data_5KMF # _model_server_result.job_id 7CmB6WloB0cF4OAaZa43_g _model_server_result.datetime_utc '2024-11-16 09:41:49' _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 5kmf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1301}' # _entry.id 5KMF # _exptl.entry_id 5KMF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 418.44 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description nimodipine _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 5KMF _cell.length_a 125.28 _cell.length_b 125.365 _cell.length_c 191.625 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KMF _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y _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 E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id OD1 _struct_conn.ptnr1_label_comp_id ASP _struct_conn.ptnr1_label_seq_id 196 _struct_conn.ptnr1_auth_asym_id C _struct_conn.ptnr1_auth_comp_id ASP _struct_conn.ptnr1_auth_seq_id 1178 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id L _struct_conn.ptnr2_label_atom_id CA _struct_conn.ptnr2_label_comp_id CA _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id C _struct_conn.ptnr2_auth_comp_id CA _struct_conn.ptnr2_auth_seq_id 1301 _struct_conn.ptnr2_symmetry 1_555 _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 3.182 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C21 H26 N2 O7' _chem_comp.formula_weight 418.44 _chem_comp.id 6U9 _chem_comp.mon_nstd_flag . _chem_comp.name nimodipine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '~{O}3-(2-methoxyethyl) ~{O}5-propan-2-yl (4~{S})-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate' # 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 O24 N22 6U9 doub 1 n n N22 O23 6U9 sing 2 n n N22 C18 6U9 sing 3 n n C01 O02 6U9 sing 4 n n O02 C03 6U9 sing 5 n n C19 C18 6U9 doub 6 n y C19 C20 6U9 sing 7 n y C03 C04 6U9 sing 8 n n C18 C17 6U9 sing 9 n y C20 C21 6U9 doub 10 n y C17 C16 6U9 doub 11 n y C04 O05 6U9 sing 12 n n C21 C16 6U9 sing 13 n y O05 C06 6U9 sing 14 n n C16 C15 6U9 sing 15 n n C06 O07 6U9 doub 16 n n C06 C08 6U9 sing 17 n n C15 C08 6U9 sing 18 n n C15 C14 6U9 sing 19 n n O26 C25 6U9 doub 20 n n C08 C09 6U9 doub 21 n n C25 C14 6U9 sing 22 n n C25 O27 6U9 sing 23 n n C14 C12 6U9 doub 24 n n C09 C10 6U9 sing 25 n n C09 N11 6U9 sing 26 n n C28 O27 6U9 sing 27 n n C28 C30 6U9 sing 28 n n C28 C29 6U9 sing 29 n n C12 N11 6U9 sing 30 n n C12 C13 6U9 sing 31 n n C13 H1 6U9 sing 32 n n C13 H2 6U9 sing 33 n n C13 H3 6U9 sing 34 n n C10 H5 6U9 sing 35 n n C10 H6 6U9 sing 36 n n C10 H7 6U9 sing 37 n n C01 H8 6U9 sing 38 n n C01 H9 6U9 sing 39 n n C01 H10 6U9 sing 40 n n C03 H11 6U9 sing 41 n n C03 H12 6U9 sing 42 n n C04 H13 6U9 sing 43 n n C04 H14 6U9 sing 44 n n N11 H17 6U9 sing 45 n n C15 H20 6U9 sing 46 n n C17 H21 6U9 sing 47 n n C19 H22 6U9 sing 48 n n C20 H23 6U9 sing 49 n n C21 H24 6U9 sing 50 n n C28 H25 6U9 sing 51 n n C29 H26 6U9 sing 52 n n C29 H27 6U9 sing 53 n n C29 H28 6U9 sing 54 n n C30 H29 6U9 sing 55 n n C30 H30 6U9 sing 56 n n C30 H31 6U9 sing 57 n n # _atom_sites.entry_id 5KMF _atom_sites.fract_transf_matrix[1][1] 0.007982 _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] 0.007977 _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] 0.005219 _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 E 2 6U9 A 1 1301 3 6U9 NIM . F 3 MC3 A 1 1302 1307 MC3 PX4 . G 3 MC3 A 1 1303 1305 MC3 PX6 . H 3 MC3 A 1 1304 1307 MC3 PX7 . I 3 MC3 B 1 1301 1305 MC3 PX4 . J 3 MC3 B 1 1302 1310 MC3 PX5 . K 3 MC3 B 1 1303 1304 MC3 PX6 . L 4 CA C 1 1301 1 CA CA . M 3 MC3 C 1 1302 1304 MC3 PX4 . N 3 MC3 C 1 1303 1302 MC3 PX6 . O 3 MC3 C 1 1304 1303 MC3 PX6 . P 3 MC3 C 1 1305 1306 MC3 PX7 . Q 3 MC3 D 1 1301 1306 MC3 PX4 . R 3 MC3 D 1 1302 1308 MC3 PX5 . S 3 MC3 D 1 1303 1309 MC3 PX5 . T 3 MC3 D 1 1304 1305 MC3 PX7 . U 4 CA D 1 1305 2 CA CA . V 5 HOH A 1 1401 6 HOH HOH . W 5 HOH B 1 1401 4 HOH HOH . W 5 HOH B 2 1402 5 HOH HOH . X 5 HOH C 1 1401 15 HOH HOH . X 5 HOH C 2 1402 25 HOH HOH . X 5 HOH C 3 1403 9 HOH HOH . X 5 HOH C 4 1404 19 HOH HOH . X 5 HOH C 5 1405 14 HOH HOH . Y 5 HOH D 1 1401 23 HOH HOH . Y 5 HOH D 2 1402 8 HOH HOH . Y 5 HOH D 3 1403 24 HOH HOH . Y 5 HOH D 4 1404 28 HOH HOH . # 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 C C13 6U9 . . . E 2 -4.411 134.527 18.258 1 118.14 ? C13 6U9 1301 A 1 HETATM 2 C C12 6U9 . . . E 2 -5.308 134.287 17.073 1 119.62 ? C12 6U9 1301 A 1 HETATM 3 C C10 6U9 . . . E 2 -7.701 131.352 16.625 1 141.38 ? C10 6U9 1301 A 1 HETATM 4 C C01 6U9 . . . E 2 -12.165 131.624 10.535 1 66.04 ? C01 6U9 1301 A 1 HETATM 5 O O02 6U9 . . . E 2 -10.897 131.011 10.594 1 71.4 ? O02 6U9 1301 A 1 HETATM 6 C C03 6U9 . . . E 2 -9.807 131.781 11.118 1 80.25 ? C03 6U9 1301 A 1 HETATM 7 C C04 6U9 . . . E 2 -9.812 131.857 12.666 1 87.08 ? C04 6U9 1301 A 1 HETATM 8 O O05 6U9 . . . E 2 -8.491 132.106 13.166 1 95.1 ? O05 6U9 1301 A 1 HETATM 9 C C06 6U9 . . . E 2 -8.519 132.868 14.314 1 110.44 ? C06 6U9 1301 A 1 HETATM 10 O O07 6U9 . . . E 2 -9.619 133.145 14.833 1 107.95 ? O07 6U9 1301 A 1 HETATM 11 C C08 6U9 . . . E 2 -7.233 133.248 15.078 1 118.76 ? C08 6U9 1301 A 1 HETATM 12 C C09 6U9 . . . E 2 -7.06 132.6 16.358 1 115.27 ? C09 6U9 1301 A 1 HETATM 13 N N11 6U9 . . . E 2 -5.861 132.928 17.128 1 113.67 ? N11 6U9 1301 A 1 HETATM 14 C C14 6U9 . . . E 2 -5.478 135.096 15.889 1 114.28 ? C14 6U9 1301 A 1 HETATM 15 C C15 6U9 . . . E 2 -6.506 134.588 14.786 1 112.17 ? C15 6U9 1301 A 1 HETATM 16 C C16 6U9 . . . E 2 -5.792 134.546 13.26 1 103.79 ? C16 6U9 1301 A 1 HETATM 17 C C17 6U9 . . . E 2 -5.559 135.687 12.558 1 90.68 ? C17 6U9 1301 A 1 HETATM 18 C C18 6U9 . . . E 2 -4.864 135.663 11.292 1 87.43 ? C18 6U9 1301 A 1 HETATM 19 C C19 6U9 . . . E 2 -4.472 134.425 10.799 1 96.99 ? C19 6U9 1301 A 1 HETATM 20 C C20 6U9 . . . E 2 -4.732 133.255 11.54 1 106.76 ? C20 6U9 1301 A 1 HETATM 21 C C21 6U9 . . . E 2 -5.365 133.352 12.779 1 113 ? C21 6U9 1301 A 1 HETATM 22 N N22 6U9 . . . E 2 -4.554 136.883 10.446 1 89.5 ? N22 6U9 1301 A 1 HETATM 23 O O23 6U9 . . . E 2 -5.215 138.117 10.807 1 81.33 ? O23 6U9 1301 A 1 HETATM 24 O O24 6U9 . . . E 2 -3.783 136.92 9.463 1 76.41 ? O24 6U9 1301 A 1 HETATM 25 C C25 6U9 . . . E 2 -5.069 136.659 15.801 1 105.75 ? C25 6U9 1301 A 1 HETATM 26 O O26 6U9 . . . E 2 -5.559 137.269 14.908 1 105.29 ? O26 6U9 1301 A 1 HETATM 27 O O27 6U9 . . . E 2 -4.369 137.44 16.775 1 101.65 ? O27 6U9 1301 A 1 HETATM 28 C C28 6U9 . . . E 2 -3.972 138.864 16.642 1 79.06 ? C28 6U9 1301 A 1 HETATM 29 C C29 6U9 . . . E 2 -4.501 139.805 17.767 1 73.58 ? C29 6U9 1301 A 1 HETATM 30 C C30 6U9 . . . E 2 -2.451 138.92 16.798 1 69.59 ? C30 6U9 1301 A 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #