{ "num_pairs": 8, "pairs": [ { "index": 1, "nt1": "///A/1", "nt2": "///B/10", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -176.852, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 53.659, "chi2": -152.904, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 55.786, "C1C1_dist": 10.690, "N1N9_dist": 8.984, "C6C8_dist": 9.941, "CNNC_torsion": -4.000, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.96],N1(imino)-N3[2.93],N2(amino)-O2(carbonyl)[2.87]", "interBase_angle": 2.321, "planarity": 0.034, "simple_Shear": -0.309, "simple_Stretch": -0.091, "simple_Buckle": 1.843, "simple_Propeller": -1.410, "bp_simpleParams": [ -0.309, -0.091, 0.117, 1.843, -1.410, 0.303 ], "bp_params": [ -0.306, -0.099, 0.117, 1.881, -1.359, 0.303 ], "frame": { "rmsd": null, "origin": [ -4.864, -7.608, 8.940 ], "x_axis": [ -0.568, 0.794, -0.216 ], "y_axis": [ -0.224, 0.103, 0.969 ], "z_axis": [ 0.792, 0.599, 0.120 ], "quaternion": [ 0.404, 0.229, 0.623, 0.629 ] } }, { "index": 2, "nt1": "///A/3", "nt2": "///B/8", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -178.322, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 53.252, "chi2": -157.446, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 56.140, "C1C1_dist": 10.615, "N1N9_dist": 8.910, "C6C8_dist": 9.848, "CNNC_torsion": -14.722, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.95],N1(imino)-N3[2.88],N2(amino)-O2(carbonyl)[2.79]", "interBase_angle": 16.823, "planarity": 0.208, "simple_Shear": -0.353, "simple_Stretch": -0.164, "simple_Buckle": -8.376, "simple_Propeller": -14.590, "bp_simpleParams": [ -0.353, -0.164, 0.174, -8.376, -14.590, -0.010 ], "bp_params": [ -0.348, -0.173, 0.174, -7.970, -14.815, -0.010 ], "frame": { "rmsd": null, "origin": [ -0.340, -1.992, 6.586 ], "x_axis": [ -0.546, 0.350, 0.762 ], "y_axis": [ 0.436, -0.657, 0.614 ], "z_axis": [ 0.716, 0.668, 0.206 ], "quaternion": [ -0.028, 0.476, 0.413, 0.776 ] } }, { "index": 3, "nt1": "///A/4", "nt2": "///B/7", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -149.759, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 51.530, "chi2": -161.450, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 55.201, "C1C1_dist": 10.634, "N1N9_dist": 8.879, "C6C8_dist": 9.818, "CNNC_torsion": -16.338, "hbonds_num": 2, "hbonds_desc": "N3(imino)-N1[2.83],O4(carbonyl)-N6(amino)[3.01]", "interBase_angle": 18.891, "planarity": 0.233, "simple_Shear": -0.179, "simple_Stretch": -0.122, "simple_Buckle": -5.953, "simple_Propeller": -17.928, "bp_simpleParams": [ -0.179, -0.122, 0.111, -5.953, -17.928, -0.634 ], "bp_params": [ -0.177, -0.125, 0.111, -5.594, -18.043, -0.641 ], "frame": { "rmsd": null, "origin": [ 1.440, 1.141, 5.798 ], "x_axis": [ -0.232, -0.166, 0.959 ], "y_axis": [ 0.670, -0.741, 0.034 ], "z_axis": [ 0.705, 0.650, 0.283 ], "quaternion": [ -0.278, 0.554, 0.228, 0.751 ] } }, { "index": 4, "nt1": "///A/5", "nt2": "///B/6", "bp": "A-u", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -166.331, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 54.077, "chi2": -155.993, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 52.103, "C1C1_dist": 10.714, "N1N9_dist": 8.957, "C6C8_dist": 9.880, "CNNC_torsion": -15.585, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[2.94],N1-N3(imino)[2.83]", "interBase_angle": 16.186, "planarity": 0.202, "simple_Shear": 0.163, "simple_Stretch": -0.096, "simple_Buckle": -1.226, "simple_Propeller": -16.139, "bp_simpleParams": [ 0.163, -0.096, 0.189, -1.226, -16.139, -2.863 ], "bp_params": [ 0.160, -0.100, 0.189, -1.604, -16.106, -2.892 ], "frame": { "rmsd": null, "origin": [ 2.314, 3.895, 7.858 ], "x_axis": [ -0.091, -0.636, 0.767 ], "y_axis": [ 0.765, -0.537, -0.355 ], "z_axis": [ 0.638, 0.554, 0.535 ], "quaternion": [ -0.476, 0.477, 0.068, 0.735 ] } }, { "index": 5, "nt1": "///A/6", "nt2": "///B/5", "bp": "u-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -155.745, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 60.177, "chi2": -160.920, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 60.267, "C1C1_dist": 10.186, "N1N9_dist": 8.737, "C6C8_dist": 9.922, "CNNC_torsion": -15.668, "hbonds_num": 2, "hbonds_desc": "N3(imino)-N1[2.82],O4(carbonyl)-N6(amino)[3.41]", "interBase_angle": 14.550, "planarity": 0.211, "simple_Shear": 0.043, "simple_Stretch": -0.027, "simple_Buckle": 3.991, "simple_Propeller": -13.992, "bp_simpleParams": [ 0.043, -0.027, 0.436, 3.991, -13.992, 8.490 ], "bp_params": [ 0.043, -0.027, 0.436, 4.057, -13.973, 8.548 ], "frame": { "rmsd": null, "origin": [ 3.378, 5.119, 10.900 ], "x_axis": [ 0.251, -0.895, 0.370 ], "y_axis": [ 0.717, -0.086, -0.692 ], "z_axis": [ 0.651, 0.439, 0.620 ], "quaternion": [ 0.668, -0.423, 0.105, -0.603 ] } }, { "index": 6, "nt1": "///A/7", "nt2": "///B/4", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -158.090, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 58.243, "chi2": -160.178, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 56.825, "C1C1_dist": 10.337, "N1N9_dist": 8.764, "C6C8_dist": 9.813, "CNNC_torsion": -6.496, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[3.04],N1-N3(imino)[2.83]", "interBase_angle": 11.762, "planarity": 0.145, "simple_Shear": -0.027, "simple_Stretch": -0.127, "simple_Buckle": 6.631, "simple_Propeller": -9.715, "bp_simpleParams": [ -0.027, -0.127, 0.016, 6.631, -9.715, 2.921 ], "bp_params": [ -0.027, -0.127, 0.016, 6.640, -9.709, 2.927 ], "frame": { "rmsd": null, "origin": [ 4.403, 6.239, 13.897 ], "x_axis": [ 0.416, -0.898, -0.142 ], "y_axis": [ 0.570, 0.380, -0.729 ], "z_axis": [ 0.708, 0.222, 0.670 ], "quaternion": [ 0.785, -0.303, 0.271, -0.467 ] } }, { "index": 7, "nt1": "///A/8", "nt2": "///B/3", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -162.640, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 56.309, "chi2": -169.193, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 55.619, "C1C1_dist": 10.519, "N1N9_dist": 8.876, "C6C8_dist": 9.857, "CNNC_torsion": -5.354, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.79],N3-N1(imino)[2.85],N4(amino)-O6(carbonyl)[2.94]", "interBase_angle": 14.072, "planarity": 0.152, "simple_Shear": 0.223, "simple_Stretch": -0.145, "simple_Buckle": 8.924, "simple_Propeller": -10.881, "bp_simpleParams": [ 0.223, -0.145, -0.229, 8.924, -10.881, 1.949 ], "bp_params": [ 0.220, -0.148, -0.229, 8.754, -11.018, 1.952 ], "frame": { "rmsd": null, "origin": [ 6.106, 5.692, 17.253 ], "x_axis": [ 0.613, -0.584, -0.533 ], "y_axis": [ 0.300, 0.795, -0.527 ], "z_axis": [ 0.731, 0.163, 0.662 ], "quaternion": [ 0.876, -0.197, 0.361, -0.252 ] } }, { "index": 8, "nt1": "///A/10", "nt2": "///B/1", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -159.139, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 54.967, "chi2": -175.670, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 52.391, "C1C1_dist": 10.703, "N1N9_dist": 8.960, "C6C8_dist": 9.868, "CNNC_torsion": 1.249, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.78],N3-N1(imino)[2.91],N4(amino)-O6(carbonyl)[2.89]", "interBase_angle": 6.517, "planarity": 0.077, "simple_Shear": 0.218, "simple_Stretch": -0.142, "simple_Buckle": -4.557, "simple_Propeller": 4.659, "bp_simpleParams": [ 0.218, -0.142, 0.269, -4.557, 4.659, -0.113 ], "bp_params": [ 0.216, -0.146, 0.269, -4.483, 4.730, -0.113 ], "frame": { "rmsd": null, "origin": [ 11.765, 3.269, 21.573 ], "x_axis": [ 0.390, 0.453, -0.802 ], "y_axis": [ -0.297, 0.886, 0.356 ], "z_axis": [ 0.871, 0.099, 0.480 ], "quaternion": [ 0.830, 0.077, 0.504, 0.226 ] } } ], "num_helices": 1, "helices": [ { "index": 1, "num_stems": 1, "strand1": "GTAuAC", "strand2": "CAuATG", "bp_type": "||||||", "helix_form": "AAAAA", "helical_rise": 2.315, "helical_rise_std": 0.260, "helical_radius": 9.447, "helical_radius_std": 0.642, "helical_axis": [ 0.895, 0.321, 0.310 ], "point1": [ -1.929, -0.781, 9.841 ], "point2": [ 8.319, 2.894, 13.395 ], "num_pairs": 6, "pairs": [ { "index": 1, "nt1": "///A/3", "nt2": "///B/8", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.348, -0.173, 0.174, -7.970, -14.815, -0.010 ], "step_params": [ -1.124, -1.578, 3.138, -1.886, 4.140, 36.802 ], "heli_params": [ -3.004, 1.529, 3.001, 6.527, 2.974, 37.073 ], "bp2_params": [ -0.177, -0.125, 0.111, -5.594, -18.043, -0.641 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.138, "simple_Twist": 36.037, "simple_hRise": 2.998, "simple_hTwist": 36.314 }, { "index": 2, "nt1": "///A/4", "nt2": "///B/7", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.177, -0.125, 0.111, -5.594, -18.043, -0.641 ], "step_params": [ 0.543, -1.604, 3.118, 1.640, 15.920, 26.149 ], "heli_params": [ -5.651, -0.760, 1.883, 31.691, -3.264, 30.584 ], "bp2_params": [ 0.160, -0.100, 0.189, -1.604, -16.106, -2.892 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.118, "simple_Twist": 24.564, "simple_hRise": 1.797, "simple_hTwist": 29.250 }, { "index": 3, "nt1": "///A/5", "nt2": "///B/6", "bp": "A-u", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.160, -0.100, 0.189, -1.604, -16.106, -2.892 ], "step_params": [ 0.918, -1.302, 3.057, -0.096, 8.231, 32.959 ], "heli_params": [ -3.401, -1.586, 2.662, 14.234, 0.165, 33.943 ], "bp2_params": [ 0.043, -0.027, 0.436, 4.057, -13.973, 8.548 ], "groove_widths": [ 18.030, null, 17.489, null ], "simple_Rise": 3.057, "simple_Twist": 33.725, "simple_hRise": 2.673, "simple_hTwist": 34.687 }, { "index": 4, "nt1": "///A/6", "nt2": "///B/5", "bp": "u-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.043, -0.027, 0.436, 4.057, -13.973, 8.548 ], "step_params": [ -0.344, -1.433, 3.019, 1.813, 13.051, 28.469 ], "heli_params": [ -4.699, 0.922, 2.146, 24.920, -3.462, 31.313 ], "bp2_params": [ -0.027, -0.127, 0.016, 6.640, -9.709, 2.927 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.019, "simple_Twist": 28.992, "simple_hRise": 2.164, "simple_hTwist": 31.788 }, { "index": 5, "nt1": "///A/7", "nt2": "///B/4", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.027, -0.127, 0.016, 6.640, -9.709, 2.927 ], "step_params": [ 0.144, -1.780, 3.358, 1.208, 3.478, 31.031 ], "heli_params": [ -3.962, -0.039, 3.148, 6.473, -2.248, 31.244 ], "bp2_params": [ 0.220, -0.148, -0.229, 8.754, -11.018, 1.952 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.358, "simple_Twist": 29.557, "simple_hRise": 3.136, "simple_hTwist": 29.781 }, { "index": 6, "nt1": "///A/8", "nt2": "///B/3", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_stems": 1, "stems": [ { "index": 1, "helix_index": 1, "strand1": "GTAuAC", "strand2": "CAuATG", "bp_type": "||||||", "helix_form": "AAAAA", "helical_rise": 2.315, "helical_rise_std": 0.260, "helical_radius": 9.447, "helical_radius_std": 0.642, "helical_axis": [ 0.895, 0.321, 0.310 ], "point1": [ -1.929, -0.781, 9.841 ], "point2": [ 8.319, 2.894, 13.395 ], "num_pairs": 6, "pairs": [ { "index": 1, "nt1": "///A/3", "nt2": "///B/8", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.348, -0.173, 0.174, -7.970, -14.815, -0.010 ], "step_params": [ -1.124, -1.578, 3.138, -1.886, 4.140, 36.802 ], "heli_params": [ -3.004, 1.529, 3.001, 6.527, 2.974, 37.073 ], "bp2_params": [ -0.177, -0.125, 0.111, -5.594, -18.043, -0.641 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.138, "simple_Twist": 36.037, "simple_hRise": 2.998, "simple_hTwist": 36.314 }, { "index": 2, "nt1": "///A/4", "nt2": "///B/7", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.177, -0.125, 0.111, -5.594, -18.043, -0.641 ], "step_params": [ 0.543, -1.604, 3.118, 1.640, 15.920, 26.149 ], "heli_params": [ -5.651, -0.760, 1.883, 31.691, -3.264, 30.584 ], "bp2_params": [ 0.160, -0.100, 0.189, -1.604, -16.106, -2.892 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.118, "simple_Twist": 24.564, "simple_hRise": 1.797, "simple_hTwist": 29.250 }, { "index": 3, "nt1": "///A/5", "nt2": "///B/6", "bp": "A-u", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.160, -0.100, 0.189, -1.604, -16.106, -2.892 ], "step_params": [ 0.918, -1.302, 3.057, -0.096, 8.231, 32.959 ], "heli_params": [ -3.401, -1.586, 2.662, 14.234, 0.165, 33.943 ], "bp2_params": [ 0.043, -0.027, 0.436, 4.057, -13.973, 8.548 ], "groove_widths": [ 18.030, null, 17.489, null ], "simple_Rise": 3.057, "simple_Twist": 33.725, "simple_hRise": 2.673, "simple_hTwist": 34.687 }, { "index": 4, "nt1": "///A/6", "nt2": "///B/5", "bp": "u-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.043, -0.027, 0.436, 4.057, -13.973, 8.548 ], "step_params": [ -0.344, -1.433, 3.019, 1.813, 13.051, 28.469 ], "heli_params": [ -4.699, 0.922, 2.146, 24.920, -3.462, 31.313 ], "bp2_params": [ -0.027, -0.127, 0.016, 6.640, -9.709, 2.927 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.019, "simple_Twist": 28.992, "simple_hRise": 2.164, "simple_hTwist": 31.788 }, { "index": 5, "nt1": "///A/7", "nt2": "///B/4", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.027, -0.127, 0.016, 6.640, -9.709, 2.927 ], "step_params": [ 0.144, -1.780, 3.358, 1.208, 3.478, 31.031 ], "heli_params": [ -3.962, -0.039, 3.148, 6.473, -2.248, 31.244 ], "bp2_params": [ 0.220, -0.148, -0.229, 8.754, -11.018, 1.952 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.358, "simple_Twist": 29.557, "simple_hRise": 3.136, "simple_hTwist": 29.781 }, { "index": 6, "nt1": "///A/8", "nt2": "///B/3", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_isoCanonPairs": 2, "isoCanonPairs": [ { "index": -1, "helix_index": 0, "nt1": "///A/1", "nt2": "///B/10", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" }, { "index": -2, "helix_index": 0, "nt1": "///A/10", "nt2": "///B/1", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ], "num_stacks": 2, "stacks": [ { "index": 1, "num_nts": 3, "nts_short": "GGC", "nts_long": "///A/3,///B/9,///B/10" }, { "index": 2, "num_nts": 3, "nts_short": "CGG", "nts_long": "///A/10,///A/9,///B/3" } ], "nonStack": { "num_nts": 2, "nts_short": "GG", "nts_long": "///A/1,///B/1" }, "num_iloops": 2, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -1, 1 ], "summary": "[2] 1 1 [A.1 B.10 A.3 B.8] 1 6", "num_nts": 6, "nts_short": "G?GCGC", "nts_long": "///A/1,///A/2,///A/3,///B/8,///B/9,///B/10", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "?", "nts_long": "///A/2" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///B/9" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 1, -2 ], "summary": "[2] 1 1 [A.8 B.3 A.10 B.1] 6 1", "num_nts": 6, "nts_short": "CGCG?G", "nts_long": "///A/8,///A/9,///A/10,///B/1,///B/2,///B/3", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/9" }, { "index": 2, "num_nts": 1, "nts_short": "?", "nts_long": "///B/2" } ] } ], "dbn": { "all_chains": { "num_nts": 20, "num_chars": 21, "bseq": "G?GTAuACGC&G?GTAuACGC", "bseqUP": "G?GTAUACGC&G?GTAUACGC", "sstr": "(.((((((.(&).)))))).)", "form": "--A.AAAAA-&--AAAAAAA-" }, "chain_A": { "num_nts": 10, "num_chars": 10, "bseq": "G?GTAuACGC", "bseqUP": "G?GTAUACGC", "sstr": "(.((((((.(", "form": "--A.AAAAA-" }, "chain_B": { "num_nts": 10, "num_chars": 10, "bseq": "G?GTAuACGC", "bseqUP": "G?GTAUACGC", "sstr": ").)))))).)", "form": "--AAAAAAA-" } }, "chains": { "chain_A": { "num_nts": 10, "bseq": "G?GTAuACGC", "sstr": "(.((((((.(", "form": "--A.AAAAA-", "helical_rise": 2.362, "helical_rise_std": 0.430, "helical_axis": [ 0.874, 0.338, 0.349 ], "point1": [ -4.814, -2.405, 9.105 ], "point2": [ 13.683, 4.746, 16.490 ], "num_chars": 28, "suite": "G1a?1cG1aT1cA1au1aA1aC1aG1aC" }, "chain_B": { "num_nts": 10, "bseq": "G?GTAuACGC", "sstr": ").)))))).)", "form": "--AAAAAAA-", "helical_rise": 2.279, "helical_rise_std": 0.231, "helical_axis": [ -0.867, -0.397, -0.299 ], "point1": [ 11.077, 4.405, 14.688 ], "point2": [ -6.619, -3.703, 8.579 ], "num_chars": 28, "suite": "G1a?1aG1aT1aA1au1aA1aC1cG1aC" } }, "num_nts": 20, "nts": [ { "index": 1, "index_chain": 1, "chain_name": "A", "nt_resnum": 1, "nt_name": "DG", "nt_code": "G", "nt_id": "///A/1", "linked_nts": [ null, "///A/2" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,non-stack,isolated-canonical,internal-loop", "alpha": null, "beta": null, "gamma": 60.040, "delta": 90.505, "epsilon": -150.218, "zeta": -76.383, "epsilon_zeta": -73.834, "bb_type": "BI", "chi": -176.852, "glyco_bond": "anti", "C5prime_xyz": [ -1.624, 8.520, 1.510 ], "P_xyz": [ null, null, null ], "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": 4.845, "v1": -25.039, "v2": 34.382, "v3": -32.531, "v4": 17.619, "amplitude": 35.007, "phase_angle": 10.842, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.011, "frame": { "rmsd": 0.011, "origin": [ -4.720, -7.700, 8.932 ], "x_axis": [ -0.559, 0.801, -0.212 ], "y_axis": [ -0.210, 0.111, 0.971 ], "z_axis": [ 0.802, 0.588, 0.106 ], "quaternion": [ 0.405, 0.236, 0.625, 0.623 ] } }, { "index": 2, "index_chain": 2, "chain_name": "A", "nt_resnum": 2, "nt_name": "EXC", "nt_code": "?", "is_modified": true, "nt_id": "///A/2", "linked_nts": [ "///A/1", "///A/3" ], "nt_type": "DNA", "dbn": ".", "summary": "modified,~C3'-endo,BI,non-stack,internal-loop", "alpha": -68.841, "beta": 176.162, "gamma": 56.322, "delta": 92.967, "epsilon": -173.061, "zeta": -69.798, "epsilon_zeta": -103.263, "bb_type": "BI", "chi": null, "glyco_bond": "--", "C5prime_xyz": [ null, null, null ], "P_xyz": [ null, null, null ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": 169.257, "theta": -119.248, "eta_prime": -170.456, "theta_prime": -135.080, "eta_base": null, "theta_base": null, "v0": -6.266, "v1": -12.324, "v2": 25.315, "v3": -29.561, "v4": 22.115, "amplitude": 29.335, "phase_angle": 30.349, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.527, "filter_rmsd": null }, { "index": 3, "index_chain": 3, "chain_name": "A", "nt_resnum": 3, "nt_name": "DG", "nt_code": "G", "nt_id": "///A/3", "linked_nts": [ "///A/2", "///A/4" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop", "alpha": 143.451, "beta": -172.352, "gamma": -172.749, "delta": 90.241, "epsilon": -152.945, "zeta": -70.249, "epsilon_zeta": -82.695, "bb_type": "BI", "chi": -178.322, "glyco_bond": "anti", "C5prime_xyz": [ -1.564, 8.385, 1.680 ], "P_xyz": [ -0.197, 10.549, 1.001 ], "form": "A", "ssZp": 4.275, "Dp": 4.389, "splay_angle": 22.955, "splay_distance": 3.657, "splay_ratio": 0.202, "d22": null, "d64": null, "eta": 170.327, "theta": -174.242, "eta_prime": -176.796, "theta_prime": -164.839, "eta_base": null, "theta_base": -137.136, "v0": 4.460, "v1": -24.188, "v2": 33.832, "v3": -32.591, "v4": 17.608, "amplitude": 34.549, "phase_angle": 11.694, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "1c", "suiteness": 0.485, "filter_rmsd": 0.008, "frame": { "rmsd": 0.008, "origin": [ -0.221, -1.937, 6.418 ], "x_axis": [ -0.447, 0.430, 0.784 ], "y_axis": [ 0.383, -0.700, 0.602 ], "z_axis": [ 0.808, 0.570, 0.148 ], "quaternion": [ 0.015, 0.526, 0.387, 0.758 ] } }, { "index": 4, "index_chain": 4, "chain_name": "A", "nt_resnum": 4, "nt_name": "DT", "nt_code": "T", "nt_id": "///A/4", "linked_nts": [ "///A/3", "///A/5" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -81.113, "beta": -165.108, "gamma": 50.715, "delta": 81.066, "epsilon": -155.172, "zeta": -66.251, "epsilon_zeta": -88.921, "bb_type": "BI", "chi": -149.759, "glyco_bond": "anti", "C5prime_xyz": [ -1.315, 8.826, -0.123 ], "P_xyz": [ 1.236, 9.282, 0.487 ], "form": ".", "ssZp": 4.023, "Dp": 4.522, "splay_angle": 19.830, "splay_distance": 3.617, "splay_ratio": 0.183, "d22": null, "d64": null, "eta": 165.312, "theta": -115.734, "eta_prime": 176.596, "theta_prime": -126.195, "eta_base": -150.462, "theta_base": -105.140, "v0": -2.649, "v1": -23.705, "v2": 39.659, "v3": -42.249, "v4": 28.199, "amplitude": 42.783, "phase_angle": 22.031, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.577, "filter_rmsd": 0.109, "frame": { "rmsd": 0.005, "origin": [ 1.458, 1.238, 5.727 ], "x_axis": [ -0.119, -0.060, 0.991 ], "y_axis": [ 0.634, -0.773, 0.029 ], "z_axis": [ 0.764, 0.631, 0.130 ], "quaternion": [ -0.244, 0.617, 0.232, 0.711 ] } }, { "index": 5, "index_chain": 5, "chain_name": "A", "nt_resnum": 5, "nt_name": "DA", "nt_code": "A", "nt_id": "///A/5", "linked_nts": [ "///A/4", "///A/6" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": 141.043, "beta": -171.043, "gamma": -174.426, "delta": 86.333, "epsilon": -143.423, "zeta": -70.321, "epsilon_zeta": -73.102, "bb_type": "BI", "chi": -166.331, "glyco_bond": "anti", "C5prime_xyz": [ -1.238, 8.540, 0.868 ], "P_xyz": [ -0.257, 10.473, -0.611 ], "form": "A", "ssZp": 4.544, "Dp": 4.692, "splay_angle": 22.160, "splay_distance": 3.524, "splay_ratio": 0.194, "d22": null, "d64": null, "eta": 159.918, "theta": -171.005, "eta_prime": 175.490, "theta_prime": -162.493, "eta_base": -144.313, "theta_base": -122.787, "v0": 1.945, "v1": -26.011, "v2": 38.502, "v3": -38.686, "v4": 23.172, "amplitude": 40.046, "phase_angle": 15.966, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "1c", "suiteness": 0.807, "filter_rmsd": 0.036, "frame": { "rmsd": 0.013, "origin": [ 2.329, 3.923, 7.988 ], "x_axis": [ -0.019, -0.538, 0.842 ], "y_axis": [ 0.756, -0.560, -0.340 ], "z_axis": [ 0.655, 0.630, 0.418 ], "quaternion": [ -0.458, 0.530, 0.103, 0.706 ] } }, { "index": 6, "index_chain": 6, "chain_name": "A", "nt_resnum": 6, "nt_name": "OMU", "nt_code": "u", "is_modified": true, "nt_id": "///A/6", "linked_nts": [ "///A/5", "///A/7" ], "nt_type": "RNA", "dbn": "(", "summary": "modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -65.827, "beta": 171.534, "gamma": 49.918, "delta": 76.368, "epsilon": -147.684, "zeta": -75.757, "epsilon_zeta": -71.927, "bb_type": "BI", "chi": -155.745, "glyco_bond": "anti", "C5prime_xyz": [ -1.492, 8.750, 0.250 ], "P_xyz": [ 1.057, 9.267, 0.240 ], "form": "A", "ssZp": 4.293, "Dp": 4.694, "splay_angle": 19.827, "splay_distance": 3.192, "splay_ratio": 0.175, "d22": null, "d64": null, "eta": 160.759, "theta": -150.318, "eta_prime": 178.222, "theta_prime": -150.255, "eta_base": -130.351, "theta_base": -133.895, "v0": 1.470, "v1": -27.391, "v2": 41.617, "v3": -42.015, "v4": 25.337, "amplitude": 43.455, "phase_angle": 16.727, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.881, "filter_rmsd": 0.070, "frame": { "rmsd": 0.048, "origin": [ 3.515, 5.196, 11.052 ], "x_axis": [ 0.380, -0.837, 0.393 ], "y_axis": [ 0.712, -0.006, -0.702 ], "z_axis": [ 0.590, 0.547, 0.594 ], "quaternion": [ 0.702, -0.445, 0.070, -0.552 ] } }, { "index": 7, "index_chain": 7, "chain_name": "A", "nt_resnum": 7, "nt_name": "DA", "nt_code": "A", "nt_id": "///A/7", "linked_nts": [ "///A/6", "///A/8" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -65.118, "beta": 171.452, "gamma": 49.134, "delta": 81.527, "epsilon": -160.090, "zeta": -72.060, "epsilon_zeta": -88.030, "bb_type": "BI", "chi": -158.090, "glyco_bond": "anti", "C5prime_xyz": [ -1.628, 8.723, 0.296 ], "P_xyz": [ 0.888, 9.369, 0.116 ], "form": "A", "ssZp": 4.413, "Dp": 4.654, "splay_angle": 23.187, "splay_distance": 3.692, "splay_ratio": 0.204, "d22": null, "d64": null, "eta": 162.388, "theta": -152.267, "eta_prime": 173.089, "theta_prime": -152.965, "eta_base": -157.091, "theta_base": -128.685, "v0": -1.168, "v1": -26.278, "v2": 41.826, "v3": -43.799, "v4": 28.610, "amplitude": 44.560, "phase_angle": 20.175, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.899, "filter_rmsd": 0.028, "frame": { "rmsd": 0.019, "origin": [ 4.367, 6.229, 13.950 ], "x_axis": [ 0.489, -0.866, -0.101 ], "y_axis": [ 0.596, 0.417, -0.686 ], "z_axis": [ 0.637, 0.275, 0.720 ], "quaternion": [ 0.810, -0.297, 0.228, -0.451 ] } }, { "index": 8, "index_chain": 8, "chain_name": "A", "nt_resnum": 8, "nt_name": "DC", "nt_code": "C", "nt_id": "///A/8", "linked_nts": [ "///A/7", "///A/9" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop", "alpha": -69.899, "beta": 170.319, "gamma": 60.943, "delta": 79.536, "epsilon": -163.702, "zeta": -68.077, "epsilon_zeta": -95.626, "bb_type": "BI", "chi": -162.640, "glyco_bond": "anti", "C5prime_xyz": [ -1.381, 8.796, 0.598 ], "P_xyz": [ 1.176, 9.295, 0.282 ], "form": "A", "ssZp": 4.519, "Dp": 4.644, "splay_angle": 26.881, "splay_distance": 4.215, "splay_ratio": 0.234, "d22": null, "d64": null, "eta": 171.009, "theta": -152.033, "eta_prime": -176.184, "theta_prime": -152.550, "eta_base": -137.300, "theta_base": -132.747, "v0": -0.410, "v1": -26.886, "v2": 41.925, "v3": -43.412, "v4": 28.031, "amplitude": 44.398, "phase_angle": 19.213, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.832, "filter_rmsd": 0.059, "frame": { "rmsd": 0.007, "origin": [ 6.067, 5.550, 17.157 ], "x_axis": [ 0.685, -0.555, -0.473 ], "y_axis": [ 0.341, 0.817, -0.465 ], "z_axis": [ 0.644, 0.157, 0.749 ], "quaternion": [ 0.901, -0.172, 0.310, -0.248 ] } }, { "index": 9, "index_chain": 9, "chain_name": "A", "nt_resnum": 9, "nt_name": "DG", "nt_code": "G", "nt_id": "///A/9", "linked_nts": [ "///A/8", "///A/10" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,internal-loop", "alpha": -75.466, "beta": -177.431, "gamma": 52.001, "delta": 80.344, "epsilon": -151.909, "zeta": -68.719, "epsilon_zeta": -83.191, "bb_type": "BI", "chi": -165.634, "glyco_bond": "anti", "C5prime_xyz": [ -1.463, 8.672, 0.888 ], "P_xyz": [ 1.089, 9.094, 1.299 ], "form": "A", "ssZp": 4.509, "Dp": 4.640, "splay_angle": 24.416, "splay_distance": 3.891, "splay_ratio": 0.217, "d22": null, "d64": null, "eta": 168.352, "theta": -144.644, "eta_prime": 178.481, "theta_prime": -141.780, "eta_base": -147.936, "theta_base": -113.644, "v0": 9.387, "v1": -36.261, "v2": 48.147, "v3": -44.486, "v4": 22.053, "amplitude": 48.623, "phase_angle": 8.025, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.779, "filter_rmsd": 0.012, "frame": { "rmsd": 0.012, "origin": [ 8.405, 4.521, 20.510 ], "x_axis": [ 0.605, -0.129, -0.786 ], "y_axis": [ -0.060, 0.977, -0.207 ], "z_axis": [ 0.794, 0.172, 0.583 ], "quaternion": [ 0.889, -0.106, 0.444, -0.020 ] } }, { "index": 10, "index_chain": 10, "chain_name": "A", "nt_resnum": 10, "nt_name": "DC", "nt_code": "C", "nt_id": "///A/10", "linked_nts": [ "///A/9", null ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C3'-endo,isolated-canonical,non-pair-contact,internal-loop", "alpha": -66.039, "beta": -177.243, "gamma": 49.861, "delta": 83.803, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -159.139, "glyco_bond": "anti", "C5prime_xyz": [ -1.331, 8.800, 0.409 ], "P_xyz": [ 1.255, 9.302, 0.690 ], "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": 0.391, "v1": -24.484, "v2": 37.503, "v3": -38.201, "v4": 24.160, "amplitude": 39.432, "phase_angle": 17.992, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.933, "filter_rmsd": 0.065, "frame": { "rmsd": 0.007, "origin": [ 11.946, 3.267, 21.526 ], "x_axis": [ 0.354, 0.447, -0.821 ], "y_axis": [ -0.331, 0.882, 0.337 ], "z_axis": [ 0.875, 0.153, 0.460 ], "quaternion": [ 0.821, 0.056, 0.516, 0.237 ] } }, { "index": 11, "index_chain": 1, "chain_name": "B", "nt_resnum": 1, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/1", "linked_nts": [ null, "///B/2" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,non-stack,isolated-canonical,internal-loop", "alpha": null, "beta": null, "gamma": 57.964, "delta": 86.874, "epsilon": -153.682, "zeta": -71.083, "epsilon_zeta": -82.599, "bb_type": "BI", "chi": -175.670, "glyco_bond": "anti", "C5prime_xyz": [ -1.362, 8.483, 1.532 ], "P_xyz": [ null, null, null ], "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": 6.726, "v1": -26.927, "v2": 35.576, "v3": -32.771, "v4": 16.671, "amplitude": 35.944, "phase_angle": 8.206, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.012, "frame": { "rmsd": 0.012, "origin": [ 11.584, 3.271, 21.621 ], "x_axis": [ 0.426, 0.457, -0.781 ], "y_axis": [ 0.264, -0.888, -0.376 ], "z_axis": [ -0.866, -0.046, -0.499 ], "quaternion": [ -0.098, 0.839, 0.215, -0.491 ] } }, { "index": 12, "index_chain": 2, "chain_name": "B", "nt_resnum": 2, "nt_name": "EXC", "nt_code": "?", "is_modified": true, "nt_id": "///B/2", "linked_nts": [ "///B/1", "///B/3" ], "nt_type": "DNA", "dbn": ".", "summary": "modified,~C3'-endo,BI,non-stack,internal-loop", "alpha": -70.052, "beta": 178.830, "gamma": 51.291, "delta": 85.333, "epsilon": -150.090, "zeta": -65.990, "epsilon_zeta": -84.100, "bb_type": "BI", "chi": null, "glyco_bond": "--", "C5prime_xyz": [ null, null, null ], "P_xyz": [ null, null, null ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": 167.594, "theta": -135.116, "eta_prime": -177.696, "theta_prime": -135.208, "eta_base": null, "theta_base": null, "v0": -1.919, "v1": -20.164, "v2": 33.399, "v3": -36.267, "v4": 23.522, "amplitude": 36.024, "phase_angle": 22.006, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.868, "filter_rmsd": null }, { "index": 13, "index_chain": 3, "chain_name": "B", "nt_resnum": 3, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/3", "linked_nts": [ "///B/2", "///B/4" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop", "alpha": -69.982, "beta": 171.884, "gamma": 54.013, "delta": 77.768, "epsilon": -161.336, "zeta": -69.109, "epsilon_zeta": -92.227, "bb_type": "BI", "chi": -169.193, "glyco_bond": "anti", "C5prime_xyz": [ -1.912, 8.801, 0.949 ], "P_xyz": [ 0.498, 9.717, 1.250 ], "form": "A", "ssZp": 4.532, "Dp": 4.558, "splay_angle": 24.230, "splay_distance": 3.920, "splay_ratio": 0.216, "d22": null, "d64": null, "eta": 162.550, "theta": -153.864, "eta_prime": 179.960, "theta_prime": -152.552, "eta_base": null, "theta_base": -126.662, "v0": -4.801, "v1": -25.494, "v2": 44.270, "v3": -47.843, "v4": 33.622, "amplitude": 48.474, "phase_angle": 24.039, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.920, "filter_rmsd": 0.011, "frame": { "rmsd": 0.011, "origin": [ 6.145, 5.834, 17.348 ], "x_axis": [ 0.534, -0.613, -0.582 ], "y_axis": [ -0.250, -0.773, 0.584 ], "z_axis": [ -0.807, -0.166, -0.566 ], "quaternion": [ 0.221, 0.847, -0.255, -0.410 ] } }, { "index": 14, "index_chain": 4, "chain_name": "B", "nt_resnum": 4, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/4", "linked_nts": [ "///B/3", "///B/5" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -69.242, "beta": -178.480, "gamma": 51.679, "delta": 77.913, "epsilon": -158.053, "zeta": -69.101, "epsilon_zeta": -88.952, "bb_type": "BI", "chi": -160.178, "glyco_bond": "anti", "C5prime_xyz": [ -1.593, 8.800, 0.502 ], "P_xyz": [ 0.939, 9.474, 0.752 ], "form": "A", "ssZp": 4.445, "Dp": 4.632, "splay_angle": 22.364, "splay_distance": 3.532, "splay_ratio": 0.197, "d22": null, "d64": null, "eta": 169.808, "theta": -152.086, "eta_prime": 179.814, "theta_prime": -148.812, "eta_base": -142.547, "theta_base": -120.157, "v0": 0.271, "v1": -28.716, "v2": 44.205, "v3": -45.728, "v4": 28.693, "amplitude": 46.605, "phase_angle": 18.467, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.843, "filter_rmsd": 0.104, "frame": { "rmsd": 0.007, "origin": [ 4.439, 6.249, 13.843 ], "x_axis": [ 0.340, -0.924, -0.177 ], "y_axis": [ -0.536, -0.345, 0.771 ], "z_axis": [ -0.773, -0.167, -0.612 ], "quaternion": [ 0.309, 0.758, -0.481, -0.313 ] } }, { "index": 15, "index_chain": 5, "chain_name": "B", "nt_resnum": 5, "nt_name": "DA", "nt_code": "A", "nt_id": "///B/5", "linked_nts": [ "///B/4", "///B/6" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -65.128, "beta": 175.208, "gamma": 53.856, "delta": 84.517, "epsilon": -154.133, "zeta": -79.288, "epsilon_zeta": -74.845, "bb_type": "BI", "chi": -160.920, "glyco_bond": "anti", "C5prime_xyz": [ -1.563, 8.686, 0.522 ], "P_xyz": [ 0.953, 9.202, 0.719 ], "form": "A", "ssZp": 4.368, "Dp": 4.555, "splay_angle": 21.186, "splay_distance": 3.374, "splay_ratio": 0.185, "d22": null, "d64": null, "eta": 172.453, "theta": -152.983, "eta_prime": -174.244, "theta_prime": -153.840, "eta_base": -134.072, "theta_base": -138.336, "v0": 0.765, "v1": -27.334, "v2": 41.688, "v3": -42.758, "v4": 26.590, "amplitude": 43.789, "phase_angle": 17.822, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.896, "filter_rmsd": 0.034, "frame": { "rmsd": 0.013, "origin": [ 3.240, 5.041, 10.748 ], "x_axis": [ 0.116, -0.931, 0.346 ], "y_axis": [ -0.703, 0.169, 0.691 ], "z_axis": [ -0.701, -0.323, -0.635 ], "quaternion": [ -0.403, -0.629, 0.650, 0.141 ] } }, { "index": 16, "index_chain": 6, "chain_name": "B", "nt_resnum": 6, "nt_name": "OMU", "nt_code": "u", "is_modified": true, "nt_id": "///B/6", "linked_nts": [ "///B/5", "///B/7" ], "nt_type": "RNA", "dbn": ")", "summary": "modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -70.312, "beta": 172.874, "gamma": 54.191, "delta": 76.196, "epsilon": -147.125, "zeta": -72.113, "epsilon_zeta": -75.012, "bb_type": "BI", "chi": -155.993, "glyco_bond": "anti", "C5prime_xyz": [ -1.396, 8.765, 0.238 ], "P_xyz": [ 1.173, 9.247, 0.133 ], "form": "A", "ssZp": 4.299, "Dp": 4.714, "splay_angle": 21.558, "splay_distance": 3.492, "splay_ratio": 0.190, "d22": null, "d64": null, "eta": 164.288, "theta": -146.993, "eta_prime": 172.501, "theta_prime": -147.743, "eta_base": -159.761, "theta_base": -129.122, "v0": 2.098, "v1": -27.864, "v2": 41.605, "v3": -41.665, "v4": 24.781, "amplitude": 43.261, "phase_angle": 15.904, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.876, "filter_rmsd": 0.076, "frame": { "rmsd": 0.046, "origin": [ 2.300, 3.866, 7.728 ], "x_axis": [ -0.159, -0.721, 0.675 ], "y_axis": [ -0.778, 0.512, 0.364 ], "z_axis": [ -0.608, -0.467, -0.642 ], "quaternion": [ -0.422, -0.493, 0.761, -0.034 ] } }, { "index": 17, "index_chain": 7, "chain_name": "B", "nt_resnum": 7, "nt_name": "DA", "nt_code": "A", "nt_id": "///B/7", "linked_nts": [ "///B/6", "///B/8" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -72.008, "beta": 171.485, "gamma": 56.525, "delta": 75.135, "epsilon": -150.429, "zeta": -68.235, "epsilon_zeta": -82.194, "bb_type": "BI", "chi": -161.450, "glyco_bond": "anti", "C5prime_xyz": [ -1.536, 8.776, 0.546 ], "P_xyz": [ 0.973, 9.448, 0.308 ], "form": "A", "ssZp": 4.490, "Dp": 4.760, "splay_angle": 23.322, "splay_distance": 3.724, "splay_ratio": 0.205, "d22": null, "d64": null, "eta": 163.583, "theta": -146.534, "eta_prime": 174.071, "theta_prime": -143.466, "eta_base": -153.532, "theta_base": -107.624, "v0": 2.860, "v1": -31.573, "v2": 46.096, "v3": -45.816, "v4": 27.450, "amplitude": 47.792, "phase_angle": 15.308, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.832, "filter_rmsd": 0.033, "frame": { "rmsd": 0.010, "origin": [ 1.422, 1.044, 5.869 ], "x_axis": [ -0.333, -0.272, 0.903 ], "y_axis": [ -0.705, 0.708, -0.046 ], "z_axis": [ -0.627, -0.651, -0.428 ], "quaternion": [ -0.487, -0.311, 0.786, -0.222 ] } }, { "index": 18, "index_chain": 8, "chain_name": "B", "nt_resnum": 8, "nt_name": "DC", "nt_code": "C", "nt_id": "///B/8", "linked_nts": [ "///B/7", "///B/9" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop", "alpha": -59.690, "beta": 167.718, "gamma": 55.857, "delta": 84.677, "epsilon": -171.775, "zeta": -71.661, "epsilon_zeta": -100.114, "bb_type": "BI", "chi": -157.446, "glyco_bond": "anti", "C5prime_xyz": [ -1.533, 8.845, 0.337 ], "P_xyz": [ 1.026, 9.345, 0.123 ], "form": "A", "ssZp": 4.283, "Dp": 4.415, "splay_angle": 22.743, "splay_distance": 4.000, "splay_ratio": 0.205, "d22": null, "d64": null, "eta": 175.209, "theta": -129.512, "eta_prime": -165.916, "theta_prime": -141.449, "eta_base": -115.587, "theta_base": -126.304, "v0": 1.678, "v1": -25.996, "v2": 38.246, "v3": -38.670, "v4": 23.843, "amplitude": 39.886, "phase_angle": 16.488, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.849, "filter_rmsd": 0.061, "frame": { "rmsd": 0.010, "origin": [ -0.460, -2.046, 6.754 ], "x_axis": [ -0.631, 0.258, 0.732 ], "y_axis": [ -0.482, 0.608, -0.631 ], "z_axis": [ -0.607, -0.751, -0.259 ], "quaternion": [ -0.423, -0.071, 0.790, -0.437 ] } }, { "index": 19, "index_chain": 9, "chain_name": "B", "nt_resnum": 9, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/9", "linked_nts": [ "///B/8", "///B/10" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,internal-loop", "alpha": 127.750, "beta": -169.580, "gamma": -160.981, "delta": 96.117, "epsilon": -145.682, "zeta": -65.904, "epsilon_zeta": -79.778, "bb_type": "BI", "chi": -173.519, "glyco_bond": "anti", "C5prime_xyz": [ -1.409, 8.198, 1.509 ], "P_xyz": [ -0.038, 10.263, 0.975 ], "form": "A", "ssZp": 4.295, "Dp": 4.440, "splay_angle": 22.477, "splay_distance": 3.649, "splay_ratio": 0.199, "d22": null, "d64": null, "eta": 171.109, "theta": -163.210, "eta_prime": -176.307, "theta_prime": -154.588, "eta_base": -140.750, "theta_base": -119.592, "v0": 11.374, "v1": -29.643, "v2": 35.366, "v3": -30.767, "v4": 12.184, "amplitude": 35.371, "phase_angle": 1.018, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33t", "cluster": "1c", "suiteness": 0.154, "filter_rmsd": 0.011, "frame": { "rmsd": 0.011, "origin": [ -2.193, -5.490, 7.815 ], "x_axis": [ -0.645, 0.629, 0.434 ], "y_axis": [ -0.163, 0.442, -0.882 ], "z_axis": [ -0.747, -0.640, -0.183 ], "quaternion": [ -0.392, 0.155, 0.753, -0.505 ] } }, { "index": 20, "index_chain": 10, "chain_name": "B", "nt_resnum": 10, "nt_name": "DC", "nt_code": "C", "nt_id": "///B/10", "linked_nts": [ "///B/9", null ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,isolated-canonical,non-pair-contact,internal-loop", "alpha": -73.514, "beta": -178.567, "gamma": 54.408, "delta": 90.803, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -152.904, "glyco_bond": "anti", "C5prime_xyz": [ -1.579, 8.913, 0.039 ], "P_xyz": [ 0.920, 9.482, 0.572 ], "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": -7.137, "v1": -15.231, "v2": 30.468, "v3": -35.022, "v4": 26.450, "amplitude": 35.059, "phase_angle": 29.650, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.381, "filter_rmsd": 0.059, "frame": { "rmsd": 0.010, "origin": [ -5.009, -7.516, 8.948 ], "x_axis": [ -0.577, 0.787, -0.220 ], "y_axis": [ 0.239, -0.095, -0.966 ], "z_axis": [ -0.781, -0.610, -0.133 ], "quaternion": [ -0.221, 0.403, 0.635, -0.620 ] } } ], "num_hbonds": 30, "hbonds": [ { "index": 1, "atom1_serNum": 14, "atom2_serNum": 435, "donAcc_type": "standard", "distance": 2.960, "atom1_id": "///A/1/O6", "atom2_id": "///B/10/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 15, "atom2_serNum": 22, "donAcc_type": "unknown", "distance": 3.347, "atom1_id": "///A/1/N1", "atom2_id": "///A/2/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 15, "atom2_serNum": 433, "donAcc_type": "standard", "distance": 2.929, "atom1_id": "///A/1/N1", "atom2_id": "///B/10/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 17, "atom2_serNum": 432, "donAcc_type": "standard", "distance": 2.867, "atom1_id": "///A/1/N2", "atom2_id": "///B/10/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 22, "atom2_serNum": 67, "donAcc_type": "unknown", "distance": 3.315, "atom1_id": "///A/2/N2", "atom2_id": "///A/3/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 22, "atom2_serNum": 414, "donAcc_type": "unknown", "distance": 2.933, "atom1_id": "///A/2/N2", "atom2_id": "///B/9/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 27, "atom2_serNum": 413, "donAcc_type": "unknown", "distance": 2.948, "atom1_id": "///A/2/N7", "atom2_id": "///B/9/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 8, "atom1_serNum": 39, "atom2_serNum": 416, "donAcc_type": "standard", "distance": 2.770, "atom1_id": "///A/2/O18", "atom2_id": "///B/9/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 9, "atom1_serNum": 70, "atom2_serNum": 394, "donAcc_type": "standard", "distance": 2.946, "atom1_id": "///A/3/O6", "atom2_id": "///B/8/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 71, "atom2_serNum": 392, "donAcc_type": "standard", "distance": 2.878, "atom1_id": "///A/3/N1", "atom2_id": "///B/8/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 73, "atom2_serNum": 391, "donAcc_type": "standard", "distance": 2.793, "atom1_id": "///A/3/N2", "atom2_id": "///B/8/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 12, "atom1_serNum": 90, "atom2_serNum": 374, "donAcc_type": "standard", "distance": 2.828, "atom1_id": "///A/4/N3", "atom2_id": "///B/7/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 13, "atom1_serNum": 92, "atom2_serNum": 373, "donAcc_type": "standard", "distance": 3.009, "atom1_id": "///A/4/O4", "atom2_id": "///B/7/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 14, "atom1_serNum": 112, "atom2_serNum": 343, "donAcc_type": "standard", "distance": 2.943, "atom1_id": "///A/5/N6", "atom2_id": "///B/6/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 113, "atom2_serNum": 338, "donAcc_type": "standard", "distance": 2.831, "atom1_id": "///A/5/N1", "atom2_id": "///B/6/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 16, "atom1_serNum": 119, "atom2_serNum": 332, "donAcc_type": "standard", "distance": 2.823, "atom1_id": "///A/6/N3", "atom2_id": "///B/5/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 17, "atom1_serNum": 124, "atom2_serNum": 331, "donAcc_type": "standard", "distance": 3.408, "atom1_id": "///A/6/O4", "atom2_id": "///B/5/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 154, "atom2_serNum": 311, "donAcc_type": "standard", "distance": 3.043, "atom1_id": "///A/7/N6", "atom2_id": "///B/4/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 19, "atom1_serNum": 155, "atom2_serNum": 309, "donAcc_type": "standard", "distance": 2.835, "atom1_id": "///A/7/N1", "atom2_id": "///B/4/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 172, "atom2_serNum": 292, "donAcc_type": "standard", "distance": 2.785, "atom1_id": "///A/8/O2", "atom2_id": "///B/3/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 21, "atom1_serNum": 173, "atom2_serNum": 290, "donAcc_type": "standard", "distance": 2.851, "atom1_id": "///A/8/N3", "atom2_id": "///B/3/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 22, "atom1_serNum": 175, "atom2_serNum": 289, "donAcc_type": "standard", "distance": 2.943, "atom1_id": "///A/8/N4", "atom2_id": "///B/3/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 23, "atom1_serNum": 194, "atom2_serNum": 246, "donAcc_type": "unknown", "distance": 2.847, "atom1_id": "///A/9/O6", "atom2_id": "///B/2/N7", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 24, "atom1_serNum": 195, "atom2_serNum": 241, "donAcc_type": "unknown", "distance": 2.839, "atom1_id": "///A/9/N1", "atom2_id": "///B/2/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 25, "atom1_serNum": 197, "atom2_serNum": 258, "donAcc_type": "standard", "distance": 2.738, "atom1_id": "///A/9/N2", "atom2_id": "///B/2/O18", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 26, "atom1_serNum": 213, "atom2_serNum": 236, "donAcc_type": "standard", "distance": 2.783, "atom1_id": "///A/10/O2", "atom2_id": "///B/1/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 27, "atom1_serNum": 214, "atom2_serNum": 234, "donAcc_type": "standard", "distance": 2.908, "atom1_id": "///A/10/N3", "atom2_id": "///B/1/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 28, "atom1_serNum": 216, "atom2_serNum": 233, "donAcc_type": "standard", "distance": 2.893, "atom1_id": "///A/10/N4", "atom2_id": "///B/1/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 29, "atom1_serNum": 234, "atom2_serNum": 241, "donAcc_type": "unknown", "distance": 3.371, "atom1_id": "///B/1/N1", "atom2_id": "///B/2/N2", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 30, "atom1_serNum": 241, "atom2_serNum": 286, "donAcc_type": "unknown", "distance": 3.210, "atom1_id": "///B/2/N2", "atom2_id": "///B/3/N7", "atom_pair": "N:N", "residue_pair": "nt:nt" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "3ot0", "num_naChains": 2, "naChains": "A=10,B=10", "num_atoms": 519, "num_waters": 83, "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": 13, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 3, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 4, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 5, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 6, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 7, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 8, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 9, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 10, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 11, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 12, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 13, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }