{ "num_pairs": 12, "pairs": [ { "index": 1, "nt1": "///A/1", "nt2": "///B/24", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -116.878, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 52.220, "chi2": -117.656, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 59.466, "C1C1_dist": 10.498, "N1N9_dist": 8.857, "C6C8_dist": 9.856, "CNNC_torsion": -0.290, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[3.07],N1(imino)-N3[2.94],N2(amino)-O2(carbonyl)[2.70]", "interBase_angle": 0.191, "planarity": 0.005, "simple_Shear": -0.747, "simple_Stretch": -0.137, "simple_Buckle": 0.168, "simple_Propeller": -0.091, "bp_simpleParams": [ -0.747, -0.137, 0.002, 0.168, -0.091, 3.189 ], "bp_params": [ -0.736, -0.189, 0.002, 0.171, -0.085, 3.189 ], "frame": { "rmsd": null, "origin": [ -11.908, -7.683, -10.523 ], "x_axis": [ -0.164, -0.581, 0.797 ], "y_axis": [ 0.691, -0.644, -0.328 ], "z_axis": [ 0.704, 0.497, 0.507 ], "quaternion": [ -0.418, 0.493, 0.055, 0.761 ] } }, { "index": 2, "nt1": "///A/2", "nt2": "///B/23", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -116.508, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 54.085, "chi2": -114.388, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 56.354, "C1C1_dist": 10.491, "N1N9_dist": 8.815, "C6C8_dist": 9.798, "CNNC_torsion": -0.683, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[2.95],N1-N3(imino)[2.83]", "interBase_angle": 0.518, "planarity": 0.008, "simple_Shear": -0.244, "simple_Stretch": -0.156, "simple_Buckle": -0.075, "simple_Propeller": -0.513, "bp_simpleParams": [ -0.244, -0.156, -0.003, -0.075, -0.513, 1.032 ], "bp_params": [ -0.241, -0.161, -0.003, -0.065, -0.514, 1.031 ], "frame": { "rmsd": null, "origin": [ -10.607, -5.607, -8.182 ], "x_axis": [ 0.250, -0.848, 0.468 ], "y_axis": [ 0.668, -0.199, -0.717 ], "z_axis": [ 0.701, 0.492, 0.516 ], "quaternion": [ 0.626, -0.483, 0.093, -0.605 ] } }, { "index": 3, "nt1": "///A/3", "nt2": "///B/22", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -115.581, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 59.042, "chi2": -114.830, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 51.182, "C1C1_dist": 10.502, "N1N9_dist": 8.832, "C6C8_dist": 9.807, "CNNC_torsion": -0.766, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.73],N3-N1(imino)[2.93],N4(amino)-O6(carbonyl)[3.02]", "interBase_angle": 0.416, "planarity": 0.005, "simple_Shear": 0.838, "simple_Stretch": -0.181, "simple_Buckle": 0.138, "simple_Propeller": -0.393, "bp_simpleParams": [ 0.838, -0.181, -0.006, 0.138, -0.393, 2.191 ], "bp_params": [ 0.821, -0.247, -0.006, 0.111, -0.401, 2.190 ], "frame": { "rmsd": null, "origin": [ -8.950, -3.954, -5.746 ], "x_axis": [ 0.620, -0.781, -0.073 ], "y_axis": [ 0.370, 0.373, -0.851 ], "z_axis": [ 0.692, 0.501, 0.521 ], "quaternion": [ 0.793, -0.426, 0.241, -0.363 ] } }, { "index": 4, "nt1": "///A/4", "nt2": "///B/21", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -115.962, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 56.316, "chi2": -115.315, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 54.049, "C1C1_dist": 10.400, "N1N9_dist": 8.723, "C6C8_dist": 9.705, "CNNC_torsion": -1.460, "hbonds_num": 2, "hbonds_desc": "N3(imino)-N1[2.75],O4(carbonyl)-N6(amino)[2.86]", "interBase_angle": 0.882, "planarity": 0.013, "simple_Shear": 0.248, "simple_Stretch": -0.247, "simple_Buckle": -0.198, "simple_Propeller": -0.859, "bp_simpleParams": [ 0.248, -0.247, 0.006, -0.198, -0.859, 1.032 ], "bp_params": [ 0.243, -0.252, 0.006, -0.215, -0.855, 1.033 ], "frame": { "rmsd": null, "origin": [ -7.146, -3.091, -2.929 ], "x_axis": [ 0.719, -0.486, -0.496 ], "y_axis": [ 0.002, 0.716, -0.699 ], "z_axis": [ 0.695, 0.502, 0.515 ], "quaternion": [ 0.859, -0.349, 0.347, -0.142 ] } }, { "index": 5, "nt1": "///A/5", "nt2": "///B/20", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -113.294, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 52.059, "chi2": -115.042, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 57.166, "C1C1_dist": 10.602, "N1N9_dist": 8.907, "C6C8_dist": 9.863, "CNNC_torsion": -1.404, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.98],N1(imino)-N3[2.93],N2(amino)-O2(carbonyl)[2.76]", "interBase_angle": 0.582, "planarity": 0.009, "simple_Shear": -0.573, "simple_Stretch": -0.144, "simple_Buckle": 0.046, "simple_Propeller": -0.580, "bp_simpleParams": [ -0.573, -0.144, 0.005, 0.046, -0.580, 1.165 ], "bp_params": [ -0.565, -0.174, 0.005, 0.077, -0.576, 1.164 ], "frame": { "rmsd": null, "origin": [ -4.698, -2.755, -0.306 ], "x_axis": [ 0.630, -0.101, -0.770 ], "y_axis": [ -0.331, 0.862, -0.384 ], "z_axis": [ 0.702, 0.497, 0.510 ], "quaternion": [ 0.866, -0.254, 0.425, 0.067 ] } }, { "index": 6, "nt1": "///A/6", "nt2": "///B/19", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -116.107, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 55.529, "chi2": -115.769, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 51.092, "C1C1_dist": 10.590, "N1N9_dist": 8.837, "C6C8_dist": 9.737, "CNNC_torsion": -1.213, "hbonds_num": 2, "hbonds_desc": "N3(imino)-N1[2.86],O4(carbonyl)-N6(amino)[2.84]", "interBase_angle": 0.651, "planarity": 0.010, "simple_Shear": 0.424, "simple_Stretch": -0.205, "simple_Buckle": 0.026, "simple_Propeller": -0.650, "bp_simpleParams": [ 0.424, -0.205, 0.002, 0.026, -0.650, -2.482 ], "bp_params": [ 0.415, -0.222, 0.002, 0.001, -0.651, -2.482 ], "frame": { "rmsd": null, "origin": [ -1.988, -2.093, 1.755 ], "x_axis": [ 0.305, 0.424, -0.853 ], "y_axis": [ -0.652, 0.746, 0.138 ], "z_axis": [ 0.694, 0.514, 0.504 ], "quaternion": [ 0.799, -0.118, 0.484, 0.336 ] } }, { "index": 7, "nt1": "///A/7", "nt2": "///B/18", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -115.601, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 50.775, "chi2": -115.900, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 55.403, "C1C1_dist": 10.608, "N1N9_dist": 8.846, "C6C8_dist": 9.738, "CNNC_torsion": -1.380, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[2.83],N1-N3(imino)[2.87]", "interBase_angle": 0.635, "planarity": 0.010, "simple_Shear": -0.439, "simple_Stretch": -0.204, "simple_Buckle": -0.002, "simple_Propeller": -0.635, "bp_simpleParams": [ -0.439, -0.204, 0.004, -0.002, -0.635, -2.874 ], "bp_params": [ -0.430, -0.221, 0.004, 0.023, -0.635, -2.874 ], "frame": { "rmsd": null, "origin": [ 1.364, -1.448, 2.915 ], "x_axis": [ -0.030, 0.748, -0.663 ], "y_axis": [ -0.723, 0.442, 0.531 ], "z_axis": [ 0.690, 0.495, 0.528 ], "quaternion": [ 0.696, 0.013, 0.486, 0.528 ] } }, { "index": 8, "nt1": "///A/8", "nt2": "///B/17", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -114.973, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 57.567, "chi2": -113.153, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 51.578, "C1C1_dist": 10.593, "N1N9_dist": 8.897, "C6C8_dist": 9.851, "CNNC_torsion": -1.450, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.77],N3-N1(imino)[2.94],N4(amino)-O6(carbonyl)[2.98]", "interBase_angle": 0.597, "planarity": 0.009, "simple_Shear": 0.659, "simple_Stretch": -0.153, "simple_Buckle": -0.034, "simple_Propeller": -0.596, "bp_simpleParams": [ 0.659, -0.153, 0.001, -0.034, -0.596, 1.111 ], "bp_params": [ 0.648, -0.193, 0.001, -0.070, -0.593, 1.110 ], "frame": { "rmsd": null, "origin": [ 4.272, 0.268, 3.700 ], "x_axis": [ -0.455, 0.864, -0.214 ], "y_axis": [ -0.548, -0.083, 0.832 ], "z_axis": [ 0.701, 0.496, 0.512 ], "quaternion": [ 0.493, 0.170, 0.464, 0.716 ] } }, { "index": 9, "nt1": "///A/9", "nt2": "///B/16", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -115.279, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 54.136, "chi2": -115.985, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 56.705, "C1C1_dist": 10.380, "N1N9_dist": 8.713, "C6C8_dist": 9.705, "CNNC_torsion": -1.390, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[2.88],N1-N3(imino)[2.75]", "interBase_angle": 0.884, "planarity": 0.013, "simple_Shear": -0.279, "simple_Stretch": -0.246, "simple_Buckle": 0.209, "simple_Propeller": -0.859, "bp_simpleParams": [ -0.279, -0.246, 0.005, 0.209, -0.859, 1.527 ], "bp_params": [ -0.273, -0.253, 0.005, 0.229, -0.854, 1.527 ], "frame": { "rmsd": null, "origin": [ 7.109, 2.474, 4.000 ], "x_axis": [ -0.665, 0.721, 0.194 ], "y_axis": [ -0.273, -0.476, 0.836 ], "z_axis": [ 0.695, 0.503, 0.513 ], "quaternion": [ 0.305, 0.273, 0.411, 0.815 ] } }, { "index": 10, "nt1": "///A/10", "nt2": "///B/15", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -114.916, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 51.263, "chi2": -115.548, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 59.290, "C1C1_dist": 10.493, "N1N9_dist": 8.831, "C6C8_dist": 9.813, "CNNC_torsion": -0.454, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[3.04],N1(imino)-N3[2.94],N2(amino)-O2(carbonyl)[2.72]", "interBase_angle": 0.298, "planarity": 0.004, "simple_Shear": -0.849, "simple_Stretch": -0.173, "simple_Buckle": -0.067, "simple_Propeller": -0.290, "bp_simpleParams": [ -0.849, -0.173, -0.008, -0.067, -0.290, 2.543 ], "bp_params": [ -0.832, -0.240, -0.008, -0.044, -0.295, 2.543 ], "frame": { "rmsd": null, "origin": [ 9.290, 5.094, 4.582 ], "x_axis": [ -0.714, 0.380, 0.588 ], "y_axis": [ 0.104, -0.773, 0.626 ], "z_axis": [ 0.693, 0.508, 0.512 ], "quaternion": [ 0.080, 0.370, 0.328, 0.866 ] } }, { "index": 11, "nt1": "///A/11", "nt2": "///B/14", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -114.594, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 56.177, "chi2": -116.545, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 54.471, "C1C1_dist": 10.488, "N1N9_dist": 8.819, "C6C8_dist": 9.806, "CNNC_torsion": -0.387, "hbonds_num": 2, "hbonds_desc": "N3(imino)-N1[2.83],O4(carbonyl)-N6(amino)[2.96]", "interBase_angle": 0.411, "planarity": 0.007, "simple_Shear": 0.196, "simple_Stretch": -0.147, "simple_Buckle": 0.090, "simple_Propeller": -0.401, "bp_simpleParams": [ 0.196, -0.147, -0.004, 0.090, -0.401, 1.263 ], "bp_params": [ 0.194, -0.150, -0.004, 0.085, -0.402, 1.262 ], "frame": { "rmsd": null, "origin": [ 11.129, 7.583, 5.967 ], "x_axis": [ -0.492, -0.175, 0.853 ], "y_axis": [ 0.516, -0.848, 0.124 ], "z_axis": [ 0.701, 0.501, 0.507 ], "quaternion": [ -0.205, 0.461, 0.185, 0.844 ] } }, { "index": 12, "nt1": "///A/12", "nt2": "///B/13", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": false, "chi1": -117.651, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 59.929, "chi2": -117.057, "conf2": "anti", "pucker2": "~C2'-endo", "lambda2": 52.166, "C1C1_dist": 10.469, "N1N9_dist": 8.838, "C6C8_dist": 9.844, "CNNC_torsion": -0.007, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.68],N3-N1(imino)[2.94],N4(amino)-O6(carbonyl)[3.08]", "interBase_angle": 0.161, "planarity": 0.004, "simple_Shear": 0.787, "simple_Stretch": -0.144, "simple_Buckle": -0.132, "simple_Propeller": -0.093, "bp_simpleParams": [ 0.787, -0.144, -0.001, -0.132, -0.093, 3.514 ], "bp_params": [ 0.775, -0.202, -0.001, -0.161, 0.005, 3.513 ], "frame": { "rmsd": null, "origin": [ 12.471, 10.161, 7.743 ], "x_axis": [ -0.127, -0.625, 0.770 ], "y_axis": [ 0.702, -0.606, -0.376 ], "z_axis": [ 0.701, 0.493, 0.515 ], "quaternion": [ -0.442, 0.491, 0.039, 0.750 ] } } ], "num_helices": 1, "helices": [ { "index": 1, "num_stems": 1, "strand1": "GACTGTACAGTC", "strand2": "CTGACATGTCAG", "bp_type": "||||||||||||", "helix_form": ".B.......B.", "helical_rise": 3.209, "helical_rise_std": 0.068, "helical_radius": 10.348, "helical_radius_std": 0.145, "helical_axis": [ 0.689, 0.507, 0.518 ], "point1": [ -12.164, -9.173, -8.720 ], "point2": [ 12.160, 8.708, 9.570 ], "num_pairs": 12, "pairs": [ { "index": 1, "nt1": "///A/1", "nt2": "///B/24", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.736, -0.189, 0.002, 0.171, -0.085, 3.189 ], "step_params": [ 0.053, -1.276, 3.139, 0.323, 0.543, 34.406 ], "heli_params": [ -2.238, -0.042, 3.119, 0.918, -0.546, 34.412 ], "bp2_params": [ -0.241, -0.161, -0.003, -0.065, -0.514, 1.031 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.139, "simple_Twist": 31.721, "simple_hRise": 3.117, "simple_hTwist": 31.727 }, { "index": 2, "nt1": "///A/2", "nt2": "///B/23", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.241, -0.161, -0.003, -0.065, -0.514, 1.031 ], "step_params": [ -0.157, -0.953, 3.237, 0.439, -0.615, 38.478 ], "heli_params": [ -1.370, 0.292, 3.250, -0.934, -0.665, 38.486 ], "bp2_params": [ 0.821, -0.247, -0.006, 0.111, -0.401, 2.190 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.237, "simple_Twist": 32.600, "simple_hRise": 3.252, "simple_hTwist": 32.609 }, { "index": 3, "nt1": "///A/3", "nt2": "///B/22", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.821, -0.247, -0.006, 0.111, -0.401, 2.190 ], "step_params": [ -0.143, -1.428, 3.142, -0.300, 0.171, 30.454 ], "heli_params": [ -2.751, 0.216, 3.136, 0.326, 0.572, 30.456 ], "bp2_params": [ 0.243, -0.252, 0.006, -0.215, -0.855, 1.033 ], "groove_widths": [ 11.391, null, 21.062, null ], "simple_Rise": 3.142, "simple_Twist": 33.640, "simple_hRise": 3.136, "simple_hTwist": 33.642 }, { "index": 4, "nt1": "///A/4", "nt2": "///B/21", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.243, -0.252, 0.006, -0.215, -0.855, 1.033 ], "step_params": [ -0.111, -1.610, 3.222, 0.102, 0.569, 27.828 ], "heli_params": [ -3.479, 0.255, 3.188, 1.182, -0.212, 27.834 ], "bp2_params": [ -0.565, -0.174, 0.005, 0.077, -0.576, 1.164 ], "groove_widths": [ 11.578, 11.291, 20.851, 20.492 ], "simple_Rise": 3.222, "simple_Twist": 32.291, "simple_hRise": 3.193, "simple_hTwist": 32.296 }, { "index": 5, "nt1": "///A/5", "nt2": "///B/20", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.565, -0.174, 0.005, 0.077, -0.576, 1.164 ], "step_params": [ -0.303, -1.111, 3.272, -1.078, 0.260, 36.273 ], "heli_params": [ -1.820, 0.336, 3.272, 0.418, 1.730, 36.289 ], "bp2_params": [ 0.415, -0.222, 0.002, 0.001, -0.651, -2.482 ], "groove_widths": [ 11.612, 11.332, 20.810, 20.470 ], "simple_Rise": 3.272, "simple_Twist": 30.926, "simple_hRise": 3.271, "simple_hTwist": 30.945 }, { "index": 6, "nt1": "///A/6", "nt2": "///B/19", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.415, -0.222, 0.002, 0.001, -0.651, -2.482 ], "step_params": [ -0.040, -1.571, 3.245, 0.007, -1.781, 29.103 ], "heli_params": [ -2.729, 0.081, 3.333, -3.540, -0.015, 29.156 ], "bp2_params": [ -0.430, -0.221, 0.004, 0.023, -0.635, -2.874 ], "groove_widths": [ 11.619, 11.337, 20.866, 20.624 ], "simple_Rise": 3.245, "simple_Twist": 33.682, "simple_hRise": 3.321, "simple_hTwist": 33.728 }, { "index": 7, "nt1": "///A/7", "nt2": "///B/18", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.430, -0.221, 0.004, 0.023, -0.635, -2.874 ], "step_params": [ 0.342, -1.062, 3.282, 1.084, 0.314, 36.708 ], "heli_params": [ -1.729, -0.394, 3.281, 0.498, -1.721, 36.725 ], "bp2_params": [ 0.648, -0.193, 0.001, -0.070, -0.593, 1.110 ], "groove_widths": [ 11.640, 11.357, 20.708, 20.394 ], "simple_Rise": 3.282, "simple_Twist": 30.820, "simple_hRise": 3.281, "simple_hTwist": 30.840 }, { "index": 8, "nt1": "///A/8", "nt2": "///B/17", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.648, -0.193, 0.001, -0.070, -0.593, 1.110 ], "step_params": [ 0.161, -1.582, 3.237, -0.105, 0.549, 27.777 ], "heli_params": [ -3.424, -0.360, 3.205, 1.144, 0.218, 27.783 ], "bp2_params": [ -0.273, -0.253, 0.005, 0.229, -0.854, 1.527 ], "groove_widths": [ 11.608, 11.312, 20.773, 20.429 ], "simple_Rise": 3.237, "simple_Twist": 32.861, "simple_hRise": 3.210, "simple_hTwist": 32.866 }, { "index": 9, "nt1": "///A/9", "nt2": "///B/16", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.273, -0.253, 0.005, 0.229, -0.854, 1.527 ], "step_params": [ 0.172, -1.446, 3.137, 0.248, 0.232, 30.341 ], "heli_params": [ -2.808, -0.280, 3.128, 0.444, -0.474, 30.343 ], "bp2_params": [ -0.832, -0.240, -0.008, -0.044, -0.295, 2.543 ], "groove_widths": [ 11.420, null, 21.161, null ], "simple_Rise": 3.137, "simple_Twist": 33.432, "simple_hRise": 3.129, "simple_hTwist": 33.434 }, { "index": 10, "nt1": "///A/10", "nt2": "///B/15", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.832, -0.240, -0.008, -0.044, -0.295, 2.543 ], "step_params": [ 0.158, -0.975, 3.243, -0.424, -0.572, 38.162 ], "heli_params": [ -1.419, -0.294, 3.255, -0.875, 0.648, 38.168 ], "bp2_params": [ 0.194, -0.150, -0.004, 0.085, -0.402, 1.262 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.243, "simple_Twist": 32.475, "simple_hRise": 3.257, "simple_hTwist": 32.483 }, { "index": 11, "nt1": "///A/11", "nt2": "///B/14", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.194, -0.150, -0.004, 0.085, -0.402, 1.262 ], "step_params": [ -0.002, -1.343, 3.130, -0.291, 0.608, 34.018 ], "heli_params": [ -2.388, -0.041, 3.106, 1.039, 0.497, 34.025 ], "bp2_params": [ 0.775, -0.202, -0.001, -0.161, 0.005, 3.513 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.130, "simple_Twist": 30.850, "simple_hRise": 3.104, "simple_hTwist": 30.857 }, { "index": 12, "nt1": "///A/12", "nt2": "///B/13", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_stems": 1, "stems": [ { "index": 1, "helix_index": 1, "strand1": "GACTGTACAGTC", "strand2": "CTGACATGTCAG", "bp_type": "||||||||||||", "helix_form": ".B.......B.", "helical_rise": 3.209, "helical_rise_std": 0.068, "helical_radius": 10.348, "helical_radius_std": 0.145, "helical_axis": [ 0.689, 0.507, 0.518 ], "point1": [ -12.164, -9.173, -8.720 ], "point2": [ 12.160, 8.708, 9.570 ], "num_pairs": 12, "pairs": [ { "index": 1, "nt1": "///A/1", "nt2": "///B/24", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.736, -0.189, 0.002, 0.171, -0.085, 3.189 ], "step_params": [ 0.053, -1.276, 3.139, 0.323, 0.543, 34.406 ], "heli_params": [ -2.238, -0.042, 3.119, 0.918, -0.546, 34.412 ], "bp2_params": [ -0.241, -0.161, -0.003, -0.065, -0.514, 1.031 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.139, "simple_Twist": 31.721, "simple_hRise": 3.117, "simple_hTwist": 31.727 }, { "index": 2, "nt1": "///A/2", "nt2": "///B/23", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.241, -0.161, -0.003, -0.065, -0.514, 1.031 ], "step_params": [ -0.157, -0.953, 3.237, 0.439, -0.615, 38.478 ], "heli_params": [ -1.370, 0.292, 3.250, -0.934, -0.665, 38.486 ], "bp2_params": [ 0.821, -0.247, -0.006, 0.111, -0.401, 2.190 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.237, "simple_Twist": 32.600, "simple_hRise": 3.252, "simple_hTwist": 32.609 }, { "index": 3, "nt1": "///A/3", "nt2": "///B/22", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.821, -0.247, -0.006, 0.111, -0.401, 2.190 ], "step_params": [ -0.143, -1.428, 3.142, -0.300, 0.171, 30.454 ], "heli_params": [ -2.751, 0.216, 3.136, 0.326, 0.572, 30.456 ], "bp2_params": [ 0.243, -0.252, 0.006, -0.215, -0.855, 1.033 ], "groove_widths": [ 11.391, null, 21.062, null ], "simple_Rise": 3.142, "simple_Twist": 33.640, "simple_hRise": 3.136, "simple_hTwist": 33.642 }, { "index": 4, "nt1": "///A/4", "nt2": "///B/21", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.243, -0.252, 0.006, -0.215, -0.855, 1.033 ], "step_params": [ -0.111, -1.610, 3.222, 0.102, 0.569, 27.828 ], "heli_params": [ -3.479, 0.255, 3.188, 1.182, -0.212, 27.834 ], "bp2_params": [ -0.565, -0.174, 0.005, 0.077, -0.576, 1.164 ], "groove_widths": [ 11.578, 11.291, 20.851, 20.492 ], "simple_Rise": 3.222, "simple_Twist": 32.291, "simple_hRise": 3.193, "simple_hTwist": 32.296 }, { "index": 5, "nt1": "///A/5", "nt2": "///B/20", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.565, -0.174, 0.005, 0.077, -0.576, 1.164 ], "step_params": [ -0.303, -1.111, 3.272, -1.078, 0.260, 36.273 ], "heli_params": [ -1.820, 0.336, 3.272, 0.418, 1.730, 36.289 ], "bp2_params": [ 0.415, -0.222, 0.002, 0.001, -0.651, -2.482 ], "groove_widths": [ 11.612, 11.332, 20.810, 20.470 ], "simple_Rise": 3.272, "simple_Twist": 30.926, "simple_hRise": 3.271, "simple_hTwist": 30.945 }, { "index": 6, "nt1": "///A/6", "nt2": "///B/19", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.415, -0.222, 0.002, 0.001, -0.651, -2.482 ], "step_params": [ -0.040, -1.571, 3.245, 0.007, -1.781, 29.103 ], "heli_params": [ -2.729, 0.081, 3.333, -3.540, -0.015, 29.156 ], "bp2_params": [ -0.430, -0.221, 0.004, 0.023, -0.635, -2.874 ], "groove_widths": [ 11.619, 11.337, 20.866, 20.624 ], "simple_Rise": 3.245, "simple_Twist": 33.682, "simple_hRise": 3.321, "simple_hTwist": 33.728 }, { "index": 7, "nt1": "///A/7", "nt2": "///B/18", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.430, -0.221, 0.004, 0.023, -0.635, -2.874 ], "step_params": [ 0.342, -1.062, 3.282, 1.084, 0.314, 36.708 ], "heli_params": [ -1.729, -0.394, 3.281, 0.498, -1.721, 36.725 ], "bp2_params": [ 0.648, -0.193, 0.001, -0.070, -0.593, 1.110 ], "groove_widths": [ 11.640, 11.357, 20.708, 20.394 ], "simple_Rise": 3.282, "simple_Twist": 30.820, "simple_hRise": 3.281, "simple_hTwist": 30.840 }, { "index": 8, "nt1": "///A/8", "nt2": "///B/17", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.648, -0.193, 0.001, -0.070, -0.593, 1.110 ], "step_params": [ 0.161, -1.582, 3.237, -0.105, 0.549, 27.777 ], "heli_params": [ -3.424, -0.360, 3.205, 1.144, 0.218, 27.783 ], "bp2_params": [ -0.273, -0.253, 0.005, 0.229, -0.854, 1.527 ], "groove_widths": [ 11.608, 11.312, 20.773, 20.429 ], "simple_Rise": 3.237, "simple_Twist": 32.861, "simple_hRise": 3.210, "simple_hTwist": 32.866 }, { "index": 9, "nt1": "///A/9", "nt2": "///B/16", "bp": "A-T", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.273, -0.253, 0.005, 0.229, -0.854, 1.527 ], "step_params": [ 0.172, -1.446, 3.137, 0.248, 0.232, 30.341 ], "heli_params": [ -2.808, -0.280, 3.128, 0.444, -0.474, 30.343 ], "bp2_params": [ -0.832, -0.240, -0.008, -0.044, -0.295, 2.543 ], "groove_widths": [ 11.420, null, 21.161, null ], "simple_Rise": 3.137, "simple_Twist": 33.432, "simple_hRise": 3.129, "simple_hTwist": 33.434 }, { "index": 10, "nt1": "///A/10", "nt2": "///B/15", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.832, -0.240, -0.008, -0.044, -0.295, 2.543 ], "step_params": [ 0.158, -0.975, 3.243, -0.424, -0.572, 38.162 ], "heli_params": [ -1.419, -0.294, 3.255, -0.875, 0.648, 38.168 ], "bp2_params": [ 0.194, -0.150, -0.004, 0.085, -0.402, 1.262 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.243, "simple_Twist": 32.475, "simple_hRise": 3.257, "simple_hTwist": 32.483 }, { "index": 11, "nt1": "///A/11", "nt2": "///B/14", "bp": "T-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.194, -0.150, -0.004, 0.085, -0.402, 1.262 ], "step_params": [ -0.002, -1.343, 3.130, -0.291, 0.608, 34.018 ], "heli_params": [ -2.388, -0.041, 3.106, 1.039, 0.497, 34.025 ], "bp2_params": [ 0.775, -0.202, -0.001, -0.161, 0.005, 3.513 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.130, "simple_Twist": 30.850, "simple_hRise": 3.104, "simple_hTwist": 30.857 }, { "index": 12, "nt1": "///A/12", "nt2": "///B/13", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_stacks": 0, "stacks": [], "dbn": { "all_chains": { "num_nts": 24, "num_chars": 25, "bseq": "GACTGTACAGTC&GACTGTACAGTC", "sstr": "((((((((((((&))))))))))))", "form": "...........-&...........-" }, "chain_A": { "num_nts": 12, "num_chars": 12, "bseq": "GACTGTACAGTC", "sstr": "((((((((((((", "form": "...........-" }, "chain_B": { "num_nts": 12, "num_chars": 12, "bseq": "GACTGTACAGTC", "sstr": "))))))))))))", "form": "...........-" } }, "chains": { "chain_A": { "num_nts": 12, "bseq": "GACTGTACAGTC", "sstr": "((((((((((((", "form": "...........-", "helical_rise": 3.210, "helical_rise_std": 0.065, "helical_axis": [ 0.690, 0.513, 0.511 ], "point1": [ -12.195, -9.358, -8.629 ], "point2": [ 12.163, 8.744, 9.419 ], "num_chars": 34, "suite": "G!!A!!C!!T!!G!!T!!A!!C!!A!!G!!T!!C" }, "chain_B": { "num_nts": 12, "bseq": "GACTGTACAGTC", "sstr": "))))))))))))", "form": "...........-", "helical_rise": 3.207, "helical_rise_std": 0.063, "helical_axis": [ -0.688, -0.501, -0.525 ], "point1": [ 12.130, 8.649, 9.756 ], "point2": [ -12.130, -9.021, -8.780 ], "num_chars": 34, "suite": "G!!A!!C!!T!!G!!T!!A!!C!!A!!G!!T!!C" } }, "num_nts": 24, "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,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end", "alpha": null, "beta": null, "gamma": 56.012, "delta": 135.951, "epsilon": 171.794, "zeta": -95.931, "epsilon_zeta": -92.275, "bb_type": "BI", "chi": -116.878, "glyco_bond": "anti", "C5prime_xyz": [ -2.384, 8.520, -1.486 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 2.351, "Dp": 2.367, "splay_angle": 19.480, "splay_distance": 3.456, "splay_ratio": 0.179, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -28.051, "v1": 36.530, "v2": -30.949, "v3": 15.549, "v4": 7.583, "amplitude": 36.003, "phase_angle": 149.274, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.003, "frame": { "rmsd": 0.003, "origin": [ -11.913, -7.407, -10.785 ], "x_axis": [ -0.144, -0.599, 0.788 ], "y_axis": [ 0.696, -0.627, -0.350 ], "z_axis": [ 0.704, 0.498, 0.507 ], "quaternion": [ -0.429, 0.494, 0.049, 0.755 ] } }, { "index": 2, "index_chain": 2, "chain_name": "A", "nt_resnum": 2, "nt_name": "DA", "nt_code": "A", "nt_id": "///A/2", "linked_nts": [ "///A/1", "///A/3" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -53.137, "beta": -167.796, "gamma": 38.615, "delta": 135.441, "epsilon": 171.670, "zeta": -100.858, "epsilon_zeta": -87.473, "bb_type": "BI", "chi": -116.508, "glyco_bond": "anti", "C5prime_xyz": [ -2.419, 8.458, -1.550 ], "P_xyz": [ -0.555, 10.166, -0.855 ], "form": ".", "ssZp": 2.319, "Dp": 2.372, "splay_angle": 20.243, "splay_distance": 3.385, "splay_ratio": 0.180, "d22": null, "d64": null, "eta": 168.861, "theta": -152.986, "eta_prime": -169.708, "theta_prime": -159.817, "eta_base": -123.750, "theta_base": -115.734, "v0": -28.346, "v1": 36.613, "v2": -30.744, "v3": 15.139, "v4": 8.064, "amplitude": 36.040, "phase_angle": 148.544, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.002, "origin": [ -10.691, -5.490, -8.182 ], "x_axis": [ 0.259, -0.847, 0.464 ], "y_axis": [ 0.665, -0.192, -0.721 ], "z_axis": [ 0.700, 0.496, 0.514 ], "quaternion": [ 0.629, -0.484, 0.094, -0.601 ] } }, { "index": 3, "index_chain": 3, "chain_name": "A", "nt_resnum": 3, "nt_name": "DC", "nt_code": "C", "nt_id": "///A/3", "linked_nts": [ "///A/2", "///A/4" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -62.735, "beta": -168.885, "gamma": 51.543, "delta": 136.608, "epsilon": 171.887, "zeta": -98.718, "epsilon_zeta": -89.395, "bb_type": "BI", "chi": -115.581, "glyco_bond": "anti", "C5prime_xyz": [ -2.136, 8.496, -1.552 ], "P_xyz": [ 0.112, 9.723, -0.989 ], "form": ".", "ssZp": 2.265, "Dp": 2.302, "splay_angle": 19.807, "splay_distance": 3.421, "splay_ratio": 0.177, "d22": 4.279, "d64": 4.222, "eta": 168.225, "theta": -144.858, "eta_prime": -168.455, "theta_prime": -158.981, "eta_base": -116.939, "theta_base": -129.749, "v0": -23.910, "v1": 33.303, "v2": -29.725, "v3": 16.610, "v4": 4.373, "amplitude": 33.123, "phase_angle": 153.820, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.063, "frame": { "rmsd": 0.001, "origin": [ -8.743, -4.322, -5.673 ], "x_axis": [ 0.630, -0.772, -0.087 ], "y_axis": [ 0.359, 0.389, -0.849 ], "z_axis": [ 0.689, 0.503, 0.522 ], "quaternion": [ 0.797, -0.424, 0.244, -0.355 ] } }, { "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,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -53.951, "beta": -167.969, "gamma": 39.687, "delta": 136.358, "epsilon": 174.867, "zeta": -99.902, "epsilon_zeta": -85.231, "bb_type": "BI", "chi": -115.962, "glyco_bond": "anti", "C5prime_xyz": [ -2.273, 8.459, -1.545 ], "P_xyz": [ -0.298, 10.029, -0.836 ], "form": ".", "ssZp": 2.310, "Dp": 2.343, "splay_angle": 20.450, "splay_distance": 3.630, "splay_ratio": 0.186, "d22": null, "d64": null, "eta": 169.440, "theta": -148.670, "eta_prime": -170.982, "theta_prime": -158.467, "eta_base": -132.791, "theta_base": -133.040, "v0": -25.467, "v1": 34.511, "v2": -30.056, "v3": 16.084, "v4": 5.688, "amplitude": 34.102, "phase_angle": 151.809, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.105, "frame": { "rmsd": 0.003, "origin": [ -7.056, -3.239, -2.900 ], "x_axis": [ 0.724, -0.476, -0.499 ], "y_axis": [ -0.006, 0.719, -0.695 ], "z_axis": [ 0.689, 0.507, 0.518 ], "quaternion": [ 0.860, -0.349, 0.345, -0.137 ] } }, { "index": 5, "index_chain": 5, "chain_name": "A", "nt_resnum": 5, "nt_name": "DG", "nt_code": "G", "nt_id": "///A/5", "linked_nts": [ "///A/4", "///A/6" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -47.928, "beta": -167.227, "gamma": 31.970, "delta": 135.895, "epsilon": 169.741, "zeta": -97.779, "epsilon_zeta": -92.480, "bb_type": "BI", "chi": -113.294, "glyco_bond": "anti", "C5prime_xyz": [ -2.354, 8.439, -1.669 ], "P_xyz": [ -0.559, 10.236, -1.018 ], "form": ".", "ssZp": 2.302, "Dp": 2.333, "splay_angle": 20.245, "splay_distance": 3.477, "splay_ratio": 0.182, "d22": null, "d64": null, "eta": 169.245, "theta": -153.262, "eta_prime": -171.742, "theta_prime": -160.639, "eta_base": -138.343, "theta_base": -121.249, "v0": -26.095, "v1": 35.019, "v2": -30.278, "v3": 15.920, "v4": 6.115, "amplitude": 34.564, "phase_angle": 151.162, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.003, "frame": { "rmsd": 0.003, "origin": [ -4.845, -2.801, -0.054 ], "x_axis": [ 0.631, -0.089, -0.771 ], "y_axis": [ -0.337, 0.863, -0.376 ], "z_axis": [ 0.699, 0.497, 0.514 ], "quaternion": [ 0.867, -0.252, 0.424, 0.072 ] } }, { "index": 6, "index_chain": 6, "chain_name": "A", "nt_resnum": 6, "nt_name": "DT", "nt_code": "T", "nt_id": "///A/6", "linked_nts": [ "///A/5", "///A/7" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -53.879, "beta": -168.105, "gamma": 42.109, "delta": 136.590, "epsilon": 172.662, "zeta": -99.056, "epsilon_zeta": -88.282, "bb_type": "BI", "chi": -116.107, "glyco_bond": "anti", "C5prime_xyz": [ -2.265, 8.458, -1.538 ], "P_xyz": [ -0.245, 9.977, -0.838 ], "form": ".", "ssZp": 2.281, "Dp": 2.329, "splay_angle": 20.570, "splay_distance": 3.627, "splay_ratio": 0.187, "d22": null, "d64": null, "eta": 170.217, "theta": -148.016, "eta_prime": -168.555, "theta_prime": -159.287, "eta_base": -121.781, "theta_base": -131.595, "v0": -25.178, "v1": 34.394, "v2": -30.231, "v3": 16.400, "v4": 5.278, "amplitude": 34.084, "phase_angle": 152.493, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.105, "frame": { "rmsd": 0.003, "origin": [ -1.851, -2.087, 1.563 ], "x_axis": [ 0.323, 0.410, -0.853 ], "y_axis": [ -0.645, 0.755, 0.119 ], "z_axis": [ 0.693, 0.511, 0.509 ], "quaternion": [ 0.804, -0.122, 0.480, 0.328 ] } }, { "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,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -48.547, "beta": -167.406, "gamma": 34.724, "delta": 135.228, "epsilon": 170.749, "zeta": -92.082, "epsilon_zeta": -97.168, "bb_type": "BI", "chi": -115.601, "glyco_bond": "anti", "C5prime_xyz": [ -2.358, 8.443, -1.590 ], "P_xyz": [ -0.528, 10.187, -0.901 ], "form": ".", "ssZp": 2.339, "Dp": 2.386, "splay_angle": 20.441, "splay_distance": 3.554, "splay_ratio": 0.185, "d22": null, "d64": null, "eta": 170.663, "theta": -146.722, "eta_prime": -170.637, "theta_prime": -154.324, "eta_base": -134.625, "theta_base": -108.440, "v0": -27.261, "v1": 35.458, "v2": -29.852, "v3": 14.843, "v4": 7.585, "amplitude": 34.869, "phase_angle": 148.882, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.003, "origin": [ 1.452, -1.657, 2.999 ], "x_axis": [ -0.008, 0.740, -0.673 ], "y_axis": [ -0.723, 0.461, 0.514 ], "z_axis": [ 0.690, 0.491, 0.532 ], "quaternion": [ 0.704, 0.008, 0.484, 0.519 ] } }, { "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,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -58.654, "beta": -168.527, "gamma": 45.466, "delta": 134.317, "epsilon": 172.190, "zeta": -97.981, "epsilon_zeta": -89.830, "bb_type": "BI", "chi": -114.973, "glyco_bond": "anti", "C5prime_xyz": [ -2.354, 8.495, -1.659 ], "P_xyz": [ -0.303, 10.042, -1.145 ], "form": ".", "ssZp": 2.327, "Dp": 2.390, "splay_angle": 20.235, "splay_distance": 3.605, "splay_ratio": 0.185, "d22": null, "d64": null, "eta": 168.338, "theta": -148.413, "eta_prime": -166.866, "theta_prime": -160.036, "eta_base": -112.522, "theta_base": -132.285, "v0": -28.254, "v1": 35.672, "v2": -29.327, "v3": 13.705, "v4": 8.887, "amplitude": 35.056, "phase_angle": 146.780, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.063, "frame": { "rmsd": 0.002, "origin": [ 4.177, 0.556, 3.551 ], "x_axis": [ -0.457, 0.866, -0.203 ], "y_axis": [ -0.544, -0.092, 0.834 ], "z_axis": [ 0.703, 0.491, 0.513 ], "quaternion": [ 0.491, 0.174, 0.461, 0.718 ] } }, { "index": 9, "index_chain": 9, "chain_name": "A", "nt_resnum": 9, "nt_name": "DA", "nt_code": "A", "nt_id": "///A/9", "linked_nts": [ "///A/8", "///A/10" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -47.589, "beta": -167.563, "gamma": 33.812, "delta": 134.748, "epsilon": 171.790, "zeta": -98.749, "epsilon_zeta": -89.461, "bb_type": "BI", "chi": -115.279, "glyco_bond": "anti", "C5prime_xyz": [ -2.438, 8.429, -1.628 ], "P_xyz": [ -0.671, 10.252, -0.973 ], "form": ".", "ssZp": 2.324, "Dp": 2.374, "splay_angle": 19.628, "splay_distance": 3.510, "splay_ratio": 0.181, "d22": null, "d64": null, "eta": 171.172, "theta": -153.444, "eta_prime": -170.234, "theta_prime": -161.315, "eta_base": -134.577, "theta_base": -129.243, "v0": -28.295, "v1": 36.154, "v2": -30.066, "v3": 14.463, "v4": 8.463, "amplitude": 35.562, "phase_angle": 147.721, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.002, "origin": [ 7.236, 2.437, 3.869 ], "x_axis": [ -0.664, 0.718, 0.209 ], "y_axis": [ -0.262, -0.485, 0.834 ], "z_axis": [ 0.701, 0.499, 0.510 ], "quaternion": [ 0.301, 0.279, 0.409, 0.815 ] } }, { "index": 10, "index_chain": 10, "chain_name": "A", "nt_resnum": 10, "nt_name": "DG", "nt_code": "G", "nt_id": "///A/10", "linked_nts": [ "///A/9", "///A/11" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -48.038, "beta": -167.560, "gamma": 34.032, "delta": 136.405, "epsilon": 169.786, "zeta": -95.188, "epsilon_zeta": -95.026, "bb_type": "BI", "chi": -114.916, "glyco_bond": "anti", "C5prime_xyz": [ -2.354, 8.482, -1.587 ], "P_xyz": [ -0.534, 10.235, -0.881 ], "form": ".", "ssZp": 2.307, "Dp": 2.335, "splay_angle": 20.210, "splay_distance": 3.477, "splay_ratio": 0.182, "d22": null, "d64": null, "eta": 169.764, "theta": -149.341, "eta_prime": -170.588, "theta_prime": -157.356, "eta_base": -131.087, "theta_base": -112.301, "v0": -26.699, "v1": 35.827, "v2": -31.046, "v3": 16.337, "v4": 6.273, "amplitude": 35.418, "phase_angle": 151.230, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.002, "frame": { "rmsd": 0.002, "origin": [ 9.572, 5.027, 4.260 ], "x_axis": [ -0.709, 0.364, 0.603 ], "y_axis": [ 0.120, -0.781, 0.613 ], "z_axis": [ 0.694, 0.507, 0.510 ], "quaternion": [ 0.071, 0.375, 0.323, 0.866 ] } }, { "index": 11, "index_chain": 11, "chain_name": "A", "nt_resnum": 11, "nt_name": "DT", "nt_code": "T", "nt_id": "///A/11", "linked_nts": [ "///A/10", "///A/12" ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -53.403, "beta": -167.598, "gamma": 40.644, "delta": 137.416, "epsilon": 170.188, "zeta": -96.292, "epsilon_zeta": -93.520, "bb_type": "BI", "chi": -114.594, "glyco_bond": "anti", "C5prime_xyz": [ -2.278, 8.434, -1.555 ], "P_xyz": [ -0.274, 9.976, -0.861 ], "form": ".", "ssZp": 2.300, "Dp": 2.310, "splay_angle": 19.409, "splay_distance": 3.377, "splay_ratio": 0.176, "d22": 4.116, "d64": 4.089, "eta": 168.856, "theta": -146.525, "eta_prime": -167.493, "theta_prime": -157.312, "eta_base": -114.029, "theta_base": -118.162, "v0": -24.690, "v1": 34.690, "v2": -31.028, "v3": 17.462, "v4": 4.308, "amplitude": 34.472, "phase_angle": 154.170, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.104, "frame": { "rmsd": 0.003, "origin": [ 11.041, 7.629, 6.039 ], "x_axis": [ -0.484, -0.182, 0.856 ], "y_axis": [ 0.522, -0.845, 0.115 ], "z_axis": [ 0.703, 0.502, 0.504 ], "quaternion": [ -0.209, 0.463, 0.183, 0.842 ] } }, { "index": 12, "index_chain": 12, "chain_name": "A", "nt_resnum": 12, "nt_name": "DC", "nt_code": "C", "nt_id": "///A/12", "linked_nts": [ "///A/11", null ], "nt_type": "DNA", "dbn": "(", "summary": "anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end", "alpha": -57.878, "beta": -168.330, "gamma": 44.771, "delta": 135.192, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -117.651, "glyco_bond": "anti", "C5prime_xyz": [ -2.276, 8.537, -1.511 ], "P_xyz": [ -0.248, 10.042, -0.819 ], "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": -26.039, "v1": 33.840, "v2": -28.581, "v3": 14.322, "v4": 7.186, "amplitude": 33.325, "phase_angle": 149.053, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.063, "frame": { "rmsd": 0.001, "origin": [ 12.350, 9.980, 8.079 ], "x_axis": [ -0.106, -0.643, 0.758 ], "y_axis": [ 0.704, -0.587, -0.400 ], "z_axis": [ 0.702, 0.492, 0.515 ], "quaternion": [ -0.453, 0.492, 0.031, 0.743 ] } }, { "index": 13, "index_chain": 1, "chain_name": "B", "nt_resnum": 13, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/13", "linked_nts": [ null, "///B/14" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end", "alpha": null, "beta": null, "gamma": 55.927, "delta": 136.284, "epsilon": 172.052, "zeta": -95.757, "epsilon_zeta": -92.191, "bb_type": "BI", "chi": -117.057, "glyco_bond": "anti", "C5prime_xyz": [ -2.378, 8.522, -1.468 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 2.353, "Dp": 2.363, "splay_angle": 19.455, "splay_distance": 3.470, "splay_ratio": 0.180, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -27.749, "v1": 36.379, "v2": -31.034, "v3": 15.825, "v4": 7.203, "amplitude": 35.894, "phase_angle": 149.838, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.004, "frame": { "rmsd": 0.004, "origin": [ 12.592, 10.342, 7.407 ], "x_axis": [ -0.149, -0.606, 0.781 ], "y_axis": [ -0.698, 0.624, 0.351 ], "z_axis": [ -0.700, -0.494, -0.516 ], "quaternion": [ -0.490, -0.431, 0.756, -0.047 ] } }, { "index": 14, "index_chain": 2, "chain_name": "B", "nt_resnum": 14, "nt_name": "DA", "nt_code": "A", "nt_id": "///B/14", "linked_nts": [ "///B/13", "///B/15" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -52.227, "beta": -167.567, "gamma": 37.174, "delta": 135.393, "epsilon": 171.589, "zeta": -101.135, "epsilon_zeta": -87.276, "bb_type": "BI", "chi": -116.545, "glyco_bond": "anti", "C5prime_xyz": [ -2.428, 8.456, -1.550 ], "P_xyz": [ -0.604, 10.198, -0.840 ], "form": ".", "ssZp": 2.323, "Dp": 2.373, "splay_angle": 20.305, "splay_distance": 3.391, "splay_ratio": 0.181, "d22": null, "d64": null, "eta": 168.813, "theta": -153.923, "eta_prime": -169.948, "theta_prime": -160.105, "eta_base": -124.612, "theta_base": -116.377, "v0": -28.376, "v1": 36.593, "v2": -30.746, "v3": 15.131, "v4": 8.080, "amplitude": 36.048, "phase_angle": 148.531, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.003, "origin": [ 11.217, 7.537, 5.894 ], "x_axis": [ -0.500, -0.167, 0.850 ], "y_axis": [ -0.510, 0.850, -0.133 ], "z_axis": [ -0.700, -0.500, -0.510 ], "quaternion": [ -0.458, -0.200, 0.846, -0.187 ] } }, { "index": 15, "index_chain": 3, "chain_name": "B", "nt_resnum": 15, "nt_name": "DC", "nt_code": "C", "nt_id": "///B/15", "linked_nts": [ "///B/14", "///B/16" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -62.824, "beta": -168.830, "gamma": 51.891, "delta": 136.933, "epsilon": 172.037, "zeta": -99.575, "epsilon_zeta": -88.388, "bb_type": "BI", "chi": -115.548, "glyco_bond": "anti", "C5prime_xyz": [ -2.145, 8.495, -1.551 ], "P_xyz": [ 0.097, 9.714, -0.981 ], "form": ".", "ssZp": 2.266, "Dp": 2.301, "splay_angle": 19.853, "splay_distance": 3.425, "splay_ratio": 0.178, "d22": 4.298, "d64": 4.238, "eta": 168.226, "theta": -144.970, "eta_prime": -168.492, "theta_prime": -159.214, "eta_base": -117.502, "theta_base": -130.282, "v0": -24.075, "v1": 33.550, "v2": -30.026, "v3": 16.829, "v4": 4.340, "amplitude": 33.416, "phase_angle": 153.968, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.063, "frame": { "rmsd": 0.002, "origin": [ 9.008, 5.162, 4.904 ], "x_axis": [ -0.718, 0.396, 0.573 ], "y_axis": [ -0.089, 0.764, -0.639 ], "z_axis": [ -0.691, -0.510, -0.513 ], "quaternion": [ -0.365, 0.089, 0.865, -0.332 ] } }, { "index": 16, "index_chain": 4, "chain_name": "B", "nt_resnum": 16, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/16", "linked_nts": [ "///B/15", "///B/17" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -54.227, "beta": -168.016, "gamma": 40.049, "delta": 136.471, "epsilon": 175.099, "zeta": -101.043, "epsilon_zeta": -83.858, "bb_type": "BI", "chi": -115.985, "glyco_bond": "anti", "C5prime_xyz": [ -2.270, 8.457, -1.543 ], "P_xyz": [ -0.290, 10.018, -0.840 ], "form": ".", "ssZp": 2.309, "Dp": 2.340, "splay_angle": 20.700, "splay_distance": 3.651, "splay_ratio": 0.188, "d22": null, "d64": null, "eta": 169.589, "theta": -149.469, "eta_prime": -171.132, "theta_prime": -159.033, "eta_base": -133.297, "theta_base": -134.476, "v0": -25.449, "v1": 34.566, "v2": -30.121, "v3": 16.168, "v4": 5.614, "amplitude": 34.140, "phase_angle": 151.918, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.105, "frame": { "rmsd": 0.003, "origin": [ 6.982, 2.511, 4.131 ], "x_axis": [ -0.667, 0.724, 0.179 ], "y_axis": [ 0.283, 0.468, -0.837 ], "z_axis": [ -0.690, -0.508, -0.516 ], "quaternion": [ -0.267, 0.309, 0.814, -0.413 ] } }, { "index": 17, "index_chain": 5, "chain_name": "B", "nt_resnum": 17, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/17", "linked_nts": [ "///B/16", "///B/18" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -49.117, "beta": -167.205, "gamma": 33.347, "delta": 136.138, "epsilon": 169.682, "zeta": -97.783, "epsilon_zeta": -92.535, "bb_type": "BI", "chi": -113.153, "glyco_bond": "anti", "C5prime_xyz": [ -2.341, 8.437, -1.674 ], "P_xyz": [ -0.514, 10.197, -1.033 ], "form": ".", "ssZp": 2.291, "Dp": 2.328, "splay_angle": 20.302, "splay_distance": 3.474, "splay_ratio": 0.182, "d22": null, "d64": null, "eta": 169.221, "theta": -152.583, "eta_prime": -171.930, "theta_prime": -160.275, "eta_base": -139.584, "theta_base": -120.599, "v0": -25.819, "v1": 34.870, "v2": -30.310, "v3": 16.097, "v4": 5.846, "amplitude": 34.457, "phase_angle": 151.601, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.002, "frame": { "rmsd": 0.002, "origin": [ 4.366, -0.020, 3.849 ], "x_axis": [ -0.454, 0.863, -0.224 ], "y_axis": [ 0.552, 0.075, -0.830 ], "z_axis": [ -0.699, -0.500, -0.510 ], "quaternion": [ -0.166, 0.495, 0.714, -0.466 ] } }, { "index": 18, "index_chain": 6, "chain_name": "B", "nt_resnum": 18, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/18", "linked_nts": [ "///B/17", "///B/19" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -55.165, "beta": -168.158, "gamma": 43.481, "delta": 136.731, "epsilon": 172.429, "zeta": -98.460, "epsilon_zeta": -89.111, "bb_type": "BI", "chi": -115.900, "glyco_bond": "anti", "C5prime_xyz": [ -2.268, 8.453, -1.546 ], "P_xyz": [ -0.222, 9.947, -0.861 ], "form": ".", "ssZp": 2.271, "Dp": 2.322, "splay_angle": 20.464, "splay_distance": 3.617, "splay_ratio": 0.187, "d22": null, "d64": null, "eta": 169.739, "theta": -146.896, "eta_prime": -168.456, "theta_prime": -158.828, "eta_base": -121.288, "theta_base": -130.374, "v0": -25.117, "v1": 34.493, "v2": -30.506, "v3": 16.684, "v4": 5.060, "amplitude": 34.259, "phase_angle": 152.928, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.104, "frame": { "rmsd": 0.004, "origin": [ 1.277, -1.239, 2.830 ], "x_axis": [ -0.051, 0.756, -0.652 ], "y_axis": [ 0.722, -0.423, -0.547 ], "z_axis": [ -0.690, -0.499, -0.524 ], "quaternion": [ -0.018, 0.688, 0.537, -0.487 ] } }, { "index": 19, "index_chain": 7, "chain_name": "B", "nt_resnum": 19, "nt_name": "DA", "nt_code": "A", "nt_id": "///B/19", "linked_nts": [ "///B/18", "///B/20" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -49.104, "beta": -167.312, "gamma": 35.059, "delta": 135.196, "epsilon": 170.802, "zeta": -92.927, "epsilon_zeta": -96.271, "bb_type": "BI", "chi": -115.769, "glyco_bond": "anti", "C5prime_xyz": [ -2.375, 8.444, -1.588 ], "P_xyz": [ -0.549, 10.195, -0.905 ], "form": ".", "ssZp": 2.347, "Dp": 2.386, "splay_angle": 20.330, "splay_distance": 3.541, "splay_ratio": 0.185, "d22": null, "d64": null, "eta": 170.470, "theta": -147.460, "eta_prime": -170.566, "theta_prime": -155.098, "eta_base": -133.559, "theta_base": -110.381, "v0": -27.626, "v1": 35.698, "v2": -29.921, "v3": 14.681, "v4": 7.900, "amplitude": 35.111, "phase_angle": 148.449, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.003, "origin": [ -2.124, -2.099, 1.947 ], "x_axis": [ 0.287, 0.437, -0.853 ], "y_axis": [ 0.658, -0.737, -0.156 ], "z_axis": [ -0.696, -0.516, -0.499 ], "quaternion": [ 0.113, 0.794, 0.345, -0.488 ] } }, { "index": 20, "index_chain": 8, "chain_name": "B", "nt_resnum": 20, "nt_name": "DC", "nt_code": "C", "nt_id": "///B/20", "linked_nts": [ "///B/19", "///B/21" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -58.044, "beta": -168.487, "gamma": 45.096, "delta": 134.504, "epsilon": 172.229, "zeta": -97.859, "epsilon_zeta": -89.912, "bb_type": "BI", "chi": -115.042, "glyco_bond": "anti", "C5prime_xyz": [ -2.353, 8.495, -1.656 ], "P_xyz": [ -0.309, 10.051, -1.128 ], "form": ".", "ssZp": 2.323, "Dp": 2.388, "splay_angle": 20.153, "splay_distance": 3.608, "splay_ratio": 0.185, "d22": null, "d64": null, "eta": 168.617, "theta": -148.136, "eta_prime": -167.144, "theta_prime": -159.874, "eta_base": -114.093, "theta_base": -132.386, "v0": -28.330, "v1": 35.800, "v2": -29.446, "v3": 13.789, "v4": 8.870, "amplitude": 35.174, "phase_angle": 146.841, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.063, "frame": { "rmsd": 0.002, "origin": [ -4.551, -2.710, -0.558 ], "x_axis": [ 0.630, -0.112, -0.768 ], "y_axis": [ 0.325, -0.860, 0.392 ], "z_axis": [ -0.705, -0.497, -0.506 ], "quaternion": [ 0.257, 0.866, 0.062, -0.426 ] } }, { "index": 21, "index_chain": 9, "chain_name": "B", "nt_resnum": 21, "nt_name": "DA", "nt_code": "A", "nt_id": "///B/21", "linked_nts": [ "///B/20", "///B/22" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -46.572, "beta": -167.498, "gamma": 32.572, "delta": 134.819, "epsilon": 171.686, "zeta": -99.471, "epsilon_zeta": -88.843, "bb_type": "BI", "chi": -115.315, "glyco_bond": "anti", "C5prime_xyz": [ -2.446, 8.428, -1.627 ], "P_xyz": [ -0.714, 10.283, -0.960 ], "form": ".", "ssZp": 2.320, "Dp": 2.375, "splay_angle": 19.710, "splay_distance": 3.506, "splay_ratio": 0.182, "d22": null, "d64": null, "eta": 171.219, "theta": -154.610, "eta_prime": -170.297, "theta_prime": -161.845, "eta_base": -134.838, "theta_base": -129.596, "v0": -28.451, "v1": 36.314, "v2": -30.178, "v3": 14.479, "v4": 8.534, "amplitude": 35.721, "phase_angle": 147.654, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.038, "frame": { "rmsd": 0.002, "origin": [ -7.235, -2.943, -2.958 ], "x_axis": [ 0.714, -0.496, -0.494 ], "y_axis": [ -0.009, -0.712, 0.702 ], "z_axis": [ -0.700, -0.497, -0.513 ], "quaternion": [ 0.350, 0.857, -0.148, -0.348 ] } }, { "index": 22, "index_chain": 10, "chain_name": "B", "nt_resnum": 22, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/22", "linked_nts": [ "///B/21", "///B/23" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -48.747, "beta": -167.579, "gamma": 35.197, "delta": 136.778, "epsilon": 169.626, "zeta": -95.110, "epsilon_zeta": -95.264, "bb_type": "BI", "chi": -114.830, "glyco_bond": "anti", "C5prime_xyz": [ -2.343, 8.476, -1.594 ], "P_xyz": [ -0.495, 10.199, -0.888 ], "form": ".", "ssZp": 2.287, "Dp": 2.328, "splay_angle": 20.195, "splay_distance": 3.467, "splay_ratio": 0.182, "d22": null, "d64": null, "eta": 169.774, "theta": -148.548, "eta_prime": -170.444, "theta_prime": -157.043, "eta_base": -131.004, "theta_base": -111.443, "v0": -26.504, "v1": 35.894, "v2": -31.362, "v3": 16.804, "v4": 5.880, "amplitude": 35.543, "phase_angle": 151.930, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.002, "frame": { "rmsd": 0.002, "origin": [ -9.157, -3.586, -5.819 ], "x_axis": [ 0.611, -0.790, -0.059 ], "y_axis": [ -0.381, -0.358, 0.852 ], "z_axis": [ -0.694, -0.498, -0.519 ], "quaternion": [ 0.428, 0.789, -0.371, -0.239 ] } }, { "index": 23, "index_chain": 11, "chain_name": "B", "nt_resnum": 23, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/23", "linked_nts": [ "///B/22", "///B/24" ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -54.135, "beta": -167.616, "gamma": 41.437, "delta": 137.676, "epsilon": 170.257, "zeta": -98.073, "epsilon_zeta": -91.669, "bb_type": "BI", "chi": -114.388, "glyco_bond": "anti", "C5prime_xyz": [ -2.276, 8.429, -1.568 ], "P_xyz": [ -0.262, 9.958, -0.879 ], "form": ".", "ssZp": 2.280, "Dp": 2.302, "splay_angle": 19.507, "splay_distance": 3.349, "splay_ratio": 0.176, "d22": 4.175, "d64": 4.063, "eta": 168.640, "theta": -147.561, "eta_prime": -167.377, "theta_prime": -158.124, "eta_base": -113.268, "theta_base": -118.977, "v0": -24.670, "v1": 34.878, "v2": -31.370, "v3": 17.821, "v4": 4.067, "amplitude": 34.720, "phase_angle": 154.624, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.104, "frame": { "rmsd": 0.003, "origin": [ -10.522, -5.725, -8.183 ], "x_axis": [ 0.241, -0.848, 0.472 ], "y_axis": [ -0.671, 0.206, 0.712 ], "z_axis": [ -0.702, -0.488, -0.519 ], "quaternion": [ 0.482, 0.623, -0.609, -0.092 ] } }, { "index": 24, "index_chain": 12, "chain_name": "B", "nt_resnum": 24, "nt_name": "DC", "nt_code": "C", "nt_id": "///B/24", "linked_nts": [ "///B/23", null ], "nt_type": "DNA", "dbn": ")", "summary": "anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end", "alpha": -59.976, "beta": -168.560, "gamma": 47.491, "delta": 135.294, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -117.656, "glyco_bond": "anti", "C5prime_xyz": [ -2.236, 8.532, -1.514 ], "P_xyz": [ -0.142, 9.944, -0.845 ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -25.293, "v1": 33.194, "v2": -28.345, "v3": 14.501, "v4": 6.616, "amplitude": 32.768, "phase_angle": 149.884, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.062, "frame": { "rmsd": 0.002, "origin": [ -11.904, -7.958, -10.261 ], "x_axis": [ -0.183, -0.564, 0.805 ], "y_axis": [ -0.685, 0.661, 0.307 ], "z_axis": [ -0.705, -0.495, -0.507 ], "quaternion": [ -0.493, -0.407, 0.767, -0.061 ] } } ], "num_hbonds": 30, "hbonds": [ { "index": 1, "atom1_serNum": 14, "atom2_serNum": 747, "donAcc_type": "standard", "distance": 3.067, "atom1_id": "///A/1/O6", "atom2_id": "///B/24/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 15, "atom2_serNum": 745, "donAcc_type": "standard", "distance": 2.944, "atom1_id": "///A/1/N1", "atom2_id": "///B/24/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 17, "atom2_serNum": 744, "donAcc_type": "standard", "distance": 2.696, "atom1_id": "///A/1/N2", "atom2_id": "///B/24/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 48, "atom2_serNum": 715, "donAcc_type": "standard", "distance": 2.953, "atom1_id": "///A/2/N6", "atom2_id": "///B/23/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 49, "atom2_serNum": 713, "donAcc_type": "standard", "distance": 2.834, "atom1_id": "///A/2/N1", "atom2_id": "///B/23/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 77, "atom2_serNum": 685, "donAcc_type": "standard", "distance": 2.728, "atom1_id": "///A/3/O2", "atom2_id": "///B/22/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 78, "atom2_serNum": 683, "donAcc_type": "standard", "distance": 2.934, "atom1_id": "///A/3/N3", "atom2_id": "///B/22/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 8, "atom1_serNum": 80, "atom2_serNum": 682, "donAcc_type": "standard", "distance": 3.020, "atom1_id": "///A/3/N4", "atom2_id": "///B/22/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 9, "atom1_serNum": 108, "atom2_serNum": 651, "donAcc_type": "standard", "distance": 2.746, "atom1_id": "///A/4/N3", "atom2_id": "///B/21/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 110, "atom2_serNum": 650, "donAcc_type": "standard", "distance": 2.865, "atom1_id": "///A/4/O4", "atom2_id": "///B/21/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 142, "atom2_serNum": 620, "donAcc_type": "standard", "distance": 2.980, "atom1_id": "///A/5/O6", "atom2_id": "///B/20/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 12, "atom1_serNum": 143, "atom2_serNum": 618, "donAcc_type": "standard", "distance": 2.933, "atom1_id": "///A/5/N1", "atom2_id": "///B/20/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 13, "atom1_serNum": 145, "atom2_serNum": 617, "donAcc_type": "standard", "distance": 2.760, "atom1_id": "///A/5/N2", "atom2_id": "///B/20/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 14, "atom1_serNum": 173, "atom2_serNum": 589, "donAcc_type": "standard", "distance": 2.862, "atom1_id": "///A/6/N3", "atom2_id": "///B/19/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 175, "atom2_serNum": 588, "donAcc_type": "standard", "distance": 2.839, "atom1_id": "///A/6/O4", "atom2_id": "///B/19/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 16, "atom1_serNum": 207, "atom2_serNum": 556, "donAcc_type": "standard", "distance": 2.831, "atom1_id": "///A/7/N6", "atom2_id": "///B/18/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 17, "atom1_serNum": 208, "atom2_serNum": 554, "donAcc_type": "standard", "distance": 2.871, "atom1_id": "///A/7/N1", "atom2_id": "///B/18/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 236, "atom2_serNum": 526, "donAcc_type": "standard", "distance": 2.771, "atom1_id": "///A/8/O2", "atom2_id": "///B/17/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 19, "atom1_serNum": 237, "atom2_serNum": 524, "donAcc_type": "standard", "distance": 2.938, "atom1_id": "///A/8/N3", "atom2_id": "///B/17/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 239, "atom2_serNum": 523, "donAcc_type": "standard", "distance": 2.984, "atom1_id": "///A/8/N4", "atom2_id": "///B/17/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 21, "atom1_serNum": 269, "atom2_serNum": 491, "donAcc_type": "standard", "distance": 2.883, "atom1_id": "///A/9/N6", "atom2_id": "///B/16/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 22, "atom1_serNum": 270, "atom2_serNum": 489, "donAcc_type": "standard", "distance": 2.746, "atom1_id": "///A/9/N1", "atom2_id": "///B/16/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 23, "atom1_serNum": 301, "atom2_serNum": 461, "donAcc_type": "standard", "distance": 3.039, "atom1_id": "///A/10/O6", "atom2_id": "///B/15/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 24, "atom1_serNum": 302, "atom2_serNum": 459, "donAcc_type": "standard", "distance": 2.938, "atom1_id": "///A/10/N1", "atom2_id": "///B/15/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 25, "atom1_serNum": 304, "atom2_serNum": 458, "donAcc_type": "standard", "distance": 2.720, "atom1_id": "///A/10/N2", "atom2_id": "///B/15/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 26, "atom1_serNum": 332, "atom2_serNum": 430, "donAcc_type": "standard", "distance": 2.833, "atom1_id": "///A/11/N3", "atom2_id": "///B/14/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 27, "atom1_serNum": 334, "atom2_serNum": 429, "donAcc_type": "standard", "distance": 2.962, "atom1_id": "///A/11/O4", "atom2_id": "///B/14/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 28, "atom1_serNum": 363, "atom2_serNum": 398, "donAcc_type": "standard", "distance": 2.682, "atom1_id": "///A/12/O2", "atom2_id": "///B/13/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 29, "atom1_serNum": 364, "atom2_serNum": 396, "donAcc_type": "standard", "distance": 2.942, "atom1_id": "///A/12/N3", "atom2_id": "///B/13/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 30, "atom1_serNum": 366, "atom2_serNum": 395, "donAcc_type": "standard", "distance": 3.078, "atom1_id": "///A/12/N4", "atom2_id": "///B/13/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "1x2o", "num_naChains": 2, "naChains": "A=12,B=12", "num_atoms": 760, "num_waters": 0, "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 11, "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-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 9, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 10, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 11, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }