{ "num_pairs": 5, "pairs": [ { "index": 1, "nt1": "///A/27", "nt2": "///A/43", "bp": "U-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -151.595, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 59.967, "chi2": -148.660, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 53.738, "C1C1_dist": 10.816, "N1N9_dist": 9.200, "C6C8_dist": 10.187, "CNNC_torsion": -1.795, "hbonds_num": 2, "hbonds_desc": "N3(imino)-N1[3.35],O4(carbonyl)-N6(amino)[3.46]", "interBase_angle": 11.853, "planarity": 0.209, "simple_Shear": 0.639, "simple_Stretch": 0.221, "simple_Buckle": -1.152, "simple_Propeller": -11.797, "bp_simpleParams": [ 0.639, 0.221, -0.767, -1.152, -11.797, 3.384 ], "bp_params": [ 0.651, 0.183, -0.767, -1.839, -11.710, 3.402 ], "frame": { "rmsd": null, "origin": [ 4.220, 2.528, 4.584 ], "x_axis": [ -0.832, 0.527, 0.171 ], "y_axis": [ -0.497, -0.847, 0.190 ], "z_axis": [ 0.245, 0.073, 0.967 ], "quaternion": [ 0.268, 0.109, 0.069, 0.955 ] } }, { "index": 2, "nt1": "///A/28", "nt2": "///A/42", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -155.549, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 48.306, "chi2": -149.635, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 56.868, "C1C1_dist": 10.826, "N1N9_dist": 9.035, "C6C8_dist": 9.875, "CNNC_torsion": -19.257, "hbonds_num": 3, "hbonds_desc": "O2(carbonyl)-N2(amino)[2.94],N3-N1(imino)[2.88],N4(amino)-O6(carbonyl)[2.86]", "interBase_angle": 21.820, "planarity": 0.274, "simple_Shear": -0.738, "simple_Stretch": -0.114, "simple_Buckle": -3.992, "simple_Propeller": -21.452, "bp_simpleParams": [ -0.738, -0.114, 0.228, -3.992, -21.452, -3.554 ], "bp_params": [ -0.727, -0.170, 0.228, -2.299, -21.698, -3.618 ], "frame": { "rmsd": null, "origin": [ 5.827, 4.035, 8.040 ], "x_axis": [ -0.989, 0.135, 0.055 ], "y_axis": [ -0.131, -0.989, 0.071 ], "z_axis": [ 0.064, 0.063, 0.996 ], "quaternion": [ 0.067, 0.030, 0.033, 0.997 ] } }, { "index": 3, "nt1": "///A/29", "nt2": "///A/41", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -152.838, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 58.446, "chi2": -154.390, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 49.220, "C1C1_dist": 10.762, "N1N9_dist": 9.024, "C6C8_dist": 9.906, "CNNC_torsion": -16.668, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O4(carbonyl)[2.94],N1-N3(imino)[2.89]", "interBase_angle": 18.295, "planarity": 0.220, "simple_Shear": 0.825, "simple_Stretch": -0.019, "simple_Buckle": 1.751, "simple_Propeller": -18.211, "bp_simpleParams": [ 0.825, -0.019, 0.187, 1.751, -18.211, -2.964 ], "bp_params": [ 0.820, -0.092, 0.187, 0.130, -18.295, -3.002 ], "frame": { "rmsd": null, "origin": [ 5.348, 5.319, 11.373 ], "x_axis": [ -0.867, -0.483, -0.126 ], "y_axis": [ 0.475, -0.876, 0.089 ], "z_axis": [ -0.153, 0.018, 0.988 ], "quaternion": [ -0.248, -0.072, 0.028, 0.966 ] } }, { "index": 4, "nt1": "///A/30", "nt2": "///A/40", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -154.531, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 57.762, "chi2": -150.423, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 47.522, "C1C1_dist": 10.793, "N1N9_dist": 9.005, "C6C8_dist": 9.833, "CNNC_torsion": -15.862, "hbonds_num": 3, "hbonds_desc": "O6(carbonyl)-N4(amino)[2.81],N1(imino)-N3[2.88],N2(amino)-O2(carbonyl)[3.00]", "interBase_angle": 28.212, "planarity": 0.309, "simple_Shear": 0.651, "simple_Stretch": -0.115, "simple_Buckle": -10.298, "simple_Propeller": -26.265, "bp_simpleParams": [ 0.651, -0.115, -0.447, -10.298, -26.265, -1.513 ], "bp_params": [ 0.640, -0.168, -0.447, -12.282, -25.398, -1.543 ], "frame": { "rmsd": null, "origin": [ 3.229, 6.260, 15.165 ], "x_axis": [ -0.480, -0.853, -0.206 ], "y_axis": [ 0.809, -0.521, 0.271 ], "z_axis": [ -0.339, -0.037, 0.940 ], "quaternion": [ -0.484, -0.159, 0.068, 0.858 ] } }, { "index": 5, "nt1": "///A/31", "nt2": "///A/39", "bp": "A-P", "name": "--", "Saenger": "--", "LW": "cWW", "DSSR": "cW-W", "intra_chain": true, "chi1": -156.518, "conf1": "anti", "pucker1": "~C3'-endo", "lambda1": 55.925, "chi2": -151.239, "conf2": "anti", "pucker2": "~C3'-endo", "lambda2": 38.596, "C1C1_dist": 11.151, "N1N9_dist": 9.134, "C6C8_dist": 9.682, "CNNC_torsion": -13.902, "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.76],N1-N3(imino)[2.94]", "interBase_angle": 33.064, "planarity": 0.423, "simple_Shear": 1.414, "simple_Stretch": 0.088, "simple_Buckle": -16.128, "simple_Propeller": -28.864, "bp_simpleParams": [ 1.414, 0.088, 0.206, -16.128, -28.864, -18.796 ], "bp_params": [ 1.408, -0.158, 0.206, -20.718, -25.768, -18.979 ], "frame": { "rmsd": null, "origin": [ 0.713, 6.847, 18.554 ], "x_axis": [ 0.159, -0.964, -0.212 ], "y_axis": [ 0.927, 0.072, 0.369 ], "z_axis": [ -0.340, -0.255, 0.905 ], "quaternion": [ 0.731, 0.213, -0.044, -0.647 ] } } ], "num_helices": 1, "helices": [ { "index": 1, "num_stems": 1, "strand1": "UCAGA", "strand2": "AGUCP", "bp_type": "||||.", "helix_form": "AA..", "helical_rise": 2.653, "helical_rise_std": 0.117, "helical_radius": 9.574, "helical_radius_std": 0.575, "helical_axis": [ 0.008, -0.342, 0.940 ], "point1": [ 0.651, 5.393, 5.654 ], "point2": [ 0.732, 1.827, 15.436 ], "num_pairs": 5, "pairs": [ { "index": 1, "nt1": "///A/27", "nt2": "///A/43", "bp": "U-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.651, 0.183, -0.767, -1.839, -11.710, 3.402 ], "step_params": [ -0.562, -1.536, 3.758, -4.150, 9.682, 23.384 ], "heli_params": [ -6.411, 0.004, 2.953, 22.482, 9.636, 25.617 ], "bp2_params": [ -0.727, -0.170, 0.228, -2.299, -21.698, -3.618 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.758, "simple_Twist": 30.585, "simple_hRise": 3.184, "simple_hTwist": 32.307 }, { "index": 2, "nt1": "///A/28", "nt2": "///A/42", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.727, -0.170, 0.228, -2.299, -21.698, -3.618 ], "step_params": [ 0.113, -1.188, 3.401, -0.219, 12.740, 36.164 ], "heli_params": [ -3.385, -0.199, 2.837, 19.782, 0.339, 38.272 ], "bp2_params": [ 0.820, -0.092, 0.187, 0.130, -18.295, -3.002 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.401, "simple_Twist": 28.138, "simple_hRise": 2.628, "simple_hTwist": 30.835 }, { "index": 3, "nt1": "///A/29", "nt2": "///A/41", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.820, -0.092, 0.187, 0.130, -18.295, -3.002 ], "step_params": [ 0.128, -1.479, 4.189, 5.364, 10.119, 29.787 ], "heli_params": [ -4.935, 0.955, 3.484, 18.831, -9.983, 31.866 ], "bp2_params": [ 0.640, -0.168, -0.447, -12.282, -25.398, -1.543 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 4.189, "simple_Twist": 30.213, "simple_hRise": 3.497, "simple_hTwist": 32.264 }, { "index": 4, "nt1": "///A/30", "nt2": "///A/40", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.640, -0.168, -0.447, -12.282, -25.398, -1.543 ], "step_params": [ -0.863, -1.433, 3.919, -2.248, 12.526, 35.835 ], "heli_params": [ -4.024, 1.001, 3.300, 19.612, 3.520, 37.958 ], "bp2_params": [ 1.408, -0.158, 0.206, -20.718, -25.768, -18.979 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.919, "simple_Twist": 31.036, "simple_hRise": 3.174, "simple_hTwist": 33.484 }, { "index": 5, "nt1": "///A/31", "nt2": "///A/39", "bp": "A-P", "name": "--", "Saenger": "--", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_stems": 1, "stems": [ { "index": 1, "helix_index": 1, "strand1": "UCAG", "strand2": "AGUC", "bp_type": "||||", "helix_form": "AA.", "helical_rise": 2.843, "helical_rise_std": 0.079, "helical_radius": 9.633, "helical_radius_std": 0.145, "helical_axis": [ 0.012, -0.293, 0.956 ], "point1": [ 1.084, 5.106, 5.336 ], "point2": [ 1.186, 2.626, 13.430 ], "num_pairs": 4, "pairs": [ { "index": 1, "nt1": "///A/27", "nt2": "///A/43", "bp": "U-A", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.651, 0.183, -0.767, -1.839, -11.710, 3.402 ], "step_params": [ -0.562, -1.536, 3.758, -4.150, 9.682, 23.384 ], "heli_params": [ -6.411, 0.004, 2.953, 22.482, 9.636, 25.617 ], "bp2_params": [ -0.727, -0.170, 0.228, -2.299, -21.698, -3.618 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.758, "simple_Twist": 30.585, "simple_hRise": 3.184, "simple_hTwist": 32.307 }, { "index": 2, "nt1": "///A/28", "nt2": "///A/42", "bp": "C-G", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ -0.727, -0.170, 0.228, -2.299, -21.698, -3.618 ], "step_params": [ 0.113, -1.188, 3.401, -0.219, 12.740, 36.164 ], "heli_params": [ -3.385, -0.199, 2.837, 19.782, 0.339, 38.272 ], "bp2_params": [ 0.820, -0.092, 0.187, 0.130, -18.295, -3.002 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 3.401, "simple_Twist": 28.138, "simple_hRise": 2.628, "simple_hTwist": 30.835 }, { "index": 3, "nt1": "///A/29", "nt2": "///A/41", "bp": "A-U", "name": "WC", "Saenger": "20-XX", "LW": "cWW", "DSSR": "cW-W", "bp1_params": [ 0.820, -0.092, 0.187, 0.130, -18.295, -3.002 ], "step_params": [ 0.128, -1.479, 4.189, 5.364, 10.119, 29.787 ], "heli_params": [ -4.935, 0.955, 3.484, 18.831, -9.983, 31.866 ], "bp2_params": [ 0.640, -0.168, -0.447, -12.282, -25.398, -1.543 ], "groove_widths": [ null, null, null, null ], "simple_Rise": 4.189, "simple_Twist": 30.213, "simple_hRise": 3.497, "simple_hTwist": 32.264 }, { "index": 4, "nt1": "///A/30", "nt2": "///A/40", "bp": "G-C", "name": "WC", "Saenger": "19-XIX", "LW": "cWW", "DSSR": "cW-W" } ] } ], "num_stacks": 2, "stacks": [ { "index": 1, "num_nts": 4, "nts_short": "GACU", "nts_long": "///A/30,///A/31,///A/32,///A/33" }, { "index": 2, "num_nts": 7, "nts_short": "tUUaAPC", "nts_long": "///A/34,///A/35,///A/36,///A/37,///A/38,///A/39,///A/40" } ], "num_hairpins": 1, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 1 ], "summary": "[1] 9 [A.30 A.40] 4", "num_nts": 11, "nts_short": "GACUtUUaAPC", "nts_long": "///A/30,///A/31,///A/32,///A/33,///A/34,///A/35,///A/36,///A/37,///A/38,///A/39,///A/40", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "ACUtUUaAP", "nts_long": "///A/31,///A/32,///A/33,///A/34,///A/35,///A/36,///A/37,///A/38,///A/39" } ] } ], "dbn": { "all_chains": { "num_nts": 17, "num_chars": 17, "bseq": "UCAGACUtUUaAPCUGA", "bseqUP": "UCAGACUTUUAAUCUGA", "sstr": "((((.........))))", "form": ".AAA.....A....AA-" }, "m1_chain_A": { "num_nts": 17, "num_chars": 17, "bseq": "UCAGACUtUUaAPCUGA", "bseqUP": "UCAGACUTUUAAUCUGA", "sstr": "((((.........))))", "form": ".AAA.....A....AA-" } }, "chains": { "m1_chain_A": { "num_nts": 17, "bseq": "UCAGACUtUUaAPCUGA", "sstr": "((((.........))))", "form": ".AAA.....A....AA-", "helical_rise": 0.101, "helical_rise_std": 2.370, "helical_axis": [ -0.702, 0.672, -0.234 ], "point1": [ 0.635, -1.132, 18.699 ], "point2": [ -0.618, 0.066, 18.281 ], "num_chars": 49, "suite": "U1aC1aA1aG1aA1aC1aU1gt1aU1aU1aa1aA1aP1aC1aU1aG1aA" } }, "num_nts": 17, "nts": [ { "index": 1, "index_chain": 1, "chain_name": "A", "nt_resnum": 27, "nt_name": "U", "nt_code": "U", "nt_id": "///A/27", "linked_nts": [ null, "///A/28" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end", "alpha": null, "beta": null, "gamma": 60.414, "delta": 75.220, "epsilon": -172.246, "zeta": -74.964, "epsilon_zeta": -97.282, "bb_type": "BI", "chi": -151.595, "glyco_bond": "anti", "C5prime_xyz": [ -2.267, 8.989, -0.191 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 4.119, "Dp": 4.400, "splay_angle": 28.672, "splay_distance": 4.764, "splay_ratio": 0.250, "d22": 5.096, "d64": 5.507, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -13.848, "v1": -14.228, "v2": 33.998, "v3": -43.819, "v4": 36.743, "amplitude": 42.832, "phase_angle": 37.463, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.104, "frame": { "rmsd": 0.021, "origin": [ 3.810, 2.594, 4.286 ], "x_axis": [ -0.818, 0.506, 0.274 ], "y_axis": [ -0.477, -0.863, 0.167 ], "z_axis": [ 0.321, 0.006, 0.947 ], "quaternion": [ 0.258, 0.156, 0.045, 0.952 ] } }, { "index": 2, "index_chain": 2, "chain_name": "A", "nt_resnum": 28, "nt_name": "C", "nt_code": "C", "nt_id": "///A/28", "linked_nts": [ "///A/27", "///A/29" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -78.581, "beta": 178.673, "gamma": 67.418, "delta": 78.033, "epsilon": -161.013, "zeta": -63.115, "epsilon_zeta": -97.898, "bb_type": "BI", "chi": -155.549, "glyco_bond": "anti", "C5prime_xyz": [ -1.866, 8.968, 0.097 ], "P_xyz": [ 0.592, 9.843, -0.221 ], "form": "A", "ssZp": 4.264, "Dp": 4.577, "splay_angle": 22.487, "splay_distance": 3.677, "splay_ratio": 0.197, "d22": null, "d64": null, "eta": 173.168, "theta": -144.317, "eta_prime": 179.485, "theta_prime": -144.567, "eta_base": -158.051, "theta_base": -109.568, "v0": -6.227, "v1": -20.841, "v2": 37.271, "v3": -42.557, "v4": 31.090, "amplitude": 41.917, "phase_angle": 27.232, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.427, "filter_rmsd": 0.072, "frame": { "rmsd": 0.018, "origin": [ 6.206, 4.077, 8.127 ], "x_axis": [ -0.955, 0.174, 0.240 ], "y_axis": [ -0.165, -0.985, 0.058 ], "z_axis": [ 0.247, 0.016, 0.969 ], "quaternion": [ 0.086, 0.123, 0.019, 0.989 ] } }, { "index": 3, "index_chain": 3, "chain_name": "A", "nt_resnum": 29, "nt_name": "A", "nt_code": "A", "nt_id": "///A/29", "linked_nts": [ "///A/28", "///A/30" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -85.138, "beta": 178.593, "gamma": 66.428, "delta": 79.068, "epsilon": -164.907, "zeta": -65.730, "epsilon_zeta": -99.177, "bb_type": "BI", "chi": -152.838, "glyco_bond": "anti", "C5prime_xyz": [ -1.713, 8.835, 0.080 ], "P_xyz": [ 0.795, 9.567, -0.255 ], "form": "A", "ssZp": 4.272, "Dp": 4.573, "splay_angle": 24.672, "splay_distance": 4.028, "splay_ratio": 0.217, "d22": null, "d64": null, "eta": 163.533, "theta": -149.169, "eta_prime": 179.397, "theta_prime": -149.495, "eta_base": -129.985, "theta_base": -125.445, "v0": -3.580, "v1": -22.078, "v2": 36.759, "v3": -40.619, "v4": 28.130, "amplitude": 40.222, "phase_angle": 23.950, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.487, "filter_rmsd": 0.038, "frame": { "rmsd": 0.009, "origin": [ 4.957, 5.163, 11.410 ], "x_axis": [ -0.892, -0.451, 0.031 ], "y_axis": [ 0.451, -0.888, 0.091 ], "z_axis": [ -0.014, 0.095, 0.995 ], "quaternion": [ -0.232, 0.004, 0.048, 0.971 ] } }, { "index": 4, "index_chain": 4, "chain_name": "A", "nt_resnum": 30, "nt_name": "G", "nt_code": "G", "nt_id": "///A/30", "linked_nts": [ "///A/29", "///A/31" ], "nt_type": "RNA", "dbn": "(", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop", "alpha": -80.619, "beta": 176.406, "gamma": 68.613, "delta": 78.427, "epsilon": -164.251, "zeta": -66.953, "epsilon_zeta": -97.298, "bb_type": "BI", "chi": -154.531, "glyco_bond": "anti", "C5prime_xyz": [ -1.692, 8.902, 0.202 ], "P_xyz": [ 0.811, 9.600, -0.227 ], "form": "A", "ssZp": 4.345, "Dp": 4.594, "splay_angle": 26.603, "splay_distance": 4.311, "splay_ratio": 0.233, "d22": null, "d64": null, "eta": 169.654, "theta": -149.915, "eta_prime": -176.202, "theta_prime": -150.278, "eta_base": -138.045, "theta_base": -129.219, "v0": -3.297, "v1": -22.595, "v2": 37.375, "v3": -41.081, "v4": 28.238, "amplitude": 40.756, "phase_angle": 23.502, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.478, "filter_rmsd": 0.009, "frame": { "rmsd": 0.009, "origin": [ 3.083, 6.039, 14.866 ], "x_axis": [ -0.544, -0.839, 0.006 ], "y_axis": [ 0.827, -0.536, 0.168 ], "z_axis": [ -0.138, 0.096, 0.986 ], "quaternion": [ -0.476, -0.038, 0.075, 0.876 ] } }, { "index": 5, "index_chain": 5, "chain_name": "A", "nt_resnum": 31, "nt_name": "A", "nt_code": "A", "nt_id": "///A/31", "linked_nts": [ "///A/30", "///A/32" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop", "alpha": -79.624, "beta": 179.016, "gamma": 67.895, "delta": 78.873, "epsilon": -156.895, "zeta": -62.570, "epsilon_zeta": -94.326, "bb_type": "BI", "chi": -156.518, "glyco_bond": "anti", "C5prime_xyz": [ -1.713, 8.825, 0.320 ], "P_xyz": [ 0.802, 9.558, 0.071 ], "form": ".", "ssZp": 4.378, "Dp": 4.636, "splay_angle": 30.767, "splay_distance": 5.033, "splay_ratio": 0.269, "d22": null, "d64": null, "eta": 172.934, "theta": -139.784, "eta_prime": -175.460, "theta_prime": -138.322, "eta_base": -142.097, "theta_base": -110.422, "v0": -3.515, "v1": -22.646, "v2": 37.532, "v3": -41.421, "v4": 28.647, "amplitude": 41.019, "phase_angle": 23.796, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.517, "filter_rmsd": 0.039, "frame": { "rmsd": 0.008, "origin": [ 0.717, 6.136, 18.469 ], "x_axis": [ -0.063, -0.997, -0.031 ], "y_axis": [ 0.979, -0.068, 0.194 ], "z_axis": [ -0.196, -0.018, 0.980 ], "quaternion": [ 0.680, 0.078, -0.061, -0.727 ] } }, { "index": 6, "index_chain": 6, "chain_name": "A", "nt_resnum": 32, "nt_name": "C", "nt_code": "C", "nt_id": "///A/32", "linked_nts": [ "///A/31", "///A/33" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,non-pair-contact,hairpin-loop", "alpha": -77.335, "beta": -179.775, "gamma": 64.083, "delta": 80.040, "epsilon": -114.631, "zeta": -73.542, "epsilon_zeta": -41.089, "bb_type": "--", "chi": -163.375, "glyco_bond": "anti", "C5prime_xyz": [ -1.897, 8.895, 0.583 ], "P_xyz": [ 0.594, 9.740, 0.734 ], "form": ".", "ssZp": 4.215, "Dp": 4.677, "splay_angle": 38.698, "splay_distance": 6.603, "splay_ratio": 0.334, "d22": 4.154, "d64": 4.626, "eta": -179.925, "theta": -116.565, "eta_prime": -167.765, "theta_prime": -113.674, "eta_base": -129.570, "theta_base": -86.823, "v0": -4.189, "v1": -21.630, "v2": 36.554, "v3": -40.741, "v4": 28.647, "amplitude": 40.262, "phase_angle": 24.785, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.697, "filter_rmsd": 0.070, "frame": { "rmsd": 0.016, "origin": [ -1.143, 3.461, 22.306 ], "x_axis": [ 0.566, -0.808, -0.161 ], "y_axis": [ 0.824, 0.550, 0.138 ], "z_axis": [ -0.023, -0.211, 0.977 ], "quaternion": [ 0.879, 0.099, 0.039, -0.464 ] } }, { "index": 7, "index_chain": 7, "chain_name": "A", "nt_resnum": 33, "nt_name": "U", "nt_code": "U", "nt_id": "///A/33", "linked_nts": [ "///A/32", "///A/34" ], "nt_type": "RNA", "dbn": ".", "summary": "u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop", "alpha": -71.693, "beta": 175.284, "gamma": 59.307, "delta": 77.764, "epsilon": -179.067, "zeta": -76.114, "epsilon_zeta": -102.952, "bb_type": "BI", "chi": -158.377, "glyco_bond": "anti", "C5prime_xyz": [ -2.400, 8.974, 0.098 ], "P_xyz": [ -0.154, 10.316, 0.292 ], "form": ".", "ssZp": 4.045, "Dp": 4.212, "splay_angle": 68.944, "splay_distance": 11.208, "splay_ratio": 0.570, "d22": 8.750, "d64": 11.416, "eta": 157.458, "theta": -153.096, "eta_prime": -178.819, "theta_prime": 172.982, "eta_base": -135.591, "theta_base": 126.088, "v0": -15.248, "v1": -11.392, "v2": 30.940, "v3": -41.483, "v4": 36.088, "amplitude": 40.710, "phase_angle": 40.534, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.404, "filter_rmsd": 0.103, "frame": { "rmsd": 0.021, "origin": [ 1.934, -0.788, 26.314 ], "x_axis": [ 0.766, -0.046, -0.642 ], "y_axis": [ 0.168, 0.977, 0.130 ], "z_axis": [ 0.621, -0.208, 0.756 ], "quaternion": [ 0.935, 0.090, 0.337, -0.057 ] } }, { "index": 8, "index_chain": 8, "chain_name": "A", "nt_resnum": 34, "nt_name": "U8U", "nt_code": "t", "is_modified": true, "nt_id": "///A/34", "linked_nts": [ "///A/33", "///A/35" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop", "alpha": 176.131, "beta": -178.470, "gamma": 57.904, "delta": 83.522, "epsilon": -167.733, "zeta": -56.620, "epsilon_zeta": -111.113, "bb_type": "BI", "chi": -150.454, "glyco_bond": "anti", "C5prime_xyz": [ -2.509, 9.016, -0.464 ], "P_xyz": [ -0.446, 10.594, -0.113 ], "form": ".", "ssZp": 3.542, "Dp": 3.853, "splay_angle": 18.983, "splay_distance": 3.454, "splay_ratio": 0.173, "d22": 3.865, "d64": 3.747, "eta": 55.200, "theta": -136.456, "eta_prime": 59.329, "theta_prime": -140.203, "eta_base": 27.811, "theta_base": -109.899, "v0": -24.076, "v1": 2.178, "v2": 18.378, "v3": -33.032, "v4": 36.363, "amplitude": 36.106, "phase_angle": 59.402, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1g", "suiteness": 0.252, "filter_rmsd": 0.112, "frame": { "rmsd": 0.037, "origin": [ -6.611, 0.300, 33.484 ], "x_axis": [ -0.519, 0.798, -0.305 ], "y_axis": [ 0.850, 0.520, -0.085 ], "z_axis": [ 0.091, -0.303, -0.948 ], "quaternion": [ 0.115, 0.477, 0.864, -0.112 ] } }, { "index": 9, "index_chain": 9, "chain_name": "A", "nt_resnum": 35, "nt_name": "U", "nt_code": "U", "nt_id": "///A/35", "linked_nts": [ "///A/34", "///A/36" ], "nt_type": "RNA", "dbn": ".", "summary": "u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop", "alpha": -104.469, "beta": -170.959, "gamma": 64.281, "delta": 74.354, "epsilon": -163.666, "zeta": -70.264, "epsilon_zeta": -93.402, "bb_type": "BI", "chi": -138.297, "glyco_bond": "anti", "C5prime_xyz": [ -2.572, 8.913, -0.949 ], "P_xyz": [ -0.454, 10.401, -1.479 ], "form": ".", "ssZp": 3.509, "Dp": 4.264, "splay_angle": 31.761, "splay_distance": 5.367, "splay_ratio": 0.274, "d22": 4.317, "d64": 4.433, "eta": 147.029, "theta": -157.754, "eta_prime": 163.103, "theta_prime": -153.464, "eta_base": -154.339, "theta_base": -122.879, "v0": -23.557, "v1": -4.787, "v2": 28.459, "v3": -43.805, "v4": 42.771, "amplitude": 44.514, "phase_angle": 50.259, "puckering": "C4'-exo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.060, "filter_rmsd": 0.104, "frame": { "rmsd": 0.019, "origin": [ -8.053, 0.319, 30.345 ], "x_axis": [ 0.002, 1.000, 0.013 ], "y_axis": [ 0.995, -0.000, -0.100 ], "z_axis": [ -0.100, 0.013, -0.995 ], "quaternion": [ -0.040, 0.707, 0.706, -0.031 ] } }, { "index": 10, "index_chain": 10, "chain_name": "A", "nt_resnum": 36, "nt_name": "U", "nt_code": "U", "nt_id": "///A/36", "linked_nts": [ "///A/35", "///A/37" ], "nt_type": "RNA", "dbn": ".", "summary": "u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate", "alpha": -81.212, "beta": 176.123, "gamma": 67.729, "delta": 79.708, "epsilon": -165.682, "zeta": -66.203, "epsilon_zeta": -99.478, "bb_type": "BI", "chi": -151.898, "glyco_bond": "anti", "C5prime_xyz": [ -1.968, 8.937, -0.098 ], "P_xyz": [ 0.464, 9.825, -0.558 ], "form": "A", "ssZp": 4.161, "Dp": 4.480, "splay_angle": 21.799, "splay_distance": 3.561, "splay_ratio": 0.190, "d22": null, "d64": null, "eta": 168.306, "theta": -149.196, "eta_prime": -178.031, "theta_prime": -148.796, "eta_base": -139.174, "theta_base": -117.382, "v0": -8.361, "v1": -17.548, "v2": 34.182, "v3": -40.674, "v4": 31.229, "amplitude": 39.795, "phase_angle": 30.802, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.478, "filter_rmsd": 0.104, "frame": { "rmsd": 0.022, "origin": [ -8.110, 2.828, 25.601 ], "x_axis": [ 0.537, 0.784, 0.310 ], "y_axis": [ 0.831, -0.556, -0.033 ], "z_axis": [ 0.146, 0.276, -0.950 ], "quaternion": [ -0.089, 0.872, 0.463, 0.131 ] } }, { "index": 11, "index_chain": 11, "chain_name": "A", "nt_resnum": 37, "nt_name": "T6A", "nt_code": "a", "is_modified": true, "nt_id": "///A/37", "linked_nts": [ "///A/36", "///A/38" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop", "alpha": -82.606, "beta": 174.652, "gamma": 72.605, "delta": 86.867, "epsilon": -167.991, "zeta": -58.262, "epsilon_zeta": -109.730, "bb_type": "BI", "chi": -149.321, "glyco_bond": "anti", "C5prime_xyz": [ -1.802, 8.852, -0.102 ], "P_xyz": [ 0.653, 9.500, -0.800 ], "form": ".", "ssZp": 4.164, "Dp": 4.247, "splay_angle": 28.855, "splay_distance": 4.660, "splay_ratio": 0.250, "d22": null, "d64": null, "eta": 167.514, "theta": -133.253, "eta_prime": -173.623, "theta_prime": -137.415, "eta_base": -127.788, "theta_base": -98.448, "v0": -9.412, "v1": -11.394, "v2": 26.019, "v3": -32.111, "v4": 26.604, "amplitude": 31.888, "phase_angle": 35.316, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.312, "filter_rmsd": 0.036, "frame": { "rmsd": 0.037, "origin": [ -7.304, 5.384, 23.256 ], "x_axis": [ 0.896, 0.348, 0.274 ], "y_axis": [ 0.434, -0.816, -0.382 ], "z_axis": [ 0.090, 0.461, -0.883 ], "quaternion": [ -0.222, 0.948, 0.206, 0.096 ] } }, { "index": 12, "index_chain": 12, "chain_name": "A", "nt_resnum": 38, "nt_name": "A", "nt_code": "A", "nt_id": "///A/38", "linked_nts": [ "///A/37", "///A/39" ], "nt_type": "RNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,hairpin-loop", "alpha": -94.319, "beta": -178.102, "gamma": 74.804, "delta": 80.005, "epsilon": -156.799, "zeta": -52.207, "epsilon_zeta": -104.592, "bb_type": "BI", "chi": -154.797, "glyco_bond": "anti", "C5prime_xyz": [ -1.693, 8.829, 0.219 ], "P_xyz": [ 0.784, 9.499, -0.393 ], "form": ".", "ssZp": 4.373, "Dp": 4.667, "splay_angle": 32.828, "splay_distance": 5.355, "splay_ratio": 0.287, "d22": null, "d64": null, "eta": 162.128, "theta": -127.188, "eta_prime": -178.031, "theta_prime": -124.903, "eta_base": -119.104, "theta_base": -88.070, "v0": -2.238, "v1": -24.112, "v2": 38.670, "v3": -41.590, "v4": 27.919, "amplitude": 41.653, "phase_angle": 21.814, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.109, "filter_rmsd": 0.040, "frame": { "rmsd": 0.013, "origin": [ -4.043, 7.905, 21.084 ], "x_axis": [ 0.928, -0.372, 0.029 ], "y_axis": [ -0.288, -0.763, -0.579 ], "z_axis": [ 0.237, 0.529, -0.815 ], "quaternion": [ -0.296, 0.936, -0.176, 0.071 ] } }, { "index": 13, "index_chain": 13, "chain_name": "A", "nt_resnum": 39, "nt_name": "PSU", "nt_code": "P", "is_modified": true, "nt_id": "///A/39", "linked_nts": [ "///A/38", "///A/40" ], "nt_type": "RNA", "dbn": ".", "summary": "modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop", "alpha": -81.405, "beta": -177.445, "gamma": 71.674, "delta": 84.394, "epsilon": -167.214, "zeta": -59.024, "epsilon_zeta": -108.190, "bb_type": "BI", "chi": -151.239, "glyco_bond": "anti", "C5prime_xyz": [ -2.043, 8.959, -0.046 ], "P_xyz": [ 0.423, 9.800, -0.498 ], "form": ".", "ssZp": 4.180, "Dp": 4.244, "splay_angle": 25.832, "splay_distance": 4.284, "splay_ratio": 0.226, "d22": null, "d64": null, "eta": 171.538, "theta": -135.712, "eta_prime": -162.102, "theta_prime": -137.506, "eta_base": -105.437, "theta_base": -99.773, "v0": -9.631, "v1": -12.104, "v2": 27.361, "v3": -33.641, "v4": 27.712, "amplitude": 33.386, "phase_angle": 34.962, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.337, "filter_rmsd": 0.110, "frame": { "rmsd": 0.033, "origin": [ 0.709, 7.557, 18.640 ], "x_axis": [ 0.387, -0.869, -0.309 ], "y_axis": [ -0.802, -0.151, -0.579 ], "z_axis": [ 0.456, 0.472, -0.755 ], "quaternion": [ -0.347, 0.757, -0.552, 0.048 ] } }, { "index": 14, "index_chain": 14, "chain_name": "A", "nt_resnum": 40, "nt_name": "C", "nt_code": "C", "nt_id": "///A/40", "linked_nts": [ "///A/39", "///A/41" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop", "alpha": -92.538, "beta": -174.199, "gamma": 72.585, "delta": 79.518, "epsilon": -161.423, "zeta": -66.547, "epsilon_zeta": -94.876, "bb_type": "BI", "chi": -150.423, "glyco_bond": "anti", "C5prime_xyz": [ -1.871, 8.978, -0.240 ], "P_xyz": [ 0.638, 9.764, -0.510 ], "form": ".", "ssZp": 3.975, "Dp": 4.478, "splay_angle": 29.109, "splay_distance": 4.862, "splay_ratio": 0.253, "d22": 4.445, "d64": 4.648, "eta": 165.572, "theta": -145.385, "eta_prime": -176.696, "theta_prime": -145.296, "eta_base": -123.839, "theta_base": -122.607, "v0": -9.455, "v1": -16.451, "v2": 33.562, "v3": -40.683, "v4": 31.871, "amplitude": 39.751, "phase_angle": 32.402, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.177, "filter_rmsd": 0.072, "frame": { "rmsd": 0.020, "origin": [ 3.375, 6.481, 15.464 ], "x_axis": [ -0.374, -0.837, -0.399 ], "y_axis": [ -0.768, 0.521, -0.373 ], "z_axis": [ 0.520, 0.167, -0.838 ], "quaternion": [ 0.278, -0.485, 0.827, -0.062 ] } }, { "index": 15, "index_chain": 15, "chain_name": "A", "nt_resnum": 41, "nt_name": "U", "nt_code": "U", "nt_id": "///A/41", "linked_nts": [ "///A/40", "///A/42" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -82.477, "beta": -177.617, "gamma": 63.460, "delta": 78.058, "epsilon": -162.525, "zeta": -63.782, "epsilon_zeta": -98.743, "bb_type": "BI", "chi": -154.390, "glyco_bond": "anti", "C5prime_xyz": [ -1.923, 8.930, 0.037 ], "P_xyz": [ 0.536, 9.862, -0.065 ], "form": "A", "ssZp": 4.210, "Dp": 4.549, "splay_angle": 22.526, "splay_distance": 3.705, "splay_ratio": 0.198, "d22": null, "d64": null, "eta": 167.353, "theta": -146.865, "eta_prime": 179.904, "theta_prime": -146.341, "eta_base": -145.347, "theta_base": -112.896, "v0": -5.845, "v1": -20.677, "v2": 36.605, "v3": -41.788, "v4": 30.338, "amplitude": 41.067, "phase_angle": 26.956, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.605, "filter_rmsd": 0.105, "frame": { "rmsd": 0.022, "origin": [ 5.740, 5.475, 11.336 ], "x_axis": [ -0.819, -0.502, -0.279 ], "y_axis": [ -0.497, 0.863, -0.096 ], "z_axis": [ 0.288, 0.060, -0.956 ], "quaternion": [ 0.149, -0.262, 0.954, -0.009 ] } }, { "index": 16, "index_chain": 16, "chain_name": "A", "nt_resnum": 42, "nt_name": "G", "nt_code": "G", "nt_id": "///A/42", "linked_nts": [ "///A/41", "///A/43" ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", "alpha": -82.345, "beta": 179.974, "gamma": 62.880, "delta": 78.173, "epsilon": -163.614, "zeta": -64.688, "epsilon_zeta": -98.926, "bb_type": "BI", "chi": -149.635, "glyco_bond": "anti", "C5prime_xyz": [ -1.647, 8.901, -0.110 ], "P_xyz": [ 0.862, 9.615, -0.450 ], "form": "A", "ssZp": 4.175, "Dp": 4.594, "splay_angle": 21.328, "splay_distance": 3.528, "splay_ratio": 0.188, "d22": null, "d64": null, "eta": 164.383, "theta": -148.702, "eta_prime": 178.557, "theta_prime": -149.437, "eta_base": -134.190, "theta_base": -130.376, "v0": -3.083, "v1": -22.632, "v2": 37.174, "v3": -40.826, "v4": 27.905, "amplitude": 40.464, "phase_angle": 23.262, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.604, "filter_rmsd": 0.009, "frame": { "rmsd": 0.009, "origin": [ 5.449, 3.993, 7.953 ], "x_axis": [ -0.988, 0.088, -0.130 ], "y_axis": [ 0.101, 0.990, -0.095 ], "z_axis": [ 0.121, -0.107, -0.987 ], "quaternion": [ 0.063, 0.047, 0.996, -0.051 ] } }, { "index": 17, "index_chain": 17, "chain_name": "A", "nt_resnum": 43, "nt_name": "A", "nt_code": "A", "nt_id": "///A/43", "linked_nts": [ "///A/42", null ], "nt_type": "RNA", "dbn": ")", "summary": "anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end", "alpha": -82.138, "beta": -179.226, "gamma": 62.688, "delta": 77.913, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -148.660, "glyco_bond": "anti", "C5prime_xyz": [ -1.725, 8.850, -0.168 ], "P_xyz": [ 0.753, 9.657, -0.504 ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -4.473, "v1": -21.865, "v2": 37.199, "v3": -41.683, "v4": 29.330, "amplitude": 41.077, "phase_angle": 25.096, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.602, "filter_rmsd": 0.039, "frame": { "rmsd": 0.008, "origin": [ 4.630, 2.462, 4.882 ], "x_axis": [ -0.839, 0.541, 0.066 ], "y_axis": [ 0.519, 0.829, -0.208 ], "z_axis": [ -0.167, -0.140, -0.976 ], "quaternion": [ -0.061, 0.278, 0.954, -0.091 ] } } ], "num_hbonds": 20, "hbonds": [ { "index": 1, "atom1_serNum": 8, "atom2_serNum": 35, "donAcc_type": "acceptable", "distance": 3.056, "atom1_id": "///A/27/O2'", "atom2_id": "///A/28/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 13, "atom2_serNum": 545, "donAcc_type": "standard", "distance": 3.350, "atom1_id": "///A/27/N3", "atom2_id": "///A/43/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 15, "atom2_serNum": 544, "donAcc_type": "standard", "distance": 3.464, "atom1_id": "///A/27/O4", "atom2_id": "///A/43/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 43, "atom2_serNum": 513, "donAcc_type": "standard", "distance": 2.935, "atom1_id": "///A/28/O2", "atom2_id": "///A/42/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 44, "atom2_serNum": 511, "donAcc_type": "standard", "distance": 2.881, "atom1_id": "///A/28/N3", "atom2_id": "///A/42/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 46, "atom2_serNum": 510, "donAcc_type": "standard", "distance": 2.858, "atom1_id": "///A/28/N4", "atom2_id": "///A/42/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 77, "atom2_serNum": 480, "donAcc_type": "standard", "distance": 2.944, "atom1_id": "///A/29/N6", "atom2_id": "///A/41/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 8, "atom1_serNum": 78, "atom2_serNum": 478, "donAcc_type": "standard", "distance": 2.885, "atom1_id": "///A/29/N1", "atom2_id": "///A/41/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 9, "atom1_serNum": 110, "atom2_serNum": 449, "donAcc_type": "standard", "distance": 2.806, "atom1_id": "///A/30/O6", "atom2_id": "///A/40/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 111, "atom2_serNum": 447, "donAcc_type": "standard", "distance": 2.883, "atom1_id": "///A/30/N1", "atom2_id": "///A/40/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 113, "atom2_serNum": 446, "donAcc_type": "standard", "distance": 2.997, "atom1_id": "///A/30/N2", "atom2_id": "///A/40/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 12, "atom1_serNum": 144, "atom2_serNum": 408, "donAcc_type": "standard", "distance": 2.763, "atom1_id": "///A/31/N6", "atom2_id": "///A/39/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 13, "atom1_serNum": 145, "atom2_serNum": 404, "donAcc_type": "standard", "distance": 2.935, "atom1_id": "///A/31/N1", "atom2_id": "///A/39/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 14, "atom1_serNum": 174, "atom2_serNum": 386, "donAcc_type": "standard", "distance": 3.524, "atom1_id": "///A/32/O2", "atom2_id": "///A/38/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 201, "atom2_serNum": 240, "donAcc_type": "acceptable", "distance": 2.720, "atom1_id": "///A/33/O2'", "atom2_id": "///A/34/O5'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 16, "atom1_serNum": 206, "atom2_serNum": 292, "donAcc_type": "standard", "distance": 3.055, "atom1_id": "///A/33/N3", "atom2_id": "///A/36/OP2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 17, "atom1_serNum": 233, "atom2_serNum": 266, "donAcc_type": "acceptable", "distance": 3.180, "atom1_id": "///A/34/O2'", "atom2_id": "///A/35/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 270, "atom2_serNum": 296, "donAcc_type": "acceptable", "distance": 3.106, "atom1_id": "///A/35/O2'", "atom2_id": "///A/36/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 19, "atom1_serNum": 330, "atom2_serNum": 375, "donAcc_type": "acceptable", "distance": 3.117, "atom1_id": "///A/37/O2'", "atom2_id": "///A/38/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 338, "atom2_serNum": 344, "donAcc_type": "unknown", "distance": 2.763, "atom1_id": "///A/37/N1", "atom2_id": "///A/37/N11", "atom_pair": "N:N", "residue_pair": "nt:nt" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "1fl8", "num_naChains": 1, "naChains": "A=17", "num_atoms": 560, "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": 13, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 3, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 4, "name": "dssr-hairpins.pdb", "desc": "an ensemble of hairpin loops" }, { "index": 5, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 6, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 7, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 8, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 9, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 10, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 11, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 12, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 13, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }