data_3F88
#
_model_server_result.job_id            ilUhgmCo4BYKbLdCfdwE1w 
_model_server_result.datetime_utc      '2025-02-05 11:48:59' 
_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          3f88 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":999}' 
#
_entry.id    3F88 
#
_exptl.entry_id    3F88 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.357 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-[1-(4-methoxyphenyl)-1H-benzimidazol-6-yl]-1,3,4-oxadiazole-2(3H)-thione 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          100.84 
_cell.angle_gamma         90 
_cell.entry_id            3F88 
_cell.length_a            66.947 
_cell.length_b            111.785 
_cell.length_c            66.955 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3F88 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 software_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N 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
covale ? covale1 A C SER 181 A SER 215 1_555 A N PTR 182 A PTR 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 A C PTR 182 A PTR 216 1_555 A N ILE 183 A ILE 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale3 B C SER 181 B SER 215 1_555 B N PTR 182 B PTR 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B C PTR 182 B PTR 216 1_555 B N ILE 183 B ILE 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
#
_chem_comp.formula           'C16 H12 N4 O2 S' 
_chem_comp.formula_weight    324.357 
_chem_comp.id                3HT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-[1-(4-methoxyphenyl)-1H-benzimidazol-6-yl]-1,3,4-oxadiazole-2(3H)-thione 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C3 C4 3HT doub 17 n y 
C4 C5 3HT sing 18 n y 
C4 H4 3HT sing 19 n n 
C5 C6 3HT doub 20 n y 
C5 H5 3HT sing 21 n n 
C7 C6 3HT sing 22 n y 
C6 N9 3HT sing 23 n y 
C8 C7 3HT doub 24 n y 
C7 H7 3HT sing 25 n n 
C3 C8 3HT sing 26 n y 
C8 H8 3HT sing 27 n n 
N9 C10 3HT sing 28 n y 
C10 N11 3HT doub 29 n y 
C10 H10 3HT sing 30 n n 
C12 C13 3HT sing 31 n y 
C14 C13 3HT doub 32 n y 
C13 H13 3HT sing 33 n n 
C16 C15 3HT doub 34 n y 
C18 C15 3HT sing 35 n n 
C15 C14 3HT sing 36 n y 
N9 C17 3HT sing 37 n y 
C16 C17 3HT sing 38 n y 
C17 C12 3HT doub 39 n y 
S22 C21 3HT doub 40 n n 
O32 C21 3HT sing 41 n n 
C21 N20 3HT sing 42 n n 
N20 N19 3HT sing 43 n n 
N20 HN20 3HT sing 44 n n 
C18 N19 3HT doub 45 n n 
O32 C18 3HT sing 46 n n 
C14 H14 3HT sing 47 n n 
C16 H16 3HT sing 48 n n 
N11 C12 3HT sing 49 n y 
O2 C3 3HT sing 50 n n 
C1 O2 3HT sing 51 n n 
C1 H1 3HT sing 52 n n 
C1 H1A 3HT sing 53 n n 
C1 H1B 3HT sing 54 n n 
#
_atom_sites.entry_id                     3F88 
_atom_sites.fract_transf_matrix[1][1]    0.014937 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002861 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008946 
_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]    0.015207 
_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 3HT A 1 999 999 3HT 3HT . 
D 3 2HT A 1 998 998 2HT 2HT . 
E 2 3HT B 1 999 999 3HT 3HT . 
F 3 2HT B 1 998 998 2HT 2HT . 
G 4 HOH A 1 1000 1000 HOH HOH . 
G 4 HOH A 2 1004 1004 HOH HOH . 
G 4 HOH A 3 1005 1005 HOH HOH . 
G 4 HOH A 4 1006 1006 HOH HOH . 
G 4 HOH A 5 1009 1009 HOH HOH . 
G 4 HOH A 6 1010 1010 HOH HOH . 
G 4 HOH A 7 1011 1011 HOH HOH . 
G 4 HOH A 8 1012 1012 HOH HOH . 
G 4 HOH A 9 1013 1013 HOH HOH . 
G 4 HOH A 10 1014 1014 HOH HOH . 
G 4 HOH A 11 1016 1016 HOH HOH . 
G 4 HOH A 12 1017 1017 HOH HOH . 
G 4 HOH A 13 1018 1018 HOH HOH . 
G 4 HOH A 14 1021 1021 HOH HOH . 
G 4 HOH A 15 1022 1022 HOH HOH . 
G 4 HOH A 16 1023 1023 HOH HOH . 
G 4 HOH A 17 1025 1025 HOH HOH . 
G 4 HOH A 18 1026 1026 HOH HOH . 
G 4 HOH A 19 1028 1028 HOH HOH . 
G 4 HOH A 20 1032 1032 HOH HOH . 
G 4 HOH A 21 1036 1036 HOH HOH . 
G 4 HOH A 22 1039 1039 HOH HOH . 
G 4 HOH A 23 1042 1042 HOH HOH . 
G 4 HOH A 24 1045 1045 HOH HOH . 
G 4 HOH A 25 1046 1046 HOH HOH . 
G 4 HOH A 26 1049 1049 HOH HOH . 
G 4 HOH A 27 1050 1050 HOH HOH . 
G 4 HOH A 28 1056 1056 HOH HOH . 
G 4 HOH A 29 1057 1057 HOH HOH . 
G 4 HOH A 30 1059 1059 HOH HOH . 
G 4 HOH A 31 1061 1061 HOH HOH . 
G 4 HOH A 32 1062 1062 HOH HOH . 
G 4 HOH A 33 1063 1063 HOH HOH . 
G 4 HOH A 34 1064 1064 HOH HOH . 
G 4 HOH A 35 1065 1065 HOH HOH . 
G 4 HOH A 36 1067 1067 HOH HOH . 
G 4 HOH A 37 1068 1068 HOH HOH . 
G 4 HOH A 38 1075 1075 HOH HOH . 
G 4 HOH A 39 1076 1076 HOH HOH . 
G 4 HOH A 40 1078 1078 HOH HOH . 
G 4 HOH A 41 1079 1079 HOH HOH . 
G 4 HOH A 42 1080 1080 HOH HOH . 
G 4 HOH A 43 1081 1081 HOH HOH . 
G 4 HOH A 44 1083 1083 HOH HOH . 
G 4 HOH A 45 1084 1084 HOH HOH . 
G 4 HOH A 46 1086 1086 HOH HOH . 
G 4 HOH A 47 1087 1087 HOH HOH . 
G 4 HOH A 48 1091 1091 HOH HOH . 
G 4 HOH A 49 1092 1092 HOH HOH . 
G 4 HOH A 50 1096 1096 HOH HOH . 
G 4 HOH A 51 1097 1097 HOH HOH . 
G 4 HOH A 52 1098 1098 HOH HOH . 
G 4 HOH A 53 1099 1099 HOH HOH . 
G 4 HOH A 54 1100 1100 HOH HOH . 
G 4 HOH A 55 1101 1101 HOH HOH . 
G 4 HOH A 56 1102 1102 HOH HOH . 
G 4 HOH A 57 1103 1103 HOH HOH . 
G 4 HOH A 58 1104 1104 HOH HOH . 
G 4 HOH A 59 1105 1105 HOH HOH . 
G 4 HOH A 60 1106 1106 HOH HOH . 
G 4 HOH A 61 1107 1107 HOH HOH . 
G 4 HOH A 62 1108 1108 HOH HOH . 
G 4 HOH A 63 1109 1109 HOH HOH . 
G 4 HOH A 64 1110 1110 HOH HOH . 
G 4 HOH A 65 1111 1111 HOH HOH . 
G 4 HOH A 66 1112 1112 HOH HOH . 
G 4 HOH A 67 1120 1120 HOH HOH . 
G 4 HOH A 68 1123 1123 HOH HOH . 
G 4 HOH A 69 1124 1124 HOH HOH . 
G 4 HOH A 70 1125 1125 HOH HOH . 
G 4 HOH A 71 1127 1127 HOH HOH . 
G 4 HOH A 72 1130 1130 HOH HOH . 
G 4 HOH A 73 1132 1132 HOH HOH . 
G 4 HOH A 74 1133 1133 HOH HOH . 
G 4 HOH A 75 1134 1134 HOH HOH . 
G 4 HOH A 76 1137 1137 HOH HOH . 
G 4 HOH A 77 1139 1139 HOH HOH . 
G 4 HOH A 78 1142 1142 HOH HOH . 
H 4 HOH B 1 1001 1001 HOH HOH . 
H 4 HOH B 2 1002 1002 HOH HOH . 
H 4 HOH B 3 1003 1003 HOH HOH . 
H 4 HOH B 4 1007 1007 HOH HOH . 
H 4 HOH B 5 1008 1008 HOH HOH . 
H 4 HOH B 6 1015 1015 HOH HOH . 
H 4 HOH B 7 1019 1019 HOH HOH . 
H 4 HOH B 8 1020 1020 HOH HOH . 
H 4 HOH B 9 1024 1024 HOH HOH . 
H 4 HOH B 10 1027 1027 HOH HOH . 
H 4 HOH B 11 1029 1029 HOH HOH . 
H 4 HOH B 12 1030 1030 HOH HOH . 
H 4 HOH B 13 1031 1031 HOH HOH . 
H 4 HOH B 14 1033 1033 HOH HOH . 
H 4 HOH B 15 1034 1034 HOH HOH . 
H 4 HOH B 16 1035 1035 HOH HOH . 
H 4 HOH B 17 1037 1037 HOH HOH . 
H 4 HOH B 18 1038 1038 HOH HOH . 
H 4 HOH B 19 1040 1040 HOH HOH . 
H 4 HOH B 20 1041 1041 HOH HOH . 
H 4 HOH B 21 1043 1043 HOH HOH . 
H 4 HOH B 22 1044 1044 HOH HOH . 
H 4 HOH B 23 1047 1047 HOH HOH . 
H 4 HOH B 24 1048 1048 HOH HOH . 
H 4 HOH B 25 1051 1051 HOH HOH . 
H 4 HOH B 26 1052 1052 HOH HOH . 
H 4 HOH B 27 1053 1053 HOH HOH . 
H 4 HOH B 28 1054 1054 HOH HOH . 
H 4 HOH B 29 1055 1055 HOH HOH . 
H 4 HOH B 30 1058 1058 HOH HOH . 
H 4 HOH B 31 1060 1060 HOH HOH . 
H 4 HOH B 32 1066 1066 HOH HOH . 
H 4 HOH B 33 1069 1069 HOH HOH . 
H 4 HOH B 34 1070 1070 HOH HOH . 
H 4 HOH B 35 1071 1071 HOH HOH . 
H 4 HOH B 36 1073 1073 HOH HOH . 
H 4 HOH B 37 1074 1074 HOH HOH . 
H 4 HOH B 38 1077 1077 HOH HOH . 
H 4 HOH B 39 1082 1082 HOH HOH . 
H 4 HOH B 40 1085 1085 HOH HOH . 
H 4 HOH B 41 1089 1089 HOH HOH . 
H 4 HOH B 42 1090 1090 HOH HOH . 
H 4 HOH B 43 1093 1093 HOH HOH . 
H 4 HOH B 44 1094 1094 HOH HOH . 
H 4 HOH B 45 1095 1095 HOH HOH . 
H 4 HOH B 46 1113 1113 HOH HOH . 
H 4 HOH B 47 1114 1114 HOH HOH . 
H 4 HOH B 48 1115 1115 HOH HOH . 
H 4 HOH B 49 1116 1116 HOH HOH . 
H 4 HOH B 50 1117 1117 HOH HOH . 
H 4 HOH B 51 1118 1118 HOH HOH . 
H 4 HOH B 52 1119 1119 HOH HOH . 
H 4 HOH B 53 1121 1121 HOH HOH . 
H 4 HOH B 54 1122 1122 HOH HOH . 
H 4 HOH B 55 1126 1126 HOH HOH . 
H 4 HOH B 56 1128 1128 HOH HOH . 
H 4 HOH B 57 1129 1129 HOH HOH . 
H 4 HOH B 58 1131 1131 HOH HOH . 
H 4 HOH B 59 1135 1135 HOH HOH . 
H 4 HOH B 60 1136 1136 HOH HOH . 
H 4 HOH B 61 1138 1138 HOH HOH . 
H 4 HOH B 62 1140 1140 HOH HOH . 
H 4 HOH B 63 1141 1141 HOH HOH . 
H 4 HOH B 64 1143 1143 HOH HOH . 
H 4 HOH B 65 1144 1144 HOH HOH . 
H 4 HOH B 66 1145 1145 HOH HOH . 
H 4 HOH B 67 1146 1146 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 C4 3HT . . . C 2 4.167 -14.36 32.51 1 53.47 ? C4 3HT 999 A 1 
HETATM 2 C C5 3HT . . . C 2 4.138 -13.959 33.845 1 52.85 ? C5 3HT 999 A 1 
HETATM 3 C C6 3HT . . . C 2 5.049 -14.342 34.837 1 58.95 ? C6 3HT 999 A 1 
HETATM 4 C C7 3HT . . . C 2 6.066 -15.178 34.376 1 55.01 ? C7 3HT 999 A 1 
HETATM 5 C C8 3HT . . . C 2 6.136 -15.61 33.036 1 54.63 ? C8 3HT 999 A 1 
HETATM 6 C C10 3HT . . . C 2 3.674 -14.018 36.671 1 65.11 ? C10 3HT 999 A 1 
HETATM 7 C C13 3HT . . . C 2 5.512 -12.033 38.992 1 65.61 ? C13 3HT 999 A 1 
HETATM 8 C C15 3HT . . . C 2 7.519 -11.866 37.691 1 64.25 ? C15 3HT 999 A 1 
HETATM 9 C C17 3HT . . . C 2 5.68 -13.098 36.805 1 66.33 ? C17 3HT 999 A 1 
HETATM 10 C C21 3HT . . . C 2 10.925 -11.297 36.961 1 67.91 ? C21 3HT 999 A 1 
HETATM 11 S S22 3HT . . . C 2 12.411 -11.709 36.189 1 68.92 ? S22 3HT 999 A 1 
HETATM 12 N N20 3HT . . . C 2 10.781 -10.223 37.749 1 68.32 ? N20 3HT 999 A 1 
HETATM 13 N N19 3HT . . . C 2 9.431 -10.29 38.13 1 66.11 ? N19 3HT 999 A 1 
HETATM 14 O O32 3HT . . . C 2 9.83 -12.064 36.805 1 68.65 ? O32 3HT 999 A 1 
HETATM 15 C C18 3HT . . . C 2 8.894 -11.391 37.542 1 65.55 ? C18 3HT 999 A 1 
HETATM 16 C C14 3HT . . . C 2 6.812 -11.569 38.855 1 63.77 ? C14 3HT 999 A 1 
HETATM 17 C C16 3HT . . . C 2 6.981 -12.626 36.669 1 63.86 ? C16 3HT 999 A 1 
HETATM 18 C C12 3HT . . . C 2 4.952 -12.807 37.967 1 67.08 ? C12 3HT 999 A 1 
HETATM 19 N N11 3HT . . . C 2 3.734 -13.388 37.859 1 65.15 ? N11 3HT 999 A 1 
HETATM 20 N N9 3HT . . . C 2 4.858 -13.862 36.083 1 62.07 ? N9 3HT 999 A 1 
HETATM 21 C C3 3HT . . . C 2 5.184 -15.204 32.089 1 56.94 ? C3 3HT 999 A 1 
HETATM 22 O O2 3HT . . . C 2 5.21 -15.581 30.764 1 57.07 ? O2 3HT 999 A 1 
HETATM 23 C C1 3HT . . . C 2 5.944 -16.715 30.297 1 50.89 ? C1 3HT 999 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           23 
#