{ "num_pairs": 30, "pairs": [ { "index": 1, "nt1": "///A/1", "nt2": "///A/27", "bp": "g-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -151.833, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 53.708, "chi2": -174.426, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 51.936, "C1C1_dist": 10.748, "N1N9_dist": 8.977, "C6C8_dist": 9.855, "CNNC_torsion": 1.985, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.81],N1(imino)-N3[2.88],N2(amino)-O2(carbonyl)[2.85]", "interBase_angle": 9.468, "planarity": 0.104, "simple_Shear": -0.053, "simple_Stretch": -0.144, "simple_Buckle": 7.413, "simple_Propeller": 5.890, "bp_simpleParams": [ -0.053, -0.144, 0.202, 7.413, 5.890, -1.746 ], "bp_params": [ -0.053, -0.144, 0.202, 7.417, 5.885, -1.745 ], "frame": { "rmsd": null, "origin": [ 8.486, -8.350, -0.387 ], "x_axis": [ -0.046, 0.275, 0.960 ], "y_axis": [ 0.629, -0.739, 0.242 ], "z_axis": [ 0.776, 0.615, -0.138 ], "quaternion": [ -0.138, 0.677, 0.334, 0.642 ] } }, { "index": 2, "nt1": "///A/2", "nt2": "///A/26", "bp": "G-A", "name": "Imino", "Saenger": "08-VIII", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -141.594, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 46.308, "chi2": 174.624, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 45.670, "C1C1_dist": 12.758, "N1N9_dist": 10.733, "C6C8_dist": 11.157, "CNNC_torsion": -10.731, "hbonds_num": 2, "hbonds_desc": "O6(carbonyl)-N6(amino)[2.85],N1(imino)-N1[2.81]", "interBase_angle": 15.917, "planarity": 0.214, "simple_Shear": 0.170, "simple_Stretch": 1.437, "simple_Buckle": 8.228, "simple_Propeller": -13.626, "bp_simpleParams": [ 0.170, 1.437, -0.218, 8.228, -13.626, -15.979 ], "bp_params": [ 0.191, 1.435, -0.218, 8.006, -13.757, -16.055 ], "frame": { "rmsd": null, "origin": [ 10.006, -4.785, -0.918 ], "x_axis": [ 0.413, -0.098, 0.905 ], "y_axis": [ 0.687, -0.620, -0.380 ], "z_axis": [ 0.598, 0.779, -0.189 ], "quaternion": [ -0.389, 0.745, 0.198, 0.504 ] } }, { "index": 3, "nt1": "///A/3", "nt2": "///A/25", "bp": "A-A", "name": "--", "Saenger": "--", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -178.116, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 27.771, "chi2": -160.099, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 45.581, "C1C1_dist": 13.819, "N1N9_dist": 11.506, "C6C8_dist": 11.435, "CNNC_torsion": -7.363, "hbonds_num": 1, "hbonds_desc": "N6(amino)-N1[2.96]", "interBase_angle": 12.973, "planarity": 0.167, "simple_Shear": -1.907, "simple_Stretch": 2.329, "simple_Buckle": -1.405, "simple_Propeller": -12.897, "bp_simpleParams": [ -1.907, 2.329, -0.515, -1.405, -12.897, -35.773 ], "bp_params": [ -2.347, 1.886, -0.515, 1.291, -12.909, -35.984 ], "frame": { "rmsd": null, "origin": [ 10.924, -1.461, -0.592 ], "x_axis": [ 0.469, -0.459, 0.754 ], "y_axis": [ 0.548, -0.519, -0.656 ], "z_axis": [ 0.693, 0.721, 0.008 ], "quaternion": [ -0.489, 0.704, 0.032, 0.514 ] } }, { "index": 4, "nt1": "///A/4", "nt2": "///A/24", "bp": "A-A", "name": "--", "Saenger": "--", "LW": "cW.", "DSSR": "cW-.", "intra_chain": true, "chi1": -168.150, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 33.015, "chi2": -178.622, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 12.182, "C1C1_dist": 13.941, "N1N9_dist": 11.300, "C6C8_dist": 10.584, "CNNC_torsion": 22.954, "hbonds_num": 1, "hbonds_desc": "N1-N6(amino)[2.86]", "interBase_angle": 12.183, "planarity": 0.200, "simple_Shear": 1.826, "simple_Stretch": 2.565, "simple_Buckle": 8.004, "simple_Propeller": 9.185, "bp_simpleParams": [ 1.826, 2.565, -0.410, 8.004, 9.185, -64.922 ], "bp_params": [ 2.357, 2.087, -0.410, 9.865, 7.149, -64.831 ], "frame": { "rmsd": null, "origin": [ 11.421, 2.883, 0.392 ], "x_axis": [ 0.629, -0.773, -0.083 ], "y_axis": [ -0.086, 0.037, -0.996 ], "z_axis": [ 0.773, 0.634, -0.043 ], "quaternion": [ 0.637, -0.639, 0.336, -0.270 ] } }, { "index": 5, "nt1": "///A/5", "nt2": "///A/23", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -173.261, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 52.553, "chi2": -160.997, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 50.582, "C1C1_dist": 11.128, "N1N9_dist": 9.303, "C6C8_dist": 10.112, "CNNC_torsion": -6.152, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.92],N1(imino)-N3[3.13],N2(amino)-O2(carbonyl)[3.21]", "interBase_angle": 8.927, "planarity": 0.115, "simple_Shear": 0.182, "simple_Stretch": 0.121, "simple_Buckle": 8.900, "simple_Propeller": -0.689, "bp_simpleParams": [ 0.182, 0.121, 0.102, 8.900, -0.689, -5.063 ], "bp_params": [ 0.185, 0.117, 0.102, 8.883, -0.882, -5.048 ], "frame": { "rmsd": null, "origin": [ 16.365, 1.657, 1.764 ], "x_axis": [ 0.450, -0.822, -0.350 ], "y_axis": [ -0.286, 0.238, -0.928 ], "z_axis": [ 0.846, 0.518, -0.128 ], "quaternion": [ 0.625, -0.579, 0.478, -0.214 ] } }, { "index": 6, "nt1": "///A/6", "nt2": "///A/22", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -178.043, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 53.967, "chi2": -156.248, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 58.896, "C1C1_dist": 10.360, "N1N9_dist": 8.745, "C6C8_dist": 9.740, "CNNC_torsion": -15.692, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[2.98],N1-N3(imino)[2.82]", "interBase_angle": 7.622, "planarity": 0.139, "simple_Shear": -0.420, "simple_Stretch": -0.194, "simple_Buckle": -4.966, "simple_Propeller": -5.782, "bp_simpleParams": [ -0.420, -0.194, 0.321, -4.966, -5.782, 2.085 ], "bp_params": [ -0.413, -0.210, 0.321, -4.752, -5.960, 2.086 ], "frame": { "rmsd": null, "origin": [ 20.235, 2.037, 2.607 ], "x_axis": [ 0.129, -0.689, -0.713 ], "y_axis": [ -0.490, 0.581, -0.650 ], "z_axis": [ 0.862, 0.433, -0.263 ], "quaternion": [ 0.601, -0.450, 0.655, -0.083 ] } }, { "index": 7, "nt1": "///A/7", "nt2": "///A/21", "bp": "A-C", "name": "~Wobble", "Saenger": "--", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": 172.875, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 35.687, "chi2": 170.832, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 49.150, "C1C1_dist": 11.585, "N1N9_dist": 9.451, "C6C8_dist": 9.817, "CNNC_torsion": -37.013, "hbonds_num": 1, "hbonds_desc": "N6(amino)-N3[3.02]", "interBase_angle": 21.942, "planarity": 0.344, "simple_Shear": -2.049, "simple_Stretch": 0.309, "simple_Buckle": -15.417, "simple_Propeller": -15.613, "bp_simpleParams": [ -2.049, 0.309, 0.597, -15.417, -15.613, -23.679 ], "bp_params": [ -2.069, -0.113, 0.597, -11.930, -18.416, -23.856 ], "frame": { "rmsd": null, "origin": [ 24.228, 2.383, 4.101 ], "x_axis": [ -0.020, -0.266, -0.964 ], "y_axis": [ -0.527, 0.822, -0.216 ], "z_axis": [ 0.849, 0.504, -0.157 ], "quaternion": [ 0.641, -0.281, 0.707, 0.102 ] } }, { "index": 8, "nt1": "///A/8", "nt2": "///A/20", "bp": "A-A", "name": "--", "Saenger": "--", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -164.732, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 58.943, "chi2": -173.264, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 34.147, "C1C1_dist": 12.874, "N1N9_dist": 10.920, "C6C8_dist": 11.200, "CNNC_torsion": -3.329, "hbonds_num": 1, "hbonds_desc": "N1-N6(amino)[2.78]", "interBase_angle": 24.766, "planarity": 0.378, "simple_Shear": 2.105, "simple_Stretch": 2.048, "simple_Buckle": -24.276, "simple_Propeller": -4.903, "bp_simpleParams": [ 2.105, 2.048, 0.332, -24.276, -4.903, -21.934 ], "bp_params": [ 2.509, 1.527, 0.332, -24.756, 0.700, -21.436 ], "frame": { "rmsd": null, "origin": [ 28.420, 1.556, 3.078 ], "x_axis": [ -0.415, 0.474, -0.777 ], "y_axis": [ -0.122, 0.817, 0.564 ], "z_axis": [ 0.901, 0.329, -0.281 ], "quaternion": [ 0.529, 0.111, 0.793, 0.282 ] } }, { "index": 9, "nt1": "///A/9", "nt2": "///A/10", "bp": "G+G", "name": "Platform", "Saenger": "--", "LW": "cSH", "DSSR": "cm+M", "intra_chain": true, "chi1": -128.911, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 143.285, "chi2": -170.112, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 43.527, "C1C1_dist": 6.807, "N1N9_dist": 6.930, "C6C8_dist": 6.912, "CNNC_torsion": 20.195, "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-OP2[2.83],N2(amino)-O6(carbonyl)[2.91]", "interBase_angle": 13.267, "planarity": 0.174, "simple_Shear": 0.061, "simple_Stretch": 7.472, "simple_Buckle": -12.493, "simple_Propeller": -4.463, "bp_simpleParams": [ 0.061, 7.472, -0.062, -12.493, -4.463, 6.735 ], "bp_params": [ 7.446, 0.631, -0.062, -5.587, 12.033, 6.765 ], "frame": { "rmsd": null, "origin": [ 30.538, 2.125, 0.584 ], "x_axis": [ -0.342, 0.896, -0.285 ], "y_axis": [ 0.169, 0.357, 0.919 ], "z_axis": [ 0.924, 0.265, -0.274 ], "quaternion": [ 0.431, 0.379, 0.702, 0.422 ] } }, { "index": 10, "nt1": "///A/9", "nt2": "///A/19", "bp": "G-C", "name": "--", "Saenger": "--", "LW": "c.W", "DSSR": "c.-W", "intra_chain": true, "chi1": -128.911, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 87.384, "chi2": -143.829, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 19.702, "C1C1_dist": 12.919, "N1N9_dist": 11.505, "C6C8_dist": 12.262, "CNNC_torsion": -5.934, "hbonds_num": 1, "hbonds_desc": "N2(amino)*N4(amino)[3.29]", "interBase_angle": 18.629, "planarity": 0.266, "simple_Shear": 5.746, "simple_Stretch": 4.199, "simple_Buckle": -16.358, "simple_Propeller": -8.915, "bp_simpleParams": [ 5.746, 4.199, 0.499, -16.358, -8.915, 0.317 ], "bp_params": [ 7.117, 0.060, 0.499, -18.483, 2.335, 0.313 ], "frame": { "rmsd": null, "origin": [ 30.530, 2.322, 0.645 ], "x_axis": [ -0.411, 0.887, -0.211 ], "y_axis": [ 0.291, 0.347, 0.891 ], "z_axis": [ 0.864, 0.305, -0.401 ], "quaternion": [ 0.366, 0.401, 0.735, 0.407 ] } }, { "index": 11, "nt1": "///A/10", "nt2": "///A/19", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -170.112, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 50.450, "chi2": -143.829, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 51.355, "C1C1_dist": 10.727, "N1N9_dist": 8.884, "C6C8_dist": 9.691, "CNNC_torsion": -20.390, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.70],N1(imino)-N3[2.83],N2(amino)-O2(carbonyl)[2.88]", "interBase_angle": 16.720, "planarity": 0.207, "simple_Shear": -0.325, "simple_Stretch": -0.252, "simple_Buckle": -13.130, "simple_Propeller": -10.353, "bp_simpleParams": [ -0.325, -0.252, -0.011, -13.130, -10.353, -4.564 ], "bp_params": [ -0.319, -0.260, -0.011, -12.895, -10.644, -4.555 ], "frame": { "rmsd": null, "origin": [ 31.777, -1.116, 1.408 ], "x_axis": [ -0.333, 0.894, -0.299 ], "y_axis": [ 0.314, 0.404, 0.859 ], "z_axis": [ 0.889, 0.192, -0.415 ], "quaternion": [ 0.405, 0.412, 0.734, 0.358 ] } }, { "index": 12, "nt1": "///A/11", "nt2": "///A/18", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -149.427, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 43.442, "chi2": -160.966, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 54.798, "C1C1_dist": 10.847, "N1N9_dist": 8.939, "C6C8_dist": 9.639, "CNNC_torsion": -9.834, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.73],N1(imino)-N3[3.03],N2(amino)-O2(carbonyl)[3.23]", "interBase_angle": 5.293, "planarity": 0.060, "simple_Shear": -1.032, "simple_Stretch": -0.287, "simple_Buckle": 4.989, "simple_Propeller": 1.767, "bp_simpleParams": [ -1.032, -0.287, 0.185, 4.989, 1.767, -8.674 ], "bp_params": [ -0.999, -0.388, 0.185, 4.790, 2.252, -8.668 ], "frame": { "rmsd": null, "origin": [ 34.748, -1.023, 0.163 ], "x_axis": [ -0.329, 0.876, 0.354 ], "y_axis": [ 0.428, -0.196, 0.882 ], "z_axis": [ 0.842, 0.442, -0.311 ], "quaternion": [ 0.203, 0.543, 0.601, 0.551 ] } }, { "index": 13, "nt1": "///A/12", "nt2": "///A/17", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -155.893, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 53.533, "chi2": -154.102, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 40.872, "C1C1_dist": 10.764, "N1N9_dist": 8.785, "C6C8_dist": 9.416, "CNNC_torsion": -8.200, "hbonds_num": 4, "hbonds_desc": "O2(carbonyl)-N1(imino)[3.10],O2(carbonyl)-N2(amino)[3.23],N3-N1(imino)[2.96],N4(amino)-O6(carbonyl)[2.62]", "interBase_angle": 4.862, "planarity": 0.078, "simple_Shear": 1.211, "simple_Stretch": -0.467, "simple_Buckle": 0.755, "simple_Propeller": -4.803, "bp_simpleParams": [ 1.211, -0.467, -0.205, 0.755, -4.803, -10.773 ], "bp_params": [ 1.148, -0.605, -0.205, 0.186, -4.858, -10.782 ], "frame": { "rmsd": null, "origin": [ 37.196, 1.099, -1.374 ], "x_axis": [ -0.219, 0.412, 0.885 ], "y_axis": [ 0.633, -0.630, 0.450 ], "z_axis": [ 0.743, 0.658, -0.123 ], "quaternion": [ -0.084, 0.619, 0.422, 0.657 ] } }, { "index": 14, "nt1": "///A/13", "nt2": "///A/16", "bp": "U+G", "name": "--", "Saenger": "--", "LW": "tSW", "DSSR": "tm+W", "intra_chain": true, "chi1": -154.673, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 101.186, "chi2": 84.305, "conf2": "syn", "pucker2": "~C3'-endo", "lambda2": 14.687, "C1C1_dist": 9.375, "N1N9_dist": 8.414, "C6C8_dist": 9.623, "CNNC_torsion": 141.223, "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O6(carbonyl)[2.46],O2(carbonyl)-N1(imino)[2.57]", "interBase_angle": 17.445, "planarity": 0.249, "simple_Shear": 3.208, "simple_Stretch": 3.022, "simple_Buckle": 12.255, "simple_Propeller": -12.415, "bp_simpleParams": [ 3.208, 3.022, 0.442, 12.255, -12.415, -95.572 ], "bp_params": [ 1.366, -4.190, 0.442, -16.456, -5.790, -95.055 ], "frame": { "rmsd": null, "origin": [ 38.774, 4.294, -0.305 ], "x_axis": [ 0.616, -0.688, 0.383 ], "y_axis": [ 0.397, -0.148, -0.906 ], "z_axis": [ 0.680, 0.710, 0.182 ], "quaternion": [ 0.642, -0.629, 0.116, -0.422 ] } }, { "index": 15, "nt1": "///A/32", "nt2": "///A/47", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -138.994, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 48.797, "chi2": -162.207, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 57.479, "C1C1_dist": 10.577, "N1N9_dist": 8.824, "C6C8_dist": 9.708, "CNNC_torsion": -4.507, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.89],N1(imino)-N3[2.91],N2(amino)-O2(carbonyl)[2.87]", "interBase_angle": 10.158, "planarity": 0.121, "simple_Shear": -0.885, "simple_Stretch": -0.257, "simple_Buckle": 6.731, "simple_Propeller": 7.608, "bp_simpleParams": [ -0.885, -0.257, 0.251, 6.731, 7.608, -0.647 ], "bp_params": [ -0.861, -0.328, 0.251, 6.083, 8.135, -0.648 ], "frame": { "rmsd": null, "origin": [ -11.685, -3.841, 0.421 ], "x_axis": [ -0.250, -0.791, -0.558 ], "y_axis": [ -0.133, -0.543, 0.829 ], "z_axis": [ -0.959, 0.281, 0.030 ], "quaternion": [ -0.244, -0.562, 0.411, 0.675 ] } }, { "index": 16, "nt1": "///A/33", "nt2": "///A/46", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -159.983, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 50.059, "chi2": -149.479, "conf2": "anti", "pucker2": "----", "lambda2": 49.836, "C1C1_dist": 11.157, "N1N9_dist": 9.272, "C6C8_dist": 10.013, "CNNC_torsion": 6.118, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[2.85],N1-N3(imino)[3.17]", "interBase_angle": 13.594, "planarity": 0.187, "simple_Shear": -0.026, "simple_Stretch": 0.094, "simple_Buckle": -5.581, "simple_Propeller": 12.396, "bp_simpleParams": [ -0.026, 0.094, 0.326, -5.581, 12.396, -8.889 ], "bp_params": [ -0.026, 0.094, 0.326, -5.585, 12.394, -8.931 ], "frame": { "rmsd": null, "origin": [ -16.303, -2.209, 0.094 ], "x_axis": [ -0.048, -0.975, -0.217 ], "y_axis": [ -0.078, -0.213, 0.974 ], "z_axis": [ -0.996, 0.064, -0.065 ], "quaternion": [ 0.410, 0.555, -0.474, -0.547 ] } }, { "index": 17, "nt1": "///A/33", "nt2": "///A/50", "bp": "A-A", "name": "--", "Saenger": "--", "LW": ".SW", "DSSR": ".m-W", "intra_chain": true, "chi1": -159.983, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 79.860, "chi2": -160.174, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 24.841, "C1C1_dist": 10.676, "N1N9_dist": 9.167, "C6C8_dist": 9.670, "CNNC_torsion": -66.089, "hbonds_num": 1, "hbonds_desc": "N3-N6(amino)[3.13]", "interBase_angle": 68.439, "planarity": 0.983, "simple_Shear": 2.872, "simple_Stretch": 0.927, "simple_Buckle": -38.146, "simple_Propeller": -56.823, "bp_simpleParams": [ 2.872, 0.927, 3.240, -38.146, -56.823, -25.475 ], "bp_params": [ 2.995, -0.374, 3.240, -57.687, -36.826, -23.899 ], "frame": { "rmsd": null, "origin": [ -15.807, -0.335, 1.132 ], "x_axis": [ 0.352, -0.936, 0.012 ], "y_axis": [ -0.501, -0.177, 0.847 ], "z_axis": [ -0.791, -0.304, -0.531 ], "quaternion": [ 0.401, 0.718, -0.500, -0.271 ] } }, { "index": 18, "nt1": "///A/34", "nt2": "///A/45", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -151.490, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 50.251, "chi2": -145.806, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 51.356, "C1C1_dist": 10.802, "N1N9_dist": 8.954, "C6C8_dist": 9.748, "CNNC_torsion": -20.611, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.65],N1(imino)-N3[2.84],N2(amino)-O2(carbonyl)[2.95]", "interBase_angle": 8.805, "planarity": 0.130, "simple_Shear": -0.228, "simple_Stretch": -0.262, "simple_Buckle": -1.933, "simple_Propeller": -8.590, "bp_simpleParams": [ -0.228, -0.262, 0.216, -1.933, -8.590, -5.916 ], "bp_params": [ -0.223, -0.266, 0.216, -1.774, -8.624, -5.932 ], "frame": { "rmsd": null, "origin": [ -20.422, -1.213, -1.045 ], "x_axis": [ -0.139, -0.967, 0.215 ], "y_axis": [ -0.078, 0.227, 0.971 ], "z_axis": [ -0.987, 0.118, -0.107 ], "quaternion": [ -0.495, -0.430, 0.607, 0.449 ] } }, { "index": 19, "nt1": "///A/34", "nt2": "///A/52", "bp": "G+A", "name": "Linker", "Saenger": "--", "LW": "tSS", "DSSR": "tm+m", "intra_chain": true, "chi1": -151.490, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 83.823, "chi2": -152.654, "conf2": "anti", "pucker2": "----", "lambda2": 68.671, "C1C1_dist": 8.344, "N1N9_dist": 8.146, "C6C8_dist": 10.543, "CNNC_torsion": 164.132, "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-N1[3.41],N2(amino)-O2'(hydroxyl)[3.31],N2(amino)-N3[3.05]", "interBase_angle": 11.706, "planarity": 0.219, "simple_Shear": 7.269, "simple_Stretch": 4.096, "simple_Buckle": -3.319, "simple_Propeller": -11.226, "bp_simpleParams": [ 7.269, 4.096, -0.648, -3.319, -11.226, -162.640 ], "bp_params": [ -2.781, -7.867, -0.648, -4.893, 10.635, -162.698 ], "frame": { "rmsd": null, "origin": [ -20.480, 2.872, 0.036 ], "x_axis": [ -0.195, 0.044, 0.980 ], "y_axis": [ 0.155, 0.988, -0.013 ], "z_axis": [ -0.969, 0.149, -0.199 ], "quaternion": [ 0.631, -0.064, -0.772, -0.044 ] } }, { "index": 20, "nt1": "///A/35", "nt2": "///A/42", "bp": "A-U", "name": "--", "Saenger": "--", "LW": "tH.", "DSSR": "tM-.", "intra_chain": true, "chi1": 156.505, "conf1": "anti", "pucker1": "----", "lambda1": 56.276, "chi2": -163.013, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 14.189, "C1C1_dist": 10.767, "N1N9_dist": 8.594, "C6C8_dist": 6.794, "CNNC_torsion": 90.893, "hbonds_num": 1, "hbonds_desc": "N7*O4(carbonyl)[3.35]", "interBase_angle": 27.021, "planarity": 0.339, "simple_Shear": -0.698, "simple_Stretch": 5.840, "simple_Buckle": 16.524, "simple_Propeller": -21.380, "bp_simpleParams": [ -0.698, 5.840, -0.305, 16.524, -21.380, -166.408 ], "bp_params": [ -4.549, 3.729, -0.305, 26.718, -4.038, -166.042 ], "frame": { "rmsd": null, "origin": [ -24.779, 2.265, -3.157 ], "x_axis": [ 0.136, -0.446, 0.885 ], "y_axis": [ 0.265, 0.877, 0.401 ], "z_axis": [ -0.955, 0.180, 0.238 ], "quaternion": [ 0.750, 0.074, -0.613, -0.237 ] } }, { "index": 21, "nt1": "///A/35", "nt2": "///A/44", "bp": "A-A", "name": "--", "Saenger": "05-V", "LW": "tHW", "DSSR": "tM-W", "intra_chain": true, "chi1": 156.505, "conf1": "anti", "pucker1": "----", "lambda1": 15.039, "chi2": -158.165, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 26.338, "C1C1_dist": 12.962, "N1N9_dist": 10.290, "C6C8_dist": 9.065, "CNNC_torsion": -174.605, "hbonds_num": 2, "hbonds_desc": "N7-N6(amino)[3.90],N6(amino)-N1[3.07]", "interBase_angle": 13.328, "planarity": 0.150, "simple_Shear": -3.272, "simple_Stretch": 3.305, "simple_Buckle": -6.715, "simple_Propeller": -11.513, "bp_simpleParams": [ -3.272, 3.305, -0.143, -6.715, -11.513, -94.230 ], "bp_params": [ -4.478, 1.254, -0.143, -0.130, -13.328, -94.617 ], "frame": { "rmsd": null, "origin": [ -24.181, 2.624, -3.989 ], "x_axis": [ 0.176, -0.876, 0.450 ], "y_axis": [ 0.088, 0.469, 0.879 ], "z_axis": [ -0.980, -0.115, 0.160 ], "quaternion": [ 0.672, 0.370, -0.532, -0.359 ] } }, { "index": 22, "nt1": "///A/36", "nt2": "///A/55", "bp": "C+C", "name": "--", "Saenger": "--", "LW": "c.H", "DSSR": "c.+M", "intra_chain": true, "chi1": -128.461, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 14.582, "chi2": 177.788, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 19.975, "C1C1_dist": 13.113, "N1N9_dist": 10.307, "C6C8_dist": 8.930, "CNNC_torsion": 57.622, "hbonds_num": 1, "hbonds_desc": "N4(amino)*N4(amino)[3.02]", "interBase_angle": 11.622, "planarity": 0.266, "simple_Shear": -7.109, "simple_Stretch": 2.114, "simple_Buckle": 11.446, "simple_Propeller": -2.011, "bp_simpleParams": [ -7.109, 2.114, -1.261, 11.446, -2.011, -152.111 ], "bp_params": [ -3.715, 6.419, -1.261, 6.943, -9.319, -152.150 ], "frame": { "rmsd": null, "origin": [ -27.705, 3.188, -2.764 ], "x_axis": [ 0.016, 0.054, 0.998 ], "y_axis": [ -0.103, 0.993, -0.052 ], "z_axis": [ -0.995, -0.102, 0.021 ], "quaternion": [ 0.712, 0.017, -0.699, 0.055 ] } }, { "index": 23, "nt1": "///A/37", "nt2": "///A/40", "bp": "G-A", "name": "--", "Saenger": "--", "LW": "cHH", "DSSR": "cM-M", "intra_chain": true, "chi1": -156.084, "conf1": "anti", "pucker1": "----", "lambda1": 35.070, "chi2": -177.733, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 29.524, "C1C1_dist": 11.767, "N1N9_dist": 9.302, "C6C8_dist": 6.963, "CNNC_torsion": -8.957, "hbonds_num": 1, "hbonds_desc": "O6(carbonyl)-N6(amino)[3.02]", "interBase_angle": 36.754, "planarity": 0.489, "simple_Shear": -0.116, "simple_Stretch": 5.733, "simple_Buckle": 34.748, "simple_Propeller": 11.976, "bp_simpleParams": [ -0.116, 5.733, -0.386, 34.748, 11.976, -166.823 ], "bp_params": [ -0.274, 5.728, -0.386, 34.513, 12.637, -166.283 ], "frame": { "rmsd": null, "origin": [ -32.321, 2.715, 0.093 ], "x_axis": [ 0.102, 0.588, 0.803 ], "y_axis": [ -0.234, 0.798, -0.555 ], "z_axis": [ -0.967, -0.132, 0.219 ], "quaternion": [ 0.728, -0.145, -0.608, 0.282 ] } }, { "index": 24, "nt1": "///A/37", "nt2": "///A/56", "bp": "G+U", "name": "--", "Saenger": "--", "LW": "--", "DSSR": "--", "intra_chain": true, "chi1": -156.084, "conf1": "anti", "pucker1": "----", "lambda1": 16.926, "chi2": -167.050, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 0.457, "C1C1_dist": 14.530, "N1N9_dist": 11.671, "C6C8_dist": 10.814, "CNNC_torsion": -166.350, "hbonds_num": 1, "hbonds_desc": "O6(carbonyl)*O4(carbonyl)[3.13]", "interBase_angle": 35.122, "planarity": 0.381, "simple_Shear": -5.112, "simple_Stretch": 2.445, "simple_Buckle": 1.544, "simple_Propeller": 35.088, "bp_simpleParams": [ -5.112, 2.445, -0.774, 1.544, 35.088, -163.906 ], "bp_params": [ -0.688, 5.625, -0.774, 30.388, 17.610, -163.512 ], "frame": { "rmsd": null, "origin": [ -32.427, 2.787, 0.185 ], "x_axis": [ 0.075, 0.557, 0.827 ], "y_axis": [ -0.263, 0.811, -0.522 ], "z_axis": [ -0.962, -0.178, 0.207 ], "quaternion": [ 0.723, -0.119, -0.618, 0.283 ] } }, { "index": 25, "nt1": "///A/38", "nt2": "///A/58", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -159.385, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 54.239, "chi2": -149.913, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 51.604, "C1C1_dist": 10.704, "N1N9_dist": 8.943, "C6C8_dist": 9.823, "CNNC_torsion": 16.126, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.86],N3-N1(imino)[2.88],N4(amino)-O6(carbonyl)[2.82]", "interBase_angle": 8.463, "planarity": 0.128, "simple_Shear": 0.358, "simple_Stretch": -0.194, "simple_Buckle": -3.982, "simple_Propeller": 7.468, "bp_simpleParams": [ 0.358, -0.194, -0.215, -3.982, 7.468, -2.245 ], "bp_params": [ 0.352, -0.205, -0.215, -3.750, 7.587, -2.248 ], "frame": { "rmsd": null, "origin": [ -38.195, 4.169, 2.689 ], "x_axis": [ 0.263, 0.084, -0.961 ], "y_axis": [ 0.194, 0.971, 0.138 ], "z_axis": [ 0.945, -0.223, 0.239 ], "quaternion": [ 0.786, 0.115, 0.606, -0.035 ] } }, { "index": 26, "nt1": "///A/39", "nt2": "///A/57", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -158.211, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 48.266, "chi2": -156.003, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 58.062, "C1C1_dist": 10.825, "N1N9_dist": 9.078, "C6C8_dist": 9.969, "CNNC_torsion": -21.010, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.92],N3-N1(imino)[2.94],N4(amino)-O6(carbonyl)[2.92]", "interBase_angle": 17.770, "planarity": 0.206, "simple_Shear": -0.596, "simple_Stretch": -0.012, "simple_Buckle": 7.611, "simple_Propeller": -16.057, "bp_simpleParams": [ -0.596, -0.012, -0.093, 7.611, -16.057, -1.114 ], "bp_params": [ -0.593, -0.053, -0.093, 8.671, -15.511, -1.121 ], "frame": { "rmsd": null, "origin": [ -35.196, 1.827, 2.517 ], "x_axis": [ 0.225, 0.490, -0.842 ], "y_axis": [ 0.139, 0.839, 0.525 ], "z_axis": [ 0.964, -0.235, 0.121 ], "quaternion": [ 0.739, 0.257, 0.611, 0.119 ] } }, { "index": 27, "nt1": "///A/40", "nt2": "///A/56", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -177.733, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 52.053, "chi2": -167.050, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 53.159, "C1C1_dist": 10.633, "N1N9_dist": 8.852, "C6C8_dist": 9.695, "CNNC_torsion": -8.803, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[2.69],N1-N3(imino)[2.77]", "interBase_angle": 5.299, "planarity": 0.080, "simple_Shear": -0.040, "simple_Stretch": -0.240, "simple_Buckle": 3.365, "simple_Propeller": -4.093, "bp_simpleParams": [ -0.040, -0.240, 0.201, 3.365, -4.093, -4.402 ], "bp_params": [ -0.040, -0.240, 0.201, 3.368, -4.091, -4.402 ], "frame": { "rmsd": null, "origin": [ -31.928, 0.555, 1.926 ], "x_axis": [ 0.026, 0.894, -0.448 ], "y_axis": [ -0.047, 0.449, 0.892 ], "z_axis": [ 0.999, -0.003, 0.054 ], "quaternion": [ 0.618, 0.362, 0.585, 0.380 ] } }, { "index": 28, "nt1": "///A/41", "nt2": "///A/55", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -164.087, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 54.948, "chi2": 177.788, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 48.326, "C1C1_dist": 10.967, "N1N9_dist": 9.151, "C6C8_dist": 10.008, "CNNC_torsion": -6.853, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.89],N1(imino)-N3[2.99],N2(amino)-O2(carbonyl)[2.99]", "interBase_angle": 12.524, "planarity": 0.148, "simple_Shear": 0.580, "simple_Stretch": 0.024, "simple_Buckle": -7.645, "simple_Propeller": -9.919, "bp_simpleParams": [ 0.580, 0.024, -0.195, -7.645, -9.919, -2.614 ], "bp_params": [ 0.580, -0.014, -0.195, -8.268, -9.407, -2.616 ], "frame": { "rmsd": null, "origin": [ -28.054, 0.328, -0.687 ], "x_axis": [ 0.062, 0.986, 0.157 ], "y_axis": [ 0.031, -0.159, 0.987 ], "z_axis": [ 0.998, -0.056, -0.041 ], "quaternion": [ 0.464, 0.562, 0.453, 0.514 ] } }, { "index": 29, "nt1": "///A/42", "nt2": "///A/44", "bp": "U+A", "name": "--", "Saenger": "--", "LW": "cWH", "DSSR": "cW+M", "intra_chain": true, "chi1": -163.013, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 71.847, "chi2": -158.165, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 34.991, "C1C1_dist": 9.128, "N1N9_dist": 7.498, "C6C8_dist": 7.416, "CNNC_torsion": 17.808, "hbonds_num": 1, "hbonds_desc": "O4(carbonyl)-N6(amino)[3.16]", "interBase_angle": 35.096, "planarity": 0.659, "simple_Shear": -0.994, "simple_Stretch": 1.114, "simple_Buckle": 14.205, "simple_Propeller": -32.093, "bp_simpleParams": [ -0.994, 1.114, -1.578, 14.205, -32.093, -69.260 ], "bp_params": [ 0.859, 1.221, -1.578, -28.195, -20.899, -68.540 ], "frame": { "rmsd": null, "origin": [ -24.511, 0.002, -2.689 ], "x_axis": [ 0.304, 0.351, 0.886 ], "y_axis": [ 0.037, -0.933, 0.358 ], "z_axis": [ 0.952, -0.076, -0.296 ], "quaternion": [ 0.136, 0.796, 0.122, 0.577 ] } }, { "index": 30, "nt1": "///A/44", "nt2": "///A/54", "bp": "A-C", "name": "~Sheared", "Saenger": "--", "LW": "tSH", "DSSR": "tm-M", "intra_chain": true, "chi1": -158.165, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 95.612, "chi2": -157.509, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 26.635, "C1C1_dist": 8.724, "N1N9_dist": 7.718, "C6C8_dist": 8.303, "CNNC_torsion": 105.082, "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-N4(amino)[3.32],N3-N4(amino)[3.21]", "interBase_angle": 29.678, "planarity": 0.564, "simple_Shear": 7.794, "simple_Stretch": 1.994, "simple_Buckle": -29.610, "simple_Propeller": 2.010, "bp_simpleParams": [ 7.794, 1.994, -2.195, -29.610, 2.010, -6.473 ], "bp_params": [ 6.390, -4.889, -2.195, -16.780, 24.479, -6.556 ], "frame": { "rmsd": null, "origin": [ -23.798, -0.649, -7.566 ], "x_axis": [ 0.461, -0.223, 0.859 ], "y_axis": [ 0.270, -0.887, -0.375 ], "z_axis": [ 0.845, 0.405, -0.349 ], "quaternion": [ -0.238, 0.821, 0.014, 0.519 ] } } ], "num_multiplets": 6, "multiplets": [ { "index": 1, "num_nts": 3, "nts_short": "GGC", "nts_long": "///A/9,///A/10,///A/19", "planarity": 0.261 }, { "index": 2, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/33,///A/46,///A/50", "planarity": 0.931 }, { "index": 3, "num_nts": 3, "nts_short": "GCA", "nts_long": "///A/34,///A/45,///A/52", "planarity": 0.200 }, { "index": 4, "num_nts": 3, "nts_short": "CGC", "nts_long": "///A/36,///A/41,///A/55", "planarity": 0.243 }, { "index": 5, "num_nts": 3, "nts_short": "GAU", "nts_long": "///A/37,///A/40,///A/56", "planarity": 0.453 }, { "index": 6, "num_nts": 4, "nts_short": "AUAC", "nts_long": "///A/35,///A/42,///A/44,///A/54", "planarity": 0.918 } ], "num_helices": 2, "helices": [ { "index": 1, "num_stems": 2, "strand1": "gGAAGAAAGGCU", "strand2": "CAAACUCACCGG", "bp_type": "|...||..|||.", "helix_form": "A...A..x...", "helical_rise": 2.987, "helical_rise_std": 0.837, "helical_radius": 9.390, "helical_radius_std": 2.665, "helical_axis": [ 0.863, 0.478, -0.162 ], "point1": [ 9.550, -8.103, 2.652 ], "point2": [ 37.809, 7.553, -2.653 ], "num_pairs": 12, "pairs": [ { "index": 1, "nt1": "///A/1", "nt2": "///A/27", "bp": "g-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.053, -0.144, 0.202, 7.417, 5.885, -1.745 ], "step_params": [ -0.034, -1.423, 3.644, 13.638, -3.953, 34.582 ], "heli_params": [ -1.628, 2.111, 3.520, -6.329, -21.837, 37.301 ], "bp2_params": [ 0.191, 1.435, -0.218, 8.006, -13.757, -16.055 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.644, "simple_Twist": 33.443, "simple_hRise": 3.508, "simple_hTwist": 36.253 }, { "index": 2, "nt1": "///A/2", "nt2": "///A/26", "bp": "G-A", "name": "Imino", "Saenger": "08-VIII", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.191, 1.435, -0.218, 8.006, -13.757, -16.055 ], "step_params": [ -0.256, -1.572, 3.075, 0.615, 12.929, 18.819 ], "heli_params": [ -7.653, 0.822, 1.653, 34.715, -1.651, 22.807 ], "bp2_params": [ -2.347, 1.886, -0.515, 1.291, -12.909, -35.984 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.075, "simple_Twist": 29.679, "simple_hRise": 2.210, "simple_hTwist": 32.320 }, { "index": 3, "nt1": "///A/3", "nt2": "///A/25", "bp": "A-A", "name": "--", "Saenger": "--", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -2.347, 1.886, -0.515, 1.291, -12.909, -35.984 ], "step_params": [ -2.252, -2.038, 3.296, -5.247, 5.201, 53.875 ], "heli_params": [ -2.552, 2.143, 3.290, 5.709, 5.760, 54.342 ], "bp2_params": [ 2.357, 2.087, -0.410, 9.865, 7.149, -64.831 ], "groove_widths": [ 17.931, null, 16.197, null ], "simple_Rise": 3.296, "simple_Twist": 33.860, "simple_hRise": 3.259, "simple_hTwist": 34.634 }, { "index": 4, "nt1": "///A/4", "nt2": "///A/24", "bp": "A-A", "name": "--", "Saenger": "--", "LW": "cW.", "DSSR": "cW-.", "bp1_params": [ 2.357, 2.087, -0.410, 9.865, 7.149, -64.831 ], "step_params": [ 3.404, -2.466, 3.188, -3.024, 8.713, 16.545 ], "heli_params": [ -10.696, -11.462, 1.122, 27.658, 9.598, 18.926 ], "bp2_params": [ 0.185, 0.117, 0.102, 8.883, -0.882, -5.048 ], "groove_widths": [ 17.343, 17.076, 16.810, 13.164 ], "simple_Rise": 3.188, "simple_Twist": 25.506, "simple_hRise": 1.850, "simple_hTwist": 27.097 }, { "index": 5, "nt1": "///A/5", "nt2": "///A/23", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.185, 0.117, 0.102, 8.883, -0.882, -5.048 ], "step_params": [ 0.424, -2.134, 3.331, -3.870, 8.333, 27.975 ], "heli_params": [ -5.842, -1.597, 2.524, 16.677, 7.745, 29.417 ], "bp2_params": [ -0.413, -0.210, 0.321, -4.752, -5.960, 2.086 ], "groove_widths": [ 15.793, 15.385, 15.720, 9.815 ], "simple_Rise": 3.331, "simple_Twist": 31.066, "simple_hRise": 2.615, "simple_hTwist": 32.364 }, { "index": 6, "nt1": "///A/6", "nt2": "///A/22", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.413, -0.210, 0.321, -4.752, -5.960, 2.086 ], "step_params": [ -1.238, -2.461, 3.272, -0.608, -7.297, 28.862 ], "heli_params": [ -3.117, 2.271, 3.791, -14.349, 1.195, 29.757 ], "bp2_params": [ -2.069, -0.113, 0.597, -11.930, -18.416, -23.856 ], "groove_widths": [ 15.834, 13.803, 16.539, 12.943 ], "simple_Rise": 3.272, "simple_Twist": 36.724, "simple_hRise": 3.696, "simple_hTwist": 37.422 }, { "index": 7, "nt1": "///A/7", "nt2": "///A/21", "bp": "A-C", "name": "~Wobble", "Saenger": "--", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -2.069, -0.113, 0.597, -11.930, -18.416, -23.856 ], "step_params": [ -0.288, -2.543, 3.571, 11.631, 5.038, 50.943 ], "heli_params": [ -3.228, 1.130, 3.191, 5.755, -13.287, 52.394 ], "bp2_params": [ 2.509, 1.527, 0.332, -24.756, 0.700, -21.436 ], "groove_widths": [ 16.000, 13.137, 16.726, 14.903 ], "simple_Rise": 3.571, "simple_Twist": 29.793, "simple_hRise": 2.810, "simple_hTwist": 32.321 }, { "index": 8, "nt1": "///A/8", "nt2": "///A/20", "bp": "A-A", "name": "--", "Saenger": "--", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 2.509, 1.527, 0.332, -24.756, 0.700, -21.436 ], "step_params": [ -2.404, -2.643, 2.905, 10.958, -1.052, 37.574 ], "heli_params": [ -3.848, 4.645, 2.215, -1.592, -16.582, 39.097 ], "bp2_params": [ -0.319, -0.260, -0.011, -12.895, -10.644, -4.555 ], "groove_widths": [ 16.703, 15.112, 15.218, 14.392 ], "simple_Rise": 2.905, "simple_Twist": 50.140, "simple_hRise": 2.416, "simple_hTwist": 51.258 }, { "index": 9, "nt1": "///A/10", "nt2": "///A/19", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.319, -0.260, -0.011, -12.895, -10.644, -4.555 ], "step_params": [ -0.937, -0.099, 3.082, -6.042, 14.596, 35.392 ], "heli_params": [ -1.882, 0.698, 2.936, 22.667, 9.384, 38.654 ], "bp2_params": [ -0.999, -0.388, 0.185, 4.790, 2.252, -8.668 ], "groove_widths": [ 18.896, null, 13.882, null ], "simple_Rise": 3.082, "simple_Twist": 39.092, "simple_hRise": 2.971, "simple_hTwist": 42.047 }, { "index": 10, "nt1": "///A/11", "nt2": "///A/18", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.999, -0.388, 0.185, 4.790, 2.252, -8.668 ], "step_params": [ -0.284, -0.817, 3.479, 1.015, 17.415, 38.143 ], "heli_params": [ -3.003, 0.506, 2.852, 25.109, -1.463, 41.807 ], "bp2_params": [ 1.148, -0.605, -0.205, 0.186, -4.858, -10.782 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.479, "simple_Twist": 27.011, "simple_hRise": 2.497, "simple_hTwist": 32.066 }, { "index": 11, "nt1": "///A/12", "nt2": "///A/17", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 1.148, -0.605, -0.205, 0.186, -4.858, -10.782 ], "step_params": [ 0.489, -1.469, 3.382, 10.451, 14.851, 94.184 ], "heli_params": [ -1.258, -0.143, 3.213, 10.066, -7.084, 95.512 ], "bp2_params": [ 1.366, -4.190, 0.442, -16.456, -5.790, -95.055 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.382, "simple_Twist": 5.412, "simple_hRise": 0.089, "simple_hTwist": 18.943 }, { "index": 12, "nt1": "///A/13", "nt2": "///A/16", "bp": "U+G", "name": "--", "Saenger": "--", "LW": "tSW", "DSSR": "tm+W" } ] }, { "index": 2, "num_stems": 2, "strand1": "GAGACUGG", "strand2": "CUCAGACC", "bp_type": "|||.||||", "helix_form": ".A.x.AA", "helical_rise": 3.952, "helical_rise_std": 0.632, "helical_radius": 9.517, "helical_radius_std": 1.944, "helical_axis": [ -0.994, 0.098, -0.039 ], "point1": [ -11.226, -0.802, -0.700 ], "point2": [ -38.936, 1.922, -1.779 ], "num_pairs": 8, "pairs": [ { "index": 1, "nt1": "///A/32", "nt2": "///A/47", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.861, -0.328, 0.251, 6.083, 8.135, -0.648 ], "step_params": [ -0.642, -0.541, 4.836, 0.005, 13.830, 21.158 ], "heli_params": [ -7.040, 1.472, 3.772, 33.447, -0.013, 25.234 ], "bp2_params": [ -0.026, 0.094, 0.326, -5.585, 12.394, -8.931 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 4.836, "simple_Twist": 16.942, "simple_hRise": 3.421, "simple_hTwist": 21.838 }, { "index": 2, "nt1": "///A/33", "nt2": "///A/46", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.026, 0.094, 0.326, -5.585, 12.394, -8.931 ], "step_params": [ -0.615, -0.773, 4.276, 2.404, -3.167, 25.344 ], "heli_params": [ -0.566, 2.277, 4.264, -7.162, -5.437, 25.649 ], "bp2_params": [ -0.223, -0.266, 0.216, -1.774, -8.624, -5.932 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 4.276, "simple_Twist": 26.165, "simple_hRise": 4.265, "simple_hTwist": 26.460 }, { "index": 3, "nt1": "///A/34", "nt2": "///A/45", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.223, -0.266, 0.216, -1.774, -8.624, -5.932 ], "step_params": [ -4.648, -1.530, 3.685, -9.786, 17.938, 14.979 ], "heli_params": [ -10.146, 6.987, 2.903, 47.514, 25.921, 25.289 ], "bp2_params": [ -4.478, 1.254, -0.143, -0.130, -13.328, -94.617 ], "groove_widths": [ 18.804, null, 12.588, null ], "simple_Rise": 3.685, "simple_Twist": 33.894, "simple_hRise": 3.629, "simple_hTwist": 39.422 }, { "index": 4, "nt1": "///A/35", "nt2": "///A/44", "bp": "A-A", "name": "--", "Saenger": "05-V", "LW": "tHW", "DSSR": "tM-W", "bp1_params": [ -4.478, 1.254, -0.143, -0.130, -13.328, -94.617 ], "step_params": [ 2.503, -2.612, 4.253, -10.808, -5.211, 142.854 ], "heli_params": [ -1.343, -1.390, 4.211, -2.748, 5.698, 143.065 ], "bp2_params": [ -0.580, -0.014, -0.195, 8.268, -9.407, -2.616 ], "groove_widths": [ 17.540, 12.044, 11.761, 6.256 ], "simple_Rise": 4.253, "simple_Twist": 126.106, "simple_hRise": 4.187, "simple_hTwist": 126.425 }, { "index": 5, "nt1": "///A/55", "nt2": "///A/41", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.580, -0.014, -0.195, 8.268, -9.407, -2.616 ], "step_params": [ -0.289, -2.624, 3.862, -5.824, -2.195, 35.669 ], "heli_params": [ -3.850, -0.527, 4.008, -3.550, 9.420, 36.191 ], "bp2_params": [ 0.040, -0.240, 0.201, -3.368, -4.091, -4.402 ], "groove_widths": [ 18.850, null, 10.940, null ], "simple_Rise": 3.862, "simple_Twist": 32.078, "simple_hRise": 4.017, "simple_hTwist": 32.661 }, { "index": 6, "nt1": "///A/56", "nt2": "///A/40", "bp": "U-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.040, -0.240, 0.201, -3.368, -4.091, -4.402 ], "step_params": [ 0.043, -1.242, 3.332, 6.240, 12.569, 32.581 ], "heli_params": [ -3.811, 0.807, 2.652, 21.219, -10.535, 35.399 ], "bp2_params": [ 0.593, -0.053, -0.093, -8.671, -15.511, -1.121 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.332, "simple_Twist": 29.502, "simple_hRise": 2.562, "simple_hTwist": 32.602 }, { "index": 7, "nt1": "///A/57", "nt2": "///A/39", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.593, -0.053, -0.093, -8.671, -15.511, -1.121 ], "step_params": [ -0.205, -1.754, 3.374, -2.735, 6.341, 23.724 ], "heli_params": [ -5.970, -0.328, 2.822, 15.022, 6.480, 24.695 ], "bp2_params": [ -0.352, -0.205, -0.215, 3.750, 7.587, -2.248 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.374, "simple_Twist": 28.843, "simple_hRise": 2.937, "simple_hTwist": 29.641 }, { "index": 8, "nt1": "///A/58", "nt2": "///A/38", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_stems": 4, "stems": [ { "index": 1, "helix_index": 1, "strand1": "GA", "strand2": "CU", "bp_type": "||", "helix_form": "A", "helical_rise": 2.364, "helical_rise_std": 0.064, "helical_radius": 9.690, "helical_radius_std": 1.840, "helical_axis": [ 0.713, 0.652, -0.259 ], "point1": [ 18.839, -1.110, -1.044 ], "point2": [ 20.527, 0.432, -1.656 ], "num_pairs": 2, "pairs": [ { "index": 1, "nt1": "///A/5", "nt2": "///A/23", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.185, 0.117, 0.102, 8.883, -0.882, -5.048 ], "step_params": [ 0.424, -2.134, 3.331, -3.870, 8.333, 27.975 ], "heli_params": [ -5.842, -1.597, 2.524, 16.677, 7.745, 29.417 ], "bp2_params": [ -0.413, -0.210, 0.321, -4.752, -5.960, 2.086 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.331, "simple_Twist": 31.066, "simple_hRise": 2.615, "simple_hTwist": 32.364 }, { "index": 2, "nt1": "///A/6", "nt2": "///A/22", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W" } ] }, { "index": 2, "helix_index": 1, "strand1": "GGC", "strand2": "CCG", "bp_type": "|||", "helix_form": "..", "helical_rise": 3.324, "helical_rise_std": 0.382, "helical_radius": 7.739, "helical_radius_std": 0.522, "helical_axis": [ 0.934, 0.353, -0.045 ], "point1": [ 30.688, -0.029, 0.982 ], "point2": [ 36.990, 2.353, 0.676 ], "num_pairs": 3, "pairs": [ { "index": 1, "nt1": "///A/10", "nt2": "///A/19", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.319, -0.260, -0.011, -12.895, -10.644, -4.555 ], "step_params": [ -0.937, -0.099, 3.082, -6.042, 14.596, 35.392 ], "heli_params": [ -1.882, 0.698, 2.936, 22.667, 9.384, 38.654 ], "bp2_params": [ -0.999, -0.388, 0.185, 4.790, 2.252, -8.668 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.082, "simple_Twist": 39.092, "simple_hRise": 2.971, "simple_hTwist": 42.047 }, { "index": 2, "nt1": "///A/11", "nt2": "///A/18", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.999, -0.388, 0.185, 4.790, 2.252, -8.668 ], "step_params": [ -0.284, -0.817, 3.479, 1.015, 17.415, 38.143 ], "heli_params": [ -3.003, 0.506, 2.852, 25.109, -1.463, 41.807 ], "bp2_params": [ 1.148, -0.605, -0.205, 0.186, -4.858, -10.782 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.479, "simple_Twist": 27.011, "simple_hRise": 2.497, "simple_hTwist": 32.066 }, { "index": 3, "nt1": "///A/12", "nt2": "///A/17", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] }, { "index": 3, "helix_index": 2, "strand1": "GAG", "strand2": "CUC", "bp_type": "|||", "helix_form": ".A", "helical_rise": 4.688, "helical_rise_std": 0.142, "helical_radius": 9.322, "helical_radius_std": 1.454, "helical_axis": [ -0.946, 0.160, -0.284 ], "point1": [ -11.737, -2.178, 2.626 ], "point2": [ -20.747, -0.655, -0.076 ], "num_pairs": 3, "pairs": [ { "index": 1, "nt1": "///A/32", "nt2": "///A/47", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.861, -0.328, 0.251, 6.083, 8.135, -0.648 ], "step_params": [ -0.642, -0.541, 4.836, 0.005, 13.830, 21.158 ], "heli_params": [ -7.040, 1.472, 3.772, 33.447, -0.013, 25.234 ], "bp2_params": [ -0.026, 0.094, 0.326, -5.585, 12.394, -8.931 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 4.836, "simple_Twist": 16.942, "simple_hRise": 3.421, "simple_hTwist": 21.838 }, { "index": 2, "nt1": "///A/33", "nt2": "///A/46", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.026, 0.094, 0.326, -5.585, 12.394, -8.931 ], "step_params": [ -0.615, -0.773, 4.276, 2.404, -3.167, 25.344 ], "heli_params": [ -0.566, 2.277, 4.264, -7.162, -5.437, 25.649 ], "bp2_params": [ -0.223, -0.266, 0.216, -1.774, -8.624, -5.932 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 4.276, "simple_Twist": 26.165, "simple_hRise": 4.265, "simple_hTwist": 26.460 }, { "index": 3, "nt1": "///A/34", "nt2": "///A/45", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] }, { "index": 4, "helix_index": 2, "strand1": "CCAG", "strand2": "GGUC", "bp_type": "||||", "helix_form": "AA.", "helical_rise": 2.573, "helical_rise_std": 0.475, "helical_radius": 9.585, "helical_radius_std": 1.141, "helical_axis": [ 0.958, 0.147, 0.246 ], "point1": [ -37.147, 4.126, -2.315 ], "point2": [ -29.921, 5.234, -0.456 ], "num_pairs": 4, "pairs": [ { "index": 1, "nt1": "///A/38", "nt2": "///A/58", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.352, -0.205, -0.215, -3.750, 7.587, -2.248 ], "step_params": [ 0.205, -1.754, 3.374, 2.735, 6.341, 23.724 ], "heli_params": [ -5.970, 0.328, 2.822, 15.022, -6.480, 24.695 ], "bp2_params": [ -0.593, -0.053, -0.093, 8.671, -15.511, -1.121 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.374, "simple_Twist": 28.843, "simple_hRise": 2.937, "simple_hTwist": 29.641 }, { "index": 2, "nt1": "///A/39", "nt2": "///A/57", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.593, -0.053, -0.093, 8.671, -15.511, -1.121 ], "step_params": [ -0.043, -1.242, 3.332, -6.240, 12.569, 32.581 ], "heli_params": [ -3.811, -0.807, 2.652, 21.219, 10.535, 35.399 ], "bp2_params": [ -0.040, -0.240, 0.201, 3.368, -4.091, -4.402 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.332, "simple_Twist": 29.502, "simple_hRise": 2.562, "simple_hTwist": 32.602 }, { "index": 3, "nt1": "///A/40", "nt2": "///A/56", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.040, -0.240, 0.201, 3.368, -4.091, -4.402 ], "step_params": [ 0.289, -2.624, 3.862, 5.824, -2.195, 35.669 ], "heli_params": [ -3.850, 0.527, 4.008, -3.550, -9.420, 36.191 ], "bp2_params": [ 0.580, -0.014, -0.195, -8.268, -9.407, -2.616 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.862, "simple_Twist": 32.078, "simple_hRise": 4.017, "simple_hTwist": 32.661 }, { "index": 4, "nt1": "///A/41", "nt2": "///A/55", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_isoCanonPairs": 1, "isoCanonPairs": [ { "index": -1, "helix_index": 1, "nt1": "///A/1", "nt2": "///A/27", "bp": "g-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ], "num_coaxStacks": 2, "coaxStacks": [ { "index": 1, "helix_index": 1, "num_stems": 2, "stem_indices": [ 1, 2 ] }, { "index": 2, "helix_index": 2, "num_stems": 2, "stem_indices": [ 3, 4 ] } ], "num_stacks": 11, "stacks": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///A/12,///A/13" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/29,///A/30" }, { "index": 3, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/31,///A/32" }, { "index": 4, "num_nts": 3, "nts_short": "GAC", "nts_long": "///A/10,///A/20,///A/21" }, { "index": 5, "num_nts": 3, "nts_short": "CGG", "nts_long": "///A/15,///A/16,///A/17" }, { "index": 6, "num_nts": 3, "nts_short": "GUG", "nts_long": "///A/34,///A/42,///A/41" }, { "index": 7, "num_nts": 3, "nts_short": "CAC", "nts_long": "///A/45,///A/44,///A/55" }, { "index": 8, "num_nts": 4, "nts_short": "GAAU", "nts_long": "///A/9,///A/8,///A/7,///A/22" }, { "index": 9, "num_nts": 5, "nts_short": "gGAAG", "nts_long": "///A/1,///A/2,///A/3,///A/4,///A/5" }, { "index": 10, "num_nts": 5, "nts_short": "AAACU", "nts_long": "///A/24,///A/25,///A/26,///A/27,///A/28" }, { "index": 11, "num_nts": 5, "nts_short": "GCAAU", "nts_long": "///A/37,///A/36,///A/35,///A/52,///A/51" } ], "nonStack": { "num_nts": 9, "nts_short": "UCCAGAUCU", "nts_long": "///A/14,///A/23,///A/43,///A/48,///A/49,///A/50,///A/53,///A/54,///A/59" }, "num_atom2bases": 3, "atom2bases": [ { "index": 1, "type": "sugar", "atom": "///A/15/O4'", "nt": "///A/16", "vert_dist": 2.606 }, { "index": 2, "type": "sugar", "atom": "///A/29/O4'", "nt": "///A/28", "vert_dist": 3.337 }, { "index": 3, "type": "phosphate", "atom": "///A/27/OP1", "nt": "///A/29", "vert_dist": 3.106 } ], "num_hairpins": 3, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 2 ], "summary": "[1] 4 [A.12 A.17] 3", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///A/12,///A/13,///A/14,///A/15,///A/16,///A/17", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///A/13,///A/14,///A/15,///A/16" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ 3 ], "summary": "[1] 10 [A.34 A.45] 3", "num_nts": 12, "nts_short": "GACGCCAGUCAC", "nts_long": "///A/34,///A/35,///A/36,///A/37,///A/38,///A/39,///A/40,///A/41,///A/42,///A/43,///A/44,///A/45", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "ACGCCAGUCA", "nts_long": "///A/35,///A/36,///A/37,///A/38,///A/39,///A/40,///A/41,///A/42,///A/43,///A/44" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 13 ], "stem_indices": [ 4 ], "summary": "[1] 13 [A.41 A.55] 4", "num_nts": 15, "nts_short": "GUCACUCAGAUAUCC", "nts_long": "///A/41,///A/42,///A/43,///A/44,///A/45,///A/46,///A/47,///A/48,///A/49,///A/50,///A/51,///A/52,///A/53,///A/54,///A/55", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "UCACUCAGAUAUC", "nts_long": "///A/42,///A/43,///A/44,///A/45,///A/46,///A/47,///A/48,///A/49,///A/50,///A/51,///A/52,///A/53,///A/54" } ] } ], "num_iloops": 2, "iloops": [ { "index": 1, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 1, 2 ], "summary": "[2] 3 2 [A.6 A.22 A.10 A.19] 2 3", "num_nts": 9, "nts_short": "AAAGGCACU", "nts_long": "///A/6,///A/7,///A/8,///A/9,///A/10,///A/19,///A/20,///A/21,///A/22", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AAG", "nts_long": "///A/7,///A/8,///A/9" }, { "index": 2, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/20,///A/21" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -1, 1 ], "summary": "[2] 3 3 [A.1 A.27 A.5 A.23] 1 2", "num_nts": 10, "nts_short": "gGAAGCAAAC", "nts_long": "///A/1,///A/2,///A/3,///A/4,///A/5,///A/23,///A/24,///A/25,///A/26,///A/27", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/2,///A/3,///A/4" }, { "index": 2, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/24,///A/25,///A/26" } ] } ], "num_ssSegments": 2, "ssSegments": [ { "index": 1, "num_nts": 4, "nts_short": "UACA", "nts_long": "///A/28,///A/29,///A/30,///A/31" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/59" } ], "num_Aminors": 1, "Aminors": [ { "index": 1, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/52 vs ///A/34,///A/45", "A_nt1": { "desc": "///A/52 vs ///A/34", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-N2(amino)[3.31],N1-O2'(hydroxyl)[3.41],N3-N2(amino)[3.05]" }, "A_nt2": { "desc": "///A/52 vs ///A/45", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O3'-O2'(hydroxyl)[2.87],O2'(hydroxyl)-O2(carbonyl)[2.97]" } } ], "num_splayUnits": 3, "splayUnits": [ { "index": 1, "num_nts": 3, "nts_short": "UUC", "nts_long": "///A/13,///A/14,///A/15" }, { "index": 2, "num_nts": 3, "nts_short": "CAG", "nts_long": "///A/47,///A/48,///A/49" }, { "index": 3, "num_nts": 2, "nts_short": "UC", "nts_long": "///A/53,///A/54" } ], "num_HtypePknots": 3, "HtypePknots": [ { "index": 1, "desc": "stem#3(hairpin#2) vs stem#4(hairpin#3) L1 groove=MAJOR nts=3 ACG ///A/35,///A/36,///A/37" }, { "index": 2, "desc": "stem#3(hairpin#2) vs stem#4(hairpin#3) L2 groove=minor nts=3 UCA ///A/42,///A/43,///A/44" }, { "index": 3, "desc": "stem#3(hairpin#2) vs stem#4(hairpin#3) L3 groove=minor nts=7 AGAUAUC ///A/48,///A/49,///A/50,///A/51,///A/52,///A/53,///A/54" } ], "pseudoknot_order": 1, "pseudoknot_nts": [ { "index": 1, "symbols": "[]", "num_nts": 6, "nts_short": "GAGCUC", "nts_long": "///A/32,///A/33,///A/34,///A/45,///A/46,///A/47" } ], "dbn": { "all_chains": { "num_nts": 59, "num_chars": 59, "bseq": "gGAAGAAAGGGCUUCGGCCACUCAAACUACAGAGACGCCAGUCACUCAGAUAUCCUGGU", "bseqUP": "GGAAGAAAGGGCUUCGGCCACUCAAACUACAGAGACGCCAGUCACUCAGAUAUCCUGGU", "sstr": "(...((...(((....)))..))...)....[[[...((((...]]].......)))).", "form": "..A.A.....A...Z.AB..AA..A...B.....B..AA.B..............A..-" }, "m1_chain_A": { "num_nts": 59, "num_chars": 59, "bseq": "gGAAGAAAGGGCUUCGGCCACUCAAACUACAGAGACGCCAGUCACUCAGAUAUCCUGGU", "bseqUP": "GGAAGAAAGGGCUUCGGCCACUCAAACUACAGAGACGCCAGUCACUCAGAUAUCCUGGU", "sstr": "(...((...(((....)))..))...)....[[[...((((...]]].......)))).", "form": "..A.A.....A...Z.AB..AA..A...B.....B..AA.B..............A..-" } }, "chains": { "m1_chain_A": { "num_nts": 59, "bseq": "gGAAGAAAGGGCUUCGGCCACUCAAACUACAGAGACGCCAGUCACUCAGAUAUCCUGGU", "sstr": "(...((...(((....)))..))...)....[[[...((((...]]].......)))).", "form": "..A.A.....A...Z.AB..AA..A...B.....B..AA.B..............A..-", "helical_rise": 0.215, "helical_rise_std": 2.788, "helical_axis": [ -0.362, -0.704, -0.611 ], "point1": [ -6.031, 0.464, -5.568 ], "point2": [ -10.423, -8.064, -12.972 ], "num_chars": 175, "suite": "g1aG!!A!!A1aG1aA1eA1cA!!G0aG1aG1aC1aU!!U!!C!!G!!G1aC1aC!!A!!C1aU1aC!!A!!A1cA1aC1aU!!A1aC!!A!!G1aA1aG1eA!!C!!G!!C!!C1aA1aG!!U!!C!!A1aC1aU!!C!!A!!G!!A!!U!!A!!U!!C1aC1aU1aG1tG!!U" } }, "num_nts": 59, "nts": [ { "index": 1, "index_chain": 1, "chain_name": "A", "nt_resnum": 1, "nt_name": "GTP", "nt_code": "g", "is_modified": true, "nt_id": "///A/1", "linked_nts": [ null, "///A/2" ], "nt_type": "RNA", "dbn": "(", "summary": "modified,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,internal-loop", "alpha": null, "beta": null, "gamma": 112.499, "delta": 80.920, "epsilon": -167.017, "zeta": -81.393, "epsilon_zeta": -85.625, "bb_type": "BI", "chi": -151.833, "glyco_bond": "anti", "C5prime_xyz": [ -1.975, 8.980, -0.082 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 4.135, "Dp": 4.277, "splay_angle": 22.419, "splay_distance": 3.569, "splay_ratio": 0.195, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -11.293, "v1": -14.025, "v2": 32.385, "v3": -39.782, "v4": 32.085, "amplitude": 39.413, "phase_angle": 34.747, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.003, "frame": { "rmsd": 0.003, "origin": [ 8.521, -8.242, -0.444 ], "x_axis": [ -0.095, 0.252, 0.963 ], "y_axis": [ 0.676, -0.694, 0.248 ], "z_axis": [ 0.731, 0.675, -0.104 ], "quaternion": [ -0.163, 0.652, 0.356, 0.649 ] } }, { "index": 2, "index_chain": 2, "chain_name": "A", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///A/2", "linked_nts": [ "///A/1", "///A/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": -80.512, "beta": 165.461, "gamma": 83.903, "delta": 90.328, "epsilon": -137.824, "zeta": -94.842, "epsilon_zeta": -42.982, "bb_type": "BI", "chi": -141.594, "glyco_bond": "anti", "C5prime_xyz": [ -1.316, 8.762, -0.537 ], "P_xyz": [ 1.050, 8.871, -1.649 ], "form": ".", "ssZp": 3.564, "Dp": 4.472, "splay_angle": 21.404, "splay_distance": 3.868, "splay_ratio": 0.189, "d22": null, "d64": null, "eta": -175.554, "theta": -128.509, "eta_prime": -166.943, "theta_prime": -151.798, "eta_base": -138.128, "theta_base": -156.567, "v0": 0.507, "v1": -19.075, "v2": 29.060, "v3": -29.356, "v4": 18.315, "amplitude": 30.459, "phase_angle": 17.436, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.019, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 10.473, -5.323, -1.084 ], "x_axis": [ 0.373, 0.077, 0.925 ], "y_axis": [ 0.785, -0.558, -0.270 ], "z_axis": [ 0.495, 0.826, -0.269 ], "quaternion": [ -0.369, 0.742, 0.291, 0.479 ] } }, { "index": 3, "index_chain": 3, "chain_name": "A", "nt_resnum": 3, "nt_name": "A", "nt_code": "A", "nt_id": "///A/3", "linked_nts": [ "///A/2", "///A/4" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop", "alpha": 84.348, "beta": -137.217, "gamma": -148.531, "delta": 82.763, "epsilon": -148.323, "zeta": -120.228, "epsilon_zeta": -28.095, "bb_type": "--", "chi": -178.116, "glyco_bond": "anti", "C5prime_xyz": [ -1.239, 8.286, 1.595 ], "P_xyz": [ -0.645, 10.570, 0.449 ], "form": "A", "ssZp": 4.835, "Dp": 4.744, "splay_angle": 27.450, "splay_distance": 3.925, "splay_ratio": 0.239, "d22": null, "d64": null, "eta": 151.536, "theta": 167.729, "eta_prime": 159.421, "theta_prime": -178.378, "eta_base": 179.640, "theta_base": -142.845, "v0": 14.482, "v1": -37.662, "v2": 45.540, "v3": -37.914, "v4": 14.978, "amplitude": 45.540, "phase_angle": 0.305, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.004, "origin": [ 10.711, -1.598, -2.098 ], "x_axis": [ 0.346, -0.198, 0.917 ], "y_axis": [ 0.696, -0.601, -0.393 ], "z_axis": [ 0.629, 0.774, -0.070 ], "quaternion": [ -0.411, 0.710, 0.175, 0.544 ] } }, { "index": 4, "index_chain": 4, "chain_name": "A", "nt_resnum": 4, "nt_name": "A", "nt_code": "A", "nt_id": "///A/4", "linked_nts": [ "///A/3", "///A/5" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": 36.891, "beta": 125.683, "gamma": -6.176, "delta": 84.356, "epsilon": -152.669, "zeta": -48.498, "epsilon_zeta": -104.171, "bb_type": "BI", "chi": -168.150, "glyco_bond": "anti", "C5prime_xyz": [ -1.010, 8.468, 1.025 ], "P_xyz": [ 1.321, 8.068, 2.190 ], "form": ".", "ssZp": 4.729, "Dp": 4.679, "splay_angle": 32.681, "splay_distance": 5.127, "splay_ratio": 0.287, "d22": null, "d64": null, "eta": 177.052, "theta": -120.395, "eta_prime": -179.344, "theta_prime": -113.948, "eta_base": -145.769, "theta_base": -80.528, "v0": 11.464, "v1": -33.602, "v2": 41.693, "v3": -36.160, "v4": 15.681, "amplitude": 41.751, "phase_angle": 3.022, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.039, "frame": { "rmsd": 0.007, "origin": [ 11.914, 1.881, -0.736 ], "x_axis": [ 0.499, -0.732, 0.464 ], "y_axis": [ 0.296, -0.359, -0.885 ], "z_axis": [ 0.815, 0.579, 0.037 ], "quaternion": [ 0.542, -0.675, 0.162, -0.474 ] } }, { "index": 5, "index_chain": 5, "chain_name": "A", "nt_resnum": 5, "nt_name": "G", "nt_code": "G", "nt_id": "///A/5", "linked_nts": [ "///A/4", "///A/6" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop", "alpha": -77.698, "beta": 178.963, "gamma": 69.163, "delta": 79.086, "epsilon": -145.196, "zeta": -74.025, "epsilon_zeta": -71.171, "bb_type": "BI", "chi": -173.261, "glyco_bond": "anti", "C5prime_xyz": [ -1.789, 8.712, 1.234 ], "P_xyz": [ 0.720, 9.271, 1.744 ], "form": "A", "ssZp": 4.460, "Dp": 4.572, "splay_angle": 25.630, "splay_distance": 4.156, "splay_ratio": 0.226, "d22": null, "d64": null, "eta": 174.025, "theta": -143.448, "eta_prime": -160.293, "theta_prime": -141.242, "eta_base": -104.054, "theta_base": -114.471, "v0": -1.801, "v1": -23.837, "v2": 39.061, "v3": -41.172, "v4": 27.058, "amplitude": 41.846, "phase_angle": 21.020, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.403, "filter_rmsd": 0.006, "frame": { "rmsd": 0.006, "origin": [ 16.433, 1.622, 1.671 ], "x_axis": [ 0.466, -0.829, -0.309 ], "y_axis": [ -0.200, 0.241, -0.950 ], "z_axis": [ 0.862, 0.504, -0.053 ], "quaternion": [ 0.643, -0.565, 0.455, -0.245 ] } }, { "index": 6, "index_chain": 6, "chain_name": "A", "nt_resnum": 6, "nt_name": "A", "nt_code": "A", "nt_id": "///A/6", "linked_nts": [ "///A/5", "///A/7" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop", "alpha": -57.858, "beta": 165.886, "gamma": 62.034, "delta": 87.502, "epsilon": -158.181, "zeta": -41.876, "epsilon_zeta": -116.304, "bb_type": "BI", "chi": -178.043, "glyco_bond": "anti", "C5prime_xyz": [ -2.189, 8.670, 1.270 ], "P_xyz": [ 0.176, 9.362, 2.128 ], "form": ".", "ssZp": 3.930, "Dp": 4.133, "splay_angle": 27.761, "splay_distance": 4.758, "splay_ratio": 0.249, "d22": null, "d64": null, "eta": 175.353, "theta": -133.797, "eta_prime": -166.238, "theta_prime": -150.632, "eta_base": -123.490, "theta_base": -143.311, "v0": -14.536, "v1": -7.267, "v2": 24.801, "v3": -33.764, "v4": 30.371, "amplitude": 33.961, "phase_angle": 43.090, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.772, "filter_rmsd": 0.037, "frame": { "rmsd": 0.004, "origin": [ 20.398, 2.188, 2.780 ], "x_axis": [ 0.163, -0.654, -0.738 ], "y_axis": [ -0.528, 0.574, -0.626 ], "z_axis": [ 0.833, 0.492, -0.252 ], "quaternion": [ 0.609, -0.459, 0.645, -0.052 ] } }, { "index": 7, "index_chain": 7, "chain_name": "A", "nt_resnum": 7, "nt_name": "A", "nt_code": "A", "nt_id": "///A/7", "linked_nts": [ "///A/6", "///A/8" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop", "alpha": -143.828, "beta": 104.427, "gamma": 158.899, "delta": 92.731, "epsilon": -128.011, "zeta": -58.165, "epsilon_zeta": -69.846, "bb_type": "--", "chi": 172.875, "glyco_bond": "anti", "C5prime_xyz": [ -1.307, 7.705, 2.102 ], "P_xyz": [ -0.627, 10.110, 1.281 ], "form": ".", "ssZp": 4.420, "Dp": 4.780, "splay_angle": 25.250, "splay_distance": 4.284, "splay_ratio": 0.236, "d22": null, "d64": null, "eta": 179.826, "theta": -137.952, "eta_prime": -179.357, "theta_prime": -140.617, "eta_base": -154.874, "theta_base": -93.990, "v0": 21.557, "v1": -37.734, "v2": 38.923, "v3": -27.721, "v4": 3.996, "amplitude": 39.941, "phase_angle": 347.037, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "1e", "suiteness": 0.033, "filter_rmsd": 0.039, "frame": { "rmsd": 0.005, "origin": [ 24.532, 2.762, 5.063 ], "x_axis": [ 0.235, -0.329, -0.914 ], "y_axis": [ -0.576, 0.710, -0.404 ], "z_axis": [ 0.783, 0.622, -0.023 ], "quaternion": [ 0.693, -0.370, 0.612, 0.089 ] } }, { "index": 8, "index_chain": 8, "chain_name": "A", "nt_resnum": 8, "nt_name": "A", "nt_code": "A", "nt_id": "///A/8", "linked_nts": [ "///A/7", "///A/9" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": 158.713, "beta": 171.340, "gamma": 169.147, "delta": 94.368, "epsilon": -175.973, "zeta": -29.405, "epsilon_zeta": -146.568, "bb_type": "BI", "chi": -164.732, "glyco_bond": "anti", "C5prime_xyz": [ -1.015, 8.208, 0.955 ], "P_xyz": [ 0.636, 9.890, -0.180 ], "form": ".", "ssZp": 4.004, "Dp": 4.424, "splay_angle": 25.856, "splay_distance": 4.047, "splay_ratio": 0.226, "d22": null, "d64": null, "eta": 146.713, "theta": -149.413, "eta_prime": 178.598, "theta_prime": -137.250, "eta_base": -111.751, "theta_base": -83.438, "v0": 20.872, "v1": -37.352, "v2": 38.267, "v3": -27.273, "v4": 4.354, "amplitude": 39.230, "phase_angle": 347.274, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "1c", "suiteness": 0.149, "filter_rmsd": 0.037, "frame": { "rmsd": 0.008, "origin": [ 27.955, 2.828, 2.488 ], "x_axis": [ -0.355, 0.328, -0.875 ], "y_axis": [ -0.385, 0.802, 0.457 ], "z_axis": [ 0.852, 0.499, -0.159 ], "quaternion": [ 0.567, -0.019, 0.761, 0.314 ] } }, { "index": 9, "index_chain": 9, "chain_name": "A", "nt_resnum": 9, "nt_name": "G", "nt_code": "G", "nt_id": "///A/9", "linked_nts": [ "///A/8", "///A/10" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop", "alpha": -95.412, "beta": -172.755, "gamma": 74.012, "delta": 146.305, "epsilon": -142.029, "zeta": 164.187, "epsilon_zeta": 53.784, "bb_type": "--", "chi": -128.911, "glyco_bond": "anti", "C5prime_xyz": [ -2.016, 8.728, -0.632 ], "P_xyz": [ 0.510, 9.228, -0.115 ], "form": ".", "ssZp": 2.306, "Dp": 2.061, "splay_angle": 48.280, "splay_distance": 7.473, "splay_ratio": 0.414, "d22": null, "d64": null, "eta": 169.333, "theta": 150.148, "eta_prime": -139.031, "theta_prime": 135.217, "eta_base": -71.065, "theta_base": 146.990, "v0": -24.270, "v1": 38.955, "v2": -38.220, "v3": 25.090, "v4": -0.696, "amplitude": 40.109, "phase_angle": 162.345, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 29.291, 5.564, -0.180 ], "x_axis": [ -0.429, 0.881, -0.202 ], "y_axis": [ 0.151, 0.290, 0.945 ], "z_axis": [ 0.891, 0.375, -0.257 ], "quaternion": [ 0.389, 0.367, 0.703, 0.470 ] } }, { "index": 10, "index_chain": 10, "chain_name": "A", "nt_resnum": 10, "nt_name": "G", "nt_code": "G", "nt_id": "///A/10", "linked_nts": [ "///A/9", "///A/11" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,phosphate", "alpha": -89.329, "beta": 161.652, "gamma": 44.911, "delta": 92.699, "epsilon": -118.225, "zeta": -91.816, "epsilon_zeta": -26.409, "bb_type": "--", "chi": -170.112, "glyco_bond": "anti", "C5prime_xyz": [ -1.142, 8.390, 1.219 ], "P_xyz": [ 1.350, 8.060, 1.958 ], "form": ".", "ssZp": 4.274, "Dp": 4.640, "splay_angle": 21.935, "splay_distance": 3.491, "splay_ratio": 0.191, "d22": null, "d64": null, "eta": 179.006, "theta": -130.351, "eta_prime": 163.341, "theta_prime": -130.389, "eta_base": 162.702, "theta_base": -115.826, "v0": 10.930, "v1": -27.352, "v2": 32.508, "v3": -27.283, "v4": 10.411, "amplitude": 32.509, "phase_angle": 359.663, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "23p", "cluster": "0a", "suiteness": 0.468, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 31.785, -1.313, 1.347 ], "x_axis": [ -0.256, 0.894, -0.367 ], "y_axis": [ 0.200, 0.421, 0.885 ], "z_axis": [ 0.946, 0.152, -0.287 ], "quaternion": [ 0.469, 0.391, 0.701, 0.370 ] } }, { "index": 11, "index_chain": 11, "chain_name": "A", "nt_resnum": 11, "nt_name": "G", "nt_code": "G", "nt_id": "///A/11", "linked_nts": [ "///A/10", "///A/12" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack", "alpha": -68.984, "beta": 166.794, "gamma": 45.096, "delta": 81.449, "epsilon": -146.425, "zeta": -74.949, "epsilon_zeta": -71.475, "bb_type": "BI", "chi": -149.427, "glyco_bond": "anti", "C5prime_xyz": [ -0.915, 8.666, 0.018 ], "P_xyz": [ 1.688, 8.758, 0.198 ], "form": "A", "ssZp": 4.020, "Dp": 4.678, "splay_angle": 22.123, "splay_distance": 3.502, "splay_ratio": 0.192, "d22": null, "d64": null, "eta": 154.122, "theta": -140.440, "eta_prime": 167.008, "theta_prime": -137.607, "eta_base": -163.308, "theta_base": -103.111, "v0": 14.035, "v1": -36.709, "v2": 43.865, "v3": -36.729, "v4": 14.538, "amplitude": 43.865, "phase_angle": 0.222, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.299, "filter_rmsd": 0.009, "frame": { "rmsd": 0.009, "origin": [ 34.907, -1.381, -0.214 ], "x_axis": [ -0.379, 0.878, 0.294 ], "y_axis": [ 0.436, -0.111, 0.893 ], "z_axis": [ 0.816, 0.467, -0.340 ], "quaternion": [ 0.206, 0.518, 0.634, 0.536 ] } }, { "index": 12, "index_chain": 12, "chain_name": "A", "nt_resnum": 12, "nt_name": "C", "nt_code": "C", "nt_id": "///A/12", "linked_nts": [ "///A/11", "///A/13" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop", "alpha": -38.526, "beta": 161.783, "gamma": 36.316, "delta": 86.624, "epsilon": -157.798, "zeta": -43.439, "epsilon_zeta": -114.359, "bb_type": "BI", "chi": -155.893, "glyco_bond": "anti", "C5prime_xyz": [ -1.176, 8.726, 0.276 ], "P_xyz": [ 1.383, 8.903, 0.838 ], "form": ".", "ssZp": 4.105, "Dp": 4.488, "splay_angle": 27.230, "splay_distance": 4.388, "splay_ratio": 0.236, "d22": 3.305, "d64": 3.278, "eta": 168.214, "theta": -117.494, "eta_prime": -171.866, "theta_prime": -115.857, "eta_base": -121.024, "theta_base": -65.568, "v0": 7.283, "v1": -27.797, "v2": 36.518, "v3": -33.256, "v4": 16.509, "amplitude": 36.829, "phase_angle": 7.444, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.265, "filter_rmsd": 0.068, "frame": { "rmsd": 0.007, "origin": [ 36.803, 1.459, -0.989 ], "x_axis": [ -0.246, 0.497, 0.832 ], "y_axis": [ 0.614, -0.585, 0.530 ], "z_axis": [ 0.750, 0.641, -0.161 ], "quaternion": [ -0.045, 0.612, 0.453, 0.646 ] } }, { "index": 13, "index_chain": 13, "chain_name": "A", "nt_resnum": 13, "nt_name": "U", "nt_code": "U", "nt_id": "///A/13", "linked_nts": [ "///A/12", "///A/14" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart", "alpha": -84.656, "beta": 177.768, "gamma": 60.662, "delta": 83.446, "epsilon": -164.360, "zeta": -107.927, "epsilon_zeta": -56.433, "bb_type": "BI", "chi": -154.673, "glyco_bond": "anti", "C5prime_xyz": [ -1.662, 8.826, 0.061 ], "P_xyz": [ 0.908, 9.412, 0.213 ], "form": ".", "ssZp": 4.034, "Dp": 4.457, "splay_angle": 103.947, "splay_distance": 14.261, "splay_ratio": 0.788, "d22": 8.287, "d64": 10.699, "eta": 156.795, "theta": -175.563, "eta_prime": -171.202, "theta_prime": 154.900, "eta_base": -96.035, "theta_base": 106.827, "v0": 0.227, "v1": -24.516, "v2": 38.013, "v3": -38.598, "v4": 24.358, "amplitude": 39.990, "phase_angle": 18.088, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.356, "filter_rmsd": 0.102, "frame": { "rmsd": 0.007, "origin": [ 38.512, 4.291, 1.894 ], "x_axis": [ 0.220, -0.255, 0.942 ], "y_axis": [ 0.682, -0.650, -0.336 ], "z_axis": [ 0.698, 0.715, 0.031 ], "quaternion": [ -0.388, 0.678, 0.157, 0.605 ] } }, { "index": 14, "index_chain": 14, "chain_name": "A", "nt_resnum": 14, "nt_name": "U", "nt_code": "U", "nt_id": "///A/14", "linked_nts": [ "///A/13", "///A/15" ], "nt_type": "RNA", "dbn": ".", "summary": "turn,anti,~C2'-endo,BI,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart", "alpha": 177.518, "beta": 161.915, "gamma": 85.387, "delta": 148.570, "epsilon": -141.770, "zeta": -39.465, "epsilon_zeta": -102.305, "bb_type": "BI", "chi": -117.715, "glyco_bond": "anti", "C5prime_xyz": [ -2.062, 8.550, -1.178 ], "P_xyz": [ 0.469, 8.828, -1.798 ], "form": ".", "ssZp": 2.112, "Dp": 1.861, "splay_angle": 96.755, "splay_distance": 14.291, "splay_ratio": 0.748, "d22": 5.965, "d64": 7.697, "eta": 69.799, "theta": -29.165, "eta_prime": 97.337, "theta_prime": -61.864, "eta_base": 74.306, "theta_base": -37.257, "v0": -24.387, "v1": 39.978, "v2": -39.890, "v3": 27.319, "v4": -2.031, "amplitude": 41.481, "phase_angle": 164.081, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.105, "frame": { "rmsd": 0.004, "origin": [ 41.786, 1.953, -11.788 ], "x_axis": [ -0.228, -0.921, 0.316 ], "y_axis": [ 0.251, 0.258, 0.933 ], "z_axis": [ -0.941, 0.292, 0.172 ], "quaternion": [ 0.548, 0.292, -0.573, -0.534 ] } }, { "index": 15, "index_chain": 15, "chain_name": "A", "nt_resnum": 15, "nt_name": "C", "nt_code": "C", "nt_id": "///A/15", "linked_nts": [ "///A/14", "///A/16" ], "nt_type": "RNA", "dbn": ".", "summary": "turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart", "alpha": -124.808, "beta": -150.630, "gamma": 71.241, "delta": 146.780, "epsilon": -92.919, "zeta": 73.744, "epsilon_zeta": 193.337, "bb_type": "--", "chi": -157.139, "glyco_bond": "anti", "C5prime_xyz": [ -2.273, 8.809, 0.763 ], "P_xyz": [ -0.318, 9.109, 2.525 ], "form": "Z", "ssZp": 1.501, "Dp": 1.271, "splay_angle": 34.218, "splay_distance": 5.381, "splay_ratio": 0.306, "d22": null, "d64": null, "eta": 151.795, "theta": 136.723, "eta_prime": -147.425, "theta_prime": 84.676, "eta_base": -117.725, "theta_base": 71.029, "v0": -40.072, "v1": 52.822, "v2": -43.915, "v3": 22.546, "v4": 10.914, "amplitude": 51.242, "phase_angle": 148.984, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.066, "frame": { "rmsd": 0.005, "origin": [ 41.622, 5.224, 2.123 ], "x_axis": [ 0.751, -0.635, -0.181 ], "y_axis": [ -0.008, 0.266, -0.964 ], "z_axis": [ 0.661, 0.725, 0.194 ], "quaternion": [ 0.743, -0.568, 0.283, -0.211 ] } }, { "index": 16, "index_chain": 16, "chain_name": "A", "nt_resnum": 16, "nt_name": "G", "nt_code": "G", "nt_id": "///A/16", "linked_nts": [ "///A/15", "///A/17" ], "nt_type": "RNA", "dbn": ".", "summary": "syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor", "alpha": 100.030, "beta": -147.361, "gamma": 119.826, "delta": 81.401, "epsilon": -167.743, "zeta": -63.120, "epsilon_zeta": -104.623, "bb_type": "BI", "chi": 84.305, "glyco_bond": "syn", "C5prime_xyz": [ -5.238, 5.534, 1.990 ], "P_xyz": [ -4.694, 4.737, 4.403 ], "form": ".", "ssZp": -2.073, "Dp": 4.376, "splay_angle": 25.862, "splay_distance": 3.912, "splay_ratio": 0.241, "d22": null, "d64": null, "eta": 108.394, "theta": -149.282, "eta_prime": 103.231, "theta_prime": -151.593, "eta_base": 127.810, "theta_base": -169.928, "v0": -9.671, "v1": -19.020, "v2": 38.615, "v3": -44.791, "v4": 34.241, "amplitude": 44.763, "phase_angle": 30.385, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.022, "frame": { "rmsd": 0.022, "origin": [ 39.035, 4.296, -2.504 ], "x_axis": [ 0.757, -0.524, -0.391 ], "y_axis": [ -0.097, 0.502, -0.860 ], "z_axis": [ 0.646, 0.689, 0.329 ], "quaternion": [ 0.804, -0.481, 0.322, -0.133 ] } }, { "index": 17, "index_chain": 17, "chain_name": "A", "nt_resnum": 17, "nt_name": "G", "nt_code": "G", "nt_id": "///A/17", "linked_nts": [ "///A/16", "///A/18" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop", "alpha": -82.825, "beta": 160.768, "gamma": 93.401, "delta": 83.020, "epsilon": -138.068, "zeta": -86.669, "epsilon_zeta": -51.399, "bb_type": "BI", "chi": -154.102, "glyco_bond": "anti", "C5prime_xyz": [ -0.772, 8.595, 0.192 ], "P_xyz": [ 1.393, 8.651, -1.347 ], "form": "A", "ssZp": 4.219, "Dp": 4.794, "splay_angle": 26.495, "splay_distance": 4.031, "splay_ratio": 0.230, "d22": null, "d64": null, "eta": -173.086, "theta": -144.960, "eta_prime": -151.324, "theta_prime": -144.213, "eta_base": -149.105, "theta_base": -110.976, "v0": 15.032, "v1": -37.820, "v2": 45.651, "v3": -37.763, "v4": 14.480, "amplitude": 45.652, "phase_angle": 359.752, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.016, "frame": { "rmsd": 0.016, "origin": [ 37.590, 0.739, -1.758 ], "x_axis": [ -0.190, 0.323, 0.927 ], "y_axis": [ -0.652, 0.665, -0.365 ], "z_axis": [ -0.734, -0.674, 0.084 ], "quaternion": [ 0.624, 0.124, -0.665, 0.390 ] } }, { "index": 18, "index_chain": 18, "chain_name": "A", "nt_resnum": 18, "nt_name": "C", "nt_code": "C", "nt_id": "///A/18", "linked_nts": [ "///A/17", "///A/19" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack", "alpha": -34.071, "beta": 152.026, "gamma": 47.196, "delta": 95.902, "epsilon": -121.923, "zeta": -80.929, "epsilon_zeta": -40.995, "bb_type": "--", "chi": -160.966, "glyco_bond": "anti", "C5prime_xyz": [ -1.195, 8.624, 0.653 ], "P_xyz": [ 1.387, 8.379, 1.054 ], "form": "B", "ssZp": 3.959, "Dp": 4.391, "splay_angle": 17.853, "splay_distance": 2.980, "splay_ratio": 0.158, "d22": 4.553, "d64": 3.505, "eta": -173.376, "theta": -120.763, "eta_prime": -155.561, "theta_prime": -124.761, "eta_base": -110.683, "theta_base": -91.483, "v0": 5.377, "v1": -19.610, "v2": 25.695, "v3": -23.304, "v4": 11.366, "amplitude": 25.887, "phase_angle": 6.981, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.128, "filter_rmsd": 0.066, "frame": { "rmsd": 0.004, "origin": [ 34.589, -0.664, 0.539 ], "x_axis": [ -0.282, 0.865, 0.415 ], "y_axis": [ -0.415, 0.280, -0.866 ], "z_axis": [ -0.865, -0.416, 0.281 ], "quaternion": [ 0.565, -0.199, -0.566, 0.566 ] } }, { "index": 19, "index_chain": 19, "chain_name": "A", "nt_resnum": 19, "nt_name": "C", "nt_code": "C", "nt_id": "///A/19", "linked_nts": [ "///A/18", "///A/20" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop", "alpha": -80.930, "beta": 148.710, "gamma": 75.270, "delta": 83.518, "epsilon": -165.866, "zeta": -69.206, "epsilon_zeta": -96.660, "bb_type": "BI", "chi": -143.829, "glyco_bond": "anti", "C5prime_xyz": [ -1.412, 8.848, -0.558 ], "P_xyz": [ 1.010, 8.932, -1.542 ], "form": ".", "ssZp": 3.570, "Dp": 4.275, "splay_angle": 21.130, "splay_distance": 3.822, "splay_ratio": 0.190, "d22": null, "d64": null, "eta": 151.704, "theta": -120.199, "eta_prime": 179.434, "theta_prime": -139.463, "eta_base": -127.098, "theta_base": -117.254, "v0": -1.097, "v1": -21.267, "v2": 34.055, "v3": -35.689, "v4": 23.167, "amplitude": 36.301, "phase_angle": 20.259, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.082, "filter_rmsd": 0.065, "frame": { "rmsd": 0.004, "origin": [ 31.770, -0.920, 1.470 ], "x_axis": [ -0.395, 0.891, -0.223 ], "y_axis": [ -0.426, -0.393, -0.815 ], "z_axis": [ -0.814, -0.227, 0.535 ], "quaternion": [ 0.432, -0.340, -0.342, 0.762 ] } }, { "index": 20, "index_chain": 20, "chain_name": "A", "nt_resnum": 20, "nt_name": "A", "nt_code": "A", "nt_id": "///A/20", "linked_nts": [ "///A/19", "///A/21" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": 111.218, "beta": -160.309, "gamma": -148.064, "delta": 93.835, "epsilon": -138.906, "zeta": -70.285, "epsilon_zeta": -68.621, "bb_type": "BI", "chi": -173.264, "glyco_bond": "anti", "C5prime_xyz": [ -1.254, 8.340, 1.442 ], "P_xyz": [ -0.050, 10.548, 0.747 ], "form": ".", "ssZp": 4.457, "Dp": 4.430, "splay_angle": 31.313, "splay_distance": 5.278, "splay_ratio": 0.276, "d22": null, "d64": null, "eta": 171.118, "theta": -140.911, "eta_prime": -175.517, "theta_prime": -139.997, "eta_base": -129.247, "theta_base": -94.597, "v0": 7.679, "v1": -22.631, "v2": 28.530, "v3": -24.775, "v4": 10.827, "amplitude": 28.582, "phase_angle": 3.449, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.005, "origin": [ 28.884, 0.283, 3.669 ], "x_axis": [ -0.389, 0.628, -0.674 ], "y_axis": [ -0.149, -0.765, -0.627 ], "z_axis": [ -0.909, -0.143, 0.391 ], "quaternion": [ 0.244, -0.496, -0.241, 0.798 ] } }, { "index": 21, "index_chain": 21, "chain_name": "A", "nt_resnum": 21, "nt_name": "C", "nt_code": "C", "nt_id": "///A/21", "linked_nts": [ "///A/20", "///A/22" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": 101.068, "beta": -156.710, "gamma": -135.179, "delta": 98.919, "epsilon": -135.485, "zeta": -51.153, "epsilon_zeta": -84.332, "bb_type": "BI", "chi": 170.832, "glyco_bond": "anti", "C5prime_xyz": [ -0.952, 7.639, 2.343 ], "P_xyz": [ 0.540, 9.774, 2.607 ], "form": "A", "ssZp": 4.478, "Dp": 4.429, "splay_angle": 23.736, "splay_distance": 3.917, "splay_ratio": 0.212, "d22": 4.300, "d64": 4.375, "eta": 170.670, "theta": -149.057, "eta_prime": -168.373, "theta_prime": -137.708, "eta_base": -100.257, "theta_base": -98.046, "v0": 16.466, "v1": -25.879, "v2": 25.535, "v3": -16.740, "v4": 0.229, "amplitude": 26.833, "phase_angle": 342.105, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.068, "frame": { "rmsd": 0.009, "origin": [ 23.923, 2.003, 3.138 ], "x_axis": [ -0.247, -0.150, -0.957 ], "y_axis": [ 0.394, -0.918, 0.042 ], "z_axis": [ -0.885, -0.367, 0.286 ], "quaternion": [ -0.174, -0.588, -0.104, 0.783 ] } }, { "index": 22, "index_chain": 22, "chain_name": "A", "nt_resnum": 22, "nt_name": "U", "nt_code": "U", "nt_id": "///A/22", "linked_nts": [ "///A/21", "///A/23" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop", "alpha": -72.754, "beta": -172.738, "gamma": 40.180, "delta": 75.699, "epsilon": -160.756, "zeta": -66.050, "epsilon_zeta": -94.707, "bb_type": "BI", "chi": -156.248, "glyco_bond": "anti", "C5prime_xyz": [ -1.674, 8.812, 0.245 ], "P_xyz": [ 0.613, 9.634, 1.169 ], "form": "A", "ssZp": 4.150, "Dp": 4.563, "splay_angle": 22.911, "splay_distance": 3.823, "splay_ratio": 0.204, "d22": 4.281, "d64": 4.679, "eta": 149.415, "theta": -155.589, "eta_prime": 177.433, "theta_prime": -152.637, "eta_base": -127.109, "theta_base": -133.672, "v0": 3.259, "v1": -30.316, "v2": 44.503, "v3": -43.832, "v4": 25.502, "amplitude": 45.995, "phase_angle": 14.632, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.183, "filter_rmsd": 0.106, "frame": { "rmsd": 0.004, "origin": [ 20.072, 1.886, 2.433 ], "x_axis": [ 0.092, -0.721, -0.687 ], "y_axis": [ 0.452, -0.585, 0.673 ], "z_axis": [ -0.887, -0.372, 0.272 ], "quaternion": [ -0.441, -0.592, 0.113, 0.664 ] } }, { "index": 23, "index_chain": 23, "chain_name": "A", "nt_resnum": 23, "nt_name": "C", "nt_code": "C", "nt_id": "///A/23", "linked_nts": [ "///A/22", "///A/24" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,non-stack,canonical,helix,stem-end,coaxial-stack,internal-loop", "alpha": -66.080, "beta": 178.219, "gamma": 53.271, "delta": 76.944, "epsilon": -118.525, "zeta": -92.817, "epsilon_zeta": -25.708, "bb_type": "--", "chi": -160.997, "glyco_bond": "anti", "C5prime_xyz": [ -1.751, 8.917, 0.525 ], "P_xyz": [ 0.686, 9.738, 0.994 ], "form": ".", "ssZp": 4.180, "Dp": 4.650, "splay_angle": 32.262, "splay_distance": 5.810, "splay_ratio": 0.286, "d22": null, "d64": null, "eta": 177.297, "theta": -149.024, "eta_prime": -176.757, "theta_prime": -166.558, "eta_base": -153.491, "theta_base": 178.259, "v0": -1.136, "v1": -25.580, "v2": 40.797, "v3": -42.557, "v4": 27.653, "amplitude": 43.423, "phase_angle": 20.026, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.812, "filter_rmsd": 0.064, "frame": { "rmsd": 0.004, "origin": [ 16.297, 1.693, 1.857 ], "x_axis": [ 0.428, -0.816, -0.388 ], "y_axis": [ 0.370, -0.234, 0.899 ], "z_axis": [ -0.824, -0.529, 0.202 ], "quaternion": [ 0.591, 0.604, -0.185, -0.502 ] } }, { "index": 24, "index_chain": 24, "chain_name": "A", "nt_resnum": 24, "nt_name": "A", "nt_code": "A", "nt_id": "///A/24", "linked_nts": [ "///A/23", "///A/25" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": 29.373, "beta": -99.768, "gamma": -103.933, "delta": 97.379, "epsilon": -153.736, "zeta": -48.341, "epsilon_zeta": -105.395, "bb_type": "BI", "chi": -178.622, "glyco_bond": "anti", "C5prime_xyz": [ -1.173, 8.130, 1.636 ], "P_xyz": [ -1.426, 10.712, 1.217 ], "form": ".", "ssZp": 4.478, "Dp": 4.441, "splay_angle": 34.464, "splay_distance": 5.249, "splay_ratio": 0.298, "d22": null, "d64": null, "eta": -174.196, "theta": -161.609, "eta_prime": 171.477, "theta_prime": -146.061, "eta_base": 163.237, "theta_base": -79.089, "v0": 10.217, "v1": -24.928, "v2": 29.427, "v3": -24.467, "v4": 9.124, "amplitude": 29.432, "phase_angle": 359.017, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.005, "origin": [ 10.927, 3.885, 1.520 ], "x_axis": [ 0.490, -0.628, -0.604 ], "y_axis": [ 0.489, -0.376, 0.787 ], "z_axis": [ -0.722, -0.681, 0.123 ], "quaternion": [ 0.556, 0.660, -0.053, -0.502 ] } }, { "index": 25, "index_chain": 25, "chain_name": "A", "nt_resnum": 25, "nt_name": "A", "nt_code": "A", "nt_id": "///A/25", "linked_nts": [ "///A/24", "///A/26" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": -173.491, "beta": -171.042, "gamma": 135.867, "delta": 91.053, "epsilon": -159.916, "zeta": -59.330, "epsilon_zeta": -100.586, "bb_type": "BI", "chi": -160.099, "glyco_bond": "anti", "C5prime_xyz": [ -0.982, 8.452, 0.688 ], "P_xyz": [ 1.304, 8.971, -0.474 ], "form": "A", "ssZp": 4.131, "Dp": 4.474, "splay_angle": 22.430, "splay_distance": 3.724, "splay_ratio": 0.198, "d22": null, "d64": null, "eta": 147.074, "theta": -123.080, "eta_prime": -171.351, "theta_prime": -147.821, "eta_base": -85.575, "theta_base": -134.825, "v0": 14.276, "v1": -31.581, "v2": 35.988, "v3": -28.742, "v4": 9.232, "amplitude": 36.079, "phase_angle": 355.929, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.040, "frame": { "rmsd": 0.006, "origin": [ 11.137, -1.324, 0.914 ], "x_axis": [ 0.536, -0.673, 0.510 ], "y_axis": [ -0.393, 0.335, 0.856 ], "z_axis": [ -0.747, -0.659, -0.085 ], "quaternion": [ 0.668, 0.567, -0.470, -0.105 ] } }, { "index": 26, "index_chain": 26, "chain_name": "A", "nt_resnum": 26, "nt_name": "A", "nt_code": "A", "nt_id": "///A/26", "linked_nts": [ "///A/25", "///A/27" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop", "alpha": 159.828, "beta": 168.060, "gamma": 155.618, "delta": 86.453, "epsilon": -147.332, "zeta": -74.922, "epsilon_zeta": -72.409, "bb_type": "BI", "chi": 174.624, "glyco_bond": "anti", "C5prime_xyz": [ -0.962, 7.782, 1.996 ], "P_xyz": [ 0.721, 9.651, 1.271 ], "form": ".", "ssZp": 4.722, "Dp": 4.744, "splay_angle": 31.994, "splay_distance": 4.370, "splay_ratio": 0.278, "d22": null, "d64": null, "eta": 135.844, "theta": -168.316, "eta_prime": 156.338, "theta_prime": -159.823, "eta_base": -158.974, "theta_base": -124.895, "v0": 21.669, "v1": -41.654, "v2": 44.826, "v3": -33.651, "v4": 7.691, "amplitude": 45.391, "phase_angle": 350.947, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "1c", "suiteness": 0.148, "filter_rmsd": 0.038, "frame": { "rmsd": 0.009, "origin": [ 9.539, -4.246, -0.753 ], "x_axis": [ 0.422, -0.280, 0.862 ], "y_axis": [ -0.589, 0.639, 0.495 ], "z_axis": [ -0.690, -0.716, 0.105 ], "quaternion": [ 0.736, 0.412, -0.527, 0.105 ] } }, { "index": 27, "index_chain": 27, "chain_name": "A", "nt_resnum": 27, "nt_name": "C", "nt_code": "C", "nt_id": "///A/27", "linked_nts": [ "///A/26", "///A/28" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,internal-loop,cap-donor,phosphate", "alpha": -53.008, "beta": -178.566, "gamma": 59.336, "delta": 104.419, "epsilon": -128.365, "zeta": -56.518, "epsilon_zeta": -71.847, "bb_type": "--", "chi": -174.426, "glyco_bond": "anti", "C5prime_xyz": [ -1.050, 8.219, 1.539 ], "P_xyz": [ 1.318, 7.623, 2.543 ], "form": ".", "ssZp": 4.080, "Dp": 4.229, "splay_angle": 23.316, "splay_distance": 3.979, "splay_ratio": 0.204, "d22": 3.903, "d64": 3.706, "eta": -160.887, "theta": -94.639, "eta_prime": -147.084, "theta_prime": -98.848, "eta_base": -113.431, "theta_base": -65.340, "v0": 10.392, "v1": -18.613, "v2": 19.531, "v3": -14.038, "v4": 2.392, "amplitude": 19.954, "phase_angle": 348.184, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.057, "filter_rmsd": 0.067, "frame": { "rmsd": 0.006, "origin": [ 8.452, -8.458, -0.331 ], "x_axis": [ 0.003, 0.293, 0.956 ], "y_axis": [ -0.577, 0.781, -0.237 ], "z_axis": [ -0.817, -0.551, 0.172 ], "quaternion": [ 0.699, 0.112, -0.634, 0.311 ] } }, { "index": 28, "index_chain": 28, "chain_name": "A", "nt_resnum": 28, "nt_name": "U", "nt_code": "U", "nt_id": "///A/28", "linked_nts": [ "///A/27", "///A/29" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor", "alpha": -60.956, "beta": 171.710, "gamma": 30.600, "delta": 79.075, "epsilon": 170.203, "zeta": 29.638, "epsilon_zeta": 140.565, "bb_type": "--", "chi": -148.697, "glyco_bond": "anti", "C5prime_xyz": [ -1.850, 8.901, -0.221 ], "P_xyz": [ 0.469, 10.022, 0.141 ], "form": ".", "ssZp": 4.002, "Dp": 4.139, "splay_angle": 79.156, "splay_distance": 11.577, "splay_ratio": 0.637, "d22": null, "d64": null, "eta": 140.886, "theta": -85.805, "eta_prime": 175.422, "theta_prime": -72.581, "eta_base": -120.613, "theta_base": -45.912, "v0": -7.193, "v1": -18.508, "v2": 35.628, "v3": -40.848, "v4": 30.082, "amplitude": 40.553, "phase_angle": 28.532, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.010, "filter_rmsd": 0.105, "frame": { "rmsd": 0.003, "origin": [ 5.878, -9.758, 2.411 ], "x_axis": [ -0.279, 0.832, 0.479 ], "y_axis": [ -0.473, 0.315, -0.823 ], "z_axis": [ -0.835, -0.457, 0.306 ], "quaternion": [ 0.579, -0.158, -0.568, 0.564 ] } }, { "index": 29, "index_chain": 29, "chain_name": "A", "nt_resnum": 29, "nt_name": "A", "nt_code": "A", "nt_id": "///A/29", "linked_nts": [ "///A/28", "///A/30" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,BI,non-pair-contact,ss-non-loop,cap-donor,cap-acceptor,phosphate", "alpha": -129.772, "beta": 150.449, "gamma": 113.266, "delta": 102.566, "epsilon": -130.884, "zeta": -74.729, "epsilon_zeta": -56.155, "bb_type": "BI", "chi": -173.710, "glyco_bond": "anti", "C5prime_xyz": [ -1.332, 8.386, 1.444 ], "P_xyz": [ 1.070, 9.022, 0.564 ], "form": "B", "ssZp": 4.000, "Dp": 4.048, "splay_angle": 19.680, "splay_distance": 3.317, "splay_ratio": 0.172, "d22": null, "d64": null, "eta": -174.152, "theta": -132.821, "eta_prime": -118.297, "theta_prime": -135.690, "eta_base": -57.231, "theta_base": -100.394, "v0": 0.542, "v1": -10.571, "v2": 16.042, "v3": -16.097, "v4": 9.849, "amplitude": 16.750, "phase_angle": 16.723, "puckering": "C3'-endo", "sugar_class": "--", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.003, "origin": [ -3.500, -4.099, -1.339 ], "x_axis": [ -0.392, 0.010, -0.920 ], "y_axis": [ 0.480, -0.851, -0.214 ], "z_axis": [ -0.785, -0.526, 0.329 ], "quaternion": [ -0.146, -0.531, -0.231, 0.802 ] } }, { "index": 30, "index_chain": 30, "chain_name": "A", "nt_resnum": 30, "nt_name": "C", "nt_code": "C", "nt_id": "///A/30", "linked_nts": [ "///A/29", "///A/31" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-pair-contact,ss-non-loop", "alpha": -63.909, "beta": 146.747, "gamma": 71.873, "delta": 85.810, "epsilon": -108.602, "zeta": -100.252, "epsilon_zeta": -8.350, "bb_type": "--", "chi": -150.909, "glyco_bond": "anti", "C5prime_xyz": [ -2.222, 9.014, -0.364 ], "P_xyz": [ 0.160, 9.754, -1.154 ], "form": ".", "ssZp": 3.107, "Dp": 3.787, "splay_angle": 33.563, "splay_distance": 5.936, "splay_ratio": 0.289, "d22": null, "d64": null, "eta": 177.473, "theta": -129.665, "eta_prime": -158.302, "theta_prime": -159.691, "eta_base": -107.654, "theta_base": 159.566, "v0": -24.283, "v1": 1.729, "v2": 19.784, "v3": -34.322, "v4": 37.094, "amplitude": 37.330, "phase_angle": 57.997, "puckering": "C4'-exo", "sugar_class": "--", "bin": "33p", "cluster": "1a", "suiteness": 0.042, "filter_rmsd": 0.064, "frame": { "rmsd": 0.002, "origin": [ -6.631, -5.194, -1.348 ], "x_axis": [ -0.262, -0.624, -0.736 ], "y_axis": [ 0.446, -0.755, 0.481 ], "z_axis": [ -0.856, -0.202, 0.475 ], "quaternion": [ -0.339, -0.504, 0.088, 0.789 ] } }, { "index": 31, "index_chain": 31, "chain_name": "A", "nt_resnum": 31, "nt_name": "A", "nt_code": "A", "nt_id": "///A/31", "linked_nts": [ "///A/30", "///A/32" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,ss-non-loop", "alpha": 33.571, "beta": -146.696, "gamma": -145.701, "delta": 92.916, "epsilon": 176.729, "zeta": -47.666, "epsilon_zeta": -135.605, "bb_type": "BI", "chi": -135.221, "glyco_bond": "anti", "C5prime_xyz": [ -1.027, 8.408, -0.916 ], "P_xyz": [ -0.777, 9.644, -3.195 ], "form": ".", "ssZp": 3.747, "Dp": 4.345, "splay_angle": 31.249, "splay_distance": 4.869, "splay_ratio": 0.270, "d22": null, "d64": null, "eta": 108.585, "theta": 174.663, "eta_prime": 116.394, "theta_prime": -172.632, "eta_base": 99.398, "theta_base": -135.296, "v0": 14.560, "v1": -33.789, "v2": 38.621, "v3": -30.542, "v4": 10.388, "amplitude": 38.696, "phase_angle": 356.428, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.003, "origin": [ -8.007, -1.746, 3.284 ], "x_axis": [ 0.209, -0.265, -0.941 ], "y_axis": [ 0.086, -0.954, 0.287 ], "z_axis": [ -0.974, -0.141, -0.176 ], "quaternion": [ 0.140, 0.765, -0.058, -0.626 ] } }, { "index": 32, "index_chain": 32, "chain_name": "A", "nt_resnum": 32, "nt_name": "G", "nt_code": "G", "nt_id": "///A/32", "linked_nts": [ "///A/31", "///A/33" ], "nt_type": "RNA", "dbn": "[", "summary": "pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack", "alpha": -85.145, "beta": 165.357, "gamma": 94.436, "delta": 89.875, "epsilon": -136.119, "zeta": -86.530, "epsilon_zeta": -49.589, "bb_type": "BI", "chi": -138.994, "glyco_bond": "anti", "C5prime_xyz": [ -1.047, 8.633, -0.694 ], "P_xyz": [ 1.168, 8.527, -2.118 ], "form": ".", "ssZp": 3.409, "Dp": 4.558, "splay_angle": 29.709, "splay_distance": 4.951, "splay_ratio": 0.257, "d22": null, "d64": null, "eta": -165.960, "theta": -150.008, "eta_prime": -142.093, "theta_prime": -153.440, "eta_base": -98.238, "theta_base": -144.496, "v0": 6.693, "v1": -24.625, "v2": 32.460, "v3": -29.253, "v4": 14.335, "amplitude": 32.704, "phase_angle": 7.002, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ -11.676, -3.376, 0.529 ], "x_axis": [ -0.180, -0.807, -0.562 ], "y_axis": [ -0.185, -0.534, 0.825 ], "z_axis": [ -0.966, 0.253, -0.053 ], "quaternion": [ -0.241, -0.593, 0.418, 0.644 ] } }, { "index": 33, "index_chain": 33, "chain_name": "A", "nt_resnum": 33, "nt_name": "A", "nt_code": "A", "nt_id": "///A/33", "linked_nts": [ "///A/32", "///A/34" ], "nt_type": "RNA", "dbn": "[", "summary": "pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet", "alpha": -76.789, "beta": 149.324, "gamma": 82.080, "delta": 86.291, "epsilon": -164.328, "zeta": -83.660, "epsilon_zeta": -80.668, "bb_type": "BI", "chi": -159.983, "glyco_bond": "anti", "C5prime_xyz": [ -1.823, 8.846, 0.386 ], "P_xyz": [ 0.592, 9.409, -0.444 ], "form": ".", "ssZp": 4.057, "Dp": 4.209, "splay_angle": 27.557, "splay_distance": 4.386, "splay_ratio": 0.238, "d22": null, "d64": null, "eta": 167.452, "theta": -161.184, "eta_prime": -172.390, "theta_prime": -166.743, "eta_base": -149.623, "theta_base": -148.070, "v0": -9.064, "v1": -13.095, "v2": 28.806, "v3": -34.855, "v4": 27.663, "amplitude": 34.510, "phase_angle": 33.413, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.040, "filter_rmsd": 0.038, "frame": { "rmsd": 0.003, "origin": [ -16.468, -2.196, 0.132 ], "x_axis": [ 0.062, -0.956, -0.287 ], "y_axis": [ -0.024, -0.289, 0.957 ], "z_axis": [ -0.998, -0.052, -0.041 ], "quaternion": [ 0.428, 0.590, -0.415, -0.544 ] } }, { "index": 34, "index_chain": 34, "chain_name": "A", "nt_resnum": 34, "nt_name": "G", "nt_code": "G", "nt_id": "///A/34", "linked_nts": [ "///A/33", "///A/35" ], "nt_type": "RNA", "dbn": "[", "summary": "pseudoknotted,anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor", "alpha": -72.393, "beta": 167.369, "gamma": 77.231, "delta": 89.061, "epsilon": -118.613, "zeta": -64.780, "epsilon_zeta": -53.833, "bb_type": "--", "chi": -151.490, "glyco_bond": "anti", "C5prime_xyz": [ -1.491, 8.838, -0.032 ], "P_xyz": [ 1.074, 9.157, -0.478 ], "form": ".", "ssZp": 3.591, "Dp": 4.438, "splay_angle": 44.265, "splay_distance": 7.889, "splay_ratio": 0.379, "d22": null, "d64": null, "eta": -168.034, "theta": -141.243, "eta_prime": -161.097, "theta_prime": -159.710, "eta_base": -137.636, "theta_base": -178.610, "v0": -2.972, "v1": -17.246, "v2": 29.627, "v3": -32.166, "v4": 22.199, "amplitude": 32.364, "phase_angle": 23.734, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.180, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ -20.503, -1.123, -1.210 ], "x_axis": [ -0.210, -0.965, 0.156 ], "y_axis": [ -0.074, 0.175, 0.982 ], "z_axis": [ -0.975, 0.194, -0.108 ], "quaternion": [ -0.463, -0.425, 0.611, 0.481 ] } }, { "index": 35, "index_chain": 35, "chain_name": "A", "nt_resnum": 35, "nt_name": "A", "nt_code": "A", "nt_id": "///A/35", "linked_nts": [ "///A/34", "///A/36" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop", "alpha": -94.914, "beta": 69.642, "gamma": -168.952, "delta": 103.450, "epsilon": -122.466, "zeta": -60.947, "epsilon_zeta": -61.519, "bb_type": "--", "chi": 156.505, "glyco_bond": "anti", "C5prime_xyz": [ -2.800, 8.257, 2.122 ], "P_xyz": [ -2.955, 10.456, 0.698 ], "form": "B", "ssZp": 2.161, "Dp": 2.772, "splay_angle": 20.159, "splay_distance": 3.338, "splay_ratio": 0.175, "d22": null, "d64": null, "eta": -130.877, "theta": -153.166, "eta_prime": -150.372, "theta_prime": -151.837, "eta_base": -166.597, "theta_base": -134.944, "v0": -31.631, "v1": 19.140, "v2": -0.649, "v3": -17.400, "v4": 30.748, "amplitude": 32.147, "phase_angle": 91.156, "puckering": "O4'-endo", "sugar_class": "--", "bin": "33t", "cluster": "1e", "suiteness": 0.010, "filter_rmsd": 0.040, "frame": { "rmsd": 0.006, "origin": [ -24.450, 4.887, -4.457 ], "x_axis": [ -0.024, -0.944, -0.330 ], "y_axis": [ 0.106, -0.331, 0.938 ], "z_axis": [ -0.994, -0.012, 0.108 ], "quaternion": [ -0.434, -0.548, 0.383, 0.605 ] } }, { "index": 36, "index_chain": 36, "chain_name": "A", "nt_resnum": 36, "nt_name": "C", "nt_code": "C", "nt_id": "///A/36", "linked_nts": [ "///A/35", "///A/37" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop", "alpha": 159.349, "beta": 152.487, "gamma": 151.406, "delta": 144.307, "epsilon": -92.807, "zeta": -34.401, "epsilon_zeta": -58.406, "bb_type": "--", "chi": -128.461, "glyco_bond": "anti", "C5prime_xyz": [ -1.332, 8.518, -0.673 ], "P_xyz": [ 0.333, 9.085, -2.612 ], "form": ".", "ssZp": 1.233, "Dp": 1.498, "splay_angle": 36.553, "splay_distance": 6.392, "splay_ratio": 0.315, "d22": null, "d64": null, "eta": 153.821, "theta": -105.303, "eta_prime": -179.497, "theta_prime": -113.634, "eta_base": -157.709, "theta_base": -95.588, "v0": -9.102, "v1": 23.254, "v2": -27.863, "v3": 23.504, "v4": -9.160, "amplitude": 27.863, "phase_angle": 180.206, "puckering": "C3'-exo", "sugar_class": "~C2'-endo", "bin": "32t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.064, "frame": { "rmsd": 0.002, "origin": [ -27.436, 6.340, -4.798 ], "x_axis": [ 0.142, -0.946, 0.291 ], "y_axis": [ -0.102, 0.279, 0.955 ], "z_axis": [ -0.985, -0.166, -0.057 ], "quaternion": [ 0.584, 0.480, -0.546, -0.361 ] } }, { "index": 37, "index_chain": 37, "chain_name": "A", "nt_resnum": 37, "nt_name": "G", "nt_code": "G", "nt_id": "///A/37", "linked_nts": [ "///A/36", "///A/38" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,multiplet,hairpin-loop", "alpha": -108.054, "beta": 74.230, "gamma": 152.315, "delta": 94.484, "epsilon": -113.520, "zeta": -36.886, "epsilon_zeta": -76.634, "bb_type": "--", "chi": -156.084, "glyco_bond": "anti", "C5prime_xyz": [ -2.654, 8.994, -0.355 ], "P_xyz": [ -2.372, 9.052, -2.972 ], "form": ".", "ssZp": 2.585, "Dp": 2.869, "splay_angle": 40.338, "splay_distance": 6.888, "splay_ratio": 0.347, "d22": null, "d64": null, "eta": 167.105, "theta": -108.027, "eta_prime": -172.246, "theta_prime": -123.678, "eta_base": -151.161, "theta_base": -143.760, "v0": -38.212, "v1": 20.899, "v2": 2.787, "v3": -24.683, "v4": 39.336, "amplitude": 40.104, "phase_angle": 86.015, "puckering": "O4'-endo", "sugar_class": "--", "bin": "23t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.003, "frame": { "rmsd": 0.003, "origin": [ -32.820, 4.946, -1.648 ], "x_axis": [ 0.529, -0.655, 0.540 ], "y_axis": [ 0.140, 0.695, 0.706 ], "z_axis": [ -0.837, -0.298, 0.459 ], "quaternion": [ 0.819, 0.306, -0.420, -0.243 ] } }, { "index": 38, "index_chain": 38, "chain_name": "A", "nt_resnum": 38, "nt_name": "C", "nt_code": "C", "nt_id": "///A/38", "linked_nts": [ "///A/37", "///A/39" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop", "alpha": 112.664, "beta": -169.289, "gamma": 90.577, "delta": 78.166, "epsilon": -163.674, "zeta": -71.106, "epsilon_zeta": -92.569, "bb_type": "BI", "chi": -159.385, "glyco_bond": "anti", "C5prime_xyz": [ -1.508, 8.873, 0.498 ], "P_xyz": [ 0.955, 9.517, -0.155 ], "form": "A", "ssZp": 4.489, "Dp": 4.516, "splay_angle": 24.172, "splay_distance": 3.842, "splay_ratio": 0.212, "d22": 4.981, "d64": 5.230, "eta": 11.617, "theta": -158.071, "eta_prime": 59.371, "theta_prime": -160.749, "eta_base": 84.608, "theta_base": -144.958, "v0": -1.079, "v1": -24.604, "v2": 39.493, "v3": -41.317, "v4": 26.588, "amplitude": 42.043, "phase_angle": 20.058, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.064, "frame": { "rmsd": 0.002, "origin": [ -38.270, 4.108, 2.480 ], "x_axis": [ 0.197, 0.078, -0.977 ], "y_axis": [ 0.167, 0.980, 0.112 ], "z_axis": [ 0.966, -0.185, 0.180 ], "quaternion": [ 0.767, 0.097, 0.633, -0.029 ] } }, { "index": 39, "index_chain": 39, "chain_name": "A", "nt_resnum": 39, "nt_name": "C", "nt_code": "C", "nt_id": "///A/39", "linked_nts": [ "///A/38", "///A/40" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop", "alpha": -84.921, "beta": 166.355, "gamma": 88.125, "delta": 80.305, "epsilon": -127.493, "zeta": -76.315, "epsilon_zeta": -51.178, "bb_type": "--", "chi": -158.211, "glyco_bond": "anti", "C5prime_xyz": [ -1.289, 8.793, 0.405 ], "P_xyz": [ 1.150, 9.294, -0.383 ], "form": "A", "ssZp": 4.123, "Dp": 4.722, "splay_angle": 23.244, "splay_distance": 3.797, "splay_ratio": 0.202, "d22": null, "d64": null, "eta": -176.984, "theta": -139.811, "eta_prime": -167.933, "theta_prime": -142.702, "eta_base": -142.647, "theta_base": -117.536, "v0": 7.228, "v1": -31.553, "v2": 42.729, "v3": -39.700, "v4": 20.454, "amplitude": 43.289, "phase_angle": 9.231, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.066, "frame": { "rmsd": 0.006, "origin": [ -35.311, 1.671, 2.747 ], "x_axis": [ 0.350, 0.442, -0.826 ], "y_axis": [ 0.213, 0.821, 0.529 ], "z_axis": [ 0.912, -0.361, 0.194 ], "quaternion": [ 0.769, 0.290, 0.565, 0.074 ] } }, { "index": 40, "index_chain": 40, "chain_name": "A", "nt_resnum": 40, "nt_name": "A", "nt_code": "A", "nt_id": "///A/40", "linked_nts": [ "///A/39", "///A/41" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop", "alpha": -75.890, "beta": 150.255, "gamma": 73.477, "delta": 78.573, "epsilon": -159.439, "zeta": -59.977, "epsilon_zeta": -99.461, "bb_type": "BI", "chi": -177.733, "glyco_bond": "anti", "C5prime_xyz": [ -1.912, 8.649, 1.418 ], "P_xyz": [ 0.556, 9.451, 1.131 ], "form": ".", "ssZp": 4.530, "Dp": 4.491, "splay_angle": 26.825, "splay_distance": 4.446, "splay_ratio": 0.243, "d22": null, "d64": null, "eta": 154.385, "theta": -140.760, "eta_prime": 176.044, "theta_prime": -143.385, "eta_base": -137.212, "theta_base": -117.986, "v0": -5.910, "v1": -20.779, "v2": 37.931, "v3": -42.397, "v4": 30.390, "amplitude": 42.342, "phase_angle": 26.388, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.274, "filter_rmsd": 0.038, "frame": { "rmsd": 0.003, "origin": [ -31.823, 0.483, 1.833 ], "x_axis": [ 0.063, 0.875, -0.480 ], "y_axis": [ -0.015, 0.482, 0.876 ], "z_axis": [ 0.998, -0.048, 0.043 ], "quaternion": [ 0.630, 0.367, 0.586, 0.353 ] } }, { "index": 41, "index_chain": 41, "chain_name": "A", "nt_resnum": 41, "nt_name": "G", "nt_code": "G", "nt_id": "///A/41", "linked_nts": [ "///A/40", "///A/42" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop", "alpha": -79.200, "beta": -179.838, "gamma": 83.915, "delta": 88.238, "epsilon": -143.299, "zeta": -56.597, "epsilon_zeta": -86.702, "bb_type": "BI", "chi": -164.087, "glyco_bond": "anti", "C5prime_xyz": [ -1.842, 8.952, 0.459 ], "P_xyz": [ 0.618, 9.775, 0.783 ], "form": "B", "ssZp": 3.668, "Dp": 4.008, "splay_angle": 20.158, "splay_distance": 3.402, "splay_ratio": 0.175, "d22": null, "d64": null, "eta": -168.774, "theta": -140.445, "eta_prime": -152.385, "theta_prime": -152.388, "eta_base": -113.852, "theta_base": -133.940, "v0": -17.086, "v1": -3.244, "v2": 20.808, "v3": -31.248, "v4": 30.412, "amplitude": 32.168, "phase_angle": 49.695, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.028, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ -28.134, 0.620, -0.644 ], "x_axis": [ 0.144, 0.981, 0.133 ], "y_axis": [ -0.037, -0.129, 0.991 ], "z_axis": [ 0.989, -0.148, 0.018 ], "quaternion": [ 0.508, 0.560, 0.421, 0.501 ] } }, { "index": 42, "index_chain": 42, "chain_name": "A", "nt_resnum": 42, "nt_name": "U", "nt_code": "U", "nt_id": "///A/42", "linked_nts": [ "///A/41", "///A/43" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop", "alpha": -127.150, "beta": 107.688, "gamma": 137.726, "delta": 93.872, "epsilon": -131.926, "zeta": -46.837, "epsilon_zeta": -85.089, "bb_type": "BI", "chi": -163.013, "glyco_bond": "anti", "C5prime_xyz": [ -1.088, 8.410, 0.771 ], "P_xyz": [ -0.311, 9.631, -1.434 ], "form": ".", "ssZp": 4.296, "Dp": 4.648, "splay_angle": 53.926, "splay_distance": 8.455, "splay_ratio": 0.454, "d22": 6.294, "d64": 7.744, "eta": 171.204, "theta": -171.151, "eta_prime": -179.763, "theta_prime": 156.879, "eta_base": -146.761, "theta_base": 95.275, "v0": 15.023, "v1": -31.004, "v2": 34.439, "v3": -26.774, "v4": 7.506, "amplitude": 34.650, "phase_angle": 353.676, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.104, "frame": { "rmsd": 0.005, "origin": [ -25.109, -0.357, -1.857 ], "x_axis": [ 0.495, 0.752, 0.436 ], "y_axis": [ 0.109, -0.551, 0.827 ], "z_axis": [ 0.862, -0.362, -0.355 ], "quaternion": [ 0.384, 0.775, 0.278, 0.419 ] } }, { "index": 43, "index_chain": 43, "chain_name": "A", "nt_resnum": 43, "nt_name": "C", "nt_code": "C", "nt_id": "///A/43", "linked_nts": [ "///A/42", "///A/44" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-stack,non-pair-contact,hairpin-loop", "alpha": -128.674, "beta": 73.629, "gamma": 137.103, "delta": 76.161, "epsilon": -149.032, "zeta": -29.669, "epsilon_zeta": -119.362, "bb_type": "BI", "chi": -135.985, "glyco_bond": "anti", "C5prime_xyz": [ -2.362, 8.930, -0.900 ], "P_xyz": [ -3.198, 8.317, -3.320 ], "form": ".", "ssZp": 3.459, "Dp": 4.402, "splay_angle": 60.710, "splay_distance": 9.616, "splay_ratio": 0.506, "d22": null, "d64": null, "eta": 128.842, "theta": -131.356, "eta_prime": 128.893, "theta_prime": -125.963, "eta_base": 81.674, "theta_base": -86.387, "v0": -17.939, "v1": -10.535, "v2": 33.251, "v3": -44.426, "v4": 39.104, "amplitude": 44.481, "phase_angle": 41.624, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.064, "frame": { "rmsd": 0.003, "origin": [ -30.273, -6.851, -3.485 ], "x_axis": [ -0.111, 0.981, -0.162 ], "y_axis": [ 0.984, 0.132, 0.123 ], "z_axis": [ 0.142, -0.145, -0.979 ], "quaternion": [ 0.102, 0.659, 0.745, -0.008 ] } }, { "index": 44, "index_chain": 44, "chain_name": "A", "nt_resnum": 44, "nt_name": "A", "nt_code": "A", "nt_id": "///A/44", "linked_nts": [ "///A/43", "///A/45" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop", "alpha": -122.359, "beta": -141.309, "gamma": 61.249, "delta": 85.992, "epsilon": -144.472, "zeta": -53.704, "epsilon_zeta": -90.767, "bb_type": "BI", "chi": -158.165, "glyco_bond": "anti", "C5prime_xyz": [ -1.384, 8.783, 0.412 ], "P_xyz": [ 1.003, 9.108, 1.489 ], "form": ".", "ssZp": 4.267, "Dp": 4.513, "splay_angle": 29.410, "splay_distance": 4.743, "splay_ratio": 0.254, "d22": null, "d64": null, "eta": 148.885, "theta": -117.416, "eta_prime": -178.106, "theta_prime": -112.668, "eta_base": -124.397, "theta_base": -58.363, "v0": -0.150, "v1": -21.424, "v2": 33.503, "v3": -34.370, "v4": 21.863, "amplitude": 35.376, "phase_angle": 18.729, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.004, "origin": [ -23.912, 0.361, -3.522 ], "x_axis": [ 0.260, -0.236, 0.936 ], "y_axis": [ 0.153, -0.947, -0.281 ], "z_axis": [ 0.953, 0.216, -0.210 ], "quaternion": [ -0.160, 0.777, -0.027, 0.608 ] } }, { "index": 45, "index_chain": 45, "chain_name": "A", "nt_resnum": 45, "nt_name": "C", "nt_code": "C", "nt_id": "///A/45", "linked_nts": [ "///A/44", "///A/46" ], "nt_type": "RNA", "dbn": "]", "summary": "pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor", "alpha": -60.076, "beta": -179.530, "gamma": 35.932, "delta": 85.853, "epsilon": -136.900, "zeta": -85.716, "epsilon_zeta": -51.184, "bb_type": "BI", "chi": -145.806, "glyco_bond": "anti", "C5prime_xyz": [ -1.164, 8.732, -0.426 ], "P_xyz": [ 1.333, 9.336, 0.115 ], "form": ".", "ssZp": 3.589, "Dp": 4.626, "splay_angle": 26.394, "splay_distance": 4.404, "splay_ratio": 0.228, "d22": 4.407, "d64": 4.522, "eta": 164.371, "theta": -145.434, "eta_prime": -171.186, "theta_prime": -138.393, "eta_base": -102.016, "theta_base": -117.476, "v0": 4.807, "v1": -25.830, "v2": 35.713, "v3": -34.064, "v4": 18.575, "amplitude": 36.421, "phase_angle": 11.319, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.414, "filter_rmsd": 0.065, "frame": { "rmsd": 0.006, "origin": [ -20.342, -1.304, -0.880 ], "x_axis": [ -0.069, -0.960, 0.273 ], "y_axis": [ 0.090, -0.278, -0.956 ], "z_axis": [ 0.994, -0.042, 0.106 ], "quaternion": [ -0.435, 0.525, -0.414, 0.603 ] } }, { "index": 46, "index_chain": 46, "chain_name": "A", "nt_resnum": 46, "nt_name": "U", "nt_code": "U", "nt_id": "///A/46", "linked_nts": [ "///A/45", "///A/47" ], "nt_type": "RNA", "dbn": "]", "summary": "pseudoknotted,anti,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop", "alpha": -46.584, "beta": 150.633, "gamma": 61.812, "delta": 90.718, "epsilon": -105.216, "zeta": -94.645, "epsilon_zeta": -10.571, "bb_type": "--", "chi": -149.479, "glyco_bond": "anti", "C5prime_xyz": [ -1.984, 8.914, -0.276 ], "P_xyz": [ 0.508, 9.535, -0.691 ], "form": ".", "ssZp": 3.083, "Dp": 3.741, "splay_angle": 27.089, "splay_distance": 4.915, "splay_ratio": 0.234, "d22": 4.291, "d64": 4.601, "eta": -165.383, "theta": -118.702, "eta_prime": -151.808, "theta_prime": -135.043, "eta_base": -129.310, "theta_base": -113.649, "v0": -17.723, "v1": -1.942, "v2": 19.339, "v3": -30.141, "v4": 30.285, "amplitude": 31.418, "phase_angle": 52.010, "puckering": "C4'-exo", "sugar_class": "--", "bin": "33p", "cluster": "1a", "suiteness": 0.415, "filter_rmsd": 0.103, "frame": { "rmsd": 0.004, "origin": [ -16.137, -2.222, 0.056 ], "x_axis": [ -0.164, -0.975, -0.149 ], "y_axis": [ 0.113, 0.132, -0.985 ], "z_axis": [ 0.980, -0.179, 0.089 ], "quaternion": [ 0.514, -0.392, 0.549, -0.529 ] } }, { "index": 47, "index_chain": 47, "chain_name": "A", "nt_resnum": 47, "nt_name": "C", "nt_code": "C", "nt_id": "///A/47", "linked_nts": [ "///A/46", "///A/48" ], "nt_type": "RNA", "dbn": "]", "summary": "pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,splayed-apart", "alpha": 47.168, "beta": -110.839, "gamma": -128.160, "delta": 82.010, "epsilon": -97.194, "zeta": -130.405, "epsilon_zeta": 33.211, "bb_type": "--", "chi": -162.207, "glyco_bond": "anti", "C5prime_xyz": [ -0.815, 8.451, 0.696 ], "P_xyz": [ -0.509, 10.559, -0.816 ], "form": ".", "ssZp": 4.065, "Dp": 4.865, "splay_angle": 127.752, "splay_distance": 17.831, "splay_ratio": 0.898, "d22": null, "d64": null, "eta": 154.671, "theta": 135.575, "eta_prime": 162.987, "theta_prime": 156.972, "eta_base": -159.838, "theta_base": -153.829, "v0": 17.075, "v1": -39.852, "v2": 46.853, "v3": -37.871, "v4": 13.028, "amplitude": 46.894, "phase_angle": 357.607, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.068, "frame": { "rmsd": 0.007, "origin": [ -11.694, -4.306, 0.313 ], "x_axis": [ -0.318, -0.773, -0.549 ], "y_axis": [ 0.081, 0.554, -0.828 ], "z_axis": [ 0.945, -0.308, -0.114 ], "quaternion": [ 0.530, -0.246, 0.705, -0.403 ] } }, { "index": 48, "index_chain": 48, "chain_name": "A", "nt_resnum": 48, "nt_name": "A", "nt_code": "A", "nt_id": "///A/48", "linked_nts": [ "///A/47", "///A/49" ], "nt_type": "RNA", "dbn": ".", "summary": "turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart", "alpha": -85.468, "beta": -177.953, "gamma": -167.295, "delta": 143.691, "epsilon": -138.106, "zeta": 96.314, "epsilon_zeta": 125.580, "bb_type": "--", "chi": -142.359, "glyco_bond": "anti", "C5prime_xyz": [ -2.093, 8.769, -0.112 ], "P_xyz": [ -0.733, 10.560, -1.460 ], "form": ".", "ssZp": 1.654, "Dp": 1.850, "splay_angle": 127.656, "splay_distance": 15.495, "splay_ratio": 0.899, "d22": null, "d64": null, "eta": -10.244, "theta": 28.597, "eta_prime": -33.114, "theta_prime": 39.508, "eta_base": -88.756, "theta_base": 103.962, "v0": -27.239, "v1": 40.152, "v2": -37.331, "v3": 22.880, "v4": 2.521, "amplitude": 40.338, "phase_angle": 157.738, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.002, "origin": [ 3.510, -1.538, -8.584 ], "x_axis": [ -0.247, -0.179, -0.952 ], "y_axis": [ -0.934, 0.306, 0.185 ], "z_axis": [ 0.258, 0.935, -0.243 ], "quaternion": [ 0.452, -0.415, 0.670, 0.418 ] } }, { "index": 49, "index_chain": 49, "chain_name": "A", "nt_resnum": 49, "nt_name": "G", "nt_code": "G", "nt_id": "///A/49", "linked_nts": [ "///A/48", "///A/50" ], "nt_type": "RNA", "dbn": ".", "summary": "~C3'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart", "alpha": -76.836, "beta": 111.773, "gamma": 147.178, "delta": 99.331, "epsilon": -80.985, "zeta": -52.492, "epsilon_zeta": -28.493, "bb_type": "--", "chi": -71.391, "glyco_bond": "--", "C5prime_xyz": [ -2.345, 6.126, -3.313 ], "P_xyz": [ -3.746, 4.596, -4.919 ], "form": ".", "ssZp": -2.523, "Dp": 4.562, "splay_angle": 84.108, "splay_distance": 13.668, "splay_ratio": 0.670, "d22": null, "d64": null, "eta": -82.935, "theta": -136.238, "eta_prime": -84.695, "theta_prime": -162.947, "eta_base": -128.810, "theta_base": 166.090, "v0": 21.178, "v1": -34.004, "v2": 33.359, "v3": -22.015, "v4": 0.659, "amplitude": 34.991, "phase_angle": 342.431, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "23t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ -1.942, 1.245, 5.651 ], "x_axis": [ -0.287, 0.691, 0.663 ], "y_axis": [ -0.718, 0.303, -0.626 ], "z_axis": [ -0.634, -0.656, 0.410 ], "quaternion": [ 0.597, 0.012, -0.543, 0.590 ] } }, { "index": 50, "index_chain": 50, "chain_name": "A", "nt_resnum": 50, "nt_name": "A", "nt_code": "A", "nt_id": "///A/50", "linked_nts": [ "///A/49", "///A/51" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C2'-endo,BII,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,phosphate", "alpha": -53.690, "beta": -76.320, "gamma": -124.553, "delta": 163.728, "epsilon": -74.452, "zeta": 143.583, "epsilon_zeta": 141.965, "bb_type": "BII", "chi": -160.174, "glyco_bond": "anti", "C5prime_xyz": [ -1.820, 8.179, 1.308 ], "P_xyz": [ -1.078, 10.164, -0.228 ], "form": ".", "ssZp": 0.037, "Dp": 0.134, "splay_angle": 34.419, "splay_distance": 5.704, "splay_ratio": 0.296, "d22": null, "d64": null, "eta": 155.937, "theta": 99.478, "eta_prime": 156.000, "theta_prime": 133.944, "eta_base": 132.989, "theta_base": 170.184, "v0": -10.747, "v1": 34.184, "v2": -42.853, "v3": 38.271, "v4": -17.463, "amplitude": 42.997, "phase_angle": 184.683, "puckering": "C3'-exo", "sugar_class": "~C2'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.036, "frame": { "rmsd": 0.007, "origin": [ -15.146, 1.526, 2.132 ], "x_axis": [ 0.360, -0.871, 0.336 ], "y_axis": [ 0.880, 0.197, -0.432 ], "z_axis": [ 0.310, 0.451, 0.837 ], "quaternion": [ 0.774, -0.285, -0.008, -0.566 ] } }, { "index": 51, "index_chain": 51, "chain_name": "A", "nt_resnum": 51, "nt_name": "U", "nt_code": "U", "nt_id": "///A/51", "linked_nts": [ "///A/50", "///A/52" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,BI,non-pair-contact,hairpin-loop", "alpha": -65.296, "beta": 102.097, "gamma": 85.821, "delta": 83.617, "epsilon": -158.392, "zeta": -51.599, "epsilon_zeta": -106.793, "bb_type": "BI", "chi": -177.940, "glyco_bond": "anti", "C5prime_xyz": [ -2.721, 8.902, 0.802 ], "P_xyz": [ -0.312, 9.468, -0.067 ], "form": ".", "ssZp": 3.764, "Dp": 3.610, "splay_angle": 9.369, "splay_distance": 2.171, "splay_ratio": 0.110, "d22": null, "d64": null, "eta": -162.798, "theta": -123.733, "eta_prime": -138.674, "theta_prime": -145.682, "eta_base": -102.182, "theta_base": -103.026, "v0": -35.942, "v1": 11.430, "v2": 15.136, "v3": -35.847, "v4": 44.929, "amplitude": 44.304, "phase_angle": 70.023, "puckering": "C4'-exo", "sugar_class": "--", "bin": "23p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.104, "frame": { "rmsd": 0.006, "origin": [ -18.897, 5.532, 0.576 ], "x_axis": [ -0.040, 0.795, 0.605 ], "y_axis": [ 0.861, 0.335, -0.382 ], "z_axis": [ -0.507, 0.506, -0.698 ], "quaternion": [ -0.386, 0.575, 0.720, 0.043 ] } }, { "index": 52, "index_chain": 52, "chain_name": "A", "nt_resnum": 52, "nt_name": "A", "nt_code": "A", "nt_id": "///A/52", "linked_nts": [ "///A/51", "///A/53" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor", "alpha": -119.366, "beta": 148.314, "gamma": 133.208, "delta": 81.416, "epsilon": -108.617, "zeta": -99.093, "epsilon_zeta": -9.524, "bb_type": "--", "chi": -152.654, "glyco_bond": "anti", "C5prime_xyz": [ -3.050, 8.870, -0.619 ], "P_xyz": [ -2.074, 10.040, -2.774 ], "form": ".", "ssZp": 2.809, "Dp": 3.235, "splay_angle": 48.139, "splay_distance": 8.085, "splay_ratio": 0.411, "d22": null, "d64": null, "eta": -170.840, "theta": -130.340, "eta_prime": -160.419, "theta_prime": -119.253, "eta_base": -104.935, "theta_base": -71.202, "v0": -37.743, "v1": 12.407, "v2": 15.790, "v3": -38.010, "v4": 47.344, "amplitude": 46.774, "phase_angle": 70.270, "puckering": "C4'-exo", "sugar_class": "--", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.002, "origin": [ -20.457, 6.867, 1.281 ], "x_axis": [ 0.069, 0.990, 0.120 ], "y_axis": [ 0.298, 0.095, -0.950 ], "z_axis": [ -0.952, 0.102, -0.288 ], "quaternion": [ -0.468, 0.562, 0.573, -0.370 ] } }, { "index": 53, "index_chain": 53, "chain_name": "A", "nt_resnum": 53, "nt_name": "U", "nt_code": "U", "nt_id": "///A/53", "linked_nts": [ "///A/52", "///A/54" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart", "alpha": 113.173, "beta": -125.253, "gamma": -161.225, "delta": 163.691, "epsilon": -84.065, "zeta": -83.867, "epsilon_zeta": -0.197, "bb_type": "--", "chi": -134.022, "glyco_bond": "anti", "C5prime_xyz": [ -1.603, 8.518, -0.140 ], "P_xyz": [ 0.250, 9.118, -1.945 ], "form": ".", "ssZp": 0.259, "Dp": 0.457, "splay_angle": 108.591, "splay_distance": 15.418, "splay_ratio": 0.812, "d22": 7.453, "d64": 9.349, "eta": -121.659, "theta": -85.955, "eta_prime": -119.558, "theta_prime": -49.468, "eta_base": -80.147, "theta_base": -11.063, "v0": -16.864, "v1": 40.196, "v2": -46.188, "v3": 38.456, "v4": -13.539, "amplitude": 46.217, "phase_angle": 177.959, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.104, "frame": { "rmsd": 0.003, "origin": [ -20.482, 11.914, -5.035 ], "x_axis": [ 0.890, 0.105, -0.444 ], "y_axis": [ -0.157, -0.843, -0.515 ], "z_axis": [ -0.429, 0.528, -0.733 ], "quaternion": [ -0.280, 0.931, -0.014, -0.234 ] } }, { "index": 54, "index_chain": 54, "chain_name": "A", "nt_resnum": 54, "nt_name": "C", "nt_code": "C", "nt_id": "///A/54", "linked_nts": [ "///A/53", "///A/55" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,phosphate,splayed-apart", "alpha": 37.701, "beta": 92.008, "gamma": 19.685, "delta": 77.232, "epsilon": -154.021, "zeta": -30.048, "epsilon_zeta": -123.973, "bb_type": "BI", "chi": -157.509, "glyco_bond": "anti", "C5prime_xyz": [ -2.066, 9.112, 0.207 ], "P_xyz": [ 0.460, 9.095, 1.097 ], "form": ".", "ssZp": 4.270, "Dp": 4.233, "splay_angle": 81.695, "splay_distance": 11.818, "splay_ratio": 0.655, "d22": 5.199, "d64": 7.463, "eta": 146.714, "theta": -88.547, "eta_prime": -169.473, "theta_prime": -84.494, "eta_base": -159.288, "theta_base": -61.514, "v0": -21.489, "v1": -4.532, "v2": 27.173, "v3": -40.344, "v4": 38.747, "amplitude": 41.380, "phase_angle": 48.954, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.067, "frame": { "rmsd": 0.006, "origin": [ -23.684, -1.659, -11.610 ], "x_axis": [ 0.646, -0.165, 0.745 ], "y_axis": [ -0.346, 0.807, 0.479 ], "z_axis": [ -0.680, -0.567, 0.464 ], "quaternion": [ 0.854, 0.306, -0.417, 0.053 ] } }, { "index": 55, "index_chain": 55, "chain_name": "A", "nt_resnum": 55, "nt_name": "C", "nt_code": "C", "nt_id": "///A/55", "linked_nts": [ "///A/54", "///A/56" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop", "alpha": -95.745, "beta": -161.395, "gamma": 74.053, "delta": 80.703, "epsilon": -142.552, "zeta": -72.158, "epsilon_zeta": -70.394, "bb_type": "BI", "chi": 177.788, "glyco_bond": "anti", "C5prime_xyz": [ -1.287, 8.294, 1.892 ], "P_xyz": [ 1.279, 8.192, 2.472 ], "form": ".", "ssZp": 4.801, "Dp": 4.707, "splay_angle": 32.667, "splay_distance": 4.938, "splay_ratio": 0.286, "d22": 4.779, "d64": 5.308, "eta": 176.180, "theta": -137.966, "eta_prime": -148.426, "theta_prime": -133.259, "eta_base": -93.200, "theta_base": -110.295, "v0": 9.285, "v1": -32.506, "v2": 42.303, "v3": -37.886, "v4": 18.048, "amplitude": 42.552, "phase_angle": 6.199, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.010, "filter_rmsd": 0.065, "frame": { "rmsd": 0.005, "origin": [ -27.974, 0.035, -0.729 ], "x_axis": [ -0.018, 0.983, 0.185 ], "y_axis": [ -0.104, 0.182, -0.978 ], "z_axis": [ -0.994, -0.037, 0.099 ], "quaternion": [ 0.562, -0.419, -0.525, 0.483 ] } }, { "index": 56, "index_chain": 56, "chain_name": "A", "nt_resnum": 56, "nt_name": "U", "nt_code": "U", "nt_id": "///A/56", "linked_nts": [ "///A/55", "///A/57" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet", "alpha": -48.793, "beta": -176.626, "gamma": 50.774, "delta": 89.264, "epsilon": -135.654, "zeta": -75.590, "epsilon_zeta": -60.064, "bb_type": "BI", "chi": -167.050, "glyco_bond": "anti", "C5prime_xyz": [ -1.411, 8.579, 0.931 ], "P_xyz": [ 0.987, 8.835, 1.925 ], "form": "A", "ssZp": 4.240, "Dp": 4.546, "splay_angle": 20.164, "splay_distance": 3.346, "splay_ratio": 0.177, "d22": null, "d64": null, "eta": -168.488, "theta": -131.791, "eta_prime": -155.896, "theta_prime": -129.318, "eta_base": -123.703, "theta_base": -99.549, "v0": 5.489, "v1": -24.726, "v2": 33.480, "v3": -31.296, "v4": 16.348, "amplitude": 33.956, "phase_angle": 9.601, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.657, "filter_rmsd": 0.105, "frame": { "rmsd": 0.004, "origin": [ -32.034, 0.627, 2.019 ], "x_axis": [ -0.012, 0.910, -0.415 ], "y_axis": [ 0.076, -0.413, -0.907 ], "z_axis": [ -0.997, -0.042, -0.064 ], "quaternion": [ -0.357, 0.605, 0.407, -0.583 ] } }, { "index": 57, "index_chain": 57, "chain_name": "A", "nt_resnum": 57, "nt_name": "G", "nt_code": "G", "nt_id": "///A/57", "linked_nts": [ "///A/56", "///A/58" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack", "alpha": -61.625, "beta": 159.062, "gamma": 57.290, "delta": 80.980, "epsilon": -165.511, "zeta": -55.778, "epsilon_zeta": -109.733, "bb_type": "BI", "chi": -156.003, "glyco_bond": "anti", "C5prime_xyz": [ -1.970, 8.934, 0.078 ], "P_xyz": [ 0.532, 9.689, 0.022 ], "form": ".", "ssZp": 3.995, "Dp": 4.332, "splay_angle": 21.697, "splay_distance": 3.827, "splay_ratio": 0.196, "d22": null, "d64": null, "eta": 160.130, "theta": -136.065, "eta_prime": -176.422, "theta_prime": -143.862, "eta_base": -129.107, "theta_base": -135.627, "v0": -8.370, "v1": -17.140, "v2": 34.430, "v3": -40.252, "v4": 30.613, "amplitude": 39.906, "phase_angle": 30.370, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.733, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ -35.081, 1.984, 2.287 ], "x_axis": [ 0.093, 0.521, -0.848 ], "y_axis": [ -0.063, -0.847, -0.527 ], "z_axis": [ -0.994, 0.103, -0.046 ], "quaternion": [ -0.224, 0.705, 0.162, -0.654 ] } }, { "index": 58, "index_chain": 58, "chain_name": "A", "nt_resnum": 58, "nt_name": "G", "nt_code": "G", "nt_id": "///A/58", "linked_nts": [ "///A/57", "///A/59" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack", "alpha": -169.105, "beta": 145.713, "gamma": 169.451, "delta": 156.182, "epsilon": -73.459, "zeta": -34.033, "epsilon_zeta": -39.426, "bb_type": "--", "chi": -149.913, "glyco_bond": "anti", "C5prime_xyz": [ -1.603, 8.555, 0.655 ], "P_xyz": [ -0.039, 10.286, -0.559 ], "form": ".", "ssZp": 0.580, "Dp": 0.221, "splay_angle": 60.302, "splay_distance": 10.375, "splay_ratio": 0.503, "d22": null, "d64": null, "eta": -119.671, "theta": -77.178, "eta_prime": -131.851, "theta_prime": -70.038, "eta_base": -123.680, "theta_base": -71.681, "v0": -14.418, "v1": 34.543, "v2": -40.443, "v3": 33.682, "v4": -12.050, "amplitude": 40.457, "phase_angle": 178.514, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32t", "cluster": "1t", "suiteness": 0.147, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ -38.120, 4.229, 2.897 ], "x_axis": [ 0.329, 0.087, -0.940 ], "y_axis": [ -0.219, -0.962, -0.165 ], "z_axis": [ -0.919, 0.260, -0.298 ], "quaternion": [ -0.132, 0.804, -0.041, -0.578 ] } }, { "index": 59, "index_chain": 59, "chain_name": "A", "nt_resnum": 59, "nt_name": "U", "nt_code": "U", "nt_id": "///A/59", "linked_nts": [ "///A/58", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-stack,ss-non-loop", "alpha": -68.357, "beta": 150.619, "gamma": 1.717, "delta": 82.256, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -115.982, "glyco_bond": "anti", "C5prime_xyz": [ -2.866, 8.311, -2.164 ], "P_xyz": [ -1.197, 10.206, -2.792 ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -27.753, "v1": 2.116, "v2": 22.372, "v3": -39.083, "v4": 42.171, "amplitude": 42.475, "phase_angle": 58.217, "puckering": "C4'-exo", "sugar_class": "--", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.105, "frame": { "rmsd": 0.004, "origin": [ -46.879, 0.761, -1.447 ], "x_axis": [ 0.840, 0.390, -0.378 ], "y_axis": [ 0.543, -0.592, 0.596 ], "z_axis": [ 0.008, -0.706, -0.709 ], "quaternion": [ 0.367, 0.886, 0.263, -0.104 ] } } ], "num_hbonds": 93, "hbonds": [ { "index": 1, "atom1_serNum": 3, "atom2_serNum": 7, "donAcc_type": "acceptable", "distance": 2.372, "atom1_id": "///A/1/O2G", "atom2_id": "///A/1/O1B", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 8, "atom2_serNum": 13, "donAcc_type": "acceptable", "distance": 2.355, "atom1_id": "///A/1/O2B", "atom2_id": "///A/1/O5'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 20, "atom2_serNum": 51, "donAcc_type": "acceptable", "distance": 2.643, "atom1_id": "///A/1/O2'", "atom2_id": "///A/2/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 27, "atom2_serNum": 873, "donAcc_type": "standard", "distance": 2.808, "atom1_id": "///A/1/O6", "atom2_id": "///A/27/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 28, "atom2_serNum": 871, "donAcc_type": "standard", "distance": 2.875, "atom1_id": "///A/1/N1", "atom2_id": "///A/27/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 30, "atom2_serNum": 870, "donAcc_type": "standard", "distance": 2.848, "atom1_id": "///A/1/N2", "atom2_id": "///A/27/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 62, "atom2_serNum": 840, "donAcc_type": "standard", "distance": 2.845, "atom1_id": "///A/2/O6", "atom2_id": "///A/26/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 8, "atom1_serNum": 63, "atom2_serNum": 841, "donAcc_type": "standard", "distance": 2.810, "atom1_id": "///A/2/N1", "atom2_id": "///A/26/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 9, "atom1_serNum": 96, "atom2_serNum": 808, "donAcc_type": "standard", "distance": 2.960, "atom1_id": "///A/3/N6", "atom2_id": "///A/25/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 129, "atom2_serNum": 808, "donAcc_type": "standard", "distance": 3.244, "atom1_id": "///A/4/N6", "atom2_id": "///A/25/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 130, "atom2_serNum": 774, "donAcc_type": "standard", "distance": 2.861, "atom1_id": "///A/4/N1", "atom2_id": "///A/24/N6", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 12, "atom1_serNum": 162, "atom2_serNum": 743, "donAcc_type": "standard", "distance": 2.924, "atom1_id": "///A/5/O6", "atom2_id": "///A/23/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 13, "atom1_serNum": 163, "atom2_serNum": 741, "donAcc_type": "standard", "distance": 3.130, "atom1_id": "///A/5/N1", "atom2_id": "///A/23/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 14, "atom1_serNum": 165, "atom2_serNum": 740, "donAcc_type": "standard", "distance": 3.208, "atom1_id": "///A/5/N2", "atom2_id": "///A/23/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 189, "atom2_serNum": 218, "donAcc_type": "acceptable", "distance": 2.855, "atom1_id": "///A/6/O2'", "atom2_id": "///A/7/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 16, "atom1_serNum": 196, "atom2_serNum": 713, "donAcc_type": "standard", "distance": 2.983, "atom1_id": "///A/6/N6", "atom2_id": "///A/22/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 17, "atom1_serNum": 197, "atom2_serNum": 711, "donAcc_type": "standard", "distance": 2.822, "atom1_id": "///A/6/N1", "atom2_id": "///A/22/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 229, "atom2_serNum": 680, "donAcc_type": "standard", "distance": 3.023, "atom1_id": "///A/7/N6", "atom2_id": "///A/21/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 19, "atom1_serNum": 263, "atom2_serNum": 649, "donAcc_type": "standard", "distance": 2.785, "atom1_id": "///A/8/N1", "atom2_id": "///A/20/N6", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 288, "atom2_serNum": 314, "donAcc_type": "acceptable", "distance": 2.834, "atom1_id": "///A/9/O2'", "atom2_id": "///A/10/OP2", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 21, "atom1_serNum": 298, "atom2_serNum": 329, "donAcc_type": "standard", "distance": 2.912, "atom1_id": "///A/9/N2", "atom2_id": "///A/10/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 22, "atom1_serNum": 298, "atom2_serNum": 618, "donAcc_type": "questionable", "distance": 3.290, "atom1_id": "///A/9/N2", "atom2_id": "///A/19/N4", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 23, "atom1_serNum": 329, "atom2_serNum": 618, "donAcc_type": "standard", "distance": 2.700, "atom1_id": "///A/10/O6", "atom2_id": "///A/19/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 24, "atom1_serNum": 330, "atom2_serNum": 616, "donAcc_type": "standard", "distance": 2.826, "atom1_id": "///A/10/N1", "atom2_id": "///A/19/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 25, "atom1_serNum": 332, "atom2_serNum": 615, "donAcc_type": "standard", "distance": 2.880, "atom1_id": "///A/10/N2", "atom2_id": "///A/19/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 26, "atom1_serNum": 363, "atom2_serNum": 587, "donAcc_type": "standard", "distance": 2.729, "atom1_id": "///A/11/O6", "atom2_id": "///A/18/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 27, "atom1_serNum": 364, "atom2_serNum": 585, "donAcc_type": "standard", "distance": 3.026, "atom1_id": "///A/11/N1", "atom2_id": "///A/18/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 28, "atom1_serNum": 366, "atom2_serNum": 584, "donAcc_type": "standard", "distance": 3.235, "atom1_id": "///A/11/N2", "atom2_id": "///A/18/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 29, "atom1_serNum": 394, "atom2_serNum": 554, "donAcc_type": "standard", "distance": 3.102, "atom1_id": "///A/12/O2", "atom2_id": "///A/17/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 30, "atom1_serNum": 394, "atom2_serNum": 556, "donAcc_type": "standard", "distance": 3.231, "atom1_id": "///A/12/O2", "atom2_id": "///A/17/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 31, "atom1_serNum": 395, "atom2_serNum": 554, "donAcc_type": "standard", "distance": 2.958, "atom1_id": "///A/12/N3", "atom2_id": "///A/17/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 32, "atom1_serNum": 397, "atom2_serNum": 553, "donAcc_type": "standard", "distance": 2.622, "atom1_id": "///A/12/N4", "atom2_id": "///A/17/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 33, "atom1_serNum": 421, "atom2_serNum": 519, "donAcc_type": "acceptable", "distance": 2.456, "atom1_id": "///A/13/O2'", "atom2_id": "///A/16/O6", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 34, "atom1_serNum": 425, "atom2_serNum": 520, "donAcc_type": "standard", "distance": 2.575, "atom1_id": "///A/13/O2", "atom2_id": "///A/16/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 35, "atom1_serNum": 443, "atom2_serNum": 488, "donAcc_type": "standard", "distance": 3.336, "atom1_id": "///A/14/OP2", "atom2_id": "///A/15/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 36, "atom1_serNum": 451, "atom2_serNum": 474, "donAcc_type": "acceptable", "distance": 2.819, "atom1_id": "///A/14/O2'", "atom2_id": "///A/15/O5'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 37, "atom1_serNum": 451, "atom2_serNum": 516, "donAcc_type": "acceptable", "distance": 2.582, "atom1_id": "///A/14/O2'", "atom2_id": "///A/16/N7", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 38, "atom1_serNum": 481, "atom2_serNum": 485, "donAcc_type": "acceptable", "distance": 3.041, "atom1_id": "///A/15/O2'", "atom2_id": "///A/15/O2", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 39, "atom1_serNum": 897, "atom2_serNum": 918, "donAcc_type": "acceptable", "distance": 2.687, "atom1_id": "///A/28/O2'", "atom2_id": "///A/29/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 40, "atom1_serNum": 960, "atom2_serNum": 987, "donAcc_type": "acceptable", "distance": 3.525, "atom1_id": "///A/30/O2'", "atom2_id": "///A/31/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 41, "atom1_serNum": 1024, "atom2_serNum": 1054, "donAcc_type": "acceptable", "distance": 3.116, "atom1_id": "///A/32/O2'", "atom2_id": "///A/33/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 42, "atom1_serNum": 1031, "atom2_serNum": 1514, "donAcc_type": "standard", "distance": 2.886, "atom1_id": "///A/32/O6", "atom2_id": "///A/47/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 43, "atom1_serNum": 1032, "atom2_serNum": 1512, "donAcc_type": "standard", "distance": 2.914, "atom1_id": "///A/32/N1", "atom2_id": "///A/47/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 44, "atom1_serNum": 1034, "atom2_serNum": 1511, "donAcc_type": "standard", "distance": 2.873, "atom1_id": "///A/32/N2", "atom2_id": "///A/47/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 45, "atom1_serNum": 1034, "atom2_serNum": 1609, "donAcc_type": "standard", "distance": 3.066, "atom1_id": "///A/32/N2", "atom2_id": "///A/50/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 46, "atom1_serNum": 1058, "atom2_serNum": 1084, "donAcc_type": "acceptable", "distance": 3.036, "atom1_id": "///A/33/O2'", "atom2_id": "///A/34/O5'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 47, "atom1_serNum": 1058, "atom2_serNum": 1087, "donAcc_type": "acceptable", "distance": 2.666, "atom1_id": "///A/33/O2'", "atom2_id": "///A/34/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 48, "atom1_serNum": 1065, "atom2_serNum": 1484, "donAcc_type": "standard", "distance": 2.846, "atom1_id": "///A/33/N6", "atom2_id": "///A/46/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 49, "atom1_serNum": 1066, "atom2_serNum": 1482, "donAcc_type": "standard", "distance": 3.166, "atom1_id": "///A/33/N1", "atom2_id": "///A/46/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 50, "atom1_serNum": 1068, "atom2_serNum": 1612, "donAcc_type": "standard", "distance": 3.130, "atom1_id": "///A/33/N3", "atom2_id": "///A/50/N6", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 51, "atom1_serNum": 1091, "atom2_serNum": 1676, "donAcc_type": "acceptable", "distance": 3.412, "atom1_id": "///A/34/O2'", "atom2_id": "///A/52/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 52, "atom1_serNum": 1098, "atom2_serNum": 1453, "donAcc_type": "standard", "distance": 2.652, "atom1_id": "///A/34/O6", "atom2_id": "///A/45/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 53, "atom1_serNum": 1099, "atom2_serNum": 1451, "donAcc_type": "standard", "distance": 2.841, "atom1_id": "///A/34/N1", "atom2_id": "///A/45/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 54, "atom1_serNum": 1101, "atom2_serNum": 1450, "donAcc_type": "standard", "distance": 2.946, "atom1_id": "///A/34/N2", "atom2_id": "///A/45/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 55, "atom1_serNum": 1101, "atom2_serNum": 1668, "donAcc_type": "acceptable", "distance": 3.308, "atom1_id": "///A/34/N2", "atom2_id": "///A/52/O2'", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 56, "atom1_serNum": 1101, "atom2_serNum": 1678, "donAcc_type": "standard", "distance": 3.046, "atom1_id": "///A/34/N2", "atom2_id": "///A/52/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 57, "atom1_serNum": 1129, "atom2_serNum": 1359, "donAcc_type": "questionable", "distance": 3.355, "atom1_id": "///A/35/N7", "atom2_id": "///A/42/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 58, "atom1_serNum": 1129, "atom2_serNum": 1420, "donAcc_type": "standard", "distance": 3.900, "atom1_id": "///A/35/N7", "atom2_id": "///A/44/N6", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 59, "atom1_serNum": 1132, "atom2_serNum": 1421, "donAcc_type": "standard", "distance": 3.074, "atom1_id": "///A/35/N6", "atom2_id": "///A/44/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 60, "atom1_serNum": 1133, "atom2_serNum": 1697, "donAcc_type": "questionable", "distance": 3.166, "atom1_id": "///A/35/N1", "atom2_id": "///A/53/O4'", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 61, "atom1_serNum": 1165, "atom2_serNum": 1722, "donAcc_type": "standard", "distance": 2.733, "atom1_id": "///A/36/N4", "atom2_id": "///A/54/OP1", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 62, "atom1_serNum": 1165, "atom2_serNum": 1769, "donAcc_type": "questionable", "distance": 3.016, "atom1_id": "///A/36/N4", "atom2_id": "///A/55/N4", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 63, "atom1_serNum": 1196, "atom2_serNum": 1292, "donAcc_type": "standard", "distance": 3.022, "atom1_id": "///A/37/O6", "atom2_id": "///A/40/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 64, "atom1_serNum": 1196, "atom2_serNum": 1800, "donAcc_type": "questionable", "distance": 3.129, "atom1_id": "///A/37/O6", "atom2_id": "///A/56/O4", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 65, "atom1_serNum": 1223, "atom2_serNum": 1250, "donAcc_type": "acceptable", "distance": 3.023, "atom1_id": "///A/38/O2'", "atom2_id": "///A/39/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 66, "atom1_serNum": 1227, "atom2_serNum": 1867, "donAcc_type": "standard", "distance": 2.855, "atom1_id": "///A/38/O2", "atom2_id": "///A/58/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 67, "atom1_serNum": 1228, "atom2_serNum": 1865, "donAcc_type": "standard", "distance": 2.884, "atom1_id": "///A/38/N3", "atom2_id": "///A/58/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 68, "atom1_serNum": 1230, "atom2_serNum": 1864, "donAcc_type": "standard", "distance": 2.824, "atom1_id": "///A/38/N4", "atom2_id": "///A/58/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 69, "atom1_serNum": 1258, "atom2_serNum": 1833, "donAcc_type": "standard", "distance": 2.923, "atom1_id": "///A/39/O2", "atom2_id": "///A/57/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 70, "atom1_serNum": 1259, "atom2_serNum": 1831, "donAcc_type": "standard", "distance": 2.940, "atom1_id": "///A/39/N3", "atom2_id": "///A/57/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 71, "atom1_serNum": 1261, "atom2_serNum": 1830, "donAcc_type": "standard", "distance": 2.918, "atom1_id": "///A/39/N4", "atom2_id": "///A/57/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 72, "atom1_serNum": 1292, "atom2_serNum": 1800, "donAcc_type": "standard", "distance": 2.691, "atom1_id": "///A/40/N6", "atom2_id": "///A/56/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 73, "atom1_serNum": 1293, "atom2_serNum": 1798, "donAcc_type": "standard", "distance": 2.770, "atom1_id": "///A/40/N1", "atom2_id": "///A/56/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 74, "atom1_serNum": 1318, "atom2_serNum": 1348, "donAcc_type": "acceptable", "distance": 2.586, "atom1_id": "///A/41/O2'", "atom2_id": "///A/42/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 75, "atom1_serNum": 1325, "atom2_serNum": 1769, "donAcc_type": "standard", "distance": 2.889, "atom1_id": "///A/41/O6", "atom2_id": "///A/55/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 76, "atom1_serNum": 1326, "atom2_serNum": 1767, "donAcc_type": "standard", "distance": 2.990, "atom1_id": "///A/41/N1", "atom2_id": "///A/55/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 77, "atom1_serNum": 1328, "atom2_serNum": 1766, "donAcc_type": "standard", "distance": 2.992, "atom1_id": "///A/41/N2", "atom2_id": "///A/55/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 78, "atom1_serNum": 1359, "atom2_serNum": 1420, "donAcc_type": "standard", "distance": 3.161, "atom1_id": "///A/42/O4", "atom2_id": "///A/44/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 79, "atom1_serNum": 1389, "atom2_serNum": 1766, "donAcc_type": "standard", "distance": 2.734, "atom1_id": "///A/43/N4", "atom2_id": "///A/55/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 80, "atom1_serNum": 1389, "atom2_serNum": 1789, "donAcc_type": "standard", "distance": 2.764, "atom1_id": "///A/43/N4", "atom2_id": "///A/56/O4'", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 81, "atom1_serNum": 1413, "atom2_serNum": 1738, "donAcc_type": "acceptable", "distance": 3.321, "atom1_id": "///A/44/O2'", "atom2_id": "///A/54/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 82, "atom1_serNum": 1423, "atom2_serNum": 1738, "donAcc_type": "standard", "distance": 3.207, "atom1_id": "///A/44/N3", "atom2_id": "///A/54/N4", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 83, "atom1_serNum": 1442, "atom2_serNum": 1738, "donAcc_type": "standard", "distance": 3.132, "atom1_id": "///A/45/O4'", "atom2_id": "///A/54/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 84, "atom1_serNum": 1446, "atom2_serNum": 1666, "donAcc_type": "acceptable", "distance": 2.874, "atom1_id": "///A/45/O2'", "atom2_id": "///A/52/O3'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 85, "atom1_serNum": 1446, "atom2_serNum": 1692, "donAcc_type": "acceptable", "distance": 2.603, "atom1_id": "///A/45/O2'", "atom2_id": "///A/53/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 86, "atom1_serNum": 1450, "atom2_serNum": 1668, "donAcc_type": "acceptable", "distance": 2.967, "atom1_id": "///A/45/O2", "atom2_id": "///A/52/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 87, "atom1_serNum": 1475, "atom2_serNum": 1636, "donAcc_type": "questionable", "distance": 3.151, "atom1_id": "///A/46/O3'", "atom2_id": "///A/51/O3'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 88, "atom1_serNum": 1477, "atom2_serNum": 1638, "donAcc_type": "acceptable", "distance": 2.616, "atom1_id": "///A/46/O2'", "atom2_id": "///A/51/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 89, "atom1_serNum": 1507, "atom2_serNum": 1569, "donAcc_type": "acceptable", "distance": 2.490, "atom1_id": "///A/47/O2'", "atom2_id": "///A/49/O3'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 90, "atom1_serNum": 1507, "atom2_serNum": 1596, "donAcc_type": "acceptable", "distance": 2.658, "atom1_id": "///A/47/O2'", "atom2_id": "///A/50/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 91, "atom1_serNum": 1507, "atom2_serNum": 1601, "donAcc_type": "acceptable", "distance": 2.540, "atom1_id": "///A/47/O2'", "atom2_id": "///A/50/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 92, "atom1_serNum": 1511, "atom2_serNum": 1609, "donAcc_type": "questionable", "distance": 2.756, "atom1_id": "///A/47/O2", "atom2_id": "///A/50/N7", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 93, "atom1_serNum": 1605, "atom2_serNum": 1615, "donAcc_type": "acceptable", "distance": 3.118, "atom1_id": "///A/50/O2'", "atom2_id": "///A/50/N3", "atom_pair": "O:N", "residue_pair": "nt:nt" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "2m58", "num_naChains": 1, "naChains": "A=59", "num_atoms": 1911, "num_waters": 0, "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 14, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-multiplets.pdb", "desc": "an ensemble of multiplets" }, { "index": 3, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 4, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 5, "name": "dssr-hairpins.pdb", "desc": "an ensemble of hairpin loops" }, { "index": 6, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 7, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 8, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 9, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 10, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 11, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 12, "name": "dssr-Aminors.pdb", "desc": "an ensemble of A minor motifs (types I and II)" }, { "index": 13, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 14, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" } ], "time_used": "999" } }