{ "num_pairs": 10, "pairs": [ { "index": 1, "nt1": "///B/2", "nt2": "///C/61", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -95.376, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 53.770, "chi2": -150.138, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 54.417, "C1C1_dist": 10.698, "N1N9_dist": 8.980, "C6C8_dist": 9.926, "CNNC_torsion": -10.166, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.91],N1(imino)-N3[2.93],N2(amino)-O2(carbonyl)[2.82]", "interBase_angle": 3.694, "planarity": 0.059, "simple_Shear": -0.194, "simple_Stretch": -0.100, "simple_Buckle": 1.987, "simple_Propeller": -3.114, "bp_simpleParams": [ -0.194, -0.100, 0.004, 1.987, -3.114, 0.020 ], "bp_params": [ -0.192, -0.103, 0.004, 2.034, -3.084, 0.020 ], "frame": { "rmsd": null, "origin": [ 200.242, 99.570, 94.930 ], "x_axis": [ 0.959, -0.252, -0.128 ], "y_axis": [ 0.267, 0.957, 0.113 ], "z_axis": [ 0.094, -0.142, 0.985 ], "quaternion": [ 0.988, 0.065, 0.056, -0.131 ] } }, { "index": 2, "nt1": "///B/3", "nt2": "///C/60", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -91.904, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 56.071, "chi2": -109.372, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 53.182, "C1C1_dist": 10.657, "N1N9_dist": 8.950, "C6C8_dist": 9.873, "CNNC_torsion": -0.690, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.87],N3-N1(imino)[2.95],N4(amino)-O6(carbonyl)[2.89]", "interBase_angle": 16.494, "planarity": 0.176, "simple_Shear": 0.259, "simple_Stretch": -0.103, "simple_Buckle": 12.519, "simple_Propeller": -10.739, "bp_simpleParams": [ 0.259, -0.103, -0.502, 12.519, -10.739, 0.386 ], "bp_params": [ 0.257, -0.107, -0.502, 12.359, -10.923, 0.385 ], "frame": { "rmsd": null, "origin": [ 200.821, 98.770, 97.824 ], "x_axis": [ 0.974, 0.207, -0.088 ], "y_axis": [ -0.179, 0.951, 0.253 ], "z_axis": [ 0.136, -0.231, 0.963 ], "quaternion": [ 0.986, 0.123, 0.057, 0.098 ] } }, { "index": 3, "nt1": "///B/4", "nt2": "///C/59", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -127.723, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 50.928, "chi2": -115.071, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 53.368, "C1C1_dist": 10.735, "N1N9_dist": 8.933, "C6C8_dist": 9.816, "CNNC_torsion": -4.904, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.84],N1(imino)-N3[2.83],N2(amino)-O2(carbonyl)[2.77]", "interBase_angle": 9.266, "planarity": 0.103, "simple_Shear": -0.242, "simple_Stretch": -0.196, "simple_Buckle": -6.840, "simple_Propeller": -6.252, "bp_simpleParams": [ -0.242, -0.196, -0.169, -6.840, -6.252, -1.076 ], "bp_params": [ -0.239, -0.200, -0.169, -6.731, -6.369, -1.076 ], "frame": { "rmsd": null, "origin": [ 200.736, 97.610, 101.481 ], "x_axis": [ 0.633, 0.763, -0.132 ], "y_axis": [ -0.743, 0.646, 0.177 ], "z_axis": [ 0.220, -0.014, 0.975 ], "quaternion": [ 0.902, 0.053, 0.097, 0.417 ] } }, { "index": 4, "nt1": "///B/5", "nt2": "///C/58", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -100.249, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 54.385, "chi2": -132.255, "conf2": "anti", "pucker2": "----", "lambda2": 55.532, "C1C1_dist": 10.495, "N1N9_dist": 8.809, "C6C8_dist": 9.777, "CNNC_torsion": -3.173, "hbonds_num": 2, "hbonds_desc": "N3(imino)-N1[2.76],O4(carbonyl)-N6(amino)[2.88]", "interBase_angle": 7.486, "planarity": 0.098, "simple_Shear": -0.095, "simple_Stretch": -0.183, "simple_Buckle": 6.398, "simple_Propeller": -3.887, "bp_simpleParams": [ -0.095, -0.183, -0.007, 6.398, -3.887, -0.288 ], "bp_params": [ -0.092, -0.185, -0.007, 6.454, -3.794, -0.288 ], "frame": { "rmsd": null, "origin": [ 201.951, 97.863, 104.370 ], "x_axis": [ 0.184, 0.973, -0.137 ], "y_axis": [ -0.954, 0.211, 0.214 ], "z_axis": [ 0.238, 0.091, 0.967 ], "quaternion": [ 0.768, 0.040, 0.122, 0.627 ] } }, { "index": 5, "nt1": "///B/6", "nt2": "///C/57", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -167.941, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 54.367, "chi2": -118.927, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 53.782, "C1C1_dist": 10.698, "N1N9_dist": 8.963, "C6C8_dist": 9.923, "CNNC_torsion": -20.316, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[3.00],N1(imino)-N3[2.89],N2(amino)-O2(carbonyl)[2.74]", "interBase_angle": 14.028, "planarity": 0.187, "simple_Shear": -0.113, "simple_Stretch": -0.109, "simple_Buckle": -2.611, "simple_Propeller": -13.783, "bp_simpleParams": [ -0.113, -0.109, 0.235, -2.611, -13.783, 1.120 ], "bp_params": [ -0.112, -0.110, 0.235, -2.531, -13.798, 1.128 ], "frame": { "rmsd": null, "origin": [ 203.122, 97.074, 107.803 ], "x_axis": [ -0.372, 0.928, 0.024 ], "y_axis": [ -0.919, -0.372, 0.133 ], "z_axis": [ 0.132, 0.027, 0.991 ], "quaternion": [ 0.558, 0.047, 0.049, 0.827 ] } }, { "index": 6, "nt1": "///B/7", "nt2": "///C/56", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -155.804, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 52.015, "chi2": -113.631, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 52.540, "C1C1_dist": 10.697, "N1N9_dist": 8.885, "C6C8_dist": 9.762, "CNNC_torsion": -13.808, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.84],N1(imino)-N3[2.83],N2(amino)-O2(carbonyl)[2.83]", "interBase_angle": 17.365, "planarity": 0.206, "simple_Shear": -0.291, "simple_Stretch": -0.219, "simple_Buckle": -10.137, "simple_Propeller": -14.098, "bp_simpleParams": [ -0.291, -0.219, 0.035, -10.137, -14.098, -1.876 ], "bp_params": [ -0.287, -0.224, 0.035, -9.851, -14.300, -1.884 ], "frame": { "rmsd": null, "origin": [ 204.693, 97.750, 111.071 ], "x_axis": [ -0.846, 0.530, 0.052 ], "y_axis": [ -0.520, -0.844, 0.131 ], "z_axis": [ 0.113, 0.084, 0.990 ], "quaternion": [ 0.274, 0.043, 0.056, 0.959 ] } }, { "index": 7, "nt1": "///B/8", "nt2": "///C/55", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -117.477, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 52.180, "chi2": -152.772, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 52.028, "C1C1_dist": 10.722, "N1N9_dist": 8.905, "C6C8_dist": 9.794, "CNNC_torsion": -10.486, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.77],N1(imino)-N3[2.79],N2(amino)-O2(carbonyl)[2.78]", "interBase_angle": 15.346, "planarity": 0.195, "simple_Shear": -0.025, "simple_Stretch": -0.235, "simple_Buckle": -0.347, "simple_Propeller": -15.342, "bp_simpleParams": [ -0.025, -0.235, -0.130, -0.347, -15.342, -0.912 ], "bp_params": [ -0.026, -0.234, -0.130, -0.411, -15.340, -0.920 ], "frame": { "rmsd": null, "origin": [ 204.823, 98.327, 114.236 ], "x_axis": [ -0.997, -0.068, -0.028 ], "y_axis": [ 0.063, -0.987, 0.148 ], "z_axis": [ -0.038, 0.145, 0.989 ], "quaternion": [ -0.033, -0.017, 0.073, 0.997 ] } }, { "index": 8, "nt1": "///B/9", "nt2": "///C/54", "bp": "c-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -133.486, "conf1": "anti", "pucker1": "----", "lambda1": 53.248, "chi2": -172.242, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 52.621, "C1C1_dist": 10.739, "N1N9_dist": 8.998, "C6C8_dist": 9.933, "CNNC_torsion": -14.279, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[3.02],N3-N1(imino)[2.87],N4(amino)-O6(carbonyl)[2.72]", "interBase_angle": 17.106, "planarity": 0.255, "simple_Shear": 0.173, "simple_Stretch": -0.142, "simple_Buckle": -2.186, "simple_Propeller": -16.965, "bp_simpleParams": [ 0.173, -0.142, 0.137, -2.186, -16.965, -2.307 ], "bp_params": [ 0.171, -0.145, 0.137, -2.437, -16.931, -2.332 ], "frame": { "rmsd": null, "origin": [ 203.571, 99.344, 117.337 ], "x_axis": [ -0.752, -0.658, 0.047 ], "y_axis": [ 0.657, -0.742, 0.132 ], "z_axis": [ -0.051, 0.130, 0.990 ], "quaternion": [ -0.352, -0.001, 0.070, 0.933 ] } }, { "index": 9, "nt1": "///B/10", "nt2": "///C/53", "bp": "G-c", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -118.254, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 51.401, "chi2": -115.478, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 50.910, "C1C1_dist": 10.870, "N1N9_dist": 9.050, "C6C8_dist": 9.950, "CNNC_torsion": 0.269, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.80],N1(imino)-N3[2.92],N2(amino)-O2(carbonyl)[2.88]", "interBase_angle": 1.756, "planarity": 0.237, "simple_Shear": -0.195, "simple_Stretch": -0.113, "simple_Buckle": -1.219, "simple_Propeller": -1.264, "bp_simpleParams": [ -0.195, -0.113, -0.152, -1.219, -1.264, -2.074 ], "bp_params": [ -0.193, -0.116, -0.152, -1.200, -1.282, -2.074 ], "frame": { "rmsd": null, "origin": [ 203.339, 101.215, 120.558 ], "x_axis": [ -0.446, -0.889, 0.105 ], "y_axis": [ 0.894, -0.438, 0.094 ], "z_axis": [ -0.037, 0.136, 0.990 ], "quaternion": [ 0.526, -0.020, -0.068, -0.848 ] } }, { "index": 10, "nt1": "///B/11", "nt2": "///C/52", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -115.159, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 55.924, "chi2": -153.804, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 57.664, "C1C1_dist": 10.193, "N1N9_dist": 8.583, "C6C8_dist": 9.641, "CNNC_torsion": -6.951, "hbonds_num": 2, "hbonds_desc": "N3(imino)-N1[2.63],O4(carbonyl)-N6(amino)[3.01]", "interBase_angle": 19.010, "planarity": 0.248, "simple_Shear": -0.079, "simple_Stretch": -0.243, "simple_Buckle": 13.341, "simple_Propeller": -13.543, "bp_simpleParams": [ -0.079, -0.243, -0.185, 13.341, -13.543, 5.317 ], "bp_params": [ -0.074, -0.245, -0.185, 13.615, -13.268, 5.315 ], "frame": { "rmsd": null, "origin": [ 202.548, 100.956, 123.677 ], "x_axis": [ 0.027, -1.000, 0.008 ], "y_axis": [ 0.999, 0.028, 0.030 ], "z_axis": [ -0.031, 0.007, 1.000 ], "quaternion": [ 0.717, 0.008, -0.013, -0.697 ] } } ], "num_helices": 1, "helices": [ { "index": 1, "num_stems": 1, "strand1": "GCGTGGGcGT", "strand2": "CGCACCCGcA", "bp_type": "||||||||||", "helix_form": "BBBB..B..", "helical_rise": 3.239, "helical_rise_std": 0.498, "helical_radius": 10.028, "helical_radius_std": 0.503, "helical_axis": [ 0.048, -0.004, 0.999 ], "point1": [ 201.828, 98.745, 95.113 ], "point2": [ 203.239, 98.623, 124.257 ], "num_pairs": 10, "pairs": [ { "index": 1, "nt1": "///B/2", "nt2": "///C/61", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.192, -0.103, 0.004, 2.034, -3.084, 0.020 ], "step_params": [ 0.242, -0.231, 3.039, 5.104, 2.659, 26.550 ], "heli_params": [ -1.117, 0.684, 2.995, 5.705, -10.951, 27.155 ], "bp2_params": [ 0.257, -0.107, -0.502, 12.359, -10.923, 0.385 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.039, "simple_Twist": 24.398, "simple_hRise": 2.985, "simple_hTwist": 25.057 }, { "index": 2, "nt1": "///B/3", "nt2": "///C/60", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.257, -0.107, -0.502, 12.359, -10.923, 0.385 ], "step_params": [ -1.004, -0.223, 3.697, -8.335, 10.457, 36.906 ], "heli_params": [ -1.782, 0.342, 3.639, 15.892, 12.667, 39.174 ], "bp2_params": [ -0.239, -0.200, -0.169, -6.731, -6.369, -1.076 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.697, "simple_Twist": 39.005, "simple_hRise": 3.653, "simple_hTwist": 41.149 }, { "index": 3, "nt1": "///B/4", "nt2": "///C/59", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.239, -0.200, -0.169, -6.731, -6.369, -1.076 ], "step_params": [ 0.349, -0.408, 3.098, -1.696, 5.906, 28.072 ], "heli_params": [ -2.059, -1.060, 2.927, 11.993, 3.445, 28.724 ], "bp2_params": [ -0.092, -0.185, -0.007, 6.454, -3.794, -0.288 ], "groove_widths": [ 14.200, null, 19.489, null ], "simple_Rise": 3.098, "simple_Twist": 27.650, "simple_hRise": 2.923, "simple_hTwist": 28.312 }, { "index": 4, "nt1": "///B/5", "nt2": "///C/58", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.092, -0.185, -0.007, 6.454, -3.794, -0.288 ], "step_params": [ -1.041, -0.427, 3.538, -6.469, -3.129, 33.667 ], "heli_params": [ -0.176, 0.633, 3.692, -5.327, 11.013, 34.404 ], "bp2_params": [ -0.112, -0.110, 0.235, -2.531, -13.798, 1.128 ], "groove_widths": [ 14.305, 14.039, 16.174, 15.308 ], "simple_Rise": 3.538, "simple_Twist": 33.621, "simple_hRise": 3.692, "simple_hTwist": 34.359 }, { "index": 5, "nt1": "///B/6", "nt2": "///C/57", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.112, -0.110, 0.235, -2.531, -13.798, 1.128 ], "step_params": [ -0.370, -1.199, 3.469, 1.231, 3.164, 35.978 ], "heli_params": [ -2.400, 0.777, 3.341, 5.109, -1.987, 36.133 ], "bp2_params": [ -0.287, -0.224, 0.035, -9.851, -14.300, -1.884 ], "groove_widths": [ 13.350, 13.060, 18.855, 18.248 ], "simple_Rise": 3.469, "simple_Twist": 36.630, "simple_hRise": 3.344, "simple_hTwist": 36.782 }, { "index": 6, "nt1": "///B/7", "nt2": "///C/56", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.287, -0.224, 0.035, -9.851, -14.300, -1.884 ], "step_params": [ 0.043, -0.205, 3.213, 1.345, 9.269, 35.083 ], "heli_params": [ -1.597, 0.115, 3.061, 15.047, -2.183, 36.274 ], "bp2_params": [ -0.026, -0.234, -0.130, -0.411, -15.340, -0.920 ], "groove_widths": [ 12.653, 12.377, 16.740, 16.295 ], "simple_Rise": 3.213, "simple_Twist": 34.118, "simple_hRise": 3.054, "simple_hTwist": 35.343 }, { "index": 7, "nt1": "///B/8", "nt2": "///C/55", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.026, -0.234, -0.130, -0.411, -15.340, -0.920 ], "step_params": [ 0.803, -0.957, 3.264, -0.524, 1.042, 37.484 ], "heli_params": [ -1.624, -1.317, 3.226, 1.621, 0.815, 37.502 ], "bp2_params": [ 0.171, -0.145, 0.137, -2.437, -16.931, -2.332 ], "groove_widths": [ 13.312, null, 16.875, null ], "simple_Rise": 3.264, "simple_Twist": 36.457, "simple_hRise": 3.225, "simple_hTwist": 36.475 }, { "index": 8, "nt1": "///B/9", "nt2": "///C/54", "bp": "c-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.171, -0.145, 0.137, -2.437, -16.931, -2.332 ], "step_params": [ -1.081, -0.935, 3.448, -0.449, -0.738, 22.350 ], "heli_params": [ -2.119, 2.608, 3.497, -1.903, 1.158, 22.366 ], "bp2_params": [ -0.193, -0.116, -0.152, -1.200, -1.282, -2.074 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.448, "simple_Twist": 23.988, "simple_hRise": 3.494, "simple_hTwist": 24.004 }, { "index": 9, "nt1": "///B/10", "nt2": "///C/53", "bp": "G-c", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.193, -0.116, -0.152, -1.200, -1.282, -2.074 ], "step_params": [ 0.618, -0.566, 3.118, -1.969, 7.139, 27.824 ], "heli_params": [ -2.620, -1.651, 2.838, 14.523, 4.006, 28.774 ], "bp2_params": [ -0.074, -0.245, -0.185, 13.615, -13.268, 5.315 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.118, "simple_Twist": 27.954, "simple_hRise": 2.840, "simple_hTwist": 28.900 }, { "index": 10, "nt1": "///B/11", "nt2": "///C/52", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_stems": 1, "stems": [ { "index": 1, "helix_index": 1, "strand1": "GCGTGGGcGT", "strand2": "CGCACCCGcA", "bp_type": "||||||||||", "helix_form": "BBBB..B..", "helical_rise": 3.239, "helical_rise_std": 0.498, "helical_radius": 10.028, "helical_radius_std": 0.503, "helical_axis": [ 0.048, -0.004, 0.999 ], "point1": [ 201.828, 98.745, 95.113 ], "point2": [ 203.239, 98.623, 124.257 ], "num_pairs": 10, "pairs": [ { "index": 1, "nt1": "///B/2", "nt2": "///C/61", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.192, -0.103, 0.004, 2.034, -3.084, 0.020 ], "step_params": [ 0.242, -0.231, 3.039, 5.104, 2.659, 26.550 ], "heli_params": [ -1.117, 0.684, 2.995, 5.705, -10.951, 27.155 ], "bp2_params": [ 0.257, -0.107, -0.502, 12.359, -10.923, 0.385 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.039, "simple_Twist": 24.398, "simple_hRise": 2.985, "simple_hTwist": 25.057 }, { "index": 2, "nt1": "///B/3", "nt2": "///C/60", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.257, -0.107, -0.502, 12.359, -10.923, 0.385 ], "step_params": [ -1.004, -0.223, 3.697, -8.335, 10.457, 36.906 ], "heli_params": [ -1.782, 0.342, 3.639, 15.892, 12.667, 39.174 ], "bp2_params": [ -0.239, -0.200, -0.169, -6.731, -6.369, -1.076 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.697, "simple_Twist": 39.005, "simple_hRise": 3.653, "simple_hTwist": 41.149 }, { "index": 3, "nt1": "///B/4", "nt2": "///C/59", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.239, -0.200, -0.169, -6.731, -6.369, -1.076 ], "step_params": [ 0.349, -0.408, 3.098, -1.696, 5.906, 28.072 ], "heli_params": [ -2.059, -1.060, 2.927, 11.993, 3.445, 28.724 ], "bp2_params": [ -0.092, -0.185, -0.007, 6.454, -3.794, -0.288 ], "groove_widths": [ 14.200, null, 19.489, null ], "simple_Rise": 3.098, "simple_Twist": 27.650, "simple_hRise": 2.923, "simple_hTwist": 28.312 }, { "index": 4, "nt1": "///B/5", "nt2": "///C/58", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.092, -0.185, -0.007, 6.454, -3.794, -0.288 ], "step_params": [ -1.041, -0.427, 3.538, -6.469, -3.129, 33.667 ], "heli_params": [ -0.176, 0.633, 3.692, -5.327, 11.013, 34.404 ], "bp2_params": [ -0.112, -0.110, 0.235, -2.531, -13.798, 1.128 ], "groove_widths": [ 14.305, 14.039, 16.174, 15.308 ], "simple_Rise": 3.538, "simple_Twist": 33.621, "simple_hRise": 3.692, "simple_hTwist": 34.359 }, { "index": 5, "nt1": "///B/6", "nt2": "///C/57", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.112, -0.110, 0.235, -2.531, -13.798, 1.128 ], "step_params": [ -0.370, -1.199, 3.469, 1.231, 3.164, 35.978 ], "heli_params": [ -2.400, 0.777, 3.341, 5.109, -1.987, 36.133 ], "bp2_params": [ -0.287, -0.224, 0.035, -9.851, -14.300, -1.884 ], "groove_widths": [ 13.350, 13.060, 18.855, 18.248 ], "simple_Rise": 3.469, "simple_Twist": 36.630, "simple_hRise": 3.344, "simple_hTwist": 36.782 }, { "index": 6, "nt1": "///B/7", "nt2": "///C/56", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.287, -0.224, 0.035, -9.851, -14.300, -1.884 ], "step_params": [ 0.043, -0.205, 3.213, 1.345, 9.269, 35.083 ], "heli_params": [ -1.597, 0.115, 3.061, 15.047, -2.183, 36.274 ], "bp2_params": [ -0.026, -0.234, -0.130, -0.411, -15.340, -0.920 ], "groove_widths": [ 12.653, 12.377, 16.740, 16.295 ], "simple_Rise": 3.213, "simple_Twist": 34.118, "simple_hRise": 3.054, "simple_hTwist": 35.343 }, { "index": 7, "nt1": "///B/8", "nt2": "///C/55", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.026, -0.234, -0.130, -0.411, -15.340, -0.920 ], "step_params": [ 0.803, -0.957, 3.264, -0.524, 1.042, 37.484 ], "heli_params": [ -1.624, -1.317, 3.226, 1.621, 0.815, 37.502 ], "bp2_params": [ 0.171, -0.145, 0.137, -2.437, -16.931, -2.332 ], "groove_widths": [ 13.312, null, 16.875, null ], "simple_Rise": 3.264, "simple_Twist": 36.457, "simple_hRise": 3.225, "simple_hTwist": 36.475 }, { "index": 8, "nt1": "///B/9", "nt2": "///C/54", "bp": "c-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.171, -0.145, 0.137, -2.437, -16.931, -2.332 ], "step_params": [ -1.081, -0.935, 3.448, -0.449, -0.738, 22.350 ], "heli_params": [ -2.119, 2.608, 3.497, -1.903, 1.158, 22.366 ], "bp2_params": [ -0.193, -0.116, -0.152, -1.200, -1.282, -2.074 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.448, "simple_Twist": 23.988, "simple_hRise": 3.494, "simple_hTwist": 24.004 }, { "index": 9, "nt1": "///B/10", "nt2": "///C/53", "bp": "G-c", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.193, -0.116, -0.152, -1.200, -1.282, -2.074 ], "step_params": [ 0.618, -0.566, 3.118, -1.969, 7.139, 27.824 ], "heli_params": [ -2.620, -1.651, 2.838, 14.523, 4.006, 28.774 ], "bp2_params": [ -0.074, -0.245, -0.185, 13.615, -13.268, 5.315 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.118, "simple_Twist": 27.954, "simple_hRise": 2.840, "simple_hTwist": 28.900 }, { "index": 10, "nt1": "///B/11", "nt2": "///C/52", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_stacks": 2, "stacks": [ { "index": 1, "num_nts": 2, "nts_short": "AG", "nts_long": "///B/1,///B/2" }, { "index": 2, "num_nts": 2, "nts_short": "TA", "nts_long": "///C/51,///C/52" } ], "num_ssSegments": 2, "ssSegments": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///B/1" }, { "index": 2, "num_nts": 1, "nts_short": "T", "nts_long": "///C/51" } ], "dbn": { "all_chains": { "num_nts": 22, "num_chars": 23, "bseq": "AGCGTGGGcGT&TAcGCCCACGC", "bseqUP": "AGCGTGGGCGT&TACGCCCACGC", "sstr": ".((((((((((&.))))))))))", "form": ".BBBBA...B-&AA.BB..BBB-" }, "chain_B": { "num_nts": 11, "num_chars": 11, "bseq": "AGCGTGGGcGT", "bseqUP": "AGCGTGGGCGT", "sstr": ".((((((((((", "form": ".BBBBA...B-" }, "chain_C": { "num_nts": 11, "num_chars": 11, "bseq": "TAcGCCCACGC", "bseqUP": "TACGCCCACGC", "sstr": ".))))))))))", "form": "AA.BB..BBB-" } }, "chains": { "chain_B": { "num_nts": 11, "bseq": "AGCGTGGGcGT", "sstr": ".((((((((((", "form": ".BBBBA...B-", "helical_rise": 3.298, "helical_rise_std": 0.540, "helical_axis": [ 0.096, -0.051, 0.994 ], "point1": [ 200.282, 99.367, 91.247 ], "point2": [ 203.447, 97.667, 124.154 ], "num_chars": 31, "suite": "A!!G!!C4bG!!T4nG1aG1bG!!c1bG!!T" }, "chain_C": { "num_nts": 11, "bseq": "TAcGCCCACGC", "sstr": ".))))))))))", "form": "AA.BB..BBB-", "helical_rise": 3.318, "helical_rise_std": 0.453, "helical_axis": [ -0.051, -0.064, -0.997 ], "point1": [ 203.644, 99.835, 127.577 ], "point2": [ 201.956, 97.705, 94.370 ], "num_chars": 31, "suite": "T1aA1bc!!G!!C1bC!!C!!A1bC!!G!!C" } }, "num_nts": 22, "nts": [ { "index": 1, "index_chain": 1, "chain_name": "B", "nt_resnum": 1, "nt_name": "DA", "nt_code": "A", "nt_id": "///B/1", "linked_nts": [ null, "///B/2" ], "nt_type": "DNA", "dbn": ".", "summary": "syn,~C2'-endo,BI,non-pair-contact,ss-non-loop", "alpha": null, "beta": null, "gamma": 40.332, "delta": 132.681, "epsilon": -161.785, "zeta": -88.285, "epsilon_zeta": -73.500, "bb_type": "BI", "chi": 52.476, "glyco_bond": "syn", "C5prime_xyz": [ -5.358, 3.728, 1.009 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": -2.319, "Dp": 2.356, "splay_angle": 35.726, "splay_distance": 5.942, "splay_ratio": 0.307, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -20.003, "v1": 27.993, "v2": -24.989, "v3": 14.088, "v4": 3.474, "amplitude": 27.785, "phase_angle": 154.077, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.039, "frame": { "rmsd": 0.009, "origin": [ 205.117, 100.016, 91.734 ], "x_axis": [ -0.559, -0.825, 0.086 ], "y_axis": [ -0.829, 0.559, -0.027 ], "z_axis": [ -0.026, -0.086, -0.996 ], "quaternion": [ -0.032, -0.468, 0.882, -0.032 ] } }, { "index": 2, "index_chain": 2, "chain_name": "B", "nt_resnum": 2, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/2", "linked_nts": [ "///B/1", "///B/3" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end", "alpha": -61.768, "beta": 179.789, "gamma": 42.917, "delta": 131.551, "epsilon": -179.566, "zeta": -97.867, "epsilon_zeta": -81.699, "bb_type": "BI", "chi": -95.376, "glyco_bond": "anti", "C5prime_xyz": [ -2.399, 7.880, -2.594 ], "P_xyz": [ -0.278, 9.355, -2.862 ], "form": "B", "ssZp": 1.618, "Dp": 2.076, "splay_angle": 16.260, "splay_distance": 2.833, "splay_ratio": 0.143, "d22": null, "d64": null, "eta": 160.884, "theta": -145.831, "eta_prime": -164.664, "theta_prime": -157.318, "eta_base": 167.385, "theta_base": -120.689, "v0": -27.491, "v1": 34.620, "v2": -28.968, "v3": 13.946, "v4": 8.170, "amplitude": 34.267, "phase_angle": 147.712, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.014, "frame": { "rmsd": 0.014, "origin": [ 200.137, 99.545, 94.939 ], "x_axis": [ 0.961, -0.256, -0.101 ], "y_axis": [ 0.268, 0.955, 0.131 ], "z_axis": [ 0.063, -0.153, 0.986 ], "quaternion": [ 0.988, 0.072, 0.042, -0.133 ] } }, { "index": 3, "index_chain": 3, "chain_name": "B", "nt_resnum": 3, "nt_name": "DC", "nt_code": "C", "nt_id": "///B/3", "linked_nts": [ "///B/2", "///B/4" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,canonical,non-pair-contact,helix,stem", "alpha": -61.224, "beta": 173.657, "gamma": 48.005, "delta": 142.760, "epsilon": -140.912, "zeta": -173.482, "epsilon_zeta": 32.570, "bb_type": "--", "chi": -91.904, "glyco_bond": "anti", "C5prime_xyz": [ -3.548, 7.871, -2.148 ], "P_xyz": [ -1.745, 9.496, -3.020 ], "form": "B", "ssZp": 2.379, "Dp": 2.197, "splay_angle": 25.012, "splay_distance": 4.074, "splay_ratio": 0.218, "d22": null, "d64": null, "eta": 170.958, "theta": 174.608, "eta_prime": -164.753, "theta_prime": 169.746, "eta_base": -127.124, "theta_base": -145.785, "v0": -39.755, "v1": 49.973, "v2": -39.475, "v3": 18.103, "v4": 12.971, "amplitude": 48.102, "phase_angle": 145.150, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.059, "frame": { "rmsd": 0.010, "origin": [ 200.922, 98.804, 97.558 ], "x_axis": [ 0.983, 0.182, 0.004 ], "y_axis": [ -0.172, 0.919, 0.356 ], "z_axis": [ 0.061, -0.350, 0.935 ], "quaternion": [ 0.979, 0.180, 0.015, 0.090 ] } }, { "index": 4, "index_chain": 4, "chain_name": "B", "nt_resnum": 4, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/4", "linked_nts": [ "///B/3", "///B/5" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate", "alpha": -54.497, "beta": 155.878, "gamma": 40.253, "delta": 143.120, "epsilon": -164.601, "zeta": -82.134, "epsilon_zeta": -82.467, "bb_type": "BI", "chi": -127.723, "glyco_bond": "anti", "C5prime_xyz": [ -1.538, 8.680, -0.853 ], "P_xyz": [ 0.845, 9.033, 0.069 ], "form": "B", "ssZp": 2.022, "Dp": 2.086, "splay_angle": 18.360, "splay_distance": 3.253, "splay_ratio": 0.163, "d22": null, "d64": null, "eta": 172.490, "theta": -102.618, "eta_prime": -172.041, "theta_prime": -122.149, "eta_base": -128.091, "theta_base": -94.432, "v0": -20.940, "v1": 34.650, "v2": -34.448, "v3": 22.946, "v4": -1.325, "amplitude": 35.919, "phase_angle": 163.543, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "4b", "suiteness": 0.390, "filter_rmsd": 0.014, "frame": { "rmsd": 0.014, "origin": [ 200.716, 97.455, 101.396 ], "x_axis": [ 0.650, 0.756, -0.078 ], "y_axis": [ -0.747, 0.654, 0.118 ], "z_axis": [ 0.141, -0.019, 0.990 ], "quaternion": [ 0.907, 0.038, 0.060, 0.414 ] } }, { "index": 5, "index_chain": 5, "chain_name": "B", "nt_resnum": 5, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/5", "linked_nts": [ "///B/4", "///B/6" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem", "alpha": -76.748, "beta": 176.616, "gamma": 45.045, "delta": 133.274, "epsilon": -131.985, "zeta": -179.746, "epsilon_zeta": 47.761, "bb_type": "BII", "chi": -100.249, "glyco_bond": "anti", "C5prime_xyz": [ -3.398, 7.978, -2.154 ], "P_xyz": [ -1.656, 9.854, -2.552 ], "form": "B", "ssZp": 1.860, "Dp": 1.946, "splay_angle": 22.596, "splay_distance": 3.823, "splay_ratio": 0.196, "d22": null, "d64": null, "eta": 161.107, "theta": -171.750, "eta_prime": -166.317, "theta_prime": 165.909, "eta_base": -127.715, "theta_base": -146.604, "v0": -42.686, "v1": 47.062, "v2": -33.783, "v3": 10.380, "v4": 19.638, "amplitude": 46.649, "phase_angle": 136.402, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.101, "frame": { "rmsd": 0.015, "origin": [ 202.029, 97.798, 104.353 ], "x_axis": [ 0.195, 0.975, -0.106 ], "y_axis": [ -0.939, 0.217, 0.268 ], "z_axis": [ 0.285, 0.047, 0.957 ], "quaternion": [ 0.770, 0.072, 0.127, 0.622 ] } }, { "index": 6, "index_chain": 6, "chain_name": "B", "nt_resnum": 6, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/6", "linked_nts": [ "///B/5", "///B/7" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate", "alpha": 81.932, "beta": -133.972, "gamma": -171.489, "delta": 94.651, "epsilon": -145.980, "zeta": -68.469, "epsilon_zeta": -77.511, "bb_type": "BI", "chi": -167.941, "glyco_bond": "anti", "C5prime_xyz": [ -1.130, 8.340, 1.286 ], "P_xyz": [ 0.571, 9.607, -0.222 ], "form": "A", "ssZp": 4.320, "Dp": 4.522, "splay_angle": 22.681, "splay_distance": 3.642, "splay_ratio": 0.198, "d22": null, "d64": null, "eta": 159.627, "theta": -157.807, "eta_prime": 156.210, "theta_prime": -157.330, "eta_base": -145.145, "theta_base": -132.233, "v0": 15.745, "v1": -31.458, "v2": 34.614, "v3": -26.568, "v4": 7.198, "amplitude": 34.888, "phase_angle": 352.811, "puckering": "C2'-exo", "sugar_class": "~C3'-endo", "bin": "23t", "cluster": "4n", "suiteness": 0.290, "filter_rmsd": 0.015, "frame": { "rmsd": 0.015, "origin": [ 203.209, 97.045, 107.911 ], "x_axis": [ -0.364, 0.920, 0.144 ], "y_axis": [ -0.918, -0.380, 0.110 ], "z_axis": [ 0.156, -0.092, 0.983 ], "quaternion": [ 0.557, 0.091, 0.005, 0.826 ] } }, { "index": 7, "index_chain": 7, "chain_name": "B", "nt_resnum": 7, "nt_name": "DG", "nt_code": "G", "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,phosphate", "alpha": -72.057, "beta": 176.328, "gamma": 56.573, "delta": 88.081, "epsilon": -164.326, "zeta": -70.102, "epsilon_zeta": -94.225, "bb_type": "BI", "chi": -155.804, "glyco_bond": "anti", "C5prime_xyz": [ -1.491, 8.836, 0.307 ], "P_xyz": [ 1.037, 9.341, 0.657 ], "form": ".", "ssZp": 4.049, "Dp": 4.288, "splay_angle": 19.877, "splay_distance": 3.159, "splay_ratio": 0.173, "d22": null, "d64": null, "eta": 166.163, "theta": -146.991, "eta_prime": -173.365, "theta_prime": -140.076, "eta_base": -132.883, "theta_base": -107.034, "v0": -0.957, "v1": -21.820, "v2": 34.618, "v3": -36.295, "v4": 23.486, "amplitude": 36.855, "phase_angle": 20.066, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.504, "filter_rmsd": 0.009, "frame": { "rmsd": 0.009, "origin": [ 204.875, 97.770, 111.067 ], "x_axis": [ -0.820, 0.546, 0.175 ], "y_axis": [ -0.546, -0.836, 0.049 ], "z_axis": [ 0.173, -0.056, 0.983 ], "quaternion": [ 0.286, 0.091, -0.002, 0.954 ] } }, { "index": 8, "index_chain": 8, "chain_name": "B", "nt_resnum": 8, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/8", "linked_nts": [ "///B/7", "///B/9" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate", "alpha": -63.529, "beta": -179.033, "gamma": 61.998, "delta": 146.011, "epsilon": -174.646, "zeta": -82.005, "epsilon_zeta": -92.641, "bb_type": "BI", "chi": -117.477, "glyco_bond": "anti", "C5prime_xyz": [ -1.826, 8.549, -1.222 ], "P_xyz": [ 0.701, 9.041, -0.785 ], "form": ".", "ssZp": 2.235, "Dp": 2.096, "splay_angle": 19.668, "splay_distance": 3.640, "splay_ratio": 0.181, "d22": null, "d64": null, "eta": 168.931, "theta": -108.627, "eta_prime": -149.606, "theta_prime": -138.443, "eta_base": -108.904, "theta_base": -95.213, "v0": -17.415, "v1": 32.269, "v2": -33.660, "v3": 24.564, "v4": -4.583, "amplitude": 34.315, "phase_angle": 168.786, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "1b", "suiteness": 0.746, "filter_rmsd": 0.016, "frame": { "rmsd": 0.016, "origin": [ 204.830, 98.434, 114.155 ], "x_axis": [ -0.994, -0.040, 0.103 ], "y_axis": [ 0.055, -0.988, 0.145 ], "z_axis": [ 0.096, 0.150, 0.984 ], "quaternion": [ -0.024, 0.050, 0.074, 0.996 ] } }, { "index": 9, "index_chain": 9, "chain_name": "B", "nt_resnum": 9, "nt_name": "5HC", "nt_code": "c", "is_modified": true, "nt_id": "///B/9", "linked_nts": [ "///B/8", "///B/10" ], "nt_type": "DNA", "dbn": "(", "summary": "modified,anti,BI,canonical,non-pair-contact,helix,stem", "alpha": -73.244, "beta": 171.659, "gamma": 50.451, "delta": 93.604, "epsilon": -173.177, "zeta": -87.077, "epsilon_zeta": -86.100, "bb_type": "BI", "chi": -133.486, "glyco_bond": "anti", "C5prime_xyz": [ -2.826, 8.752, -1.323 ], "P_xyz": [ -0.992, 10.505, -1.580 ], "form": ".", "ssZp": 2.707, "Dp": 2.779, "splay_angle": 20.683, "splay_distance": 3.646, "splay_ratio": 0.181, "d22": null, "d64": null, "eta": 168.199, "theta": -169.601, "eta_prime": -172.428, "theta_prime": -168.295, "eta_base": -115.334, "theta_base": -149.069, "v0": -39.711, "v1": 25.906, "v2": 1.018, "v3": -27.426, "v4": 40.195, "amplitude": 43.304, "phase_angle": 88.652, "puckering": "O4'-endo", "sugar_class": "--", "bin": "23p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.084, "frame": { "rmsd": 0.064, "origin": [ 203.456, 99.350, 117.399 ], "x_axis": [ -0.763, -0.617, 0.191 ], "y_axis": [ 0.642, -0.758, 0.114 ], "z_axis": [ 0.074, 0.210, 0.975 ], "quaternion": [ -0.337, 0.071, 0.087, 0.935 ] } }, { "index": 10, "index_chain": 10, "chain_name": "B", "nt_resnum": 10, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/10", "linked_nts": [ "///B/9", "///B/11" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -49.476, "beta": 179.003, "gamma": 38.287, "delta": 125.475, "epsilon": -171.212, "zeta": -92.638, "epsilon_zeta": -78.575, "bb_type": "BI", "chi": -118.254, "glyco_bond": "anti", "C5prime_xyz": [ -2.349, 8.555, -1.612 ], "P_xyz": [ -0.415, 10.218, -1.285 ], "form": "B", "ssZp": 2.259, "Dp": 2.341, "splay_angle": 18.324, "splay_distance": 3.259, "splay_ratio": 0.163, "d22": null, "d64": null, "eta": 174.921, "theta": -142.400, "eta_prime": -167.775, "theta_prime": -148.471, "eta_base": -145.757, "theta_base": -109.422, "v0": -34.379, "v1": 36.328, "v2": -24.615, "v3": 5.771, "v4": 17.753, "amplitude": 36.439, "phase_angle": 132.495, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "1b", "suiteness": 0.033, "filter_rmsd": 0.022, "frame": { "rmsd": 0.022, "origin": [ 203.333, 101.316, 120.467 ], "x_axis": [ -0.462, -0.879, 0.114 ], "y_axis": [ 0.886, -0.455, 0.085 ], "z_axis": [ -0.023, 0.141, 0.990 ], "quaternion": [ 0.518, -0.027, -0.066, -0.853 ] } }, { "index": 11, "index_chain": 11, "chain_name": "B", "nt_resnum": 11, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/11", "linked_nts": [ "///B/10", null ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end", "alpha": -62.884, "beta": 171.986, "gamma": 46.814, "delta": 123.257, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -115.159, "glyco_bond": "anti", "C5prime_xyz": [ -3.153, 8.353, -1.747 ], "P_xyz": [ -1.246, 10.051, -2.137 ], "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": -41.758, "v1": 40.630, "v2": -23.939, "v3": 0.974, "v4": 25.340, "amplitude": 42.145, "phase_angle": 124.611, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.102, "frame": { "rmsd": 0.010, "origin": [ 202.427, 100.989, 123.581 ], "x_axis": [ 0.063, -0.990, 0.129 ], "y_axis": [ 0.986, 0.081, 0.142 ], "z_axis": [ -0.151, 0.119, 0.981 ], "quaternion": [ 0.729, 0.008, -0.096, -0.678 ] } }, { "index": 12, "index_chain": 1, "chain_name": "C", "nt_resnum": 51, "nt_name": "DT", "nt_code": "T", "nt_id": "///C/51", "linked_nts": [ null, "///C/52" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,ss-non-loop", "alpha": null, "beta": null, "gamma": 42.181, "delta": 93.333, "epsilon": -133.562, "zeta": -81.397, "epsilon_zeta": -52.164, "bb_type": "BI", "chi": -164.467, "glyco_bond": "anti", "C5prime_xyz": [ -1.288, 8.563, 0.912 ], "P_xyz": [ null, null, null ], "form": "A", "ssZp": 4.284, "Dp": 4.535, "splay_angle": 22.788, "splay_distance": 3.753, "splay_ratio": 0.199, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": 9.096, "v1": -26.233, "v2": 32.306, "v3": -27.875, "v4": 11.884, "amplitude": 32.338, "phase_angle": 2.551, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.102, "frame": { "rmsd": 0.010, "origin": [ 201.613, 100.628, 127.363 ], "x_axis": [ 0.557, -0.795, -0.241 ], "y_axis": [ -0.820, -0.573, -0.007 ], "z_axis": [ -0.132, 0.201, -0.971 ], "quaternion": [ -0.059, 0.880, -0.459, -0.106 ] } }, { "index": 13, "index_chain": 2, "chain_name": "C", "nt_resnum": 52, "nt_name": "DA", "nt_code": "A", "nt_id": "///C/52", "linked_nts": [ "///C/51", "///C/53" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end", "alpha": -40.339, "beta": 161.640, "gamma": 34.391, "delta": 80.262, "epsilon": -158.052, "zeta": -83.252, "epsilon_zeta": -74.800, "bb_type": "BI", "chi": -153.804, "glyco_bond": "anti", "C5prime_xyz": [ -1.550, 8.853, 0.133 ], "P_xyz": [ 0.922, 9.598, 0.550 ], "form": "A", "ssZp": 4.106, "Dp": 4.448, "splay_angle": 19.949, "splay_distance": 3.204, "splay_ratio": 0.173, "d22": null, "d64": null, "eta": 165.103, "theta": -160.671, "eta_prime": -176.326, "theta_prime": -150.148, "eta_base": -131.389, "theta_base": -131.593, "v0": -3.157, "v1": -21.888, "v2": 37.110, "v3": -40.261, "v4": 27.574, "amplitude": 40.394, "phase_angle": 23.265, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.172, "filter_rmsd": 0.038, "frame": { "rmsd": 0.006, "origin": [ 202.668, 100.924, 123.774 ], "x_axis": [ -0.022, -0.994, -0.104 ], "y_axis": [ -0.996, 0.013, 0.093 ], "z_axis": [ -0.091, 0.105, -0.990 ], "quaternion": [ 0.004, -0.699, 0.712, 0.070 ] } }, { "index": 14, "index_chain": 3, "chain_name": "C", "nt_resnum": 53, "nt_name": "5HC", "nt_code": "c", "is_modified": true, "nt_id": "///C/53", "linked_nts": [ "///C/52", "///C/54" ], "nt_type": "DNA", "dbn": ")", "summary": "modified,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -49.407, "beta": 175.235, "gamma": 42.242, "delta": 136.340, "epsilon": -151.344, "zeta": -55.216, "epsilon_zeta": -96.127, "bb_type": "BI", "chi": -115.478, "glyco_bond": "anti", "C5prime_xyz": [ -1.851, 8.660, -1.280 ], "P_xyz": [ 0.696, 9.189, -0.971 ], "form": ".", "ssZp": 2.767, "Dp": 2.829, "splay_angle": 21.205, "splay_distance": 3.828, "splay_ratio": 0.188, "d22": null, "d64": null, "eta": 175.009, "theta": -108.683, "eta_prime": -160.369, "theta_prime": -135.505, "eta_base": -138.723, "theta_base": -112.167, "v0": -20.663, "v1": 31.654, "v2": -27.197, "v3": 9.310, "v4": 6.800, "amplitude": 31.648, "phase_angle": 149.246, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "1b", "suiteness": 0.439, "filter_rmsd": 0.085, "frame": { "rmsd": 0.067, "origin": [ 203.345, 101.114, 120.648 ], "x_axis": [ -0.429, -0.898, 0.096 ], "y_axis": [ -0.902, 0.420, -0.102 ], "z_axis": [ 0.052, -0.130, -0.990 ], "quaternion": [ -0.013, -0.534, 0.843, -0.069 ] } }, { "index": 15, "index_chain": 4, "chain_name": "C", "nt_resnum": 54, "nt_name": "DG", "nt_code": "G", "nt_id": "///C/54", "linked_nts": [ "///C/53", "///C/55" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -110.753, "beta": 77.663, "gamma": 179.135, "delta": 120.383, "epsilon": -151.201, "zeta": -68.245, "epsilon_zeta": -82.956, "bb_type": "BI", "chi": -172.242, "glyco_bond": "anti", "C5prime_xyz": [ -1.972, 8.626, 1.183 ], "P_xyz": [ -1.935, 10.372, -0.795 ], "form": "B", "ssZp": 2.290, "Dp": 2.460, "splay_angle": 18.842, "splay_distance": 3.357, "splay_ratio": 0.168, "d22": null, "d64": null, "eta": -121.898, "theta": -174.794, "eta_prime": -134.797, "theta_prime": -163.950, "eta_base": -102.237, "theta_base": -127.387, "v0": -22.880, "v1": 22.831, "v2": -14.234, "v3": 1.758, "v4": 13.351, "amplitude": 23.437, "phase_angle": 127.398, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "22t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.014, "frame": { "rmsd": 0.014, "origin": [ 203.686, 99.337, 117.275 ], "x_axis": [ -0.722, -0.686, -0.095 ], "y_axis": [ -0.670, 0.726, -0.155 ], "z_axis": [ 0.175, -0.048, -0.983 ], "quaternion": [ 0.073, -0.366, 0.926, -0.055 ] } }, { "index": 16, "index_chain": 5, "chain_name": "C", "nt_resnum": 55, "nt_name": "DC", "nt_code": "C", "nt_id": "///C/55", "linked_nts": [ "///C/54", "///C/56" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate", "alpha": 146.568, "beta": 179.919, "gamma": 151.456, "delta": 87.653, "epsilon": -161.910, "zeta": -77.787, "epsilon_zeta": -84.122, "bb_type": "BI", "chi": -152.772, "glyco_bond": "anti", "C5prime_xyz": [ -1.767, 8.998, -0.036 ], "P_xyz": [ -0.257, 10.215, -1.805 ], "form": "B", "ssZp": 3.781, "Dp": 4.039, "splay_angle": 20.086, "splay_distance": 3.292, "splay_ratio": 0.176, "d22": 4.335, "d64": 3.591, "eta": 122.669, "theta": -175.192, "eta_prime": 155.940, "theta_prime": -163.655, "eta_base": -154.603, "theta_base": -126.956, "v0": -10.721, "v1": -10.543, "v2": 26.585, "v3": -33.490, "v4": 28.043, "amplitude": 33.299, "phase_angle": 37.025, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "23t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.063, "frame": { "rmsd": 0.004, "origin": [ 204.815, 98.220, 114.317 ], "x_axis": [ -0.983, -0.095, -0.159 ], "y_axis": [ -0.071, 0.986, -0.152 ], "z_axis": [ 0.171, -0.139, -0.975 ], "quaternion": [ 0.083, -0.042, 0.993, -0.073 ] } }, { "index": 17, "index_chain": 6, "chain_name": "C", "nt_resnum": 56, "nt_name": "DC", "nt_code": "C", "nt_id": "///C/56", "linked_nts": [ "///C/55", "///C/57" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate", "alpha": -59.796, "beta": 174.148, "gamma": 59.501, "delta": 145.556, "epsilon": -178.462, "zeta": -94.398, "epsilon_zeta": -84.064, "bb_type": "BI", "chi": -113.631, "glyco_bond": "anti", "C5prime_xyz": [ -2.027, 8.527, -1.372 ], "P_xyz": [ 0.484, 9.123, -0.996 ], "form": ".", "ssZp": 2.284, "Dp": 2.223, "splay_angle": 21.378, "splay_distance": 3.742, "splay_ratio": 0.191, "d22": 4.147, "d64": 4.014, "eta": 162.788, "theta": -119.367, "eta_prime": -155.698, "theta_prime": -143.681, "eta_base": -114.078, "theta_base": -105.148, "v0": -24.051, "v1": 37.922, "v2": -35.954, "v3": 23.123, "v4": 0.348, "amplitude": 38.143, "phase_angle": 160.494, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "1b", "suiteness": 0.798, "filter_rmsd": 0.064, "frame": { "rmsd": 0.011, "origin": [ 204.511, 97.730, 111.076 ], "x_axis": [ -0.865, 0.497, -0.067 ], "y_axis": [ 0.499, 0.839, -0.216 ], "z_axis": [ -0.051, -0.221, -0.974 ], "quaternion": [ 0.004, 0.260, 0.959, -0.114 ] } }, { "index": 18, "index_chain": 7, "chain_name": "C", "nt_resnum": 57, "nt_name": "DC", "nt_code": "C", "nt_id": "///C/57", "linked_nts": [ "///C/56", "///C/58" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -68.596, "beta": -173.025, "gamma": 51.106, "delta": 124.081, "epsilon": -170.583, "zeta": -82.017, "epsilon_zeta": -88.566, "bb_type": "BI", "chi": -118.927, "glyco_bond": "anti", "C5prime_xyz": [ -2.355, 8.548, -1.771 ], "P_xyz": [ -0.286, 10.133, -1.490 ], "form": ".", "ssZp": 2.065, "Dp": 2.252, "splay_angle": 19.518, "splay_distance": 3.603, "splay_ratio": 0.176, "d22": null, "d64": null, "eta": 172.267, "theta": -132.973, "eta_prime": -166.515, "theta_prime": -145.375, "eta_base": -117.128, "theta_base": -102.713, "v0": -32.433, "v1": 34.277, "v2": -23.705, "v3": 5.873, "v4": 16.350, "amplitude": 34.510, "phase_angle": 133.386, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.063, "frame": { "rmsd": 0.008, "origin": [ 203.035, 97.102, 107.695 ], "x_axis": [ -0.377, 0.921, -0.097 ], "y_axis": [ 0.920, 0.361, -0.154 ], "z_axis": [ -0.107, -0.147, -0.983 ], "quaternion": [ -0.003, 0.558, 0.825, -0.091 ] } }, { "index": 19, "index_chain": 8, "chain_name": "C", "nt_resnum": 58, "nt_name": "DA", "nt_code": "A", "nt_id": "///C/58", "linked_nts": [ "///C/57", "///C/59" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,BI,canonical,non-pair-contact,helix,stem", "alpha": -64.819, "beta": 166.780, "gamma": 51.071, "delta": 90.045, "epsilon": -178.055, "zeta": -92.190, "epsilon_zeta": -85.865, "bb_type": "BI", "chi": -132.255, "glyco_bond": "anti", "C5prime_xyz": [ -3.195, 8.585, -1.431 ], "P_xyz": [ -1.491, 10.423, -2.066 ], "form": "B", "ssZp": 2.985, "Dp": 3.053, "splay_angle": 17.703, "splay_distance": 3.038, "splay_ratio": 0.154, "d22": null, "d64": null, "eta": 167.437, "theta": -177.854, "eta_prime": -174.345, "theta_prime": -174.279, "eta_base": -123.407, "theta_base": -144.361, "v0": -39.007, "v1": 19.199, "v2": 6.059, "v3": -28.921, "v4": 43.078, "amplitude": 42.738, "phase_angle": 81.850, "puckering": "O4'-endo", "sugar_class": "--", "bin": "23p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.040, "frame": { "rmsd": 0.010, "origin": [ 201.872, 97.927, 104.387 ], "x_axis": [ 0.175, 0.970, -0.169 ], "y_axis": [ 0.966, -0.202, -0.160 ], "z_axis": [ -0.189, -0.135, -0.973 ], "quaternion": [ -0.008, 0.766, 0.632, -0.117 ] } }, { "index": 20, "index_chain": 9, "chain_name": "C", "nt_resnum": 59, "nt_name": "DC", "nt_code": "C", "nt_id": "///C/59", "linked_nts": [ "///C/58", "///C/60" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -54.451, "beta": 168.296, "gamma": 54.284, "delta": 130.454, "epsilon": -165.459, "zeta": -101.728, "epsilon_zeta": -63.731, "bb_type": "BI", "chi": -115.071, "glyco_bond": "anti", "C5prime_xyz": [ -2.540, 8.531, -1.656 ], "P_xyz": [ -0.326, 9.760, -1.754 ], "form": "B", "ssZp": 2.228, "Dp": 2.253, "splay_angle": 20.792, "splay_distance": 3.608, "splay_ratio": 0.182, "d22": null, "d64": null, "eta": 175.982, "theta": -138.287, "eta_prime": -161.200, "theta_prime": -149.857, "eta_base": -130.443, "theta_base": -104.179, "v0": -33.861, "v1": 39.513, "v2": -29.767, "v3": 11.310, "v4": 14.013, "amplitude": 38.693, "phase_angle": 140.293, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "1b", "suiteness": 0.183, "filter_rmsd": 0.061, "frame": { "rmsd": 0.008, "origin": [ 200.755, 97.764, 101.565 ], "x_axis": [ 0.611, 0.770, -0.183 ], "y_axis": [ 0.733, -0.638, -0.235 ], "z_axis": [ -0.298, 0.010, -0.955 ], "quaternion": [ -0.068, 0.895, 0.420, -0.134 ] } }, { "index": 21, "index_chain": 10, "chain_name": "C", "nt_resnum": 60, "nt_name": "DG", "nt_code": "G", "nt_id": "///C/60", "linked_nts": [ "///C/59", "///C/61" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -53.657, "beta": 173.822, "gamma": 34.953, "delta": 128.021, "epsilon": -159.908, "zeta": -78.464, "epsilon_zeta": -81.444, "bb_type": "BI", "chi": -109.372, "glyco_bond": "anti", "C5prime_xyz": [ -2.691, 8.333, -1.893 ], "P_xyz": [ -0.681, 9.946, -1.936 ], "form": "B", "ssZp": 2.333, "Dp": 2.364, "splay_angle": 18.834, "splay_distance": 3.304, "splay_ratio": 0.165, "d22": null, "d64": null, "eta": 167.458, "theta": -145.879, "eta_prime": -170.352, "theta_prime": -161.639, "eta_base": -117.916, "theta_base": -128.377, "v0": -32.566, "v1": 35.498, "v2": -25.229, "v3": 7.307, "v4": 15.647, "amplitude": 35.395, "phase_angle": 135.463, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.010, "frame": { "rmsd": 0.010, "origin": [ 200.720, 98.736, 98.091 ], "x_axis": [ 0.959, 0.220, -0.181 ], "y_axis": [ 0.194, -0.970, -0.148 ], "z_axis": [ -0.208, 0.107, -0.972 ], "quaternion": [ -0.064, 0.988, 0.105, -0.098 ] } }, { "index": 22, "index_chain": 11, "chain_name": "C", "nt_resnum": 61, "nt_name": "DC", "nt_code": "C", "nt_id": "///C/61", "linked_nts": [ "///C/60", null ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end", "alpha": -114.444, "beta": 90.396, "gamma": 155.128, "delta": 150.753, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -150.138, "glyco_bond": "anti", "C5prime_xyz": [ -2.051, 8.776, 0.481 ], "P_xyz": [ -0.930, 10.071, -1.451 ], "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": -26.772, "v1": 43.675, "v2": -43.018, "v3": 28.537, "v4": -1.544, "amplitude": 44.973, "phase_angle": 163.044, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.060, "frame": { "rmsd": 0.012, "origin": [ 200.348, 99.596, 94.922 ], "x_axis": [ 0.956, -0.249, -0.154 ], "y_axis": [ -0.265, -0.960, -0.095 ], "z_axis": [ -0.124, 0.132, -0.983 ], "quaternion": [ -0.058, 0.987, -0.130, -0.070 ] } } ], "num_hbonds": 123, "hbonds": [ { "index": 1, "atom1_serNum": 31, "atom2_serNum": 130, "donAcc_type": "standard", "distance": 3.074, "atom1_id": "///A/353/N", "atom2_id": "///A/364/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 2, "atom1_serNum": 34, "atom2_serNum": 127, "donAcc_type": "standard", "distance": 2.917, "atom1_id": "///A/353/O", "atom2_id": "///A/364/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 3, "atom1_serNum": 48, "atom2_serNum": 108, "donAcc_type": "standard", "distance": 2.771, "atom1_id": "///A/355/N", "atom2_id": "///A/362/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 4, "atom1_serNum": 65, "atom2_serNum": 90, "donAcc_type": "standard", "distance": 2.997, "atom1_id": "///A/357/O", "atom2_id": "///A/360/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 5, "atom1_serNum": 147, "atom2_serNum": 178, "donAcc_type": "standard", "distance": 3.191, "atom1_id": "///A/366/O", "atom2_id": "///A/370/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 6, "atom1_serNum": 151, "atom2_serNum": 167, "donAcc_type": "standard", "distance": 3.224, "atom1_id": "///A/366/NE", "atom2_id": "///A/368/OD1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 7, "atom1_serNum": 153, "atom2_serNum": 962, "donAcc_type": "standard", "distance": 2.927, "atom1_id": "///A/366/NH1", "atom2_id": "///B/10/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 8, "atom1_serNum": 154, "atom2_serNum": 168, "donAcc_type": "standard", "distance": 2.876, "atom1_id": "///A/366/NH2", "atom2_id": "///A/368/OD2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 9, "atom1_serNum": 154, "atom2_serNum": 965, "donAcc_type": "standard", "distance": 2.788, "atom1_id": "///A/366/NH2", "atom2_id": "///B/10/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 10, "atom1_serNum": 154, "atom2_serNum": 1041, "donAcc_type": "questionable", "distance": 3.140, "atom1_id": "///A/366/NH2", "atom2_id": "///C/52/N6", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 11, "atom1_serNum": 158, "atom2_serNum": 186, "donAcc_type": "standard", "distance": 2.957, "atom1_id": "///A/367/O", "atom2_id": "///A/371/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 12, "atom1_serNum": 160, "atom2_serNum": 1329, "donAcc_type": "acceptable", "distance": 2.940, "atom1_id": "///A/367/OG", "atom2_id": "///A/504/O1", "atom_pair": "O:O", "residue_pair": "aa:ligand" }, { "index": 13, "atom1_serNum": 161, "atom2_serNum": 167, "donAcc_type": "standard", "distance": 2.672, "atom1_id": "///A/368/N", "atom2_id": "///A/368/OD1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 14, "atom1_serNum": 164, "atom2_serNum": 195, "donAcc_type": "standard", "distance": 3.016, "atom1_id": "///A/368/O", "atom2_id": "///A/372/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 15, "atom1_serNum": 168, "atom2_serNum": 1041, "donAcc_type": "standard", "distance": 2.981, "atom1_id": "///A/368/OD2", "atom2_id": "///C/52/N6", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 16, "atom1_serNum": 168, "atom2_serNum": 1333, "donAcc_type": "acceptable", "distance": 2.578, "atom1_id": "///A/368/OD2", "atom2_id": "///C/101/O1", "atom_pair": "O:O", "residue_pair": "aa:ligand" }, { "index": 17, "atom1_serNum": 172, "atom2_serNum": 206, "donAcc_type": "standard", "distance": 2.986, "atom1_id": "///A/369/O", "atom2_id": "///A/373/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 18, "atom1_serNum": 176, "atom2_serNum": 944, "donAcc_type": "standard", "distance": 3.094, "atom1_id": "///A/369/OE1", "atom2_id": "///B/9/N4", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 19, "atom1_serNum": 177, "atom2_serNum": 205, "donAcc_type": "questionable", "distance": 3.123, "atom1_id": "///A/369/NE2", "atom2_id": "///A/372/NH2", "atom_pair": "N:N", "residue_pair": "aa:aa" }, { "index": 20, "atom1_serNum": 177, "atom2_serNum": 908, "donAcc_type": "standard", "distance": 2.914, "atom1_id": "///A/369/NE2", "atom2_id": "///B/8/OP2", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 21, "atom1_serNum": 177, "atom2_serNum": 919, "donAcc_type": "standard", "distance": 3.069, "atom1_id": "///A/369/NE2", "atom2_id": "///B/8/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 22, "atom1_serNum": 181, "atom2_serNum": 216, "donAcc_type": "standard", "distance": 2.914, "atom1_id": "///A/370/O", "atom2_id": "///A/374/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 23, "atom1_serNum": 198, "atom2_serNum": 225, "donAcc_type": "standard", "distance": 3.149, "atom1_id": "///A/372/O", "atom2_id": "///A/375/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 24, "atom1_serNum": 204, "atom2_serNum": 922, "donAcc_type": "standard", "distance": 3.055, "atom1_id": "///A/372/NH1", "atom2_id": "///B/8/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 25, "atom1_serNum": 204, "atom2_serNum": 1115, "donAcc_type": "standard", "distance": 2.943, "atom1_id": "///A/372/NH1", "atom2_id": "///C/54/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 26, "atom1_serNum": 205, "atom2_serNum": 919, "donAcc_type": "standard", "distance": 3.177, "atom1_id": "///A/372/NH2", "atom2_id": "///B/8/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 27, "atom1_serNum": 205, "atom2_serNum": 922, "donAcc_type": "standard", "distance": 3.225, "atom1_id": "///A/372/NH2", "atom2_id": "///B/8/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 28, "atom1_serNum": 209, "atom2_serNum": 236, "donAcc_type": "standard", "distance": 2.923, "atom1_id": "///A/373/O", "atom2_id": "///A/376/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 29, "atom1_serNum": 212, "atom2_serNum": 885, "donAcc_type": "acceptable", "distance": 2.592, "atom1_id": "///A/373/ND1", "atom2_id": "///B/7/OP1", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 30, "atom1_serNum": 215, "atom2_serNum": 256, "donAcc_type": "questionable", "distance": 3.205, "atom1_id": "///A/373/NE2", "atom2_id": "///A/377/NE2", "atom_pair": "N:N", "residue_pair": "aa:aa" }, { "index": 31, "atom1_serNum": 219, "atom2_serNum": 247, "donAcc_type": "standard", "distance": 2.880, "atom1_id": "///A/374/O", "atom2_id": "///A/377/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 32, "atom1_serNum": 219, "atom2_serNum": 257, "donAcc_type": "standard", "distance": 3.165, "atom1_id": "///A/374/O", "atom2_id": "///A/378/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 33, "atom1_serNum": 228, "atom2_serNum": 264, "donAcc_type": "standard", "distance": 3.023, "atom1_id": "///A/375/O", "atom2_id": "///A/379/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 34, "atom1_serNum": 232, "atom2_serNum": 382, "donAcc_type": "standard", "distance": 2.873, "atom1_id": "///A/375/NE", "atom2_id": "///A/393/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 35, "atom1_serNum": 235, "atom2_serNum": 382, "donAcc_type": "standard", "distance": 2.837, "atom1_id": "///A/375/NH2", "atom2_id": "///A/393/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 36, "atom1_serNum": 262, "atom2_serNum": 268, "donAcc_type": "acceptable", "distance": 3.292, "atom1_id": "///A/378/OG1", "atom2_id": "///A/380/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 37, "atom1_serNum": 291, "atom2_serNum": 371, "donAcc_type": "standard", "distance": 3.078, "atom1_id": "///A/383/N", "atom2_id": "///A/392/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 38, "atom1_serNum": 294, "atom2_serNum": 368, "donAcc_type": "standard", "distance": 2.628, "atom1_id": "///A/383/O", "atom2_id": "///A/392/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 39, "atom1_serNum": 310, "atom2_serNum": 342, "donAcc_type": "standard", "distance": 2.951, "atom1_id": "///A/384/NE2", "atom2_id": "///A/389/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 40, "atom1_serNum": 311, "atom2_serNum": 351, "donAcc_type": "standard", "distance": 2.768, "atom1_id": "///A/385/N", "atom2_id": "///A/390/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 41, "atom1_serNum": 314, "atom2_serNum": 339, "donAcc_type": "standard", "distance": 2.919, "atom1_id": "///A/385/O", "atom2_id": "///A/389/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 42, "atom1_serNum": 384, "atom2_serNum": 864, "donAcc_type": "acceptable", "distance": 2.753, "atom1_id": "///A/393/OG", "atom2_id": "///B/6/OP2", "atom_pair": "O:O", "residue_pair": "aa:nt" }, { "index": 43, "atom1_serNum": 388, "atom2_serNum": 420, "donAcc_type": "standard", "distance": 3.028, "atom1_id": "///A/394/O", "atom2_id": "///A/398/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 44, "atom1_serNum": 392, "atom2_serNum": 408, "donAcc_type": "standard", "distance": 3.208, "atom1_id": "///A/394/NE", "atom2_id": "///A/396/OD1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 45, "atom1_serNum": 394, "atom2_serNum": 897, "donAcc_type": "standard", "distance": 2.999, "atom1_id": "///A/394/NH1", "atom2_id": "///B/7/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 46, "atom1_serNum": 395, "atom2_serNum": 409, "donAcc_type": "standard", "distance": 2.893, "atom1_id": "///A/394/NH2", "atom2_id": "///A/396/OD2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 47, "atom1_serNum": 395, "atom2_serNum": 900, "donAcc_type": "standard", "distance": 2.838, "atom1_id": "///A/394/NH2", "atom2_id": "///B/7/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 48, "atom1_serNum": 399, "atom2_serNum": 428, "donAcc_type": "standard", "distance": 3.069, "atom1_id": "///A/395/O", "atom2_id": "///A/399/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 49, "atom1_serNum": 402, "atom2_serNum": 408, "donAcc_type": "standard", "distance": 2.694, "atom1_id": "///A/396/N", "atom2_id": "///A/396/OD1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 50, "atom1_serNum": 405, "atom2_serNum": 437, "donAcc_type": "standard", "distance": 3.119, "atom1_id": "///A/396/O", "atom2_id": "///A/400/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 51, "atom1_serNum": 409, "atom2_serNum": 1159, "donAcc_type": "standard", "distance": 3.176, "atom1_id": "///A/396/OD2", "atom2_id": "///C/55/N4", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 52, "atom1_serNum": 409, "atom2_serNum": 1181, "donAcc_type": "standard", "distance": 3.797, "atom1_id": "///A/396/OD2", "atom2_id": "///C/56/N4", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 53, "atom1_serNum": 413, "atom2_serNum": 444, "donAcc_type": "standard", "distance": 2.944, "atom1_id": "///A/397/O", "atom2_id": "///A/401/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 54, "atom1_serNum": 419, "atom2_serNum": 875, "donAcc_type": "standard", "distance": 2.820, "atom1_id": "///A/397/NE2", "atom2_id": "///B/6/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 55, "atom1_serNum": 423, "atom2_serNum": 454, "donAcc_type": "standard", "distance": 2.928, "atom1_id": "///A/398/O", "atom2_id": "///A/402/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 56, "atom1_serNum": 431, "atom2_serNum": 459, "donAcc_type": "acceptable", "distance": 2.857, "atom1_id": "///A/399/O", "atom2_id": "///A/402/OG1", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 57, "atom1_serNum": 431, "atom2_serNum": 461, "donAcc_type": "standard", "distance": 3.772, "atom1_id": "///A/399/O", "atom2_id": "///A/403/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 58, "atom1_serNum": 436, "atom2_serNum": 1131, "donAcc_type": "standard", "distance": 2.277, "atom1_id": "///A/399/NZ", "atom2_id": "///C/55/OP2", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 59, "atom1_serNum": 440, "atom2_serNum": 461, "donAcc_type": "standard", "distance": 3.122, "atom1_id": "///A/400/O", "atom2_id": "///A/403/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 60, "atom1_serNum": 447, "atom2_serNum": 472, "donAcc_type": "standard", "distance": 2.866, "atom1_id": "///A/401/O", "atom2_id": "///A/404/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 61, "atom1_serNum": 447, "atom2_serNum": 477, "donAcc_type": "acceptable", "distance": 2.646, "atom1_id": "///A/401/O", "atom2_id": "///A/404/OG1", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 62, "atom1_serNum": 450, "atom2_serNum": 821, "donAcc_type": "acceptable", "distance": 2.706, "atom1_id": "///A/401/ND1", "atom2_id": "///B/4/OP1", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 63, "atom1_serNum": 453, "atom2_serNum": 488, "donAcc_type": "questionable", "distance": 3.272, "atom1_id": "///A/401/NE2", "atom2_id": "///A/405/NE2", "atom_pair": "N:N", "residue_pair": "aa:aa" }, { "index": 64, "atom1_serNum": 457, "atom2_serNum": 479, "donAcc_type": "standard", "distance": 2.900, "atom1_id": "///A/402/O", "atom2_id": "///A/405/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 65, "atom1_serNum": 464, "atom2_serNum": 496, "donAcc_type": "standard", "distance": 2.802, "atom1_id": "///A/403/O", "atom2_id": "///A/407/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 66, "atom1_serNum": 470, "atom2_serNum": 632, "donAcc_type": "standard", "distance": 2.864, "atom1_id": "///A/403/NH1", "atom2_id": "///A/423/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 67, "atom1_serNum": 494, "atom2_serNum": 500, "donAcc_type": "acceptable", "distance": 3.262, "atom1_id": "///A/406/OG1", "atom2_id": "///A/408/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 68, "atom1_serNum": 525, "atom2_serNum": 621, "donAcc_type": "standard", "distance": 3.030, "atom1_id": "///A/411/N", "atom2_id": "///A/422/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 69, "atom1_serNum": 528, "atom2_serNum": 618, "donAcc_type": "standard", "distance": 2.773, "atom1_id": "///A/411/O", "atom2_id": "///A/422/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 70, "atom1_serNum": 541, "atom2_serNum": 603, "donAcc_type": "standard", "distance": 2.878, "atom1_id": "///A/413/N", "atom2_id": "///A/420/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 71, "atom1_serNum": 547, "atom2_serNum": 713, "donAcc_type": "questionable", "distance": 3.098, "atom1_id": "///A/414/N", "atom2_id": "///A/432/NE2", "atom_pair": "N:N", "residue_pair": "aa:aa" }, { "index": 72, "atom1_serNum": 561, "atom2_serNum": 585, "donAcc_type": "standard", "distance": 2.942, "atom1_id": "///A/415/O", "atom2_id": "///A/418/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 73, "atom1_serNum": 634, "atom2_serNum": 666, "donAcc_type": "standard", "distance": 2.943, "atom1_id": "///A/424/N", "atom2_id": "///A/427/OE1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 74, "atom1_serNum": 637, "atom2_serNum": 668, "donAcc_type": "standard", "distance": 3.401, "atom1_id": "///A/424/O", "atom2_id": "///A/428/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 75, "atom1_serNum": 641, "atom2_serNum": 657, "donAcc_type": "standard", "distance": 2.937, "atom1_id": "///A/424/NE", "atom2_id": "///A/426/OD1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 76, "atom1_serNum": 643, "atom2_serNum": 833, "donAcc_type": "standard", "distance": 3.026, "atom1_id": "///A/424/NH1", "atom2_id": "///B/4/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 77, "atom1_serNum": 644, "atom2_serNum": 658, "donAcc_type": "standard", "distance": 2.870, "atom1_id": "///A/424/NH2", "atom2_id": "///A/426/OD2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 78, "atom1_serNum": 644, "atom2_serNum": 836, "donAcc_type": "standard", "distance": 2.826, "atom1_id": "///A/424/NH2", "atom2_id": "///B/4/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 79, "atom1_serNum": 648, "atom2_serNum": 676, "donAcc_type": "standard", "distance": 2.914, "atom1_id": "///A/425/O", "atom2_id": "///A/429/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 80, "atom1_serNum": 650, "atom2_serNum": 1167, "donAcc_type": "acceptable", "distance": 2.833, "atom1_id": "///A/425/OG", "atom2_id": "///C/56/OP2", "atom_pair": "O:O", "residue_pair": "aa:nt" }, { "index": 81, "atom1_serNum": 654, "atom2_serNum": 683, "donAcc_type": "standard", "distance": 3.068, "atom1_id": "///A/426/O", "atom2_id": "///A/430/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 82, "atom1_serNum": 662, "atom2_serNum": 694, "donAcc_type": "standard", "distance": 3.038, "atom1_id": "///A/427/O", "atom2_id": "///A/431/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 83, "atom1_serNum": 671, "atom2_serNum": 704, "donAcc_type": "standard", "distance": 2.792, "atom1_id": "///A/428/O", "atom2_id": "///A/432/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 84, "atom1_serNum": 679, "atom2_serNum": 714, "donAcc_type": "standard", "distance": 2.936, "atom1_id": "///A/429/O", "atom2_id": "///A/433/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 85, "atom1_serNum": 686, "atom2_serNum": 722, "donAcc_type": "standard", "distance": 3.073, "atom1_id": "///A/430/O", "atom2_id": "///A/434/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 86, "atom1_serNum": 692, "atom2_serNum": 795, "donAcc_type": "standard", "distance": 2.980, "atom1_id": "///A/430/NH1", "atom2_id": "///B/2/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 87, "atom1_serNum": 693, "atom2_serNum": 792, "donAcc_type": "standard", "distance": 2.819, "atom1_id": "///A/430/NH2", "atom2_id": "///B/2/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 88, "atom1_serNum": 697, "atom2_serNum": 730, "donAcc_type": "standard", "distance": 3.265, "atom1_id": "///A/431/O", "atom2_id": "///A/435/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 89, "atom1_serNum": 707, "atom2_serNum": 740, "donAcc_type": "standard", "distance": 3.513, "atom1_id": "///A/432/O", "atom2_id": "///A/436/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 90, "atom1_serNum": 717, "atom2_serNum": 755, "donAcc_type": "standard", "distance": 3.128, "atom1_id": "///A/433/O", "atom2_id": "///A/437/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 91, "atom1_serNum": 795, "atom2_serNum": 1321, "donAcc_type": "standard", "distance": 2.909, "atom1_id": "///B/2/O6", "atom2_id": "///C/61/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 92, "atom1_serNum": 796, "atom2_serNum": 1319, "donAcc_type": "standard", "distance": 2.926, "atom1_id": "///B/2/N1", "atom2_id": "///C/61/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 93, "atom1_serNum": 798, "atom2_serNum": 1318, "donAcc_type": "standard", "distance": 2.817, "atom1_id": "///B/2/N2", "atom2_id": "///C/61/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 94, "atom1_serNum": 814, "atom2_serNum": 1302, "donAcc_type": "standard", "distance": 2.865, "atom1_id": "///B/3/O2", "atom2_id": "///C/60/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 95, "atom1_serNum": 815, "atom2_serNum": 1300, "donAcc_type": "standard", "distance": 2.955, "atom1_id": "///B/3/N3", "atom2_id": "///C/60/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 96, "atom1_serNum": 817, "atom2_serNum": 1299, "donAcc_type": "standard", "distance": 2.891, "atom1_id": "///B/3/N4", "atom2_id": "///C/60/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 97, "atom1_serNum": 836, "atom2_serNum": 1280, "donAcc_type": "standard", "distance": 2.840, "atom1_id": "///B/4/O6", "atom2_id": "///C/59/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 98, "atom1_serNum": 837, "atom2_serNum": 1278, "donAcc_type": "standard", "distance": 2.825, "atom1_id": "///B/4/N1", "atom2_id": "///C/59/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 99, "atom1_serNum": 839, "atom2_serNum": 1277, "donAcc_type": "standard", "distance": 2.768, "atom1_id": "///B/4/N2", "atom2_id": "///C/59/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 100, "atom1_serNum": 856, "atom2_serNum": 1256, "donAcc_type": "standard", "distance": 2.761, "atom1_id": "///B/5/N3", "atom2_id": "///C/58/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 101, "atom1_serNum": 858, "atom2_serNum": 1254, "donAcc_type": "standard", "distance": 2.878, "atom1_id": "///B/5/O4", "atom2_id": "///C/58/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 102, "atom1_serNum": 878, "atom2_serNum": 1216, "donAcc_type": "standard", "distance": 3.001, "atom1_id": "///B/6/O6", "atom2_id": "///C/57/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 103, "atom1_serNum": 879, "atom2_serNum": 1212, "donAcc_type": "standard", "distance": 2.892, "atom1_id": "///B/6/N1", "atom2_id": "///C/57/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 104, "atom1_serNum": 881, "atom2_serNum": 1210, "donAcc_type": "standard", "distance": 2.742, "atom1_id": "///B/6/N2", "atom2_id": "///C/57/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 105, "atom1_serNum": 900, "atom2_serNum": 1159, "donAcc_type": "standard", "distance": 3.255, "atom1_id": "///B/7/O6", "atom2_id": "///C/55/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 106, "atom1_serNum": 900, "atom2_serNum": 1181, "donAcc_type": "standard", "distance": 2.836, "atom1_id": "///B/7/O6", "atom2_id": "///C/56/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 107, "atom1_serNum": 901, "atom2_serNum": 1179, "donAcc_type": "standard", "distance": 2.829, "atom1_id": "///B/7/N1", "atom2_id": "///C/56/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 108, "atom1_serNum": 903, "atom2_serNum": 1178, "donAcc_type": "standard", "distance": 2.832, "atom1_id": "///B/7/N2", "atom2_id": "///C/56/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 109, "atom1_serNum": 922, "atom2_serNum": 1159, "donAcc_type": "standard", "distance": 2.770, "atom1_id": "///B/8/O6", "atom2_id": "///C/55/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 110, "atom1_serNum": 923, "atom2_serNum": 1155, "donAcc_type": "standard", "distance": 2.792, "atom1_id": "///B/8/N1", "atom2_id": "///C/55/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 111, "atom1_serNum": 925, "atom2_serNum": 1153, "donAcc_type": "standard", "distance": 2.776, "atom1_id": "///B/8/N2", "atom2_id": "///C/55/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 112, "atom1_serNum": 941, "atom2_serNum": 1121, "donAcc_type": "standard", "distance": 3.019, "atom1_id": "///B/9/O2", "atom2_id": "///C/54/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 113, "atom1_serNum": 942, "atom2_serNum": 1117, "donAcc_type": "standard", "distance": 2.875, "atom1_id": "///B/9/N3", "atom2_id": "///C/54/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 114, "atom1_serNum": 944, "atom2_serNum": 1115, "donAcc_type": "standard", "distance": 2.720, "atom1_id": "///B/9/N4", "atom2_id": "///C/54/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 115, "atom1_serNum": 965, "atom2_serNum": 1078, "donAcc_type": "standard", "distance": 2.804, "atom1_id": "///B/10/O6", "atom2_id": "///C/53/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 116, "atom1_serNum": 966, "atom2_serNum": 1076, "donAcc_type": "standard", "distance": 2.919, "atom1_id": "///B/10/N1", "atom2_id": "///C/53/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 117, "atom1_serNum": 968, "atom2_serNum": 1075, "donAcc_type": "standard", "distance": 2.878, "atom1_id": "///B/10/N2", "atom2_id": "///C/53/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 118, "atom1_serNum": 985, "atom2_serNum": 1043, "donAcc_type": "standard", "distance": 2.629, "atom1_id": "///B/11/N3", "atom2_id": "///C/52/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 119, "atom1_serNum": 987, "atom2_serNum": 1041, "donAcc_type": "standard", "distance": 3.012, "atom1_id": "///B/11/O4", "atom2_id": "///C/52/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 120, "atom1_serNum": 1078, "atom2_serNum": 1333, "donAcc_type": "acceptable", "distance": 2.731, "atom1_id": "///C/53/N4", "atom2_id": "///C/101/O1", "atom_pair": "N:O", "residue_pair": "nt:ligand" }, { "index": 121, "atom1_serNum": 1081, "atom2_serNum": 1333, "donAcc_type": "acceptable", "distance": 3.153, "atom1_id": "///C/53/O5", "atom2_id": "///C/101/O1", "atom_pair": "O:O", "residue_pair": "nt:ligand" }, { "index": 122, "atom1_serNum": 1081, "atom2_serNum": 1335, "donAcc_type": "acceptable", "distance": 2.570, "atom1_id": "///C/53/O5", "atom2_id": "///C/101/O2", "atom_pair": "O:O", "residue_pair": "nt:ligand" }, { "index": 123, "atom1_serNum": 1115, "atom2_serNum": 1335, "donAcc_type": "acceptable", "distance": 2.732, "atom1_id": "///C/54/O6", "atom2_id": "///C/101/O2", "atom_pair": "O:O", "residue_pair": "nt:ligand" } ], "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": "4r2p", "num_aaChains": 1, "aaChains": "A=89", "num_naChains": 2, "naChains": "B=11,C=11", "num_atoms": 1356, "num_waters": 143, "num_metals": 3, "metals_desc": "Zn=3", "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": 12, "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-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-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 9, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 10, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 11, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 12, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }