{ "num_pairs": 42, "pairs": [ { "index": 1, "nt1": "///A/2", "nt2": "///C/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -177.187, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 29.461, "chi2": -177.476, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 62.674, "C1C1_dist": 11.588, "N1N9_dist": 9.667, "C6C8_dist": 9.344, "CNNC_torsion": 20.183, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.91],O6(carbonyl)-N1(imino)[2.94]", "interBase_angle": 15.375, "planarity": 0.211, "simple_Shear": -2.573, "simple_Stretch": 2.884, "simple_Buckle": -15.169, "simple_Propeller": -2.507, "bp_simpleParams": [ -2.573, 2.884, 0.220, -15.169, -2.507, 89.160 ], "bp_params": [ -1.754, -3.444, 0.220, 7.825, -13.234, 89.409 ], "frame": { "rmsd": null, "origin": [ 10.193, -13.424, -16.102 ], "x_axis": [ 0.010, 0.557, 0.831 ], "y_axis": [ 0.965, 0.213, -0.155 ], "z_axis": [ -0.263, 0.803, -0.535 ], "quaternion": [ -0.415, 0.577, 0.659, 0.246 ] } }, { "index": 2, "nt1": "///A/2", "nt2": "///D/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -177.187, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 63.815, "chi2": -169.224, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 29.777, "C1C1_dist": 11.598, "N1N9_dist": 9.706, "C6C8_dist": 9.431, "CNNC_torsion": 18.186, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.96],N2(amino)-N7[2.96]", "interBase_angle": 18.353, "planarity": 0.257, "simple_Shear": -2.511, "simple_Stretch": 2.942, "simple_Buckle": -13.673, "simple_Propeller": -12.243, "bp_simpleParams": [ -2.511, 2.942, -0.123, -13.673, -12.243, -88.799 ], "bp_params": [ 1.860, 3.391, -0.123, -16.292, 8.450, -88.374 ], "frame": { "rmsd": null, "origin": [ 7.633, -13.549, -15.013 ], "x_axis": [ 0.917, 0.333, -0.220 ], "y_axis": [ -0.010, -0.533, -0.846 ], "z_axis": [ -0.399, 0.778, -0.485 ], "quaternion": [ -0.474, 0.857, 0.094, -0.181 ] } }, { "index": 3, "nt1": "///A/3", "nt2": "///C/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -168.415, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 29.061, "chi2": -167.492, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 63.159, "C1C1_dist": 11.462, "N1N9_dist": 9.528, "C6C8_dist": 9.206, "CNNC_torsion": 15.286, "hbonds_num": 1, "hbonds_desc": "O6(carbonyl)-N1(imino)[2.82]", "interBase_angle": 13.275, "planarity": 0.162, "simple_Shear": -2.663, "simple_Stretch": 2.751, "simple_Buckle": -13.144, "simple_Propeller": -1.863, "bp_simpleParams": [ -2.663, 2.751, 0.041, -13.144, -1.863, 88.079 ], "bp_params": [ -1.565, -3.494, 0.041, 6.605, -11.516, 88.273 ], "frame": { "rmsd": null, "origin": [ 8.093, -10.920, -17.552 ], "x_axis": [ 0.499, 0.616, 0.610 ], "y_axis": [ 0.820, -0.107, -0.563 ], "z_axis": [ -0.281, 0.781, -0.558 ], "quaternion": [ -0.457, 0.736, 0.488, 0.112 ] } }, { "index": 4, "nt1": "///A/3", "nt2": "///D/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -168.415, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 64.495, "chi2": -165.268, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 30.383, "C1C1_dist": 11.283, "N1N9_dist": 9.396, "C6C8_dist": 9.094, "CNNC_torsion": 12.707, "hbonds_num": 1, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.78]", "interBase_angle": 17.729, "planarity": 0.217, "simple_Shear": -2.652, "simple_Stretch": 2.724, "simple_Buckle": -14.904, "simple_Propeller": -9.601, "bp_simpleParams": [ -2.652, 2.724, 0.272, -14.904, -9.601, -86.911 ], "bp_params": [ 1.540, 3.476, 0.272, -14.449, 10.274, -86.686 ], "frame": { "rmsd": null, "origin": [ 6.546, -10.296, -15.401 ], "x_axis": [ 0.786, 0.035, -0.618 ], "y_axis": [ -0.479, -0.597, -0.643 ], "z_axis": [ -0.391, 0.801, -0.453 ], "quaternion": [ -0.429, 0.842, -0.132, -0.300 ] } }, { "index": 5, "nt1": "///A/4", "nt2": "///C/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -153.935, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 28.361, "chi2": -156.822, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 62.514, "C1C1_dist": 11.668, "N1N9_dist": 9.728, "C6C8_dist": 9.369, "CNNC_torsion": 5.038, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.95],O6(carbonyl)-N1(imino)[2.99]", "interBase_angle": 5.254, "planarity": 0.078, "simple_Shear": -2.630, "simple_Stretch": 2.953, "simple_Buckle": -4.793, "simple_Propeller": -2.152, "bp_simpleParams": [ -2.630, 2.953, -0.152, -4.793, -2.152, 88.763 ], "bp_params": [ -1.755, -3.545, -0.152, 3.789, -3.640, 88.760 ], "frame": { "rmsd": null, "origin": [ 6.261, -8.339, -18.588 ], "x_axis": [ 0.836, 0.481, 0.265 ], "y_axis": [ 0.454, -0.335, -0.826 ], "z_axis": [ -0.308, 0.810, -0.498 ], "quaternion": [ 0.501, -0.817, -0.286, 0.013 ] } }, { "index": 6, "nt1": "///A/4", "nt2": "///D/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -153.935, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 62.470, "chi2": -154.281, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 28.191, "C1C1_dist": 11.656, "N1N9_dist": 9.712, "C6C8_dist": 9.359, "CNNC_torsion": 7.770, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.94],N2(amino)-N7[2.96]", "interBase_angle": 7.801, "planarity": 0.108, "simple_Shear": -2.639, "simple_Stretch": 2.860, "simple_Buckle": -7.135, "simple_Propeller": -3.154, "bp_simpleParams": [ -2.639, 2.860, 0.044, -7.135, -3.154, -90.134 ], "bp_params": [ 1.677, 3.511, 0.044, -5.573, 5.458, -90.131 ], "frame": { "rmsd": null, "origin": [ 5.860, -7.202, -16.097 ], "x_axis": [ 0.435, -0.264, -0.861 ], "y_axis": [ -0.838, -0.469, -0.279 ], "z_axis": [ -0.330, 0.843, -0.425 ], "quaternion": [ -0.368, 0.763, -0.361, -0.390 ] } }, { "index": 7, "nt1": "///A/5", "nt2": "///C/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -155.135, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 29.381, "chi2": -151.994, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 62.988, "C1C1_dist": 11.502, "N1N9_dist": 9.584, "C6C8_dist": 9.216, "CNNC_torsion": -8.813, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.86],O6(carbonyl)-N1(imino)[2.93]", "interBase_angle": 10.430, "planarity": 0.146, "simple_Shear": -2.688, "simple_Stretch": 2.874, "simple_Buckle": 8.952, "simple_Propeller": 5.352, "bp_simpleParams": [ -2.688, 2.874, 0.206, 8.952, 5.352, 88.160 ], "bp_params": [ -1.616, -3.588, 0.206, -8.386, 6.202, 88.090 ], "frame": { "rmsd": null, "origin": [ 4.784, -5.615, -19.308 ], "x_axis": [ 0.968, 0.247, -0.035 ], "y_axis": [ 0.064, -0.384, -0.921 ], "z_axis": [ -0.241, 0.890, -0.387 ], "quaternion": [ 0.547, -0.828, -0.094, 0.084 ] } }, { "index": 8, "nt1": "///A/5", "nt2": "///D/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -155.135, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 62.123, "chi2": -151.337, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 27.251, "C1C1_dist": 11.750, "N1N9_dist": 9.788, "C6C8_dist": 9.430, "CNNC_torsion": -6.928, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.98],N2(amino)-N7[3.07]", "interBase_angle": 8.235, "planarity": 0.115, "simple_Shear": -2.678, "simple_Stretch": 2.857, "simple_Buckle": 7.932, "simple_Propeller": 2.211, "bp_simpleParams": [ -2.678, 2.857, -0.109, 7.932, 2.211, -91.617 ], "bp_params": [ 1.659, 3.547, -0.109, 4.996, -6.547, -91.656 ], "frame": { "rmsd": null, "origin": [ 5.493, -4.156, -17.034 ], "x_axis": [ 0.094, -0.497, -0.863 ], "y_axis": [ -0.971, -0.238, 0.031 ], "z_axis": [ -0.221, 0.835, -0.504 ], "quaternion": [ -0.297, 0.677, -0.541, -0.400 ] } }, { "index": 9, "nt1": "///A/6", "nt2": "///C/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -138.735, "conf1": "anti", "pucker1": "----", "lambda1": 63.661, "chi2": -137.393, "conf2": "anti", "pucker2": "----", "lambda2": 33.333, "C1C1_dist": 9.720, "N1N9_dist": 7.840, "C6C8_dist": 7.730, "CNNC_torsion": 16.672, "hbonds_num": 1, "hbonds_desc": "N3(imino)-O4(carbonyl)[2.70]", "interBase_angle": 29.801, "planarity": 0.332, "simple_Shear": -2.318, "simple_Stretch": 1.534, "simple_Buckle": -29.760, "simple_Propeller": -1.578, "bp_simpleParams": [ -2.318, 1.534, 0.712, -29.760, -1.578, -83.305 ], "bp_params": [ 0.647, 2.703, 0.712, -11.640, 27.434, -84.661 ], "frame": { "rmsd": null, "origin": [ 6.577, -2.729, -20.946 ], "x_axis": [ -0.780, -0.036, 0.625 ], "y_axis": [ -0.572, -0.362, -0.736 ], "z_axis": [ 0.253, -0.932, 0.261 ], "quaternion": [ 0.173, 0.283, -0.538, 0.775 ] } }, { "index": 10, "nt1": "///A/6", "nt2": "///D/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -138.735, "conf1": "anti", "pucker1": "----", "lambda1": 31.985, "chi2": -136.090, "conf2": "anti", "pucker2": "----", "lambda2": 60.537, "C1C1_dist": 10.351, "N1N9_dist": 8.377, "C6C8_dist": 8.223, "CNNC_torsion": 17.998, "hbonds_num": 1, "hbonds_desc": "O4(carbonyl)-N3(imino)[3.06]", "interBase_angle": 24.450, "planarity": 0.278, "simple_Shear": -2.549, "simple_Stretch": 1.754, "simple_Buckle": -24.386, "simple_Propeller": 1.770, "bp_simpleParams": [ -2.549, 1.754, -0.398, -24.386, 1.770, 88.136 ], "bp_params": [ -0.705, -3.013, -0.398, 7.267, -23.345, 89.218 ], "frame": { "rmsd": null, "origin": [ 4.572, -3.220, -20.563 ], "x_axis": [ 0.535, 0.460, 0.709 ], "y_axis": [ -0.843, 0.232, 0.485 ], "z_axis": [ 0.059, -0.857, 0.512 ], "quaternion": [ 0.755, 0.445, -0.215, 0.431 ] } }, { "index": 11, "nt1": "///B/2", "nt2": "///C/1", "bp": "G+u", "name": "--", "Saenger": "--", "LW": "tSW", "DSSR": "tm+W", "intra_chain": false, "chi1": -172.932, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 98.185, "chi2": -109.787, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 37.333, "C1C1_dist": 8.969, "N1N9_dist": 8.339, "C6C8_dist": 10.287, "CNNC_torsion": 167.190, "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O4(carbonyl)[3.25],N2(amino)-O2(carbonyl)[3.41]", "interBase_angle": 23.938, "planarity": 0.291, "simple_Shear": 5.263, "simple_Stretch": 3.484, "simple_Buckle": 20.852, "simple_Propeller": -11.757, "bp_simpleParams": [ 5.263, 3.484, 0.971, 20.852, -11.757, -117.740 ], "bp_params": [ -0.454, -6.295, 0.971, -22.011, -9.409, -116.964 ], "frame": { "rmsd": null, "origin": [ 11.200, -10.582, -9.324 ], "x_axis": [ -0.926, -0.154, 0.344 ], "y_axis": [ 0.235, 0.480, 0.845 ], "z_axis": [ -0.295, 0.864, -0.408 ], "quaternion": [ -0.191, 0.024, 0.839, 0.509 ] } }, { "index": 12, "nt1": "///B/2", "nt2": "///C/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -172.932, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 61.873, "chi2": -177.476, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 27.550, "C1C1_dist": 11.612, "N1N9_dist": 9.648, "C6C8_dist": 9.309, "CNNC_torsion": 5.907, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.80],N2(amino)-N7[2.93]", "interBase_angle": 11.196, "planarity": 0.162, "simple_Shear": -2.600, "simple_Stretch": 2.676, "simple_Buckle": -3.150, "simple_Propeller": -10.743, "bp_simpleParams": [ -2.600, 2.676, -0.005, -3.150, -10.743, -91.789 ], "bp_params": [ 1.553, 3.393, -0.005, -11.154, -0.960, -91.519 ], "frame": { "rmsd": null, "origin": [ 11.210, -12.148, -13.921 ], "x_axis": [ -0.982, -0.152, 0.111 ], "y_axis": [ 0.047, 0.371, 0.927 ], "z_axis": [ -0.182, 0.916, -0.357 ], "quaternion": [ -0.089, -0.032, 0.823, 0.560 ] } }, { "index": 13, "nt1": "///B/2", "nt2": "///D/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -172.932, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 31.027, "chi2": -169.224, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 63.259, "C1C1_dist": 11.561, "N1N9_dist": 9.670, "C6C8_dist": 9.316, "CNNC_torsion": 8.357, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.98],O6(carbonyl)-N1(imino)[3.15]", "interBase_angle": 18.880, "planarity": 0.259, "simple_Shear": -2.738, "simple_Stretch": 3.059, "simple_Buckle": -13.876, "simple_Propeller": -12.802, "bp_simpleParams": [ -2.738, 3.059, -0.412, -13.876, -12.802, 87.465 ], "bp_params": [ -1.737, -3.720, -0.412, 17.223, -7.735, 86.947 ], "frame": { "rmsd": null, "origin": [ 8.650, -12.273, -12.833 ], "x_axis": [ -0.061, -0.345, -0.937 ], "y_axis": [ -0.946, -0.279, 0.164 ], "z_axis": [ -0.318, 0.896, -0.309 ], "quaternion": [ -0.296, 0.618, -0.522, -0.508 ] } }, { "index": 14, "nt1": "///B/3", "nt2": "///C/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -167.392, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 63.923, "chi2": -167.492, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 28.505, "C1C1_dist": 11.468, "N1N9_dist": 9.546, "C6C8_dist": 9.265, "CNNC_torsion": 12.617, "hbonds_num": 1, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.73]", "interBase_angle": 16.428, "planarity": 0.201, "simple_Shear": -2.584, "simple_Stretch": 2.703, "simple_Buckle": -13.030, "simple_Propeller": -10.006, "bp_simpleParams": [ -2.584, 2.703, 0.247, -13.030, -10.006, -89.288 ], "bp_params": [ 1.608, 3.376, 0.247, -13.977, 8.634, -89.024 ], "frame": { "rmsd": null, "origin": [ 10.203, -9.731, -16.433 ], "x_axis": [ -0.807, 0.101, 0.582 ], "y_axis": [ 0.564, 0.425, 0.708 ], "z_axis": [ -0.176, 0.899, -0.400 ], "quaternion": [ -0.234, 0.205, 0.811, 0.495 ] } }, { "index": 15, "nt1": "///B/3", "nt2": "///D/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -167.392, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 27.327, "chi2": -165.268, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 61.534, "C1C1_dist": 11.690, "N1N9_dist": 9.698, "C6C8_dist": 9.364, "CNNC_torsion": 12.213, "hbonds_num": 1, "hbonds_desc": "O6(carbonyl)-N1(imino)[2.87]", "interBase_angle": 14.358, "planarity": 0.179, "simple_Shear": -2.753, "simple_Stretch": 2.690, "simple_Buckle": -13.735, "simple_Propeller": -4.185, "bp_simpleParams": [ -2.753, 2.690, -0.202, -13.735, -4.185, 92.064 ], "bp_params": [ -1.479, -3.554, -0.202, 8.962, -11.218, 92.163 ], "frame": { "rmsd": null, "origin": [ 8.655, -9.107, -14.283 ], "x_axis": [ -0.555, -0.404, -0.728 ], "y_axis": [ -0.782, -0.045, 0.621 ], "z_axis": [ -0.284, 0.914, -0.291 ], "quaternion": [ 0.165, -0.442, 0.671, 0.572 ] } }, { "index": 16, "nt1": "///B/4", "nt2": "///C/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -162.407, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 62.554, "chi2": -156.822, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 27.969, "C1C1_dist": 11.750, "N1N9_dist": 9.808, "C6C8_dist": 9.470, "CNNC_torsion": 11.039, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.99],N2(amino)-N7[3.07]", "interBase_angle": 12.341, "planarity": 0.176, "simple_Shear": -2.625, "simple_Stretch": 2.924, "simple_Buckle": -11.727, "simple_Propeller": -3.846, "bp_simpleParams": [ -2.625, 2.924, 0.247, -11.727, -3.846, -90.945 ], "bp_params": [ 1.765, 3.511, 0.247, -7.851, 9.522, -91.009 ], "frame": { "rmsd": null, "origin": [ 8.872, -7.387, -18.614 ], "x_axis": [ -0.441, 0.292, 0.849 ], "y_axis": [ 0.864, 0.396, 0.312 ], "z_axis": [ -0.245, 0.870, -0.427 ], "quaternion": [ -0.364, 0.384, 0.752, 0.393 ] } }, { "index": 17, "nt1": "///B/4", "nt2": "///D/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -162.407, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 27.815, "chi2": -154.281, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 62.626, "C1C1_dist": 11.648, "N1N9_dist": 9.705, "C6C8_dist": 9.352, "CNNC_torsion": 4.839, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.94],O6(carbonyl)-N1(imino)[2.94]", "interBase_angle": 5.938, "planarity": 0.089, "simple_Shear": -2.607, "simple_Stretch": 2.903, "simple_Buckle": -5.436, "simple_Propeller": 2.388, "bp_simpleParams": [ -2.607, 2.903, -0.052, -5.436, 2.388, 89.187 ], "bp_params": [ -1.733, -3.495, -0.052, -0.208, -5.934, 89.263 ], "frame": { "rmsd": null, "origin": [ 8.471, -6.250, -16.123 ], "x_axis": [ -0.866, -0.383, -0.322 ], "y_axis": [ -0.424, 0.219, 0.879 ], "z_axis": [ -0.266, 0.898, -0.352 ], "quaternion": [ 0.018, -0.258, 0.780, 0.569 ] } }, { "index": 18, "nt1": "///B/5", "nt2": "///C/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -154.704, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 63.442, "chi2": -151.994, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 28.393, "C1C1_dist": 11.576, "N1N9_dist": 9.658, "C6C8_dist": 9.325, "CNNC_torsion": -11.434, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.94],N2(amino)-N7[2.88]", "interBase_angle": 8.652, "planarity": 0.120, "simple_Shear": -2.589, "simple_Stretch": 2.890, "simple_Buckle": 8.133, "simple_Propeller": 2.951, "bp_simpleParams": [ -2.589, 2.890, 0.086, 8.133, 2.951, -88.693 ], "bp_params": [ 1.736, 3.471, 0.086, 5.732, -6.481, -88.713 ], "frame": { "rmsd": null, "origin": [ 7.289, -5.257, -20.330 ], "x_axis": [ -0.036, 0.376, 0.926 ], "y_axis": [ 0.939, 0.331, -0.098 ], "z_axis": [ -0.343, 0.865, -0.365 ], "quaternion": [ -0.482, 0.499, 0.658, 0.292 ] } }, { "index": 19, "nt1": "///B/5", "nt2": "///D/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -154.704, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 28.203, "chi2": -151.337, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 62.378, "C1C1_dist": 11.612, "N1N9_dist": 9.668, "C6C8_dist": 9.318, "CNNC_torsion": -9.838, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.93],O6(carbonyl)-N1(imino)[2.93]", "interBase_angle": 11.080, "planarity": 0.154, "simple_Shear": -2.651, "simple_Stretch": 2.836, "simple_Buckle": 9.849, "simple_Propeller": 5.075, "bp_simpleParams": [ -2.651, 2.836, 0.188, 9.849, 5.075, 90.022 ], "bp_params": [ -1.646, -3.515, 0.188, -8.369, 7.261, 89.984 ], "frame": { "rmsd": null, "origin": [ 7.999, -3.798, -18.056 ], "x_axis": [ -0.943, -0.316, 0.099 ], "y_axis": [ -0.072, 0.488, 0.870 ], "z_axis": [ -0.324, 0.813, -0.483 ], "quaternion": [ -0.124, -0.114, 0.854, 0.493 ] } }, { "index": 20, "nt1": "///B/6", "nt2": "///C/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -126.443, "conf1": "anti", "pucker1": "----", "lambda1": 30.314, "chi2": -137.393, "conf2": "anti", "pucker2": "----", "lambda2": 62.527, "C1C1_dist": 10.140, "N1N9_dist": 8.192, "C6C8_dist": 8.153, "CNNC_torsion": 16.741, "hbonds_num": 1, "hbonds_desc": "O4(carbonyl)-N3(imino)[2.81]", "interBase_angle": 22.263, "planarity": 0.260, "simple_Shear": -2.291, "simple_Stretch": 1.449, "simple_Buckle": -20.952, "simple_Propeller": -7.527, "bp_simpleParams": [ -2.291, 1.449, -0.553, -20.952, -7.527, 89.976 ], "bp_params": [ -0.642, -2.634, -0.553, 13.764, -17.498, 90.232 ], "frame": { "rmsd": null, "origin": [ 6.582, -1.660, -19.251 ], "x_axis": [ -0.490, -0.590, -0.641 ], "y_axis": [ 0.725, 0.132, -0.676 ], "z_axis": [ 0.484, -0.796, 0.363 ], "quaternion": [ 0.501, 0.060, 0.561, -0.656 ] } }, { "index": 21, "nt1": "///B/6", "nt2": "///D/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -126.443, "conf1": "anti", "pucker1": "----", "lambda1": 64.090, "chi2": -136.090, "conf2": "anti", "pucker2": "----", "lambda2": 31.215, "C1C1_dist": 10.130, "N1N9_dist": 8.229, "C6C8_dist": 8.154, "CNNC_torsion": 15.540, "hbonds_num": 1, "hbonds_desc": "N3(imino)-O4(carbonyl)[2.96]", "interBase_angle": 21.750, "planarity": 0.248, "simple_Shear": -2.219, "simple_Stretch": 1.792, "simple_Buckle": -21.691, "simple_Propeller": 1.601, "bp_simpleParams": [ -2.219, 1.792, 0.317, -21.691, 1.601, -84.442 ], "bp_params": [ 0.963, 2.685, 0.317, -5.640, 21.006, -85.337 ], "frame": { "rmsd": null, "origin": [ 4.577, -2.151, -18.868 ], "x_axis": [ 0.835, -0.119, -0.538 ], "y_axis": [ 0.467, 0.671, 0.576 ], "z_axis": [ 0.293, -0.732, 0.615 ], "quaternion": [ 0.883, 0.370, 0.235, -0.166 ] } }, { "index": 22, "nt1": "///E/2", "nt2": "///G/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -174.792, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 26.933, "chi2": -172.187, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 61.707, "C1C1_dist": 11.712, "N1N9_dist": 9.741, "C6C8_dist": 9.422, "CNNC_torsion": 16.330, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.98],O6(carbonyl)-N1(imino)[2.88]", "interBase_angle": 11.417, "planarity": 0.158, "simple_Shear": -2.569, "simple_Stretch": 2.797, "simple_Buckle": -11.071, "simple_Propeller": -2.788, "bp_simpleParams": [ -2.569, 2.797, 0.176, -11.071, -2.788, 91.560 ], "bp_params": [ -1.702, -3.394, 0.176, 6.531, -9.364, 91.659 ], "frame": { "rmsd": null, "origin": [ 13.225, -12.139, -5.506 ], "x_axis": [ -0.211, -0.568, -0.796 ], "y_axis": [ 0.919, 0.161, -0.359 ], "z_axis": [ 0.332, -0.807, 0.488 ], "quaternion": [ 0.600, 0.187, 0.470, -0.620 ] } }, { "index": 23, "nt1": "///E/2", "nt2": "///H/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -174.792, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 66.455, "chi2": -167.183, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 29.958, "C1C1_dist": 11.427, "N1N9_dist": 9.598, "C6C8_dist": 9.331, "CNNC_torsion": 10.497, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.88],N2(amino)-N7[2.78]", "interBase_angle": 16.749, "planarity": 0.228, "simple_Shear": -2.405, "simple_Stretch": 3.016, "simple_Buckle": -11.897, "simple_Propeller": -11.789, "bp_simpleParams": [ -2.405, 3.016, 0.162, -11.897, -11.789, -86.020 ], "bp_params": [ 1.988, 3.307, 0.162, -15.199, 7.036, -85.624 ], "frame": { "rmsd": null, "origin": [ 10.517, -12.855, -5.251 ], "x_axis": [ 0.948, 0.052, -0.314 ], "y_axis": [ 0.241, 0.528, 0.815 ], "z_axis": [ 0.208, -0.848, 0.488 ], "quaternion": [ 0.861, 0.483, 0.151, -0.055 ] } }, { "index": 24, "nt1": "///E/3", "nt2": "///G/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -166.604, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 29.162, "chi2": -167.806, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 62.315, "C1C1_dist": 11.458, "N1N9_dist": 9.506, "C6C8_dist": 9.166, "CNNC_torsion": 13.012, "hbonds_num": 1, "hbonds_desc": "O6(carbonyl)-N1(imino)[2.81]", "interBase_angle": 13.172, "planarity": 0.161, "simple_Shear": -2.753, "simple_Stretch": 2.636, "simple_Buckle": -12.406, "simple_Propeller": -4.424, "bp_simpleParams": [ -2.753, 2.636, -0.032, -12.406, -4.424, 89.744 ], "bp_params": [ -1.398, -3.546, -0.032, 8.780, -9.819, 89.787 ], "frame": { "rmsd": null, "origin": [ 13.009, -15.093, -3.488 ], "x_axis": [ 0.279, -0.437, -0.855 ], "y_axis": [ 0.913, 0.398, 0.095 ], "z_axis": [ 0.299, -0.807, 0.510 ], "quaternion": [ 0.739, 0.305, 0.390, -0.456 ] } }, { "index": 25, "nt1": "///E/3", "nt2": "///H/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -166.604, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 63.672, "chi2": -173.452, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 29.840, "C1C1_dist": 11.474, "N1N9_dist": 9.561, "C6C8_dist": 9.248, "CNNC_torsion": 11.479, "hbonds_num": 1, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.83]", "interBase_angle": 15.349, "planarity": 0.190, "simple_Shear": -2.659, "simple_Stretch": 2.786, "simple_Buckle": -13.763, "simple_Propeller": -6.795, "bp_simpleParams": [ -2.659, 2.786, 0.252, -13.763, -6.795, -88.353 ], "bp_params": [ 1.607, 3.500, 0.252, -11.382, 10.298, -88.301 ], "frame": { "rmsd": null, "origin": [ 10.877, -16.324, -4.774 ], "x_axis": [ 0.952, 0.253, 0.170 ], "y_axis": [ -0.268, 0.428, 0.863 ], "z_axis": [ 0.145, -0.867, 0.476 ], "quaternion": [ 0.845, 0.512, -0.007, 0.154 ] } }, { "index": 26, "nt1": "///E/4", "nt2": "///G/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -155.291, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 29.840, "chi2": -156.806, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 62.701, "C1C1_dist": 11.640, "N1N9_dist": 9.720, "C6C8_dist": 9.347, "CNNC_torsion": 5.946, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.96],O6(carbonyl)-N1(imino)[3.07]", "interBase_angle": 5.722, "planarity": 0.079, "simple_Shear": -2.684, "simple_Stretch": 3.023, "simple_Buckle": -4.856, "simple_Propeller": -3.026, "bp_simpleParams": [ -2.684, 3.023, -0.008, -4.856, -3.026, 87.745 ], "bp_params": [ -1.756, -3.641, -0.008, 4.663, -3.316, 87.722 ], "frame": { "rmsd": null, "origin": [ 12.866, -18.124, -2.080 ], "x_axis": [ 0.692, -0.178, -0.700 ], "y_axis": [ 0.678, 0.494, 0.545 ], "z_axis": [ 0.249, -0.851, 0.462 ], "quaternion": [ 0.814, 0.429, 0.291, -0.263 ] } }, { "index": 27, "nt1": "///E/4", "nt2": "///H/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -155.291, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 60.928, "chi2": -157.670, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 29.149, "C1C1_dist": 11.717, "N1N9_dist": 9.748, "C6C8_dist": 9.344, "CNNC_torsion": 2.770, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[3.08],N2(amino)-N7[3.05]", "interBase_angle": 4.420, "planarity": 0.069, "simple_Shear": -2.789, "simple_Stretch": 2.907, "simple_Buckle": -4.418, "simple_Propeller": -0.108, "bp_simpleParams": [ -2.789, 2.907, 0.120, -4.418, -0.108, -90.101 ], "bp_params": [ 1.579, 3.706, 0.120, -1.833, 4.022, -90.129 ], "frame": { "rmsd": null, "origin": [ 11.720, -19.511, -4.237 ], "x_axis": [ 0.707, 0.425, 0.566 ], "y_axis": [ -0.682, 0.197, 0.704 ], "z_axis": [ 0.187, -0.884, 0.429 ], "quaternion": [ 0.764, 0.520, -0.124, 0.362 ] } }, { "index": 28, "nt1": "///E/5", "nt2": "///G/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -152.218, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 29.466, "chi2": -151.609, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 62.567, "C1C1_dist": 11.609, "N1N9_dist": 9.684, "C6C8_dist": 9.327, "CNNC_torsion": -11.063, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.96],O6(carbonyl)-N1(imino)[3.01]", "interBase_angle": 13.351, "planarity": 0.185, "simple_Shear": -2.683, "simple_Stretch": 2.927, "simple_Buckle": 12.153, "simple_Propeller": 5.527, "bp_simpleParams": [ -2.683, 2.927, 0.185, 12.153, 5.527, 89.069 ], "bp_params": [ -1.692, -3.592, 0.185, -9.710, 9.163, 89.046 ], "frame": { "rmsd": null, "origin": [ 12.967, -21.128, -1.058 ], "x_axis": [ 0.870, 0.134, -0.474 ], "y_axis": [ 0.388, 0.407, 0.827 ], "z_axis": [ 0.303, -0.904, 0.303 ], "quaternion": [ 0.803, 0.539, 0.242, -0.079 ] } }, { "index": 29, "nt1": "///E/5", "nt2": "///H/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -152.218, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 61.971, "chi2": -152.155, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 28.852, "C1C1_dist": 11.601, "N1N9_dist": 9.654, "C6C8_dist": 9.295, "CNNC_torsion": -10.843, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.97],N2(amino)-N7[2.95]", "interBase_angle": 13.167, "planarity": 0.182, "simple_Shear": -2.702, "simple_Stretch": 2.836, "simple_Buckle": 11.348, "simple_Propeller": 6.677, "bp_simpleParams": [ -2.702, 2.836, -0.216, 11.348, 6.677, -90.046 ], "bp_params": [ 1.602, 3.574, -0.216, 10.469, -7.985, -89.946 ], "frame": { "rmsd": null, "origin": [ 12.890, -22.360, -3.526 ], "x_axis": [ 0.339, 0.542, 0.769 ], "y_axis": [ -0.873, -0.123, 0.471 ], "z_axis": [ 0.350, -0.831, 0.432 ], "quaternion": [ 0.642, 0.507, -0.163, 0.551 ] } }, { "index": 30, "nt1": "///E/6", "nt2": "///G/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -133.929, "conf1": "anti", "pucker1": "----", "lambda1": 62.872, "chi2": -131.717, "conf2": "anti", "pucker2": "----", "lambda2": 31.712, "C1C1_dist": 9.956, "N1N9_dist": 8.031, "C6C8_dist": 7.933, "CNNC_torsion": 19.141, "hbonds_num": 1, "hbonds_desc": "N3(imino)-O4(carbonyl)[2.77]", "interBase_angle": 26.007, "planarity": 0.295, "simple_Shear": -2.282, "simple_Stretch": 1.538, "simple_Buckle": -25.998, "simple_Propeller": 0.679, "bp_simpleParams": [ -2.282, 1.538, 0.470, -25.998, 0.679, -85.693 ], "bp_params": [ 0.690, 2.664, 0.470, -8.026, 24.737, -86.896 ], "frame": { "rmsd": null, "origin": [ 16.263, -23.267, -0.935 ], "x_axis": [ -0.961, -0.250, -0.118 ], "y_axis": [ -0.166, 0.182, 0.969 ], "z_axis": [ -0.220, 0.951, -0.216 ], "quaternion": [ -0.033, -0.135, 0.768, 0.625 ] } }, { "index": 31, "nt1": "///E/6", "nt2": "///H/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -133.929, "conf1": "anti", "pucker1": "----", "lambda1": 30.282, "chi2": -133.107, "conf2": "anti", "pucker2": "----", "lambda2": 61.933, "C1C1_dist": 10.107, "N1N9_dist": 8.142, "C6C8_dist": 8.049, "CNNC_torsion": 16.688, "hbonds_num": 1, "hbonds_desc": "O4(carbonyl)-N3(imino)[2.79]", "interBase_angle": 23.069, "planarity": 0.260, "simple_Shear": -2.288, "simple_Stretch": 1.498, "simple_Buckle": -23.013, "simple_Propeller": 1.608, "bp_simpleParams": [ -2.288, 1.498, -0.399, -23.013, 1.608, 87.813 ], "bp_params": [ -0.662, -2.653, -0.399, 6.068, -22.256, 88.820 ], "frame": { "rmsd": null, "origin": [ 14.477, -23.472, -0.150 ], "x_axis": [ 0.196, -0.300, -0.934 ], "y_axis": [ -0.872, -0.489, -0.026 ], "z_axis": [ -0.449, 0.819, -0.357 ], "quaternion": [ -0.296, 0.715, -0.410, -0.484 ] } }, { "index": 32, "nt1": "///F/2", "nt2": "///G/1", "bp": "G+u", "name": "--", "Saenger": "--", "LW": "tSW", "DSSR": "tm+W", "intra_chain": false, "chi1": -169.594, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 99.300, "chi2": -114.066, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 34.196, "C1C1_dist": 8.833, "N1N9_dist": 8.169, "C6C8_dist": 10.102, "CNNC_torsion": 163.821, "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O4(carbonyl)[2.94],N2(amino)-O2(carbonyl)[3.28]", "interBase_angle": 18.890, "planarity": 0.257, "simple_Shear": 5.091, "simple_Stretch": 3.234, "simple_Buckle": 12.991, "simple_Propeller": -13.713, "bp_simpleParams": [ 5.091, 3.234, 0.534, 12.991, -13.713, -114.482 ], "bp_params": [ -0.421, -6.017, 0.534, -18.748, -2.307, -113.789 ], "frame": { "rmsd": null, "origin": [ 11.588, -15.081, -11.862 ], "x_axis": [ -0.967, -0.203, 0.153 ], "y_axis": [ -0.056, -0.418, -0.907 ], "z_axis": [ 0.248, -0.886, 0.393 ], "quaternion": [ -0.044, 0.121, -0.538, 0.833 ] } }, { "index": 33, "nt1": "///F/2", "nt2": "///G/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -169.594, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 64.350, "chi2": -172.187, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 28.809, "C1C1_dist": 11.539, "N1N9_dist": 9.648, "C6C8_dist": 9.345, "CNNC_torsion": 9.114, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.85],N2(amino)-N7[2.86]", "interBase_angle": 12.642, "planarity": 0.176, "simple_Shear": -2.493, "simple_Stretch": 2.876, "simple_Buckle": -7.383, "simple_Propeller": -10.262, "bp_simpleParams": [ -2.493, 2.876, 0.047, -7.383, -10.262, -88.702 ], "bp_params": [ 1.804, 3.352, 0.047, -12.217, 3.251, -88.399 ], "frame": { "rmsd": null, "origin": [ 13.302, -13.148, -7.948 ], "x_axis": [ -0.909, -0.183, 0.374 ], "y_axis": [ -0.276, -0.408, -0.870 ], "z_axis": [ 0.312, -0.894, 0.320 ], "quaternion": [ 0.029, 0.211, -0.543, 0.812 ] } }, { "index": 34, "nt1": "///F/2", "nt2": "///H/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -169.594, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 27.730, "chi2": -167.183, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 60.851, "C1C1_dist": 11.835, "N1N9_dist": 9.850, "C6C8_dist": 9.495, "CNNC_torsion": 12.905, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[3.12],O6(carbonyl)-N1(imino)[3.05]", "interBase_angle": 12.182, "planarity": 0.165, "simple_Shear": -2.705, "simple_Stretch": 2.912, "simple_Buckle": -9.658, "simple_Propeller": -7.423, "bp_simpleParams": [ -2.705, 2.912, -0.047, -9.658, -7.423, 91.709 ], "bp_params": [ -1.690, -3.598, -0.047, 10.493, -6.188, 91.552 ], "frame": { "rmsd": null, "origin": [ 10.593, -13.864, -7.693 ], "x_axis": [ 0.294, 0.361, 0.885 ], "y_axis": [ -0.937, -0.072, 0.341 ], "z_axis": [ 0.186, -0.930, 0.317 ], "quaternion": [ 0.620, 0.512, -0.282, 0.523 ] } }, { "index": 35, "nt1": "///F/3", "nt2": "///G/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -166.653, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 63.822, "chi2": -167.806, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 29.215, "C1C1_dist": 11.450, "N1N9_dist": 9.532, "C6C8_dist": 9.229, "CNNC_torsion": 11.166, "hbonds_num": 1, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.80]", "interBase_angle": 13.418, "planarity": 0.164, "simple_Shear": -2.615, "simple_Stretch": 2.793, "simple_Buckle": -11.221, "simple_Propeller": -7.356, "bp_simpleParams": [ -2.615, 2.793, 0.137, -11.221, -7.356, -87.453 ], "bp_params": [ 1.640, 3.456, 0.137, -10.950, 7.755, -87.322 ], "frame": { "rmsd": null, "origin": [ 14.518, -15.580, -5.583 ], "x_axis": [ -0.905, -0.412, -0.108 ], "y_axis": [ 0.237, -0.276, -0.932 ], "z_axis": [ 0.354, -0.868, 0.347 ], "quaternion": [ -0.204, 0.077, -0.566, 0.795 ] } }, { "index": 36, "nt1": "///F/3", "nt2": "///H/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -166.653, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 28.711, "chi2": -173.452, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 61.153, "C1C1_dist": 11.561, "N1N9_dist": 9.574, "C6C8_dist": 9.240, "CNNC_torsion": 13.300, "hbonds_num": 1, "hbonds_desc": "O6(carbonyl)-N1(imino)[2.80]", "interBase_angle": 14.868, "planarity": 0.183, "simple_Shear": -2.744, "simple_Stretch": 2.618, "simple_Buckle": -13.114, "simple_Propeller": -7.007, "bp_simpleParams": [ -2.744, 2.618, -0.172, -13.114, -7.007, 91.146 ], "bp_params": [ -1.411, -3.520, -0.172, 11.365, -9.587, 91.064 ], "frame": { "rmsd": null, "origin": [ 12.386, -16.811, -6.869 ], "x_axis": [ -0.239, 0.263, 0.935 ], "y_axis": [ -0.950, -0.263, -0.169 ], "z_axis": [ 0.201, -0.928, 0.312 ], "quaternion": [ 0.450, 0.422, -0.408, 0.673 ] } }, { "index": 37, "nt1": "///F/4", "nt2": "///G/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -158.813, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 62.338, "chi2": -156.806, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 27.662, "C1C1_dist": 11.770, "N1N9_dist": 9.820, "C6C8_dist": 9.475, "CNNC_torsion": 7.515, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[2.99],N2(amino)-N7[3.07]", "interBase_angle": 9.328, "planarity": 0.139, "simple_Shear": -2.617, "simple_Stretch": 2.942, "simple_Buckle": -9.083, "simple_Propeller": -2.123, "bp_simpleParams": [ -2.617, 2.942, 0.231, -9.083, -2.123, -90.662 ], "bp_params": [ 1.782, 3.511, 0.231, -5.293, 7.681, -90.729 ], "frame": { "rmsd": null, "origin": [ 15.331, -18.093, -3.432 ], "x_axis": [ -0.677, -0.473, -0.564 ], "y_axis": [ 0.680, -0.107, -0.726 ], "z_axis": [ 0.283, -0.875, 0.394 ], "quaternion": [ -0.391, -0.095, -0.542, 0.738 ] } }, { "index": 38, "nt1": "///F/4", "nt2": "///H/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -158.813, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 27.916, "chi2": -157.670, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 61.147, "C1C1_dist": 11.666, "N1N9_dist": 9.691, "C6C8_dist": 9.317, "CNNC_torsion": 6.303, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.97],O6(carbonyl)-N1(imino)[2.93]", "interBase_angle": 7.004, "planarity": 0.109, "simple_Shear": -2.682, "simple_Stretch": 2.806, "simple_Buckle": -6.830, "simple_Propeller": 1.555, "bp_simpleParams": [ -2.682, 2.806, -0.140, -6.830, 1.555, 90.616 ], "bp_params": [ -1.591, -3.541, -0.140, 1.128, -6.913, 90.717 ], "frame": { "rmsd": null, "origin": [ 14.185, -19.481, -5.589 ], "x_axis": [ -0.673, 0.125, 0.729 ], "y_axis": [ -0.706, -0.404, -0.582 ], "z_axis": [ 0.221, -0.906, 0.360 ], "quaternion": [ 0.266, 0.304, -0.477, 0.780 ] } }, { "index": 39, "nt1": "///F/5", "nt2": "///G/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -149.247, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 63.391, "chi2": -151.609, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 29.896, "C1C1_dist": 11.607, "N1N9_dist": 9.708, "C6C8_dist": 9.362, "CNNC_torsion": -12.350, "hbonds_num": 2, "hbonds_desc": "N1(imino)-O6(carbonyl)[3.05],N2(amino)-N7[2.98]", "interBase_angle": 14.600, "planarity": 0.202, "simple_Shear": -2.656, "simple_Stretch": 3.010, "simple_Buckle": 13.586, "simple_Propeller": 5.348, "bp_simpleParams": [ -2.656, 3.010, -0.179, 13.586, 5.348, -88.232 ], "bp_params": [ 1.784, 3.596, -0.179, 10.069, -10.573, -88.255 ], "frame": { "rmsd": null, "origin": [ 15.672, -20.512, -1.501 ], "x_axis": [ -0.372, -0.413, -0.832 ], "y_axis": [ 0.915, -0.014, -0.402 ], "z_axis": [ 0.154, -0.911, 0.383 ], "quaternion": [ -0.499, -0.255, -0.494, 0.665 ] } }, { "index": 40, "nt1": "///F/5", "nt2": "///H/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -149.247, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 28.124, "chi2": -152.155, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 63.346, "C1C1_dist": 11.605, "N1N9_dist": 9.685, "C6C8_dist": 9.363, "CNNC_torsion": -14.017, "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.91],O6(carbonyl)-N1(imino)[2.89]", "interBase_angle": 11.378, "planarity": 0.156, "simple_Shear": -2.557, "simple_Stretch": 2.864, "simple_Buckle": 10.866, "simple_Propeller": 3.375, "bp_simpleParams": [ -2.557, 2.864, 0.005, 10.866, 3.375, 89.692 ], "bp_params": [ -1.753, -3.415, 0.005, -7.049, 8.932, 89.758 ], "frame": { "rmsd": null, "origin": [ 15.595, -21.744, -3.969 ], "x_axis": [ -0.921, 0.017, 0.389 ], "y_axis": [ -0.334, -0.549, -0.766 ], "z_axis": [ 0.200, -0.836, 0.511 ], "quaternion": [ 0.102, 0.171, -0.464, 0.863 ] } }, { "index": 41, "nt1": "///F/6", "nt2": "///G/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cHW", "DSSR": "cM+W", "intra_chain": false, "chi1": -130.236, "conf1": "anti", "pucker1": "----", "lambda1": 32.285, "chi2": -131.717, "conf2": "anti", "pucker2": "----", "lambda2": 63.194, "C1C1_dist": 9.966, "N1N9_dist": 8.060, "C6C8_dist": 7.962, "CNNC_torsion": 18.299, "hbonds_num": 1, "hbonds_desc": "O4(carbonyl)-N3(imino)[2.84]", "interBase_angle": 26.015, "planarity": 0.298, "simple_Shear": -2.327, "simple_Stretch": 1.620, "simple_Buckle": -26.014, "simple_Propeller": -0.240, "bp_simpleParams": [ -2.327, 1.620, -0.432, -26.014, -0.240, 85.122 ], "bp_params": [ -0.731, -2.739, -0.432, 9.076, -24.381, 86.246 ], "frame": { "rmsd": null, "origin": [ 15.628, -24.178, -2.621 ], "x_axis": [ -0.235, 0.444, 0.865 ], "y_axis": [ 0.972, 0.130, 0.197 ], "z_axis": [ -0.025, 0.886, -0.462 ], "quaternion": [ -0.329, 0.524, 0.676, 0.401 ] } }, { "index": 42, "nt1": "///F/6", "nt2": "///H/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cWH", "DSSR": "cW+M", "intra_chain": false, "chi1": -130.236, "conf1": "anti", "pucker1": "----", "lambda1": 63.097, "chi2": -133.107, "conf2": "anti", "pucker2": "----", "lambda2": 31.934, "C1C1_dist": 9.880, "N1N9_dist": 7.967, "C6C8_dist": 7.866, "CNNC_torsion": 12.793, "hbonds_num": 1, "hbonds_desc": "N3(imino)-O4(carbonyl)[2.68]", "interBase_angle": 24.010, "planarity": 0.266, "simple_Shear": -2.334, "simple_Stretch": 1.436, "simple_Buckle": -23.849, "simple_Propeller": -2.779, "bp_simpleParams": [ -2.334, 1.436, 0.760, -23.849, -2.779, -86.266 ], "bp_params": [ 0.566, 2.681, 0.760, -10.619, 21.534, -87.037 ], "frame": { "rmsd": null, "origin": [ 13.842, -24.384, -1.836 ], "x_axis": [ 0.924, 0.375, 0.078 ], "y_axis": [ 0.285, -0.537, -0.794 ], "z_axis": [ -0.255, 0.756, -0.603 ], "quaternion": [ -0.443, 0.875, 0.188, -0.051 ] } } ], "num_multiplets": 10, "multiplets": [ { "index": 1, "num_nts": 4, "nts_short": "gggg", "nts_long": "///A/3,///B/3,///C/3,///D/3", "planarity": 0.327 }, { "index": 2, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///A/4,///B/4,///C/4,///D/4", "planarity": 0.175 }, { "index": 3, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///A/5,///B/5,///C/5,///D/5", "planarity": 0.189 }, { "index": 4, "num_nts": 4, "nts_short": "UUUU", "nts_long": "///A/6,///B/6,///C/6,///D/6", "planarity": 0.427 }, { "index": 5, "num_nts": 4, "nts_short": "gggg", "nts_long": "///E/3,///F/3,///G/3,///H/3", "planarity": 0.279 }, { "index": 6, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///E/4,///F/4,///G/4,///H/4", "planarity": 0.140 }, { "index": 7, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///E/5,///F/5,///G/5,///H/5", "planarity": 0.255 }, { "index": 8, "num_nts": 4, "nts_short": "UUUU", "nts_long": "///E/6,///F/6,///G/6,///H/6", "planarity": 0.414 }, { "index": 9, "num_nts": 5, "nts_short": "GGuGG", "nts_long": "///A/2,///B/2,///C/1,///C/2,///D/2", "planarity": 0.320 }, { "index": 10, "num_nts": 5, "nts_short": "GGuGG", "nts_long": "///E/2,///F/2,///G/1,///G/2,///H/2", "planarity": 0.258 } ], "num_helices": 4, "helices": [ { "index": 1, "num_stems": 0, "strand1": "GgGGU", "strand2": "GgGGU", "bp_type": ".....", "helix_form": "...x", "helical_rise": 3.752, "helical_rise_std": 0.314, "helical_radius": 10.171, "helical_radius_std": 0.795, "helical_axis": [ -0.315, 0.868, -0.385 ], "point1": [ 9.107, -13.936, -14.013 ], "point2": [ 4.265, -0.592, -19.929 ], "num_pairs": 5, "pairs": [ { "index": 1, "nt1": "///A/2", "nt2": "///D/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "bp1_params": [ 1.860, 3.391, -0.123, -16.292, 8.450, -88.374 ], "step_params": [ -0.188, -1.327, 3.181, 2.326, -0.172, 29.783 ], "heli_params": [ -2.540, 0.834, 3.165, -0.334, -4.517, 29.872 ], "bp2_params": [ 1.540, 3.476, 0.272, -14.449, 10.274, -86.686 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.181, "simple_Twist": 31.022, "simple_hRise": 3.166, "simple_hTwist": 31.107 }, { "index": 2, "nt1": "///A/3", "nt2": "///D/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "bp1_params": [ 1.540, 3.476, 0.272, -14.449, 10.274, -86.686 ], "step_params": [ -0.300, -0.915, 3.098, 4.452, 0.712, 30.218 ], "heli_params": [ -1.869, 1.398, 3.002, 1.357, -8.479, 30.545 ], "bp2_params": [ 1.677, 3.511, 0.044, -5.573, 5.458, -90.131 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.098, "simple_Twist": 30.066, "simple_hRise": 3.001, "simple_hTwist": 30.394 }, { "index": 3, "nt1": "///A/4", "nt2": "///D/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "bp1_params": [ 1.677, 3.511, 0.044, -5.573, 5.458, -90.131 ], "step_params": [ -0.485, -0.675, 3.099, 5.075, 5.880, 23.132 ], "heli_params": [ -3.268, 2.590, 2.682, 14.161, -12.222, 24.385 ], "bp2_params": [ 1.659, 3.547, -0.109, 4.996, -6.547, -91.656 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.099, "simple_Twist": 23.276, "simple_hRise": 2.685, "simple_hTwist": 24.521 }, { "index": 4, "nt1": "///A/5", "nt2": "///D/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "bp1_params": [ 1.659, 3.547, -0.109, 4.996, -6.547, -91.656 ], "step_params": [ 0.338, -0.170, 2.842, 4.898, 8.283, 127.019 ], "heli_params": [ -0.152, -0.155, 2.841, 4.624, -2.735, 127.220 ], "bp2_params": [ 0.963, 2.685, 0.317, -5.640, 21.006, -85.337 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 2.842, "simple_Twist": -126.472, "simple_hRise": 2.839, "simple_hTwist": -126.676 }, { "index": 5, "nt1": "///B/6", "nt2": "///D/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cWH", "DSSR": "cW+M" } ] }, { "index": 2, "num_stems": 0, "strand1": "GgGGU", "strand2": "GgGGU", "bp_type": ".....", "helix_form": "...x", "helical_rise": 3.765, "helical_rise_std": 0.384, "helical_radius": 10.391, "helical_radius_std": 0.897, "helical_axis": [ -0.264, 0.832, -0.488 ], "point1": [ 9.926, -13.637, -13.998 ], "point2": [ 5.866, -0.816, -21.522 ], "num_pairs": 5, "pairs": [ { "index": 1, "nt1": "///B/2", "nt2": "///C/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "bp1_params": [ 1.553, 3.393, -0.005, -11.154, -0.960, -91.519 ], "step_params": [ -0.053, -1.449, 3.326, 2.373, -1.187, 32.684 ], "heli_params": [ -2.357, 0.511, 3.363, -2.105, -4.208, 32.788 ], "bp2_params": [ 1.608, 3.376, 0.247, -13.977, 8.634, -89.024 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.326, "simple_Twist": 32.318, "simple_hRise": 3.364, "simple_hTwist": 32.424 }, { "index": 2, "nt1": "///B/3", "nt2": "///C/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "bp1_params": [ 1.608, 3.376, 0.247, -13.977, 8.634, -89.024 ], "step_params": [ -0.309, -1.141, 3.259, 4.460, 1.074, 28.473 ], "heli_params": [ -2.527, 1.599, 3.131, 2.166, -8.993, 28.833 ], "bp2_params": [ 1.765, 3.511, 0.247, -7.851, 9.522, -91.009 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.259, "simple_Twist": 28.781, "simple_hRise": 3.133, "simple_hTwist": 29.137 }, { "index": 3, "nt1": "///B/4", "nt2": "///C/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "bp1_params": [ 1.765, 3.511, 0.247, -7.851, 9.522, -91.009 ], "step_params": [ -0.470, -0.879, 2.999, 4.882, 4.507, 23.853 ], "heli_params": [ -3.254, 2.399, 2.643, 10.642, -11.529, 24.748 ], "bp2_params": [ 1.736, 3.471, 0.086, 5.732, -6.481, -88.713 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 2.999, "simple_Twist": 24.067, "simple_hRise": 2.647, "simple_hTwist": 24.955 }, { "index": 4, "nt1": "///B/5", "nt2": "///C/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cWH", "DSSR": "cW+M", "bp1_params": [ 1.736, 3.471, 0.086, 5.732, -6.481, -88.713 ], "step_params": [ 0.201, -0.177, 2.684, 3.532, 8.005, 126.322 ], "heli_params": [ -0.152, -0.089, 2.679, 4.483, -1.978, 126.491 ], "bp2_params": [ 0.647, 2.703, 0.712, -11.640, 27.434, -84.661 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 2.684, "simple_Twist": -128.196, "simple_hRise": 2.685, "simple_hTwist": -128.358 }, { "index": 5, "nt1": "///A/6", "nt2": "///C/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cWH", "DSSR": "cW+M" } ] }, { "index": 3, "num_stems": 0, "strand1": "GgGGU", "strand2": "GgGGU", "bp_type": ".....", "helix_form": "...x", "helical_rise": 3.685, "helical_rise_std": 0.380, "helical_radius": 10.568, "helical_radius_std": 1.118, "helical_axis": [ 0.246, -0.867, 0.434 ], "point1": [ 11.724, -12.158, -6.638 ], "point2": [ 15.419, -25.193, -0.118 ], "num_pairs": 5, "pairs": [ { "index": 1, "nt1": "///E/2", "nt2": "///G/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "bp1_params": [ -1.702, -3.394, 0.176, 6.531, -9.364, 91.659 ], "step_params": [ -0.211, -1.325, 3.323, 1.976, -1.138, 29.596 ], "heli_params": [ -2.343, 0.835, 3.350, -2.223, -3.861, 29.682 ], "bp2_params": [ -1.398, -3.546, -0.032, 8.780, -9.819, 89.787 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.323, "simple_Twist": 30.889, "simple_hRise": 3.349, "simple_hTwist": 30.971 }, { "index": 2, "nt1": "///E/3", "nt2": "///G/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "bp1_params": [ -1.398, -3.546, -0.032, 8.780, -9.819, 89.787 ], "step_params": [ -0.272, -1.062, 3.160, 4.411, 1.567, 29.618 ], "heli_params": [ -2.360, 1.392, 3.029, 3.041, -8.561, 29.977 ], "bp2_params": [ -1.756, -3.641, -0.008, 4.663, -3.316, 87.722 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.160, "simple_Twist": 29.329, "simple_hRise": 3.028, "simple_hTwist": 29.692 }, { "index": 3, "nt1": "///E/4", "nt2": "///G/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "bp1_params": [ -1.756, -3.641, -0.008, 4.663, -3.316, 87.722 ], "step_params": [ -0.498, -0.656, 3.066, 6.124, 8.084, 23.160 ], "heli_params": [ -3.592, 2.724, 2.489, 19.010, -14.401, 25.255 ], "bp2_params": [ -1.692, -3.592, 0.185, -9.710, 9.163, 89.046 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.066, "simple_Twist": 23.071, "simple_hRise": 2.486, "simple_hTwist": 25.174 }, { "index": 4, "nt1": "///E/5", "nt2": "///G/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "bp1_params": [ -1.692, -3.592, 0.185, -9.710, 9.163, 89.046 ], "step_params": [ 0.353, -0.276, 2.898, 2.100, 9.940, 124.754 ], "heli_params": [ -0.229, -0.184, 2.886, 5.605, -1.184, 124.989 ], "bp2_params": [ -0.662, -2.653, -0.399, 6.068, -22.256, 88.820 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 2.898, "simple_Twist": -129.459, "simple_hRise": 2.904, "simple_hTwist": -129.671 }, { "index": 5, "nt1": "///E/6", "nt2": "///H/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cHW", "DSSR": "cM+W" } ] }, { "index": 4, "num_stems": 0, "strand1": "GgGGU", "strand2": "GgGGU", "bp_type": ".....", "helix_form": "...x", "helical_rise": 3.715, "helical_rise_std": 0.416, "helical_radius": 10.203, "helical_radius_std": 0.672, "helical_axis": [ 0.275, -0.890, 0.364 ], "point1": [ 11.573, -12.373, -6.915 ], "point2": [ 15.753, -25.900, -1.385 ], "num_pairs": 5, "pairs": [ { "index": 1, "nt1": "///F/2", "nt2": "///H/2", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "bp1_params": [ -1.690, -3.598, -0.047, 10.493, -6.188, 91.552 ], "step_params": [ -0.131, -1.172, 3.345, 0.858, -0.210, 31.598 ], "heli_params": [ -2.111, 0.403, 3.347, -0.386, -1.575, 31.610 ], "bp2_params": [ -1.411, -3.520, -0.172, 11.365, -9.587, 91.064 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.345, "simple_Twist": 31.715, "simple_hRise": 3.347, "simple_hTwist": 31.727 }, { "index": 2, "nt1": "///F/3", "nt2": "///H/3", "bp": "g+g", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "bp1_params": [ -1.411, -3.520, -0.172, 11.365, -9.587, 91.064 ], "step_params": [ -0.300, -1.132, 3.261, 2.494, 2.059, 28.849 ], "heli_params": [ -2.704, 1.137, 3.138, 4.117, -4.987, 29.026 ], "bp2_params": [ -1.591, -3.541, -0.140, 1.128, -6.913, 90.717 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.261, "simple_Twist": 28.934, "simple_hRise": 3.138, "simple_hTwist": 29.110 }, { "index": 3, "nt1": "///F/4", "nt2": "///H/4", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "bp1_params": [ -1.591, -3.541, -0.140, 1.128, -6.913, 90.717 ], "step_params": [ -0.429, -0.800, 2.985, 7.341, 6.254, 24.378 ], "heli_params": [ -3.233, 2.668, 2.475, 14.124, -16.578, 26.190 ], "bp2_params": [ -1.753, -3.415, 0.005, -7.049, 8.932, 89.758 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 2.985, "simple_Twist": 23.498, "simple_hRise": 2.451, "simple_hTwist": 25.374 }, { "index": 4, "nt1": "///F/5", "nt2": "///H/5", "bp": "G+G", "name": "--", "Saenger": "06-VI", "LW": "cHW", "DSSR": "cM+W", "bp1_params": [ -1.753, -3.415, 0.005, -7.049, 8.932, 89.758 ], "step_params": [ 0.226, -0.169, 2.768, 3.847, 10.140, 123.959 ], "heli_params": [ -0.169, -0.100, 2.761, 5.739, -2.177, 124.232 ], "bp2_params": [ -0.731, -2.739, -0.432, 9.076, -24.381, 86.246 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 2.768, "simple_Twist": -129.919, "simple_hRise": 2.769, "simple_hTwist": -130.158 }, { "index": 5, "nt1": "///F/6", "nt2": "///G/6", "bp": "U+U", "name": "Metal", "Saenger": "--", "LW": "cHW", "DSSR": "cM+W" } ] } ], "num_stacks": 8, "stacks": [ { "index": 1, "num_nts": 2, "nts_short": "uu", "nts_long": "///D/1,///F/1" }, { "index": 2, "num_nts": 5, "nts_short": "GgGGU", "nts_long": "///A/2,///A/3,///A/4,///A/5,///A/6" }, { "index": 3, "num_nts": 5, "nts_short": "GgGGU", "nts_long": "///D/2,///D/3,///D/4,///D/5,///D/6" }, { "index": 4, "num_nts": 5, "nts_short": "GgGGU", "nts_long": "///G/2,///G/3,///G/4,///G/5,///G/6" }, { "index": 5, "num_nts": 5, "nts_short": "GgGGU", "nts_long": "///H/2,///H/3,///H/4,///H/5,///H/6" }, { "index": 6, "num_nts": 6, "nts_short": "uGgGGU", "nts_long": "///C/1,///E/2,///E/3,///E/4,///E/5,///E/6" }, { "index": 7, "num_nts": 6, "nts_short": "UGGgGu", "nts_long": "///C/6,///C/5,///C/4,///C/3,///C/2,///G/1" }, { "index": 8, "num_nts": 10, "nts_short": "UGGgGGgGGU", "nts_long": "///B/6,///B/5,///B/4,///B/3,///B/2,///F/2,///F/3,///F/4,///F/5,///F/6" } ], "nonStack": { "num_nts": 1, "nts_short": "u", "nts_long": "///E/1" }, "num_atom2bases": 6, "atom2bases": [ { "index": 1, "type": "sugar", "atom": "///F/2/O2'", "nt": "///A/2", "vert_dist": 3.500 }, { "index": 2, "type": "sugar", "atom": "///F/1/O4'", "nt": "///D/1", "vert_dist": 2.910 }, { "index": 3, "type": "sugar", "atom": "///F/2/O4'", "nt": "///D/2", "vert_dist": 2.814 }, { "index": 4, "type": "phosphate", "atom": "///H/4/O3'", "nt": "///F/1", "vert_dist": 3.396 }, { "index": 5, "type": "sugar", "atom": "///H/4/O2'", "nt": "///F/1", "vert_dist": 3.433 }, { "index": 6, "type": "sugar", "atom": "///B/2/O4'", "nt": "///H/2", "vert_dist": 2.901 } ], "num_ssSegments": 8, "ssSegments": [ { "index": 1, "num_nts": 5, "nts_short": "GgGGU", "nts_long": "///A/2,///A/3,///A/4,///A/5,///A/6" }, { "index": 2, "num_nts": 5, "nts_short": "GgGGU", "nts_long": "///B/2,///B/3,///B/4,///B/5,///B/6" }, { "index": 3, "num_nts": 6, "nts_short": "uGgGGU", "nts_long": "///C/1,///C/2,///C/3,///C/4,///C/5,///C/6" }, { "index": 4, "num_nts": 6, "nts_short": "uGgGGU", "nts_long": "///D/1,///D/2,///D/3,///D/4,///D/5,///D/6" }, { "index": 5, "num_nts": 6, "nts_short": "uGgGGU", "nts_long": "///E/1,///E/2,///E/3,///E/4,///E/5,///E/6" }, { "index": 6, "num_nts": 6, "nts_short": "uGgGGU", "nts_long": "///F/1,///F/2,///F/3,///F/4,///F/5,///F/6" }, { "index": 7, "num_nts": 6, "nts_short": "uGgGGU", "nts_long": "///G/1,///G/2,///G/3,///G/4,///G/5,///G/6" }, { "index": 8, "num_nts": 5, "nts_short": "GgGGU", "nts_long": "///H/2,///H/3,///H/4,///H/5,///H/6" } ], "num_Gtetrads": 8, "Gtetrads": [ { "index": 1, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///A/2,///D/2,///B/2,///C/2", "planarity": 0.322, "G1G2_simpleParams": [ -2.511, 2.942, -0.123, -13.673, -12.243, -88.799 ], "G2G3_simpleParams": [ -2.738, 3.059, 0.412, -13.876, -12.802, -87.465 ], "G3G4_simpleParams": [ -2.600, 2.676, -0.005, -3.150, -10.743, -91.789 ], "G4G1_simpleParams": [ -2.573, 2.884, -0.220, -15.169, -2.507, -89.160 ], "type": "other", "direction": "WC-->Major", "ONZ_class": "--", "glyco_bond": "----", "sugar_pucker": "3333", "groove_type": "----", "groove_distPP": [ null, 16.531, 17.321, null ], "rmsd": 0.247, "frame": { "rmsd": null, "origin": [ 9.528, -13.229, -14.285 ], "x_axis": [ 0.595, 0.512, 0.619 ], "y_axis": [ 0.748, -0.072, -0.660 ], "z_axis": [ -0.293, 0.856, -0.425 ], "quaternion": [ 0.524, -0.723, -0.435, -0.113 ] } }, { "index": 2, "num_nts": 4, "nts_short": "gggg", "nts_long": "///A/3,///D/3,///B/3,///C/3", "planarity": 0.327, "G1G2_simpleParams": [ -2.652, 2.724, 0.272, -14.904, -9.601, -86.911 ], "G2G3_simpleParams": [ -2.753, 2.690, 0.202, -13.735, -4.185, -92.064 ], "G3G4_simpleParams": [ -2.584, 2.703, 0.247, -13.030, -10.006, -89.288 ], "G4G1_simpleParams": [ -2.663, 2.751, -0.041, -13.144, -1.863, -88.079 ], "type": "other", "direction": "WC-->Major", "ONZ_class": "--", "glyco_bond": "----", "sugar_pucker": "3333", "groove_type": "----", "groove_distPP": [ 14.852, 14.966, 14.963, 14.807 ], "rmsd": 0.299, "frame": { "rmsd": null, "origin": [ 8.524, -10.471, -15.735 ], "x_axis": [ 0.904, 0.390, 0.177 ], "y_axis": [ 0.320, -0.337, -0.885 ], "z_axis": [ -0.286, 0.857, -0.430 ], "quaternion": [ 0.533, -0.817, -0.217, 0.033 ] } }, { "index": 3, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///A/4,///D/4,///B/4,///C/4", "planarity": 0.175, "G1G2_simpleParams": [ -2.639, 2.860, 0.044, -7.135, -3.154, -90.134 ], "G2G3_simpleParams": [ -2.607, 2.903, 0.052, -5.436, 2.388, -89.187 ], "G3G4_simpleParams": [ -2.625, 2.924, 0.247, -11.727, -3.846, -90.945 ], "G4G1_simpleParams": [ -2.630, 2.953, 0.152, -4.793, -2.152, -88.763 ], "type": "other", "direction": "WC-->Major", "ONZ_class": "--", "glyco_bond": "----", "sugar_pucker": "3333", "groove_type": "----", "groove_distPP": [ 14.963, 14.985, 15.082, 14.859 ], "rmsd": 0.125, "frame": { "rmsd": null, "origin": [ 7.434, -7.531, -17.244 ], "x_axis": [ 0.944, 0.180, -0.277 ], "y_axis": [ -0.161, -0.482, -0.861 ], "z_axis": [ -0.288, 0.857, -0.427 ], "quaternion": [ 0.509, -0.845, -0.006, 0.167 ] } }, { "index": 4, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///A/5,///D/5,///B/5,///C/5", "planarity": 0.189, "G1G2_simpleParams": [ -2.678, 2.857, -0.109, 7.932, 2.211, -91.617 ], "G2G3_simpleParams": [ -2.651, 2.836, -0.188, 9.849, 5.075, -90.022 ], "G3G4_simpleParams": [ -2.589, 2.890, 0.086, 8.133, 2.951, -88.693 ], "G4G1_simpleParams": [ -2.688, 2.874, -0.206, 8.952, 5.352, -88.160 ], "type": "other", "direction": "WC-->Major", "ONZ_class": "--", "glyco_bond": "----", "sugar_pucker": "3333", "groove_type": "----", "groove_distPP": [ 15.076, 14.887, 15.064, 15.012 ], "rmsd": 0.097, "frame": { "rmsd": null, "origin": [ 6.317, -4.436, -18.850 ], "x_axis": [ 0.804, -0.037, -0.594 ], "y_axis": [ -0.523, -0.519, -0.676 ], "z_axis": [ -0.283, 0.854, -0.437 ], "quaternion": [ -0.460, 0.831, -0.169, -0.264 ] } }, { "index": 5, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///E/2,///H/2,///F/2,///G/2", "planarity": 0.262, "G1G2_simpleParams": [ -2.405, 3.016, 0.162, -11.897, -11.789, -86.020 ], "G2G3_simpleParams": [ -2.705, 2.912, 0.047, -9.658, -7.423, -91.709 ], "G3G4_simpleParams": [ -2.493, 2.876, 0.047, -7.383, -10.262, -88.702 ], "G4G1_simpleParams": [ -2.569, 2.797, -0.176, -11.071, -2.788, -91.560 ], "type": "other", "direction": "WC-->Major", "ONZ_class": "--", "glyco_bond": "----", "sugar_pucker": "3333", "groove_type": "----", "groove_distPP": [ 14.234, 15.578, 17.502, 18.035 ], "rmsd": 0.252, "frame": { "rmsd": null, "origin": [ 11.805, -12.658, -6.737 ], "x_axis": [ 0.341, -0.310, -0.888 ], "y_axis": [ 0.903, 0.370, 0.217 ], "z_axis": [ 0.261, -0.876, 0.406 ], "quaternion": [ 0.727, 0.376, 0.395, -0.417 ] } }, { "index": 6, "num_nts": 4, "nts_short": "gggg", "nts_long": "///E/3,///H/3,///F/3,///G/3", "planarity": 0.279, "G1G2_simpleParams": [ -2.659, 2.786, 0.252, -13.763, -6.795, -88.353 ], "G2G3_simpleParams": [ -2.744, 2.618, 0.172, -13.114, -7.007, -91.146 ], "G3G4_simpleParams": [ -2.615, 2.793, 0.137, -11.221, -7.356, -87.453 ], "G4G1_simpleParams": [ -2.753, 2.636, 0.032, -12.406, -4.424, -89.744 ], "type": "other", "direction": "WC-->Major", "ONZ_class": "--", "glyco_bond": "----", "sugar_pucker": "3333", "groove_type": "----", "groove_distPP": [ 15.345, 15.257, 14.964, 14.695 ], "rmsd": 0.151, "frame": { "rmsd": null, "origin": [ 12.595, -15.534, -5.376 ], "x_axis": [ 0.771, -0.078, -0.633 ], "y_axis": [ 0.585, 0.479, 0.654 ], "z_axis": [ 0.252, -0.875, 0.414 ], "quaternion": [ 0.816, 0.468, 0.271, -0.203 ] } }, { "index": 7, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///E/4,///H/4,///F/4,///G/4", "planarity": 0.140, "G1G2_simpleParams": [ -2.789, 2.907, 0.120, -4.418, -0.108, -90.101 ], "G2G3_simpleParams": [ -2.682, 2.806, 0.140, -6.830, 1.555, -90.616 ], "G3G4_simpleParams": [ -2.617, 2.942, 0.231, -9.083, -2.123, -90.662 ], "G4G1_simpleParams": [ -2.684, 3.023, 0.008, -4.856, -3.026, -87.745 ], "type": "planar", "direction": "WC-->Major", "ONZ_class": "--", "glyco_bond": "----", "sugar_pucker": "3333", "groove_type": "----", "groove_distPP": [ 15.140, 14.876, 14.981, 14.783 ], "rmsd": 0.074, "frame": { "rmsd": null, "origin": [ 13.473, -18.585, -3.904 ], "x_axis": [ 0.962, 0.152, -0.226 ], "y_axis": [ 0.136, 0.450, 0.883 ], "z_axis": [ 0.236, -0.880, 0.412 ], "quaternion": [ 0.840, 0.525, 0.137, 0.005 ] } }, { "index": 8, "num_nts": 4, "nts_short": "GGGG", "nts_long": "///E/5,///H/5,///F/5,///G/5", "planarity": 0.255, "G1G2_simpleParams": [ -2.702, 2.836, -0.216, 11.348, 6.677, -90.046 ], "G2G3_simpleParams": [ -2.557, 2.864, -0.005, 10.866, 3.375, -89.692 ], "G3G4_simpleParams": [ -2.656, 3.010, -0.179, 13.586, 5.348, -88.232 ], "G4G1_simpleParams": [ -2.683, 2.927, -0.185, 12.153, 5.527, -89.069 ], "type": "bowl", "direction": "WC-->Major", "ONZ_class": "--", "glyco_bond": "----", "sugar_pucker": "3333", "groove_type": "----", "groove_distPP": [ 14.971, 15.026, 15.010, 15.003 ], "rmsd": 0.049, "frame": { "rmsd": null, "origin": [ 14.407, -21.822, -2.327 ], "x_axis": [ 0.933, 0.333, 0.134 ], "y_axis": [ -0.254, 0.349, 0.902 ], "z_axis": [ 0.254, -0.876, 0.410 ], "quaternion": [ 0.820, 0.542, 0.036, 0.179 ] } } ], "num_splayUnits": 2, "splayUnits": [ { "index": 1, "num_nts": 2, "nts_short": "uG", "nts_long": "///D/1,///D/2" }, { "index": 2, "num_nts": 2, "nts_short": "uG", "nts_long": "///F/1,///F/2" } ], "dbn": { "all_chains": { "num_nts": 45, "num_chars": 52, "bseq": "GgGGU&GgGGU&uGgGGU&uGgGGU&uGgGGU&uGgGGU&uGgGGU&GgGGU", "bseqUP": "GGGGU&GGGGU&UGGGGU&UGGGGU&UGGGGU&UGGGGU&UGGGGU&GGGGU", "sstr": ".....&.....&......&......&......&......&......&.....", "form": "AAA.-&AAA.-&.AAA.-&.AAA.-&.AAA.-&.AAA.-&.AAA.-&AAA.-" }, "chain_A": { "num_nts": 5, "num_chars": 5, "bseq": "GgGGU", "bseqUP": "GGGGU", "sstr": ".....", "form": "AAA.-" }, "chain_B": { "num_nts": 5, "num_chars": 5, "bseq": "GgGGU", "bseqUP": "GGGGU", "sstr": ".....", "form": "AAA.-" }, "chain_C": { "num_nts": 6, "num_chars": 6, "bseq": "uGgGGU", "bseqUP": "UGGGGU", "sstr": "......", "form": ".AAA.-" }, "chain_D": { "num_nts": 6, "num_chars": 6, "bseq": "uGgGGU", "bseqUP": "UGGGGU", "sstr": "......", "form": ".AAA.-" }, "chain_E": { "num_nts": 6, "num_chars": 6, "bseq": "uGgGGU", "bseqUP": "UGGGGU", "sstr": "......", "form": ".AAA.-" }, "chain_F": { "num_nts": 6, "num_chars": 6, "bseq": "uGgGGU", "bseqUP": "UGGGGU", "sstr": "......", "form": ".AAA.-" }, "chain_G": { "num_nts": 6, "num_chars": 6, "bseq": "uGgGGU", "bseqUP": "UGGGGU", "sstr": "......", "form": ".AAA.-" }, "chain_H": { "num_nts": 5, "num_chars": 5, "bseq": "GgGGU", "bseqUP": "GGGGU", "sstr": ".....", "form": "AAA.-" } }, "chains": { "chain_A": { "num_nts": 5, "bseq": "GgGGU", "sstr": ".....", "form": "AAA.-", "helical_rise": 3.676, "helical_rise_std": 0.107, "helical_axis": [ -0.418, 0.711, -0.565 ], "point1": [ 8.888, -12.928, -14.587 ], "point2": [ 2.589, -2.215, -23.089 ], "num_chars": 13, "suite": "G1ag1aG1aG5zU" }, "chain_B": { "num_nts": 5, "bseq": "GgGGU", "sstr": ".....", "form": "AAA.-", "helical_rise": 3.587, "helical_rise_std": 0.115, "helical_axis": [ -0.090, 0.971, -0.222 ], "point1": [ 9.995, -11.942, -13.985 ], "point2": [ 8.674, 2.312, -17.245 ], "num_chars": 13, "suite": "G1ag1aG1aG5zU" }, "chain_C": { "num_nts": 6, "bseq": "uGgGGU", "sstr": "......", "form": ".AAA.-", "helical_rise": 3.279, "helical_rise_std": 0.449, "helical_axis": [ 0.092, 0.654, -0.751 ], "point1": [ 8.654, -10.601, -11.585 ], "point2": [ 10.169, 0.213, -24.012 ], "num_chars": 16, "suite": "u!!G1ag1aG1aG5zU" }, "chain_D": { "num_nts": 6, "bseq": "uGgGGU", "sstr": "......", "form": ".AAA.-", "helical_rise": 3.663, "helical_rise_std": 0.658, "helical_axis": [ -0.578, 0.786, -0.220 ], "point1": [ 7.435, -17.163, -14.369 ], "point2": [ -3.057, -2.885, -18.366 ], "num_chars": 16, "suite": "u!!G1ag1aG1aG5zU" }, "chain_E": { "num_nts": 6, "bseq": "uGgGGU", "sstr": "......", "form": ".AAA.-", "helical_rise": 3.618, "helical_rise_std": 0.233, "helical_axis": [ 0.181, -0.761, 0.622 ], "point1": [ 7.763, -6.326, -1.181 ], "point2": [ 11.022, -20.017, 10.012 ], "num_chars": 16, "suite": "u!!G1ag1aG1aG5zU" }, "chain_F": { "num_nts": 6, "bseq": "uGgGGU", "sstr": "......", "form": ".AAA.-", "helical_rise": 0.411, "helical_rise_std": 1.179, "helical_axis": [ 0.377, -0.337, -0.863 ], "point1": [ 12.267, -22.468, -8.108 ], "point2": [ 13.319, -23.410, -10.517 ], "num_chars": 16, "suite": "u6dG1ag1aG1aG5zU" }, "chain_G": { "num_nts": 6, "bseq": "uGgGGU", "sstr": "......", "form": ".AAA.-", "helical_rise": 3.113, "helical_rise_std": 0.443, "helical_axis": [ 0.717, -0.489, 0.497 ], "point1": [ 11.035, -16.149, -8.411 ], "point2": [ 22.301, -23.824, -0.608 ], "num_chars": 16, "suite": "u!!G1ag1aG1aG5zU" }, "chain_H": { "num_nts": 5, "bseq": "GgGGU", "sstr": ".....", "form": "AAA.-", "helical_rise": 3.484, "helical_rise_std": 0.097, "helical_axis": [ -0.070, -0.949, 0.308 ], "point1": [ 10.789, -14.410, -6.400 ], "point2": [ 9.799, -27.892, -2.026 ], "num_chars": 13, "suite": "G!!g1aG1aG5zU" } }, "num_nts": 45, "nts": [ { "index": 1, "index_chain": 1, "chain_name": "A", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///A/2", "linked_nts": [ null, "///A/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-acceptor", "alpha": null, "beta": null, "gamma": 93.906, "delta": 93.925, "epsilon": -138.939, "zeta": -78.033, "epsilon_zeta": -60.907, "bb_type": "BI", "chi": -177.187, "glyco_bond": "anti", "C5prime_xyz": [ -1.144, 8.272, 1.472 ], "P_xyz": [ null, null, null ], "form": "A", "ssZp": 4.656, "Dp": 4.669, "splay_angle": 23.686, "splay_distance": 3.757, "splay_ratio": 0.209, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": 10.196, "v1": -30.038, "v2": 37.304, "v3": -32.417, "v4": 14.187, "amplitude": 37.362, "phase_angle": 3.176, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 8.494, -14.191, -16.623 ], "x_axis": [ 0.647, 0.645, 0.407 ], "y_axis": [ 0.688, -0.265, -0.676 ], "z_axis": [ -0.328, 0.717, -0.615 ], "quaternion": [ -0.438, 0.795, 0.419, 0.025 ] } }, { "index": 2, "index_chain": 2, "chain_name": "A", "nt_resnum": 3, "nt_name": "I", "nt_code": "g", "is_modified": true, "nt_id": "///A/3", "linked_nts": [ "///A/2", "///A/4" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -74.818, "beta": 171.771, "gamma": 66.503, "delta": 88.014, "epsilon": -152.460, "zeta": -85.332, "epsilon_zeta": -67.128, "bb_type": "BI", "chi": -168.415, "glyco_bond": "anti", "C5prime_xyz": [ -1.478, 8.773, 1.001 ], "P_xyz": [ 1.087, 9.221, 1.104 ], "form": "A", "ssZp": 4.495, "Dp": 4.522, "splay_angle": 20.969, "splay_distance": 3.345, "splay_ratio": 0.184, "d22": null, "d64": null, "eta": 168.570, "theta": -151.363, "eta_prime": -175.022, "theta_prime": -151.807, "eta_base": -138.849, "theta_base": -134.260, "v0": -2.779, "v1": -16.759, "v2": 28.369, "v3": -30.812, "v4": 21.295, "amplitude": 30.956, "phase_angle": 23.591, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.422, "filter_rmsd": 0.070, "frame": { "rmsd": 0.070, "origin": [ 6.265, -11.198, -17.056 ], "x_axis": [ 0.892, 0.452, -0.019 ], "y_axis": [ 0.250, -0.527, -0.812 ], "z_axis": [ -0.377, 0.720, -0.583 ], "quaternion": [ -0.442, 0.866, 0.202, -0.114 ] } }, { "index": 3, "index_chain": 3, "chain_name": "A", "nt_resnum": 4, "nt_name": "G", "nt_code": "G", "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,multiplet,ss-non-loop,G-tetrad", "alpha": -58.001, "beta": 171.145, "gamma": 50.390, "delta": 83.920, "epsilon": -148.342, "zeta": -79.511, "epsilon_zeta": -68.831, "bb_type": "BI", "chi": -153.935, "glyco_bond": "anti", "C5prime_xyz": [ -1.374, 8.822, 0.195 ], "P_xyz": [ 1.208, 9.256, 0.357 ], "form": "A", "ssZp": 4.157, "Dp": 4.540, "splay_angle": 20.323, "splay_distance": 3.333, "splay_ratio": 0.177, "d22": null, "d64": null, "eta": 173.853, "theta": -149.998, "eta_prime": -176.234, "theta_prime": -151.602, "eta_base": -147.716, "theta_base": -139.273, "v0": 2.777, "v1": -26.022, "v2": 37.878, "v3": -37.322, "v4": 21.930, "amplitude": 39.149, "phase_angle": 14.640, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.759, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 4.747, -8.229, -17.319 ], "x_axis": [ 0.900, 0.147, -0.411 ], "y_axis": [ -0.261, -0.574, -0.776 ], "z_axis": [ -0.350, 0.805, -0.479 ], "quaternion": [ -0.460, 0.859, -0.033, -0.221 ] } }, { "index": 4, "index_chain": 4, "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,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": -66.828, "beta": 164.593, "gamma": 55.174, "delta": 79.761, "epsilon": -148.646, "zeta": 56.141, "epsilon_zeta": 155.213, "bb_type": "--", "chi": -155.135, "glyco_bond": "anti", "C5prime_xyz": [ -1.530, 8.877, 0.162 ], "P_xyz": [ 0.980, 9.504, -0.213 ], "form": ".", "ssZp": 4.263, "Dp": 4.640, "splay_angle": 28.885, "splay_distance": 4.602, "splay_ratio": 0.250, "d22": null, "d64": null, "eta": 163.511, "theta": -19.206, "eta_prime": 174.104, "theta_prime": -60.759, "eta_base": -160.630, "theta_base": -84.231, "v0": -0.071, "v1": -25.077, "v2": 38.923, "v3": -40.097, "v4": 25.504, "amplitude": 41.097, "phase_angle": 18.720, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.914, "filter_rmsd": 0.012, "frame": { "rmsd": 0.012, "origin": [ 3.861, -5.035, -17.666 ], "x_axis": [ 0.760, -0.168, -0.628 ], "y_axis": [ -0.624, -0.461, -0.631 ], "z_axis": [ -0.183, 0.871, -0.455 ], "quaternion": [ -0.459, 0.818, -0.242, -0.248 ] } }, { "index": 5, "index_chain": 5, "chain_name": "A", "nt_resnum": 6, "nt_name": "U", "nt_code": "U", "nt_id": "///A/6", "linked_nts": [ "///A/5", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop", "alpha": 166.052, "beta": 144.739, "gamma": 48.031, "delta": 136.741, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -138.735, "glyco_bond": "anti", "C5prime_xyz": [ -2.021, 8.838, -0.436 ], "P_xyz": [ 0.419, 9.305, 0.399 ], "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": -29.089, "v1": 38.570, "v2": -33.111, "v3": 17.294, "v4": 7.213, "amplitude": 38.031, "phase_angle": 150.533, "puckering": "C2'-endo", "sugar_class": "--", "bin": "32p", "cluster": "5z", "suiteness": 0.665, "filter_rmsd": 0.104, "frame": { "rmsd": 0.006, "origin": [ 5.641, -3.562, -21.646 ], "x_axis": [ -0.205, 0.319, 0.925 ], "y_axis": [ -0.979, -0.069, -0.193 ], "z_axis": [ 0.002, -0.945, 0.327 ], "quaternion": [ 0.513, 0.367, -0.450, 0.633 ] } }, { "index": 6, "index_chain": 1, "chain_name": "B", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///B/2", "linked_nts": [ null, "///B/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-donor", "alpha": null, "beta": -173.033, "gamma": 46.995, "delta": 76.807, "epsilon": -146.774, "zeta": -82.880, "epsilon_zeta": -63.894, "bb_type": "BI", "chi": -172.932, "glyco_bond": "anti", "C5prime_xyz": [ -1.820, 8.778, 1.150 ], "P_xyz": [ 0.428, 9.589, 2.209 ], "form": "A", "ssZp": 4.583, "Dp": 4.610, "splay_angle": 24.386, "splay_distance": 3.807, "splay_ratio": 0.213, "d22": null, "d64": null, "eta": null, "theta": -160.765, "eta_prime": null, "theta_prime": -154.074, "eta_base": null, "theta_base": -119.899, "v0": -4.154, "v1": -23.903, "v2": 41.047, "v3": -44.446, "v4": 30.740, "amplitude": 44.825, "phase_angle": 23.693, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 10.528, -11.639, -12.261 ], "x_axis": [ -0.732, -0.301, -0.611 ], "y_axis": [ -0.660, 0.092, 0.746 ], "z_axis": [ -0.168, 0.949, -0.266 ], "quaternion": [ 0.153, -0.332, 0.723, 0.586 ] } }, { "index": 7, "index_chain": 2, "chain_name": "B", "nt_resnum": 3, "nt_name": "I", "nt_code": "g", "is_modified": true, "nt_id": "///B/3", "linked_nts": [ "///B/2", "///B/4" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -58.911, "beta": 171.708, "gamma": 54.858, "delta": 87.443, "epsilon": -150.643, "zeta": -81.850, "epsilon_zeta": -68.793, "bb_type": "BI", "chi": -167.392, "glyco_bond": "anti", "C5prime_xyz": [ -1.331, 8.744, 0.944 ], "P_xyz": [ 1.259, 9.028, 1.216 ], "form": "A", "ssZp": 4.551, "Dp": 4.597, "splay_angle": 22.619, "splay_distance": 3.606, "splay_ratio": 0.198, "d22": null, "d64": null, "eta": 173.906, "theta": -148.055, "eta_prime": -175.061, "theta_prime": -147.874, "eta_base": -133.466, "theta_base": -129.699, "v0": -0.217, "v1": -19.627, "v2": 30.523, "v3": -31.473, "v4": 20.117, "amplitude": 32.265, "phase_angle": 18.909, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.788, "filter_rmsd": 0.070, "frame": { "rmsd": 0.070, "origin": [ 10.484, -8.821, -14.820 ], "x_axis": [ -0.976, -0.197, -0.092 ], "y_axis": [ -0.139, 0.245, 0.960 ], "z_axis": [ -0.166, 0.949, -0.266 ], "quaternion": [ -0.024, -0.107, 0.789, 0.605 ] } }, { "index": 8, "index_chain": 3, "chain_name": "B", "nt_resnum": 4, "nt_name": "G", "nt_code": "G", "nt_id": "///B/4", "linked_nts": [ "///B/3", "///B/5" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -65.204, "beta": 169.184, "gamma": 57.967, "delta": 81.304, "epsilon": -148.351, "zeta": -81.483, "epsilon_zeta": -66.868, "bb_type": "BI", "chi": -162.407, "glyco_bond": "anti", "C5prime_xyz": [ -1.424, 8.789, 0.648 ], "P_xyz": [ 1.150, 9.274, 0.635 ], "form": "A", "ssZp": 4.445, "Dp": 4.619, "splay_angle": 20.499, "splay_distance": 3.273, "splay_ratio": 0.179, "d22": null, "d64": null, "eta": 170.555, "theta": -153.864, "eta_prime": -177.910, "theta_prime": -153.929, "eta_base": -146.134, "theta_base": -139.479, "v0": 1.951, "v1": -26.809, "v2": 39.869, "v3": -39.864, "v4": 24.037, "amplitude": 41.472, "phase_angle": 15.981, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.832, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 9.969, -6.325, -17.371 ], "x_axis": [ -0.923, -0.086, 0.376 ], "y_axis": [ 0.316, 0.391, 0.865 ], "z_axis": [ -0.221, 0.917, -0.333 ], "quaternion": [ -0.184, 0.071, 0.813, 0.547 ] } }, { "index": 9, "index_chain": 4, "chain_name": "B", "nt_resnum": 5, "nt_name": "G", "nt_code": "G", "nt_id": "///B/5", "linked_nts": [ "///B/4", "///B/6" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": -69.226, "beta": 168.839, "gamma": 59.272, "delta": 81.885, "epsilon": -150.155, "zeta": 57.361, "epsilon_zeta": 152.484, "bb_type": "--", "chi": -154.704, "glyco_bond": "anti", "C5prime_xyz": [ -1.364, 8.821, 0.179 ], "P_xyz": [ 1.192, 9.256, -0.180 ], "form": ".", "ssZp": 4.263, "Dp": 4.634, "splay_angle": 28.649, "splay_distance": 4.569, "splay_ratio": 0.248, "d22": null, "d64": null, "eta": 167.976, "theta": -17.251, "eta_prime": 177.808, "theta_prime": -58.087, "eta_base": -156.360, "theta_base": -87.691, "v0": 2.206, "v1": -26.773, "v2": 39.485, "v3": -39.239, "v4": 23.561, "amplitude": 40.985, "phase_angle": 15.553, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.876, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 8.872, -4.319, -19.712 ], "x_axis": [ -0.684, 0.042, 0.728 ], "y_axis": [ 0.618, 0.563, 0.548 ], "z_axis": [ -0.387, 0.825, -0.412 ], "quaternion": [ -0.342, 0.203, 0.815, 0.421 ] } }, { "index": 10, "index_chain": 5, "chain_name": "B", "nt_resnum": 6, "nt_name": "U", "nt_code": "U", "nt_id": "///B/6", "linked_nts": [ "///B/5", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop", "alpha": 172.043, "beta": 149.761, "gamma": 38.748, "delta": 140.186, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -126.443, "glyco_bond": "anti", "C5prime_xyz": [ -1.923, 8.691, -0.993 ], "P_xyz": [ 0.478, 9.337, -0.158 ], "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": -25.105, "v1": 36.944, "v2": -34.340, "v3": 20.832, "v4": 2.464, "amplitude": 37.157, "phase_angle": 157.544, "puckering": "C2'-endo", "sugar_class": "--", "bin": "32p", "cluster": "5z", "suiteness": 0.671, "filter_rmsd": 0.104, "frame": { "rmsd": 0.006, "origin": [ 5.651, -1.424, -18.256 ], "x_axis": [ 0.259, -0.469, -0.844 ], "y_axis": [ 0.848, 0.529, -0.033 ], "z_axis": [ 0.462, -0.707, 0.535 ], "quaternion": [ 0.762, 0.221, 0.429, -0.432 ] } }, { "index": 11, "index_chain": 1, "chain_name": "C", "nt_resnum": 1, "nt_name": "U33", "nt_code": "u", "is_modified": true, "nt_id": "///C/1", "linked_nts": [ null, "///C/2" ], "nt_type": "DNA", "dbn": ".", "summary": "modified,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop", "alpha": null, "beta": null, "gamma": 62.138, "delta": 122.775, "epsilon": 16.716, "zeta": 104.221, "epsilon_zeta": -87.505, "bb_type": "--", "chi": -109.787, "glyco_bond": "anti", "C5prime_xyz": [ -1.567, 8.850, -0.452 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 0.180, "Dp": 0.266, "splay_angle": 56.846, "splay_distance": 9.713, "splay_ratio": 0.479, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -1.673, "v1": 21.614, "v2": -38.094, "v3": 37.543, "v4": -26.888, "amplitude": 40.371, "phase_angle": 199.338, "puckering": "C3'-exo", "sugar_class": "~C2'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.064, "frame": { "rmsd": 0.061, "origin": [ 11.871, -9.526, -6.387 ], "x_axis": [ -0.327, 0.426, 0.844 ], "y_axis": [ 0.852, 0.519, 0.068 ], "z_axis": [ -0.409, 0.741, -0.533 ], "quaternion": [ -0.406, 0.414, 0.771, 0.262 ] } }, { "index": 12, "index_chain": 2, "chain_name": "C", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///C/2", "linked_nts": [ "///C/1", "///C/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": 77.960, "beta": 116.830, "gamma": 164.728, "delta": 92.194, "epsilon": -143.307, "zeta": -75.299, "epsilon_zeta": -68.008, "bb_type": "BI", "chi": -177.476, "glyco_bond": "anti", "C5prime_xyz": [ -1.380, 8.417, 1.600 ], "P_xyz": [ -0.902, 10.734, 0.469 ], "form": "A", "ssZp": 4.439, "Dp": 4.452, "splay_angle": 23.257, "splay_distance": 3.745, "splay_ratio": 0.204, "d22": null, "d64": null, "eta": 108.959, "theta": 166.514, "eta_prime": 122.876, "theta_prime": -177.870, "eta_base": 142.303, "theta_base": -147.074, "v0": 4.718, "v1": -22.467, "v2": 30.581, "v3": -28.584, "v4": 15.234, "amplitude": 31.055, "phase_angle": 10.022, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.006, "frame": { "rmsd": 0.006, "origin": [ 11.892, -12.657, -15.581 ], "x_axis": [ -0.663, 0.217, 0.716 ], "y_axis": [ 0.723, 0.434, 0.538 ], "z_axis": [ -0.194, 0.874, -0.445 ], "quaternion": [ -0.285, 0.295, 0.797, 0.443 ] } }, { "index": 13, "index_chain": 3, "chain_name": "C", "nt_resnum": 3, "nt_name": "I", "nt_code": "g", "is_modified": true, "nt_id": "///C/3", "linked_nts": [ "///C/2", "///C/4" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -84.282, "beta": 173.870, "gamma": 68.193, "delta": 87.925, "epsilon": -151.465, "zeta": -88.076, "epsilon_zeta": -63.389, "bb_type": "BI", "chi": -167.492, "glyco_bond": "anti", "C5prime_xyz": [ -1.522, 8.826, 0.927 ], "P_xyz": [ 1.022, 9.351, 1.047 ], "form": "A", "ssZp": 4.454, "Dp": 4.490, "splay_angle": 22.340, "splay_distance": 3.562, "splay_ratio": 0.195, "d22": null, "d64": null, "eta": 164.120, "theta": -153.130, "eta_prime": -178.821, "theta_prime": -153.411, "eta_base": -140.459, "theta_base": -133.376, "v0": -4.907, "v1": -15.364, "v2": 28.092, "v3": -31.729, "v4": 23.227, "amplitude": 31.594, "phase_angle": 27.235, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.366, "filter_rmsd": 0.070, "frame": { "rmsd": 0.070, "origin": [ 9.921, -10.641, -18.047 ], "x_axis": [ -0.205, 0.491, 0.847 ], "y_axis": [ 0.962, 0.262, 0.081 ], "z_axis": [ -0.182, 0.831, -0.526 ], "quaternion": [ -0.364, 0.514, 0.706, 0.323 ] } }, { "index": 14, "index_chain": 4, "chain_name": "C", "nt_resnum": 4, "nt_name": "G", "nt_code": "G", "nt_id": "///C/4", "linked_nts": [ "///C/3", "///C/5" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -52.575, "beta": 167.269, "gamma": 47.416, "delta": 83.047, "epsilon": -145.058, "zeta": -83.858, "epsilon_zeta": -61.200, "bb_type": "BI", "chi": -156.822, "glyco_bond": "anti", "C5prime_xyz": [ -1.325, 8.820, 0.335 ], "P_xyz": [ 1.253, 9.240, 0.497 ], "form": "A", "ssZp": 4.253, "Dp": 4.593, "splay_angle": 19.911, "splay_distance": 3.248, "splay_ratio": 0.174, "d22": null, "d64": null, "eta": 174.338, "theta": -151.407, "eta_prime": -176.097, "theta_prime": -150.977, "eta_base": -145.545, "theta_base": -138.550, "v0": 1.859, "v1": -25.582, "v2": 38.057, "v3": -37.938, "v4": 22.931, "amplitude": 39.576, "phase_angle": 15.929, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.656, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 7.776, -8.448, -19.857 ], "x_axis": [ 0.280, 0.578, 0.767 ], "y_axis": [ 0.922, 0.060, -0.382 ], "z_axis": [ -0.266, 0.814, -0.516 ], "quaternion": [ -0.454, 0.659, 0.569, 0.190 ] } }, { "index": 15, "index_chain": 5, "chain_name": "C", "nt_resnum": 5, "nt_name": "G", "nt_code": "G", "nt_id": "///C/5", "linked_nts": [ "///C/4", "///C/6" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": -56.927, "beta": 164.005, "gamma": 47.703, "delta": 81.883, "epsilon": -153.174, "zeta": 60.029, "epsilon_zeta": 146.797, "bb_type": "--", "chi": -151.994, "glyco_bond": "anti", "C5prime_xyz": [ -1.519, 8.878, 0.020 ], "P_xyz": [ 1.019, 9.452, -0.133 ], "form": ".", "ssZp": 4.154, "Dp": 4.557, "splay_angle": 29.067, "splay_distance": 4.715, "splay_ratio": 0.251, "d22": null, "d64": null, "eta": 166.527, "theta": -22.211, "eta_prime": 177.362, "theta_prime": -62.800, "eta_base": -158.950, "theta_base": -85.671, "v0": 0.032, "v1": -24.563, "v2": 38.028, "v3": -39.068, "v4": 24.839, "amplitude": 40.116, "phase_angle": 18.567, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.806, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 5.707, -6.195, -20.949 ], "x_axis": [ 0.654, 0.434, 0.619 ], "y_axis": [ 0.695, -0.023, -0.718 ], "z_axis": [ -0.297, 0.901, -0.317 ], "quaternion": [ 0.573, -0.706, -0.400, -0.114 ] } }, { "index": 16, "index_chain": 6, "chain_name": "C", "nt_resnum": 6, "nt_name": "U", "nt_code": "U", "nt_id": "///C/6", "linked_nts": [ "///C/5", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop", "alpha": 176.444, "beta": 138.986, "gamma": 41.505, "delta": 134.338, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -137.393, "glyco_bond": "anti", "C5prime_xyz": [ -2.262, 8.848, -0.556 ], "P_xyz": [ 0.132, 9.496, 0.284 ], "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": -32.349, "v1": 40.236, "v2": -32.506, "v3": 14.832, "v4": 10.771, "amplitude": 39.400, "phase_angle": 145.591, "puckering": "C2'-endo", "sugar_class": "--", "bin": "32p", "cluster": "5z", "suiteness": 0.464, "filter_rmsd": 0.103, "frame": { "rmsd": 0.007, "origin": [ 7.513, -1.897, -20.247 ], "x_axis": [ -0.871, -0.491, 0.021 ], "y_axis": [ 0.070, -0.166, -0.984 ], "z_axis": [ 0.487, -0.855, 0.179 ], "quaternion": [ -0.189, 0.170, -0.618, 0.744 ] } }, { "index": 17, "index_chain": 1, "chain_name": "D", "nt_resnum": 1, "nt_name": "U33", "nt_code": "u", "is_modified": true, "nt_id": "///D/1", "linked_nts": [ null, "///D/2" ], "nt_type": "DNA", "dbn": ".", "summary": "modified,anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,cap-acceptor,splayed-apart", "alpha": null, "beta": null, "gamma": 71.549, "delta": 139.640, "epsilon": -134.756, "zeta": -54.320, "epsilon_zeta": -80.435, "bb_type": "BI", "chi": -165.260, "glyco_bond": "anti", "C5prime_xyz": [ -1.740, 8.553, 1.235 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 1.715, "Dp": 1.944, "splay_angle": 90.629, "splay_distance": 14.387, "splay_ratio": 0.712, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -15.438, "v1": 24.527, "v2": -24.304, "v3": 15.844, "v4": -0.298, "amplitude": 25.507, "phase_angle": 162.334, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.063, "frame": { "rmsd": 0.063, "origin": [ -0.337, -25.242, -11.322 ], "x_axis": [ 0.692, -0.667, 0.277 ], "y_axis": [ 0.484, 0.143, -0.863 ], "z_axis": [ 0.536, 0.731, 0.422 ], "quaternion": [ 0.751, -0.531, 0.086, -0.383 ] } }, { "index": 18, "index_chain": 2, "chain_name": "D", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///D/2", "linked_nts": [ "///D/1", "///D/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-acceptor,splayed-apart", "alpha": 169.213, "beta": 172.950, "gamma": -176.043, "delta": 89.626, "epsilon": -155.038, "zeta": -64.086, "epsilon_zeta": -90.952, "bb_type": "BI", "chi": -169.224, "glyco_bond": "anti", "C5prime_xyz": [ -1.040, 8.419, 1.166 ], "P_xyz": [ 0.167, 10.502, 0.179 ], "form": "A", "ssZp": 4.541, "Dp": 4.582, "splay_angle": 21.673, "splay_distance": 3.532, "splay_ratio": 0.192, "d22": null, "d64": null, "eta": 177.879, "theta": -177.649, "eta_prime": -144.519, "theta_prime": -167.991, "eta_base": -103.848, "theta_base": -143.126, "v0": 11.619, "v1": -30.815, "v2": 36.841, "v3": -31.245, "v4": 12.681, "amplitude": 36.844, "phase_angle": 0.754, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "23t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 6.772, -12.908, -13.404 ], "x_axis": [ 0.585, -0.011, -0.811 ], "y_axis": [ -0.668, -0.574, -0.474 ], "z_axis": [ -0.460, 0.819, -0.343 ], "quaternion": [ -0.409, 0.791, -0.215, -0.402 ] } }, { "index": 19, "index_chain": 3, "chain_name": "D", "nt_resnum": 3, "nt_name": "I", "nt_code": "g", "is_modified": true, "nt_id": "///D/3", "linked_nts": [ "///D/2", "///D/4" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -94.233, "beta": 178.539, "gamma": 76.062, "delta": 87.861, "epsilon": -155.386, "zeta": -82.308, "epsilon_zeta": -73.078, "bb_type": "BI", "chi": -165.268, "glyco_bond": "anti", "C5prime_xyz": [ -1.652, 8.888, 0.796 ], "P_xyz": [ 0.892, 9.487, 0.807 ], "form": "A", "ssZp": 4.373, "Dp": 4.413, "splay_angle": 21.242, "splay_distance": 3.413, "splay_ratio": 0.186, "d22": null, "d64": null, "eta": 165.629, "theta": -151.026, "eta_prime": -175.199, "theta_prime": -152.623, "eta_base": -139.917, "theta_base": -129.702, "v0": -7.363, "v1": -12.922, "v2": 26.569, "v3": -31.609, "v4": 24.672, "amplitude": 31.265, "phase_angle": 31.811, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.097, "filter_rmsd": 0.070, "frame": { "rmsd": 0.070, "origin": [ 6.827, -9.393, -13.747 ], "x_axis": [ 0.183, -0.258, -0.949 ], "y_axis": [ -0.900, -0.433, -0.055 ], "z_axis": [ -0.397, 0.864, -0.311 ], "quaternion": [ -0.331, 0.694, -0.417, -0.484 ] } }, { "index": 20, "index_chain": 4, "chain_name": "D", "nt_resnum": 4, "nt_name": "G", "nt_code": "G", "nt_id": "///D/4", "linked_nts": [ "///D/3", "///D/5" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -63.328, "beta": 174.652, "gamma": 49.545, "delta": 82.799, "epsilon": -149.954, "zeta": -82.202, "epsilon_zeta": -67.752, "bb_type": "BI", "chi": -154.281, "glyco_bond": "anti", "C5prime_xyz": [ -1.362, 8.829, 0.190 ], "P_xyz": [ 1.209, 9.310, 0.354 ], "form": "A", "ssZp": 4.210, "Dp": 4.580, "splay_angle": 20.425, "splay_distance": 3.279, "splay_ratio": 0.177, "d22": null, "d64": null, "eta": 169.766, "theta": -154.785, "eta_prime": 179.636, "theta_prime": -154.212, "eta_base": -145.315, "theta_base": -139.139, "v0": 2.114, "v1": -26.172, "v2": 38.762, "v3": -38.527, "v4": 23.121, "amplitude": 40.249, "phase_angle": 15.624, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.809, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 6.973, -6.176, -14.875 ], "x_axis": [ -0.308, -0.460, -0.833 ], "y_axis": [ -0.900, -0.144, 0.412 ], "z_axis": [ -0.310, 0.876, -0.370 ], "quaternion": [ 0.211, -0.549, 0.619, 0.520 ] } }, { "index": 21, "index_chain": 5, "chain_name": "D", "nt_resnum": 5, "nt_name": "G", "nt_code": "G", "nt_id": "///D/5", "linked_nts": [ "///D/4", "///D/6" ], "nt_type": "RNA", "dbn": ".", "summary": "turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": -63.296, "beta": 166.783, "gamma": 53.141, "delta": 82.185, "epsilon": -149.213, "zeta": 62.293, "epsilon_zeta": 148.494, "bb_type": "--", "chi": -151.337, "glyco_bond": "anti", "C5prime_xyz": [ -1.312, 8.815, 0.009 ], "P_xyz": [ 1.253, 9.222, -0.285 ], "form": ".", "ssZp": 4.145, "Dp": 4.625, "splay_angle": 29.867, "splay_distance": 4.771, "splay_ratio": 0.258, "d22": null, "d64": null, "eta": 167.356, "theta": -14.634, "eta_prime": 176.910, "theta_prime": -56.829, "eta_base": -157.683, "theta_base": -82.834, "v0": 4.032, "v1": -28.100, "v2": 39.844, "v3": -38.599, "v4": 22.014, "amplitude": 40.905, "phase_angle": 13.075, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.894, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 7.125, -3.277, -16.401 ], "x_axis": [ -0.614, -0.574, -0.541 ], "y_axis": [ -0.746, 0.199, 0.635 ], "z_axis": [ -0.257, 0.794, -0.551 ], "quaternion": [ 0.092, -0.429, 0.769, 0.465 ] } }, { "index": 22, "index_chain": 6, "chain_name": "D", "nt_resnum": 6, "nt_name": "U", "nt_code": "U", "nt_id": "///D/6", "linked_nts": [ "///D/5", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop", "alpha": 170.823, "beta": 142.589, "gamma": 41.881, "delta": 135.863, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -136.090, "glyco_bond": "anti", "C5prime_xyz": [ -2.055, 8.817, -0.543 ], "P_xyz": [ 0.371, 9.314, 0.309 ], "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": -28.106, "v1": 37.171, "v2": -31.773, "v3": 16.478, "v4": 7.089, "amplitude": 36.596, "phase_angle": 150.251, "puckering": "C2'-endo", "sugar_class": "--", "bin": "32p", "cluster": "5z", "suiteness": 0.565, "filter_rmsd": 0.104, "frame": { "rmsd": 0.006, "origin": [ 3.502, -2.879, -19.480 ], "x_axis": [ 0.964, 0.244, 0.104 ], "y_axis": [ -0.241, 0.638, 0.731 ], "z_axis": [ 0.112, -0.730, 0.674 ], "quaternion": [ 0.905, 0.404, 0.002, 0.134 ] } }, { "index": 23, "index_chain": 1, "chain_name": "E", "nt_resnum": 1, "nt_name": "U33", "nt_code": "u", "is_modified": true, "nt_id": "///E/1", "linked_nts": [ null, "///E/2" ], "nt_type": "DNA", "dbn": ".", "summary": "modified,anti,~C2'-endo,non-stack,ss-non-loop", "alpha": null, "beta": null, "gamma": 66.246, "delta": 130.209, "epsilon": -86.103, "zeta": -70.758, "epsilon_zeta": -15.345, "bb_type": "--", "chi": -145.870, "glyco_bond": "anti", "C5prime_xyz": [ -1.735, 8.785, 0.059 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 1.467, "Dp": 1.774, "splay_angle": 78.027, "splay_distance": 13.181, "splay_ratio": 0.630, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -16.361, "v1": 20.308, "v2": -16.782, "v3": 7.611, "v4": 5.481, "amplitude": 20.188, "phase_angle": 146.230, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.065, "frame": { "rmsd": 0.061, "origin": [ 10.743, -0.926, 2.882 ], "x_axis": [ -0.529, 0.558, -0.639 ], "y_axis": [ 0.734, -0.079, -0.675 ], "z_axis": [ -0.427, -0.826, -0.368 ], "quaternion": [ 0.079, 0.479, 0.674, -0.557 ] } }, { "index": 24, "index_chain": 2, "chain_name": "E", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///E/2", "linked_nts": [ "///E/1", "///E/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad", "alpha": -81.663, "beta": 84.193, "gamma": 167.740, "delta": 90.654, "epsilon": -142.420, "zeta": -78.334, "epsilon_zeta": -64.086, "bb_type": "BI", "chi": -174.792, "glyco_bond": "anti", "C5prime_xyz": [ -1.050, 8.286, 1.451 ], "P_xyz": [ -1.355, 10.480, 0.043 ], "form": "A", "ssZp": 4.673, "Dp": 4.685, "splay_angle": 23.608, "splay_distance": 3.716, "splay_ratio": 0.208, "d22": null, "d64": null, "eta": -140.962, "theta": 150.479, "eta_prime": -120.020, "theta_prime": 172.388, "eta_base": -90.278, "theta_base": -160.236, "v0": 13.278, "v1": -31.474, "v2": 36.574, "v3": -29.915, "v4": 10.710, "amplitude": 36.599, "phase_angle": 357.900, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "23t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 11.874, -12.000, -4.177 ], "x_axis": [ 0.543, -0.357, -0.760 ], "y_axis": [ 0.786, 0.534, 0.311 ], "z_axis": [ 0.295, -0.766, 0.571 ], "quaternion": [ 0.814, 0.331, 0.324, -0.351 ] } }, { "index": 25, "index_chain": 3, "chain_name": "E", "nt_resnum": 3, "nt_name": "I", "nt_code": "g", "is_modified": true, "nt_id": "///E/3", "linked_nts": [ "///E/2", "///E/4" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -72.377, "beta": 170.888, "gamma": 65.626, "delta": 88.823, "epsilon": -153.207, "zeta": -82.300, "epsilon_zeta": -70.907, "bb_type": "BI", "chi": -166.604, "glyco_bond": "anti", "C5prime_xyz": [ -1.405, 8.782, 0.904 ], "P_xyz": [ 1.180, 9.146, 0.963 ], "form": "A", "ssZp": 4.458, "Dp": 4.500, "splay_angle": 21.509, "splay_distance": 3.442, "splay_ratio": 0.188, "d22": null, "d64": null, "eta": 170.811, "theta": -149.292, "eta_prime": -172.640, "theta_prime": -150.465, "eta_base": -140.164, "theta_base": -133.968, "v0": -2.357, "v1": -16.929, "v2": 28.279, "v3": -30.467, "v4": 20.804, "amplitude": 30.690, "phase_angle": 22.863, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.547, "filter_rmsd": 0.070, "frame": { "rmsd": 0.070, "origin": [ 11.191, -15.480, -3.067 ], "x_axis": [ 0.871, -0.121, -0.477 ], "y_axis": [ 0.448, 0.595, 0.667 ], "z_axis": [ 0.203, -0.795, 0.572 ], "quaternion": [ 0.872, 0.419, 0.195, -0.163 ] } }, { "index": 26, "index_chain": 4, "chain_name": "E", "nt_resnum": 4, "nt_name": "G", "nt_code": "G", "nt_id": "///E/4", "linked_nts": [ "///E/3", "///E/5" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -68.007, "beta": 172.448, "gamma": 58.234, "delta": 83.129, "epsilon": -146.261, "zeta": -80.757, "epsilon_zeta": -65.504, "bb_type": "BI", "chi": -155.291, "glyco_bond": "anti", "C5prime_xyz": [ -1.386, 8.841, 0.248 ], "P_xyz": [ 1.196, 9.294, 0.225 ], "form": "A", "ssZp": 4.199, "Dp": 4.557, "splay_angle": 20.046, "splay_distance": 3.255, "splay_ratio": 0.174, "d22": null, "d64": null, "eta": 172.199, "theta": -150.569, "eta_prime": -177.403, "theta_prime": -151.921, "eta_base": -148.924, "theta_base": -138.355, "v0": 0.741, "v1": -24.523, "v2": 37.469, "v3": -38.036, "v4": 23.649, "amplitude": 39.293, "phase_angle": 17.528, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.780, "filter_rmsd": 0.006, "frame": { "rmsd": 0.006, "origin": [ 11.024, -18.864, -2.460 ], "x_axis": [ 0.980, 0.172, -0.104 ], "y_axis": [ 0.011, 0.471, 0.882 ], "z_axis": [ 0.201, -0.865, 0.460 ], "quaternion": [ 0.853, 0.512, 0.090, 0.047 ] } }, { "index": 27, "index_chain": 5, "chain_name": "E", "nt_resnum": 5, "nt_name": "G", "nt_code": "G", "nt_id": "///E/5", "linked_nts": [ "///E/4", "///E/6" ], "nt_type": "RNA", "dbn": ".", "summary": "turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": -71.215, "beta": 167.878, "gamma": 55.416, "delta": 79.485, "epsilon": -149.457, "zeta": 59.105, "epsilon_zeta": 151.437, "bb_type": "--", "chi": -152.218, "glyco_bond": "anti", "C5prime_xyz": [ -1.390, 8.854, 0.025 ], "P_xyz": [ 1.142, 9.351, -0.372 ], "form": ".", "ssZp": 4.183, "Dp": 4.663, "splay_angle": 30.447, "splay_distance": 4.809, "splay_ratio": 0.263, "d22": null, "d64": null, "eta": 161.218, "theta": -15.768, "eta_prime": 171.165, "theta_prime": -59.770, "eta_base": -162.547, "theta_base": -89.328, "v0": 1.358, "v1": -27.505, "v2": 41.398, "v3": -41.758, "v4": 25.676, "amplitude": 43.254, "phase_angle": 16.843, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.902, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 11.562, -22.056, -2.115 ], "x_axis": [ 0.851, 0.483, 0.205 ], "y_axis": [ -0.335, 0.200, 0.920 ], "z_axis": [ 0.404, -0.852, 0.333 ], "quaternion": [ 0.772, 0.574, 0.064, 0.265 ] } }, { "index": 28, "index_chain": 6, "chain_name": "E", "nt_resnum": 6, "nt_name": "U", "nt_code": "U", "nt_id": "///E/6", "linked_nts": [ "///E/5", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop", "alpha": 160.793, "beta": 144.620, "gamma": 49.302, "delta": 137.260, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -133.929, "glyco_bond": "anti", "C5prime_xyz": [ -2.014, 8.790, -0.626 ], "P_xyz": [ 0.488, 9.203, 0.030 ], "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": -26.928, "v1": 36.882, "v2": -32.400, "v3": 17.782, "v4": 5.542, "amplitude": 36.477, "phase_angle": 152.654, "puckering": "C2'-endo", "sugar_class": "--", "bin": "32p", "cluster": "5z", "suiteness": 0.687, "filter_rmsd": 0.104, "frame": { "rmsd": 0.006, "origin": [ 15.658, -22.888, 0.264 ], "x_axis": [ -0.548, -0.406, -0.731 ], "y_axis": [ -0.716, -0.224, 0.661 ], "z_axis": [ -0.432, 0.886, -0.168 ], "quaternion": [ 0.122, -0.459, 0.611, 0.633 ] } }, { "index": 29, "index_chain": 1, "chain_name": "F", "nt_resnum": 1, "nt_name": "U33", "nt_code": "u", "is_modified": true, "nt_id": "///F/1", "linked_nts": [ null, "///F/2" ], "nt_type": "DNA", "dbn": ".", "summary": "modified,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,cap-acceptor,splayed-apart", "alpha": null, "beta": null, "gamma": 62.677, "delta": 142.517, "epsilon": -163.539, "zeta": 59.252, "epsilon_zeta": 137.209, "bb_type": "--", "chi": -129.216, "glyco_bond": "anti", "C5prime_xyz": [ -1.669, 8.604, -0.683 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 2.147, "Dp": 2.209, "splay_angle": 123.727, "splay_distance": 16.752, "splay_ratio": 0.882, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -12.820, "v1": 23.644, "v2": -25.098, "v3": 18.330, "v4": -3.535, "amplitude": 25.542, "phase_angle": 169.298, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.064, "frame": { "rmsd": 0.061, "origin": [ 2.132, -27.495, -8.005 ], "x_axis": [ 0.583, -0.810, -0.060 ], "y_axis": [ 0.549, 0.447, -0.706 ], "z_axis": [ 0.599, 0.379, 0.705 ], "quaternion": [ 0.827, -0.328, 0.199, -0.411 ] } }, { "index": 30, "index_chain": 2, "chain_name": "F", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///F/2", "linked_nts": [ "///F/1", "///F/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-donor,phosphate,splayed-apart", "alpha": 48.925, "beta": -175.236, "gamma": 47.432, "delta": 82.555, "epsilon": -153.736, "zeta": -75.034, "epsilon_zeta": -78.703, "bb_type": "BI", "chi": -169.594, "glyco_bond": "anti", "C5prime_xyz": [ -1.521, 8.692, 1.072 ], "P_xyz": [ 0.884, 9.205, 1.964 ], "form": "A", "ssZp": 4.545, "Dp": 4.588, "splay_angle": 23.684, "splay_distance": 3.735, "splay_ratio": 0.208, "d22": null, "d64": null, "eta": -51.040, "theta": -152.996, "eta_prime": -8.357, "theta_prime": -149.061, "eta_base": 71.819, "theta_base": -122.806, "v0": 3.281, "v1": -28.191, "v2": 40.537, "v3": -39.779, "v4": 23.260, "amplitude": 41.815, "phase_angle": 14.199, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "23p", "cluster": "6d", "suiteness": 0.050, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 12.026, -14.018, -9.062 ], "x_axis": [ -0.444, 0.104, 0.890 ], "y_axis": [ -0.859, -0.332, -0.390 ], "z_axis": [ 0.255, -0.938, 0.236 ], "quaternion": [ 0.339, 0.404, -0.468, 0.709 ] } }, { "index": 31, "index_chain": 3, "chain_name": "F", "nt_resnum": 3, "nt_name": "I", "nt_code": "g", "is_modified": true, "nt_id": "///F/3", "linked_nts": [ "///F/2", "///F/4" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -84.455, "beta": 174.975, "gamma": 73.971, "delta": 85.008, "epsilon": -150.948, "zeta": -86.631, "epsilon_zeta": -64.317, "bb_type": "BI", "chi": -166.653, "glyco_bond": "anti", "C5prime_xyz": [ -1.417, 8.799, 0.914 ], "P_xyz": [ 1.167, 9.175, 0.808 ], "form": "A", "ssZp": 4.507, "Dp": 4.585, "splay_angle": 22.787, "splay_distance": 3.599, "splay_ratio": 0.199, "d22": null, "d64": null, "eta": 170.421, "theta": -151.858, "eta_prime": -176.330, "theta_prime": -152.549, "eta_base": -138.767, "theta_base": -134.288, "v0": -1.892, "v1": -19.780, "v2": 32.200, "v3": -34.193, "v4": 22.932, "amplitude": 34.632, "phase_angle": 21.600, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.288, "filter_rmsd": 0.070, "frame": { "rmsd": 0.070, "origin": [ 14.209, -16.454, -7.258 ], "x_axis": [ -0.812, -0.123, 0.570 ], "y_axis": [ -0.492, -0.380, -0.783 ], "z_axis": [ 0.313, -0.917, 0.248 ], "quaternion": [ 0.118, 0.283, -0.544, 0.781 ] } }, { "index": 32, "index_chain": 4, "chain_name": "F", "nt_resnum": 4, "nt_name": "G", "nt_code": "G", "nt_id": "///F/4", "linked_nts": [ "///F/3", "///F/5" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -52.766, "beta": 168.065, "gamma": 47.998, "delta": 83.945, "epsilon": -147.235, "zeta": -80.850, "epsilon_zeta": -66.385, "bb_type": "BI", "chi": -158.813, "glyco_bond": "anti", "C5prime_xyz": [ -1.332, 8.785, 0.462 ], "P_xyz": [ 1.260, 9.134, 0.712 ], "form": "A", "ssZp": 4.313, "Dp": 4.577, "splay_angle": 19.412, "splay_distance": 3.131, "splay_ratio": 0.169, "d22": null, "d64": null, "eta": 174.668, "theta": -150.226, "eta_prime": -175.618, "theta_prime": -150.774, "eta_base": -145.869, "theta_base": -139.023, "v0": 2.121, "v1": -25.406, "v2": 37.570, "v3": -37.404, "v4": 22.365, "amplitude": 39.003, "phase_angle": 15.581, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.720, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 15.954, -18.803, -5.163 ], "x_axis": [ -0.963, -0.244, 0.115 ], "y_axis": [ -0.026, -0.340, -0.940 ], "z_axis": [ 0.268, -0.908, 0.321 ], "quaternion": [ -0.067, 0.118, -0.570, 0.810 ] } }, { "index": 33, "index_chain": 5, "chain_name": "F", "nt_resnum": 5, "nt_name": "G", "nt_code": "G", "nt_id": "///F/5", "linked_nts": [ "///F/4", "///F/6" ], "nt_type": "RNA", "dbn": ".", "summary": "turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": -67.298, "beta": 170.697, "gamma": 50.460, "delta": 81.391, "epsilon": -158.144, "zeta": 68.623, "epsilon_zeta": 133.233, "bb_type": "--", "chi": -149.247, "glyco_bond": "anti", "C5prime_xyz": [ -1.315, 8.812, -0.152 ], "P_xyz": [ 1.227, 9.292, -0.486 ], "form": ".", "ssZp": 4.128, "Dp": 4.616, "splay_angle": 29.510, "splay_distance": 4.669, "splay_ratio": 0.255, "d22": null, "d64": null, "eta": 162.467, "theta": -17.131, "eta_prime": 172.683, "theta_prime": -60.539, "eta_base": -162.784, "theta_base": -88.688, "v0": 2.976, "v1": -27.803, "v2": 40.293, "v3": -39.696, "v4": 23.382, "amplitude": 41.638, "phase_angle": 14.599, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.912, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 16.973, -20.824, -3.000 ], "x_axis": [ -0.903, -0.291, -0.315 ], "y_axis": [ 0.415, -0.411, -0.812 ], "z_axis": [ 0.107, -0.864, 0.492 ], "quaternion": [ -0.211, -0.062, -0.500, 0.838 ] } }, { "index": 34, "index_chain": 6, "chain_name": "F", "nt_resnum": 6, "nt_name": "U", "nt_code": "U", "nt_id": "///F/6", "linked_nts": [ "///F/5", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop", "alpha": 171.456, "beta": 142.930, "gamma": 37.143, "delta": 139.876, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -130.236, "glyco_bond": "anti", "C5prime_xyz": [ -2.013, 8.733, -0.759 ], "P_xyz": [ 0.395, 9.221, 0.145 ], "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": -26.307, "v1": 37.713, "v2": -34.232, "v3": 20.065, "v4": 3.700, "amplitude": 37.571, "phase_angle": 155.661, "puckering": "C2'-endo", "sugar_class": "--", "bin": "32p", "cluster": "5z", "suiteness": 0.550, "filter_rmsd": 0.103, "frame": { "rmsd": 0.007, "origin": [ 14.389, -24.711, -3.107 ], "x_axis": [ 0.485, 0.586, 0.649 ], "y_axis": [ 0.873, -0.281, -0.398 ], "z_axis": [ -0.051, 0.760, -0.648 ], "quaternion": [ -0.373, 0.777, 0.470, 0.192 ] } }, { "index": 35, "index_chain": 1, "chain_name": "G", "nt_resnum": 1, "nt_name": "U33", "nt_code": "u", "is_modified": true, "nt_id": "///G/1", "linked_nts": [ null, "///G/2" ], "nt_type": "DNA", "dbn": ".", "summary": "modified,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop", "alpha": null, "beta": null, "gamma": 25.809, "delta": 128.660, "epsilon": 20.794, "zeta": 80.909, "epsilon_zeta": -60.116, "bb_type": "--", "chi": -114.066, "glyco_bond": "anti", "C5prime_xyz": [ -1.332, 8.308, -1.286 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 0.293, "Dp": 0.404, "splay_angle": 53.619, "splay_distance": 9.379, "splay_ratio": 0.454, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": 11.084, "v1": -11.267, "v2": 7.217, "v3": -0.309, "v4": -5.563, "amplitude": 11.512, "phase_angle": 308.822, "puckering": "C1'-endo", "sugar_class": "~C2'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.095, "frame": { "rmsd": 0.091, "origin": [ 11.149, -16.144, -14.663 ], "x_axis": [ -0.545, -0.568, -0.617 ], "y_axis": [ 0.805, -0.148, -0.574 ], "z_axis": [ 0.235, -0.810, 0.538 ], "quaternion": [ -0.460, -0.128, -0.463, 0.747 ] } }, { "index": 36, "index_chain": 2, "chain_name": "G", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///G/2", "linked_nts": [ "///G/1", "///G/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": 71.969, "beta": 112.714, "gamma": -178.700, "delta": 92.163, "epsilon": -155.674, "zeta": -62.806, "epsilon_zeta": -92.868, "bb_type": "BI", "chi": -172.187, "glyco_bond": "anti", "C5prime_xyz": [ -1.133, 8.417, 1.330 ], "P_xyz": [ -1.117, 10.895, 0.486 ], "form": "A", "ssZp": 4.444, "Dp": 4.467, "splay_angle": 23.520, "splay_distance": 3.811, "splay_ratio": 0.206, "d22": null, "d64": null, "eta": 131.242, "theta": 161.805, "eta_prime": 120.396, "theta_prime": -179.343, "eta_base": 138.001, "theta_base": -148.024, "v0": 9.666, "v1": -27.210, "v2": 33.180, "v3": -28.462, "v4": 12.115, "amplitude": 33.202, "phase_angle": 2.076, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.006, "frame": { "rmsd": 0.006, "origin": [ 14.577, -12.278, -6.835 ], "x_axis": [ -0.812, -0.498, -0.304 ], "y_axis": [ 0.455, -0.214, -0.864 ], "z_axis": [ 0.365, -0.840, 0.400 ], "quaternion": [ -0.306, 0.020, -0.547, 0.779 ] } }, { "index": 37, "index_chain": 3, "chain_name": "G", "nt_resnum": 3, "nt_name": "I", "nt_code": "g", "is_modified": true, "nt_id": "///G/3", "linked_nts": [ "///G/2", "///G/4" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -98.265, "beta": 179.905, "gamma": 76.017, "delta": 87.632, "epsilon": -152.402, "zeta": -83.503, "epsilon_zeta": -68.899, "bb_type": "BI", "chi": -167.806, "glyco_bond": "anti", "C5prime_xyz": [ -1.580, 8.817, 0.965 ], "P_xyz": [ 0.931, 9.433, 1.074 ], "form": "A", "ssZp": 4.447, "Dp": 4.482, "splay_angle": 21.805, "splay_distance": 3.472, "splay_ratio": 0.190, "d22": null, "d64": null, "eta": 163.928, "theta": -152.616, "eta_prime": -177.554, "theta_prime": -153.043, "eta_base": -139.756, "theta_base": -131.014, "v0": -4.779, "v1": -15.611, "v2": 28.327, "v3": -31.990, "v4": 23.327, "amplitude": 31.801, "phase_angle": 27.033, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.049, "filter_rmsd": 0.069, "frame": { "rmsd": 0.069, "origin": [ 14.827, -14.706, -3.909 ], "x_axis": [ -0.448, -0.585, -0.676 ], "y_axis": [ 0.804, 0.066, -0.591 ], "z_axis": [ 0.390, -0.808, 0.441 ], "quaternion": [ 0.514, 0.106, 0.518, -0.675 ] } }, { "index": 38, "index_chain": 4, "chain_name": "G", "nt_resnum": 4, "nt_name": "G", "nt_code": "G", "nt_id": "///G/4", "linked_nts": [ "///G/3", "///G/5" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad", "alpha": -64.894, "beta": 172.796, "gamma": 52.925, "delta": 82.617, "epsilon": -140.359, "zeta": -88.936, "epsilon_zeta": -51.423, "bb_type": "BI", "chi": -156.806, "glyco_bond": "anti", "C5prime_xyz": [ -1.303, 8.802, 0.339 ], "P_xyz": [ 1.273, 9.222, 0.425 ], "form": "A", "ssZp": 4.255, "Dp": 4.649, "splay_angle": 20.390, "splay_distance": 3.307, "splay_ratio": 0.177, "d22": null, "d64": null, "eta": 172.261, "theta": -152.627, "eta_prime": -178.787, "theta_prime": -151.871, "eta_base": -146.421, "theta_base": -140.252, "v0": 2.496, "v1": -26.646, "v2": 39.086, "v3": -38.751, "v4": 23.013, "amplitude": 40.497, "phase_angle": 15.173, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.816, "filter_rmsd": 0.006, "frame": { "rmsd": 0.006, "origin": [ 14.708, -17.384, -1.701 ], "x_axis": [ 0.031, -0.477, -0.879 ], "y_axis": [ 0.955, 0.275, -0.115 ], "z_axis": [ 0.296, -0.835, 0.464 ], "quaternion": [ 0.665, 0.271, 0.441, -0.538 ] } }, { "index": 39, "index_chain": 5, "chain_name": "G", "nt_resnum": 5, "nt_name": "G", "nt_code": "G", "nt_id": "///G/5", "linked_nts": [ "///G/4", "///G/6" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": -53.221, "beta": 160.728, "gamma": 44.013, "delta": 79.749, "epsilon": -155.023, "zeta": 63.913, "epsilon_zeta": 141.064, "bb_type": "--", "chi": -151.609, "glyco_bond": "anti", "C5prime_xyz": [ -1.419, 8.867, -0.019 ], "P_xyz": [ 1.131, 9.362, -0.246 ], "form": ".", "ssZp": 4.176, "Dp": 4.620, "splay_angle": 30.123, "splay_distance": 4.760, "splay_ratio": 0.260, "d22": null, "d64": null, "eta": 163.958, "theta": -16.436, "eta_prime": 174.044, "theta_prime": -59.868, "eta_base": -162.958, "theta_base": -87.971, "v0": 0.748, "v1": -26.710, "v2": 40.651, "v3": -41.275, "v4": 25.808, "amplitude": 42.641, "phase_angle": 17.574, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.619, "filter_rmsd": 0.006, "frame": { "rmsd": 0.006, "origin": [ 14.371, -20.200, -0.002 ], "x_axis": [ 0.348, -0.188, -0.918 ], "y_axis": [ 0.916, 0.276, 0.291 ], "z_axis": [ 0.199, -0.942, 0.268 ], "quaternion": [ 0.688, 0.448, 0.406, -0.401 ] } }, { "index": 40, "index_chain": 6, "chain_name": "G", "nt_resnum": 6, "nt_name": "U", "nt_code": "U", "nt_id": "///G/6", "linked_nts": [ "///G/5", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop", "alpha": 165.440, "beta": 144.354, "gamma": 45.505, "delta": 141.010, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -131.717, "glyco_bond": "anti", "C5prime_xyz": [ -1.977, 8.755, -0.688 ], "P_xyz": [ 0.484, 9.177, 0.110 ], "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": -25.810, "v1": 38.201, "v2": -35.467, "v3": 21.615, "v4": 2.413, "amplitude": 38.339, "phase_angle": 157.682, "puckering": "C2'-endo", "sugar_class": "--", "bin": "32p", "cluster": "5z", "suiteness": 0.801, "filter_rmsd": 0.104, "frame": { "rmsd": 0.005, "origin": [ 16.868, -23.646, -2.135 ], "x_axis": [ -0.835, 0.141, 0.533 ], "y_axis": [ 0.551, 0.209, 0.808 ], "z_axis": [ 0.002, 0.968, -0.252 ], "quaternion": [ -0.175, 0.228, 0.758, 0.586 ] } }, { "index": 41, "index_chain": 1, "chain_name": "H", "nt_resnum": 2, "nt_name": "G", "nt_code": "G", "nt_id": "///H/2", "linked_nts": [ null, "///H/3" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-acceptor", "alpha": null, "beta": -144.032, "gamma": 144.473, "delta": 76.780, "epsilon": 94.347, "zeta": 48.421, "epsilon_zeta": 45.927, "bb_type": "--", "chi": -167.183, "glyco_bond": "anti", "C5prime_xyz": [ -1.023, 8.557, 0.970 ], "P_xyz": [ 1.056, 9.084, -0.533 ], "form": "A", "ssZp": 3.659, "Dp": 3.640, "splay_angle": 21.833, "splay_distance": 3.734, "splay_ratio": 0.195, "d22": null, "d64": null, "eta": null, "theta": -133.643, "eta_prime": null, "theta_prime": -152.543, "eta_base": null, "theta_base": -132.868, "v0": 11.465, "v1": -35.396, "v2": 44.610, "v3": -39.002, "v4": 17.581, "amplitude": 44.721, "phase_angle": 4.050, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.007, "frame": { "rmsd": 0.007, "origin": [ 9.159, -13.710, -6.325 ], "x_axis": [ 0.881, 0.277, 0.383 ], "y_axis": [ -0.459, 0.303, 0.835 ], "z_axis": [ 0.115, -0.912, 0.394 ], "quaternion": [ 0.803, 0.544, -0.083, 0.229 ] } }, { "index": 42, "index_chain": 2, "chain_name": "H", "nt_resnum": 3, "nt_name": "I", "nt_code": "g", "is_modified": true, "nt_id": "///H/3", "linked_nts": [ "///H/2", "///H/4" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": 107.226, "beta": 152.697, "gamma": 167.438, "delta": 104.930, "epsilon": -135.056, "zeta": -82.806, "epsilon_zeta": -52.251, "bb_type": "BI", "chi": -173.452, "glyco_bond": "anti", "C5prime_xyz": [ -0.732, 8.119, 1.395 ], "P_xyz": [ 0.851, 9.975, 0.498 ], "form": "A", "ssZp": 4.531, "Dp": 4.558, "splay_angle": 21.832, "splay_distance": 3.550, "splay_ratio": 0.192, "d22": null, "d64": null, "eta": 153.202, "theta": -164.529, "eta_prime": 172.979, "theta_prime": -157.550, "eta_base": -144.824, "theta_base": -135.842, "v0": 12.311, "v1": -21.010, "v2": 21.571, "v3": -15.031, "v4": 1.775, "amplitude": 22.228, "phase_angle": 346.030, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.070, "frame": { "rmsd": 0.070, "origin": [ 10.562, -17.167, -6.481 ], "x_axis": [ 0.512, 0.360, 0.780 ], "y_axis": [ -0.855, 0.123, 0.504 ], "z_axis": [ 0.085, -0.925, 0.371 ], "quaternion": [ 0.708, 0.504, -0.245, 0.429 ] } }, { "index": 43, "index_chain": 3, "chain_name": "H", "nt_resnum": 4, "nt_name": "G", "nt_code": "G", "nt_id": "///H/4", "linked_nts": [ "///H/3", "///H/5" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,cap-donor", "alpha": -54.072, "beta": 165.795, "gamma": 42.825, "delta": 80.237, "epsilon": -148.204, "zeta": -82.589, "epsilon_zeta": -65.615, "bb_type": "BI", "chi": -157.670, "glyco_bond": "anti", "C5prime_xyz": [ -1.510, 8.886, 0.352 ], "P_xyz": [ 1.032, 9.461, 0.643 ], "form": "A", "ssZp": 4.285, "Dp": 4.577, "splay_angle": 20.220, "splay_distance": 3.268, "splay_ratio": 0.176, "d22": null, "d64": null, "eta": 162.920, "theta": -154.818, "eta_prime": -179.482, "theta_prime": -153.941, "eta_base": -147.051, "theta_base": -137.059, "v0": -1.530, "v1": -23.949, "v2": 38.675, "v3": -40.624, "v4": 26.684, "amplitude": 41.333, "phase_angle": 20.663, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.045, "filter_rmsd": 0.005, "frame": { "rmsd": 0.005, "origin": [ 12.415, -20.159, -6.014 ], "x_axis": [ 0.022, 0.407, 0.913 ], "y_axis": [ -0.985, -0.149, 0.091 ], "z_axis": [ 0.173, -0.901, 0.398 ], "quaternion": [ 0.564, 0.440, -0.328, 0.617 ] } }, { "index": 44, "index_chain": 4, "chain_name": "H", "nt_resnum": 5, "nt_name": "G", "nt_code": "G", "nt_id": "///H/5", "linked_nts": [ "///H/4", "///H/6" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate", "alpha": -61.590, "beta": 166.626, "gamma": 50.378, "delta": 80.287, "epsilon": -151.710, "zeta": 66.132, "epsilon_zeta": 142.157, "bb_type": "--", "chi": -152.155, "glyco_bond": "anti", "C5prime_xyz": [ -1.382, 8.840, 0.038 ], "P_xyz": [ 1.167, 9.334, -0.251 ], "form": ".", "ssZp": 4.202, "Dp": 4.656, "splay_angle": 29.395, "splay_distance": 4.681, "splay_ratio": 0.254, "d22": null, "d64": null, "eta": 166.126, "theta": -18.703, "eta_prime": 175.251, "theta_prime": -61.083, "eta_base": -157.578, "theta_base": -89.689, "v0": 2.826, "v1": -28.058, "v2": 40.863, "v3": -40.361, "v4": 23.928, "amplitude": 42.280, "phase_angle": 14.876, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.881, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 14.217, -22.664, -4.938 ], "x_axis": [ -0.414, 0.390, 0.823 ], "y_axis": [ -0.862, -0.457, -0.217 ], "z_axis": [ 0.292, -0.799, 0.526 ], "quaternion": [ 0.404, 0.360, -0.328, 0.774 ] } }, { "index": 45, "index_chain": 5, "chain_name": "H", "nt_resnum": 6, "nt_name": "U", "nt_code": "U", "nt_id": "///H/6", "linked_nts": [ "///H/5", null ], "nt_type": "RNA", "dbn": ".", "summary": "anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop", "alpha": 176.116, "beta": 135.353, "gamma": 39.234, "delta": 134.025, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -133.107, "glyco_bond": "anti", "C5prime_xyz": [ -2.159, 8.803, -0.788 ], "P_xyz": [ 0.260, 9.312, 0.056 ], "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": -30.942, "v1": 38.444, "v2": -31.282, "v3": 14.346, "v4": 10.239, "amplitude": 37.794, "phase_angle": 145.861, "puckering": "C2'-endo", "sugar_class": "--", "bin": "32p", "cluster": "5z", "suiteness": 0.396, "filter_rmsd": 0.104, "frame": { "rmsd": 0.005, "origin": [ 13.296, -24.057, -0.565 ], "x_axis": [ 0.796, 0.050, -0.604 ], "y_axis": [ -0.407, -0.693, -0.594 ], "z_axis": [ -0.448, 0.719, -0.531 ], "quaternion": [ -0.378, 0.869, -0.103, -0.303 ] } } ], "num_hbonds": 102, "hbonds": [ { "index": 1, "atom1_serNum": 12, "atom2_serNum": 259, "donAcc_type": "standard", "distance": 2.911, "atom1_id": "///A/2/N7", "atom2_id": "///C/2/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 15, "atom2_serNum": 257, "donAcc_type": "standard", "distance": 2.945, "atom1_id": "///A/2/O6", "atom2_id": "///C/2/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 16, "atom2_serNum": 385, "donAcc_type": "standard", "distance": 2.958, "atom1_id": "///A/2/N1", "atom2_id": "///D/2/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 18, "atom2_serNum": 382, "donAcc_type": "standard", "distance": 2.955, "atom1_id": "///A/2/N2", "atom2_id": "///D/2/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 31, "atom2_serNum": 49, "donAcc_type": "acceptable", "distance": 3.011, "atom1_id": "///A/3/O2'", "atom2_id": "///A/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 38, "atom2_serNum": 280, "donAcc_type": "standard", "distance": 2.820, "atom1_id": "///A/3/O6", "atom2_id": "///C/3/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 39, "atom2_serNum": 408, "donAcc_type": "standard", "distance": 2.780, "atom1_id": "///A/3/N1", "atom2_id": "///D/3/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 8, "atom1_serNum": 53, "atom2_serNum": 72, "donAcc_type": "acceptable", "distance": 3.082, "atom1_id": "///A/4/O2'", "atom2_id": "///A/5/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 9, "atom1_serNum": 57, "atom2_serNum": 304, "donAcc_type": "standard", "distance": 2.945, "atom1_id": "///A/4/N7", "atom2_id": "///C/4/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 60, "atom2_serNum": 302, "donAcc_type": "standard", "distance": 2.994, "atom1_id": "///A/4/O6", "atom2_id": "///C/4/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 61, "atom2_serNum": 430, "donAcc_type": "standard", "distance": 2.937, "atom1_id": "///A/4/N1", "atom2_id": "///D/4/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 12, "atom1_serNum": 63, "atom2_serNum": 427, "donAcc_type": "standard", "distance": 2.963, "atom1_id": "///A/4/N2", "atom2_id": "///D/4/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 13, "atom1_serNum": 68, "atom2_serNum": 99, "donAcc_type": "acceptable", "distance": 2.687, "atom1_id": "///A/5/OP2", "atom2_id": "///A/6/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 14, "atom1_serNum": 80, "atom2_serNum": 327, "donAcc_type": "standard", "distance": 2.859, "atom1_id": "///A/5/N7", "atom2_id": "///C/5/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 83, "atom2_serNum": 325, "donAcc_type": "standard", "distance": 2.933, "atom1_id": "///A/5/O6", "atom2_id": "///C/5/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 16, "atom1_serNum": 84, "atom2_serNum": 453, "donAcc_type": "standard", "distance": 2.982, "atom1_id": "///A/5/N1", "atom2_id": "///D/5/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 17, "atom1_serNum": 86, "atom2_serNum": 450, "donAcc_type": "standard", "distance": 3.069, "atom1_id": "///A/5/N2", "atom2_id": "///D/5/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 104, "atom2_serNum": 347, "donAcc_type": "standard", "distance": 2.698, "atom1_id": "///A/6/N3", "atom2_id": "///C/6/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 19, "atom1_serNum": 106, "atom2_serNum": 474, "donAcc_type": "standard", "distance": 3.061, "atom1_id": "///A/6/O4", "atom2_id": "///D/6/N3", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 120, "atom2_serNum": 229, "donAcc_type": "acceptable", "distance": 3.251, "atom1_id": "///B/2/O2'", "atom2_id": "///C/1/O4", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 21, "atom1_serNum": 124, "atom2_serNum": 388, "donAcc_type": "standard", "distance": 2.984, "atom1_id": "///B/2/N7", "atom2_id": "///D/2/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 22, "atom1_serNum": 127, "atom2_serNum": 386, "donAcc_type": "standard", "distance": 3.146, "atom1_id": "///B/2/O6", "atom2_id": "///D/2/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 23, "atom1_serNum": 128, "atom2_serNum": 256, "donAcc_type": "standard", "distance": 2.805, "atom1_id": "///B/2/N1", "atom2_id": "///C/2/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 24, "atom1_serNum": 130, "atom2_serNum": 228, "donAcc_type": "standard", "distance": 3.409, "atom1_id": "///B/2/N2", "atom2_id": "///C/1/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 25, "atom1_serNum": 130, "atom2_serNum": 253, "donAcc_type": "standard", "distance": 2.935, "atom1_id": "///B/2/N2", "atom2_id": "///C/2/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 26, "atom1_serNum": 143, "atom2_serNum": 161, "donAcc_type": "acceptable", "distance": 3.064, "atom1_id": "///B/3/O2'", "atom2_id": "///B/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 27, "atom1_serNum": 150, "atom2_serNum": 409, "donAcc_type": "standard", "distance": 2.865, "atom1_id": "///B/3/O6", "atom2_id": "///D/3/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 28, "atom1_serNum": 151, "atom2_serNum": 279, "donAcc_type": "standard", "distance": 2.733, "atom1_id": "///B/3/N1", "atom2_id": "///C/3/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 29, "atom1_serNum": 169, "atom2_serNum": 433, "donAcc_type": "standard", "distance": 2.942, "atom1_id": "///B/4/N7", "atom2_id": "///D/4/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 30, "atom1_serNum": 172, "atom2_serNum": 431, "donAcc_type": "standard", "distance": 2.942, "atom1_id": "///B/4/O6", "atom2_id": "///D/4/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 31, "atom1_serNum": 173, "atom2_serNum": 301, "donAcc_type": "standard", "distance": 2.988, "atom1_id": "///B/4/N1", "atom2_id": "///C/4/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 32, "atom1_serNum": 175, "atom2_serNum": 298, "donAcc_type": "standard", "distance": 3.068, "atom1_id": "///B/4/N2", "atom2_id": "///C/4/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 33, "atom1_serNum": 180, "atom2_serNum": 211, "donAcc_type": "acceptable", "distance": 2.370, "atom1_id": "///B/5/OP2", "atom2_id": "///B/6/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 34, "atom1_serNum": 192, "atom2_serNum": 456, "donAcc_type": "standard", "distance": 2.928, "atom1_id": "///B/5/N7", "atom2_id": "///D/5/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 35, "atom1_serNum": 195, "atom2_serNum": 454, "donAcc_type": "standard", "distance": 2.935, "atom1_id": "///B/5/O6", "atom2_id": "///D/5/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 36, "atom1_serNum": 196, "atom2_serNum": 324, "donAcc_type": "standard", "distance": 2.942, "atom1_id": "///B/5/N1", "atom2_id": "///C/5/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 37, "atom1_serNum": 198, "atom2_serNum": 321, "donAcc_type": "standard", "distance": 2.881, "atom1_id": "///B/5/N2", "atom2_id": "///C/5/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 38, "atom1_serNum": 211, "atom2_serNum": 456, "donAcc_type": "acceptable", "distance": 3.487, "atom1_id": "///B/6/O2'", "atom2_id": "///D/5/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 39, "atom1_serNum": 216, "atom2_serNum": 476, "donAcc_type": "standard", "distance": 2.958, "atom1_id": "///B/6/N3", "atom2_id": "///D/6/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 40, "atom1_serNum": 218, "atom2_serNum": 345, "donAcc_type": "standard", "distance": 2.807, "atom1_id": "///B/6/O4", "atom2_id": "///C/6/N3", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 41, "atom1_serNum": 235, "atom2_serNum": 775, "donAcc_type": "standard", "distance": 3.071, "atom1_id": "///C/1/O4'", "atom2_id": "///G/2/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 42, "atom1_serNum": 240, "atom2_serNum": 765, "donAcc_type": "acceptable", "distance": 3.400, "atom1_id": "///C/2/OP1", "atom2_id": "///G/2/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 43, "atom1_serNum": 245, "atom2_serNum": 761, "donAcc_type": "questionable", "distance": 2.870, "atom1_id": "///C/2/O4'", "atom2_id": "///G/2/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 44, "atom1_serNum": 249, "atom2_serNum": 268, "donAcc_type": "acceptable", "distance": 3.233, "atom1_id": "///C/2/O2'", "atom2_id": "///C/3/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 45, "atom1_serNum": 249, "atom2_serNum": 756, "donAcc_type": "acceptable", "distance": 3.413, "atom1_id": "///C/2/O2'", "atom2_id": "///G/2/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 46, "atom1_serNum": 272, "atom2_serNum": 290, "donAcc_type": "acceptable", "distance": 2.908, "atom1_id": "///C/3/O2'", "atom2_id": "///C/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 47, "atom1_serNum": 294, "atom2_serNum": 313, "donAcc_type": "acceptable", "distance": 3.118, "atom1_id": "///C/4/O2'", "atom2_id": "///C/5/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 48, "atom1_serNum": 309, "atom2_serNum": 340, "donAcc_type": "acceptable", "distance": 2.742, "atom1_id": "///C/5/OP2", "atom2_id": "///C/6/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 49, "atom1_serNum": 401, "atom2_serNum": 419, "donAcc_type": "acceptable", "distance": 2.954, "atom1_id": "///D/3/O2'", "atom2_id": "///D/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 50, "atom1_serNum": 423, "atom2_serNum": 442, "donAcc_type": "acceptable", "distance": 3.107, "atom1_id": "///D/4/O2'", "atom2_id": "///D/5/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 51, "atom1_serNum": 438, "atom2_serNum": 469, "donAcc_type": "acceptable", "distance": 2.376, "atom1_id": "///D/5/OP2", "atom2_id": "///D/6/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 52, "atom1_serNum": 511, "atom2_serNum": 775, "donAcc_type": "standard", "distance": 2.977, "atom1_id": "///E/2/N7", "atom2_id": "///G/2/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 53, "atom1_serNum": 514, "atom2_serNum": 773, "donAcc_type": "standard", "distance": 2.879, "atom1_id": "///E/2/O6", "atom2_id": "///G/2/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 54, "atom1_serNum": 515, "atom2_serNum": 884, "donAcc_type": "standard", "distance": 2.880, "atom1_id": "///E/2/N1", "atom2_id": "///H/2/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 55, "atom1_serNum": 517, "atom2_serNum": 881, "donAcc_type": "standard", "distance": 2.780, "atom1_id": "///E/2/N2", "atom2_id": "///H/2/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 56, "atom1_serNum": 530, "atom2_serNum": 548, "donAcc_type": "acceptable", "distance": 3.048, "atom1_id": "///E/3/O2'", "atom2_id": "///E/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 57, "atom1_serNum": 537, "atom2_serNum": 796, "donAcc_type": "standard", "distance": 2.812, "atom1_id": "///E/3/O6", "atom2_id": "///G/3/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 58, "atom1_serNum": 538, "atom2_serNum": 907, "donAcc_type": "standard", "distance": 2.830, "atom1_id": "///E/3/N1", "atom2_id": "///H/3/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 59, "atom1_serNum": 552, "atom2_serNum": 571, "donAcc_type": "acceptable", "distance": 3.256, "atom1_id": "///E/4/O2'", "atom2_id": "///E/5/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 60, "atom1_serNum": 556, "atom2_serNum": 820, "donAcc_type": "standard", "distance": 2.962, "atom1_id": "///E/4/N7", "atom2_id": "///G/4/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 61, "atom1_serNum": 559, "atom2_serNum": 818, "donAcc_type": "standard", "distance": 3.070, "atom1_id": "///E/4/O6", "atom2_id": "///G/4/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 62, "atom1_serNum": 560, "atom2_serNum": 929, "donAcc_type": "standard", "distance": 3.081, "atom1_id": "///E/4/N1", "atom2_id": "///H/4/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 63, "atom1_serNum": 562, "atom2_serNum": 926, "donAcc_type": "standard", "distance": 3.053, "atom1_id": "///E/4/N2", "atom2_id": "///H/4/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 64, "atom1_serNum": 567, "atom2_serNum": 598, "donAcc_type": "acceptable", "distance": 2.650, "atom1_id": "///E/5/OP2", "atom2_id": "///E/6/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 65, "atom1_serNum": 579, "atom2_serNum": 843, "donAcc_type": "standard", "distance": 2.960, "atom1_id": "///E/5/N7", "atom2_id": "///G/5/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 66, "atom1_serNum": 582, "atom2_serNum": 841, "donAcc_type": "standard", "distance": 3.011, "atom1_id": "///E/5/O6", "atom2_id": "///G/5/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 67, "atom1_serNum": 583, "atom2_serNum": 952, "donAcc_type": "standard", "distance": 2.970, "atom1_id": "///E/5/N1", "atom2_id": "///H/5/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 68, "atom1_serNum": 585, "atom2_serNum": 949, "donAcc_type": "standard", "distance": 2.948, "atom1_id": "///E/5/N2", "atom2_id": "///H/5/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 69, "atom1_serNum": 585, "atom2_serNum": 968, "donAcc_type": "acceptable", "distance": 3.284, "atom1_id": "///E/5/N2", "atom2_id": "///H/6/O2'", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 70, "atom1_serNum": 598, "atom2_serNum": 843, "donAcc_type": "acceptable", "distance": 3.399, "atom1_id": "///E/6/O2'", "atom2_id": "///G/5/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 71, "atom1_serNum": 603, "atom2_serNum": 863, "donAcc_type": "standard", "distance": 2.766, "atom1_id": "///E/6/N3", "atom2_id": "///G/6/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 72, "atom1_serNum": 605, "atom2_serNum": 973, "donAcc_type": "standard", "distance": 2.785, "atom1_id": "///E/6/O4", "atom2_id": "///H/6/N3", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 73, "atom1_serNum": 624, "atom2_serNum": 650, "donAcc_type": "questionable", "distance": 3.076, "atom1_id": "///F/1/O5'", "atom2_id": "///F/3/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 74, "atom1_serNum": 627, "atom2_serNum": 900, "donAcc_type": "acceptable", "distance": 3.402, "atom1_id": "///F/2/OP1", "atom2_id": "///H/3/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 75, "atom1_serNum": 636, "atom2_serNum": 745, "donAcc_type": "acceptable", "distance": 2.938, "atom1_id": "///F/2/O2'", "atom2_id": "///G/1/O4", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 76, "atom1_serNum": 640, "atom2_serNum": 887, "donAcc_type": "standard", "distance": 3.121, "atom1_id": "///F/2/N7", "atom2_id": "///H/2/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 77, "atom1_serNum": 643, "atom2_serNum": 885, "donAcc_type": "standard", "distance": 3.047, "atom1_id": "///F/2/O6", "atom2_id": "///H/2/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 78, "atom1_serNum": 644, "atom2_serNum": 772, "donAcc_type": "standard", "distance": 2.847, "atom1_id": "///F/2/N1", "atom2_id": "///G/2/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 79, "atom1_serNum": 646, "atom2_serNum": 744, "donAcc_type": "standard", "distance": 3.282, "atom1_id": "///F/2/N2", "atom2_id": "///G/1/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 80, "atom1_serNum": 646, "atom2_serNum": 769, "donAcc_type": "standard", "distance": 2.856, "atom1_id": "///F/2/N2", "atom2_id": "///G/2/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 81, "atom1_serNum": 659, "atom2_serNum": 677, "donAcc_type": "acceptable", "distance": 3.100, "atom1_id": "///F/3/O2'", "atom2_id": "///F/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 82, "atom1_serNum": 666, "atom2_serNum": 908, "donAcc_type": "standard", "distance": 2.796, "atom1_id": "///F/3/O6", "atom2_id": "///H/3/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 83, "atom1_serNum": 667, "atom2_serNum": 795, "donAcc_type": "standard", "distance": 2.799, "atom1_id": "///F/3/N1", "atom2_id": "///G/3/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 84, "atom1_serNum": 681, "atom2_serNum": 700, "donAcc_type": "acceptable", "distance": 3.263, "atom1_id": "///F/4/O2'", "atom2_id": "///F/5/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 85, "atom1_serNum": 685, "atom2_serNum": 932, "donAcc_type": "standard", "distance": 2.972, "atom1_id": "///F/4/N7", "atom2_id": "///H/4/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 86, "atom1_serNum": 688, "atom2_serNum": 930, "donAcc_type": "standard", "distance": 2.929, "atom1_id": "///F/4/O6", "atom2_id": "///H/4/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 87, "atom1_serNum": 689, "atom2_serNum": 817, "donAcc_type": "standard", "distance": 2.986, "atom1_id": "///F/4/N1", "atom2_id": "///G/4/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 88, "atom1_serNum": 691, "atom2_serNum": 814, "donAcc_type": "standard", "distance": 3.072, "atom1_id": "///F/4/N2", "atom2_id": "///G/4/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 89, "atom1_serNum": 696, "atom2_serNum": 727, "donAcc_type": "acceptable", "distance": 2.627, "atom1_id": "///F/5/OP2", "atom2_id": "///F/6/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 90, "atom1_serNum": 708, "atom2_serNum": 955, "donAcc_type": "standard", "distance": 2.910, "atom1_id": "///F/5/N7", "atom2_id": "///H/5/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 91, "atom1_serNum": 711, "atom2_serNum": 953, "donAcc_type": "standard", "distance": 2.892, "atom1_id": "///F/5/O6", "atom2_id": "///H/5/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 92, "atom1_serNum": 712, "atom2_serNum": 840, "donAcc_type": "standard", "distance": 3.051, "atom1_id": "///F/5/N1", "atom2_id": "///G/5/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 93, "atom1_serNum": 714, "atom2_serNum": 837, "donAcc_type": "standard", "distance": 2.981, "atom1_id": "///F/5/N2", "atom2_id": "///G/5/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 94, "atom1_serNum": 732, "atom2_serNum": 975, "donAcc_type": "standard", "distance": 2.684, "atom1_id": "///F/6/N3", "atom2_id": "///H/6/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 95, "atom1_serNum": 734, "atom2_serNum": 861, "donAcc_type": "standard", "distance": 2.835, "atom1_id": "///F/6/O4", "atom2_id": "///G/6/N3", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 96, "atom1_serNum": 788, "atom2_serNum": 806, "donAcc_type": "acceptable", "distance": 3.049, "atom1_id": "///G/3/O2'", "atom2_id": "///G/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 97, "atom1_serNum": 810, "atom2_serNum": 829, "donAcc_type": "acceptable", "distance": 3.209, "atom1_id": "///G/4/O2'", "atom2_id": "///G/5/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 98, "atom1_serNum": 825, "atom2_serNum": 856, "donAcc_type": "acceptable", "distance": 2.593, "atom1_id": "///G/5/OP2", "atom2_id": "///G/6/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 99, "atom1_serNum": 877, "atom2_serNum": 891, "donAcc_type": "acceptable", "distance": 2.851, "atom1_id": "///H/2/O2'", "atom2_id": "///H/3/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 100, "atom1_serNum": 900, "atom2_serNum": 918, "donAcc_type": "acceptable", "distance": 3.162, "atom1_id": "///H/3/O2'", "atom2_id": "///H/4/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 101, "atom1_serNum": 922, "atom2_serNum": 941, "donAcc_type": "acceptable", "distance": 3.140, "atom1_id": "///H/4/O2'", "atom2_id": "///H/5/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 102, "atom1_serNum": 937, "atom2_serNum": 968, "donAcc_type": "acceptable", "distance": 2.608, "atom1_id": "///H/5/OP2", "atom2_id": "///H/6/O2'", "atom_pair": "O:O", "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": "2grb", "num_naChains": 8, "naChains": "A=5,B=5,C=6,D=6,E=6,F=6,G=6,H=5", "num_atoms": 1160, "num_waters": 178, "num_metals": 12, "metals_desc": "K=11,Sr=1", "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-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 4, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 5, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 6, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 7, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 8, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 9, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 10, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 11, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 12, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 13, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 14, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }