data_1V9G # _model_server_result.job_id 9wN9FWuAXPYS1ckdiKKrXA _model_server_result.datetime_utc '2025-07-09 17:10:20' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1v9g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":13}' # _entry.id 1V9G # _exptl.entry_id 1V9G _exptl.method 'NEUTRON DIFFRACTION' # _entity.details ? _entity.formula_weight 216.434 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N,N'-BIS(3-AMMONIOPROPYL)BUTANE-1,4-DIAMINIUM" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 1V9G _cell.length_a 18.46 _cell.length_b 30.76 _cell.length_c 43.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V9G _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H20 N4 4' _chem_comp.formula_weight 216.434 _chem_comp.id SPW _chem_comp.mon_nstd_flag . _chem_comp.name "N,N'-BIS(3-AMMONIOPROPYL)BUTANE-1,4-DIAMINIUM" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'SPERMINE (FULLY DEUTERATED FORM)' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 SPW sing 77 n n N1 D1A SPW sing 78 n n N1 D1B SPW sing 79 n n N1 D1C SPW sing 80 n n C2 C3 SPW sing 81 n n C2 H2A SPW sing 82 n n C2 H2B SPW sing 83 n n C3 C4 SPW sing 84 n n C3 H3A SPW sing 85 n n C3 H3B SPW sing 86 n n C4 N5 SPW sing 87 n n C4 H4A SPW sing 88 n n C4 H4B SPW sing 89 n n N5 C6 SPW sing 90 n n N5 D5A SPW sing 91 n n N5 D5B SPW sing 92 n n C6 C7 SPW sing 93 n n C6 H6A SPW sing 94 n n C6 H6B SPW sing 95 n n C7 C8 SPW sing 96 n n C7 H7A SPW sing 97 n n C7 H7B SPW sing 98 n n C8 C9 SPW sing 99 n n C8 H8A SPW sing 100 n n C8 H8B SPW sing 101 n n C9 N10 SPW sing 102 n n C9 H9A SPW sing 103 n n C9 H9B SPW sing 104 n n N10 C11 SPW sing 105 n n N10 DXT SPW sing 106 n n N10 DXU SPW sing 107 n n C11 C12 SPW sing 108 n n C11 H111 SPW sing 109 n n C11 H112 SPW sing 110 n n C12 C13 SPW sing 111 n n C12 H121 SPW sing 112 n n C12 H122 SPW sing 113 n n C13 N14 SPW sing 114 n n C13 H131 SPW sing 115 n n C13 H132 SPW sing 116 n n N14 DXX SPW sing 117 n n N14 DXY SPW sing 118 n n N14 DXZ SPW sing 119 n n # _atom_sites.entry_id 1V9G _atom_sites.fract_transf_matrix[1][1] 0.054171 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.03251 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.023159 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SPW A 1 13 13 SPW SPW . D 3 DOD A 1 102 102 DOD DOD . D 3 DOD A 2 104 104 DOD DOD . D 3 DOD A 3 106 106 DOD DOD . D 3 DOD A 4 108 108 DOD DOD . D 3 DOD A 5 109 109 DOD DOD . D 3 DOD A 6 110 110 DOD DOD . D 3 DOD A 7 111 111 DOD DOD . D 3 DOD A 8 114 114 DOD DOD . D 3 DOD A 9 117 117 DOD DOD . D 3 DOD A 10 120 120 DOD DOD . D 3 DOD A 11 122 122 DOD DOD . D 3 DOD A 12 126 126 DOD DOD . D 3 DOD A 13 127 127 DOD DOD . D 3 DOD A 14 128 128 DOD DOD . D 3 DOD A 15 129 129 DOD DOD . D 3 DOD A 16 131 131 DOD DOD . D 3 DOD A 17 132 132 DOD DOD . D 3 DOD A 18 133 133 DOD DOD . D 3 DOD A 19 134 134 DOD DOD . D 3 DOD A 20 135 135 DOD DOD . D 3 DOD A 21 137 137 DOD DOD . D 3 DOD A 22 138 138 DOD DOD . D 3 DOD A 23 142 142 DOD DOD . D 3 DOD A 24 143 143 DOD DOD . E 3 DOD B 1 100 100 DOD DOD . E 3 DOD B 2 101 101 DOD DOD . E 3 DOD B 3 103 103 DOD DOD . E 3 DOD B 4 105 105 DOD DOD . E 3 DOD B 5 107 107 DOD DOD . E 3 DOD B 6 112 112 DOD DOD . E 3 DOD B 7 113 113 DOD DOD . E 3 DOD B 8 115 115 DOD DOD . E 3 DOD B 9 116 116 DOD DOD . E 3 DOD B 10 118 118 DOD DOD . E 3 DOD B 11 119 119 DOD DOD . E 3 DOD B 12 121 121 DOD DOD . E 3 DOD B 13 123 123 DOD DOD . E 3 DOD B 14 124 124 DOD DOD . E 3 DOD B 15 125 125 DOD DOD . E 3 DOD B 16 130 130 DOD DOD . E 3 DOD B 17 136 136 DOD DOD . E 3 DOD B 18 139 139 DOD DOD . E 3 DOD B 19 140 140 DOD DOD . E 3 DOD B 20 141 141 DOD DOD . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 SPW . . . C 2 24.259 18.417 27.355 1 17.28 ? N1 SPW 13 A 1 HETATM 2 C C2 SPW . . . C 2 23.674 17.123 26.97 1 17.61 ? C2 SPW 13 A 1 HETATM 3 C C3 SPW . . . C 2 22.994 17.179 25.601 1 18.12 ? C3 SPW 13 A 1 HETATM 4 C C4 SPW . . . C 2 22.387 15.818 25.242 1 18.84 ? C4 SPW 13 A 1 HETATM 5 N N5 SPW . . . C 2 23.358 14.957 24.475 1 19.35 ? N5 SPW 13 A 1 HETATM 6 C C6 SPW . . . C 2 22.756 13.666 23.972 1 19.41 ? C6 SPW 13 A 1 HETATM 7 C C7 SPW . . . C 2 23.803 12.878 23.183 1 19.94 ? C7 SPW 13 A 1 HETATM 8 C C8 SPW . . . C 2 23.197 12.183 21.962 1 20.38 ? C8 SPW 13 A 1 HETATM 9 C C9 SPW . . . C 2 24.255 11.404 21.17 1 21.02 ? C9 SPW 13 A 1 HETATM 10 N N10 SPW . . . C 2 23.677 10.709 19.957 1 21.22 ? N10 SPW 13 A 1 HETATM 11 C C11 SPW . . . C 2 24.697 10.5 18.867 1 22.01 ? C11 SPW 13 A 1 HETATM 12 C C12 SPW . . . C 2 24.275 9.4 17.894 1 22.53 ? C12 SPW 13 A 1 HETATM 13 C C13 SPW . . . C 2 25.322 9.194 16.797 1 23.34 ? C13 SPW 13 A 1 HETATM 14 N N14 SPW . . . C 2 24.911 8.129 15.862 1 24.02 ? N14 SPW 13 A 1 HETATM 15 D D1A SPW . . . C 2 23.534 19.15 27.405 1 17.44 ? D1A SPW 13 A 1 HETATM 16 D D1B SPW . . . C 2 24.97 18.689 26.649 1 17.63 ? D1B SPW 13 A 1 HETATM 17 D D1C SPW . . . C 2 24.703 18.338 28.279 1 17.21 ? D1C SPW 13 A 1 HETATM 18 D D5A SPW . . . C 2 24.117 14.74 25.067 1 19.36 ? D5A SPW 13 A 1 HETATM 19 D D5B SPW . . . C 2 23.695 15.47 23.713 1 19.62 ? D5B SPW 13 A 1 HETATM 20 D DXT SPW . . . C 2 22.947 11.249 19.599 1 21.31 ? DXT SPW 13 A 1 HETATM 21 D DXU SPW . . . C 2 23.319 9.843 20.225 1 21.6 ? DXU SPW 13 A 1 HETATM 22 D DXX SPW . . . C 2 24.007 8.406 15.426 1 24.24 ? DXX SPW 13 A 1 HETATM 23 D DXY SPW . . . C 2 24.799 7.241 16.388 1 24.25 ? DXY SPW 13 A 1 HETATM 24 D DXZ SPW . . . C 2 25.618 7.978 15.112 1 24.4 ? DXZ SPW 13 A 1 HETATM 25 H H2A SPW . . . C 2 22.943 16.802 27.717 1 17.8 ? H2A SPW 13 A 1 HETATM 26 H H2B SPW . . . C 2 24.485 16.393 26.917 1 17.77 ? H2B SPW 13 A 1 HETATM 27 H H3A SPW . . . C 2 23.727 17.438 24.836 1 18.54 ? H3A SPW 13 A 1 HETATM 28 H H3B SPW . . . C 2 22.207 17.936 25.624 1 18.31 ? H3B SPW 13 A 1 HETATM 29 H H4A SPW . . . C 2 21.503 15.98 24.637 1 18.71 ? H4A SPW 13 A 1 HETATM 30 H H4B SPW . . . C 2 22.098 15.307 26.159 1 18.44 ? H4B SPW 13 A 1 HETATM 31 H H6A SPW . . . C 2 21.905 13.884 23.317 1 19.73 ? H6A SPW 13 A 1 HETATM 32 H H6B SPW . . . C 2 22.416 13.08 24.834 1 19.8 ? H6B SPW 13 A 1 HETATM 33 H H7A SPW . . . C 2 24.271 12.125 23.818 1 19.88 ? H7A SPW 13 A 1 HETATM 34 H H7B SPW . . . C 2 24.574 13.575 22.84 1 19.9 ? H7B SPW 13 A 1 HETATM 35 H H8A SPW . . . C 2 22.754 12.937 21.314 1 20.33 ? H8A SPW 13 A 1 HETATM 36 H H8B SPW . . . C 2 22.431 11.492 22.302 1 20.4 ? H8B SPW 13 A 1 HETATM 37 H H9A SPW . . . C 2 25.016 12.103 20.828 1 20.4 ? H9A SPW 13 A 1 HETATM 38 H H9B SPW . . . C 2 24.734 10.682 21.827 1 20.76 ? H9B SPW 13 A 1 HETATM 39 H H111 SPW . . . C 2 25.657 10.226 19.309 1 21.79 ? H111 SPW 13 A 1 HETATM 40 H H112 SPW . . . C 2 24.831 11.437 18.321 1 21.85 ? H112 SPW 13 A 1 HETATM 41 H H121 SPW . . . C 2 23.323 9.664 17.433 1 22.75 ? H121 SPW 13 A 1 HETATM 42 H H122 SPW . . . C 2 24.156 8.467 18.443 1 22.99 ? H122 SPW 13 A 1 HETATM 43 H H131 SPW . . . C 2 26.267 8.913 17.26 1 23.16 ? H131 SPW 13 A 1 HETATM 44 H H132 SPW . . . C 2 25.476 10.127 16.253 1 23.19 ? H132 SPW 13 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #