data_8XGB
#
_model_server_result.job_id            Htr-lete70dVH6hUwGHq8Q 
_model_server_result.datetime_utc      '2025-03-13 17:31:40' 
_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          8xgb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    8XGB 
#
_exptl.entry_id    8XGB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              336.388 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (5~{S})-1-(3~{H}-benzimidazol-5-yl)-5-(4-propoxyphenyl)imidazolidin-2-one 
_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         120 
_cell.entry_id            8XGB 
_cell.length_a            156.421 
_cell.length_b            156.421 
_cell.length_c            80.934 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XGB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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                      3 
_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
metalc ? metalc1 A OD2 ASP 129 B ASP 159 1_555 B ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? 
metalc ? metalc2 A OE2 GLU 172 B GLU 202 1_555 B ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc3 A NE2 HIS 300 B HIS 330 1_555 B ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? 
#
_chem_comp.formula           'C19 H20 N4 O2' 
_chem_comp.formula_weight    336.388 
_chem_comp.id                A1D49 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (5~{S})-1-(3~{H}-benzimidazol-5-yl)-5-(4-propoxyphenyl)imidazolidin-2-one 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     PQ912 
#
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
O15 C14 A1D49 doub 1 n n 
N13 C14 A1D49 sing 2 n n 
N13 C12 A1D49 sing 3 n n 
C14 N16 A1D49 sing 4 n n 
C12 C11 A1D49 sing 5 n n 
N16 C11 A1D49 sing 6 n n 
N16 C17 A1D49 sing 7 n n 
C11 C08 A1D49 sing 8 n n 
C17 C18 A1D49 doub 9 n y 
C17 C25 A1D49 sing 10 n y 
C18 C19 A1D49 sing 11 n y 
C25 C24 A1D49 doub 12 n y 
C19 C20 A1D49 doub 13 n y 
C24 C20 A1D49 sing 14 n y 
C24 N23 A1D49 sing 15 n y 
C08 C09 A1D49 doub 16 n y 
C08 C07 A1D49 sing 17 n y 
C09 C10 A1D49 sing 18 n y 
C20 N21 A1D49 sing 19 n y 
N23 C22 A1D49 sing 20 n y 
N21 C22 A1D49 doub 21 n y 
C07 C06 A1D49 doub 22 n y 
C10 C05 A1D49 doub 23 n y 
C06 C05 A1D49 sing 24 n y 
C05 O04 A1D49 sing 25 n n 
O04 C03 A1D49 sing 26 n n 
C03 C02 A1D49 sing 27 n n 
C02 C01 A1D49 sing 28 n n 
C01 H011 A1D49 sing 29 n n 
C01 H012 A1D49 sing 30 n n 
C01 H013 A1D49 sing 31 n n 
C02 H022 A1D49 sing 32 n n 
C02 H021 A1D49 sing 33 n n 
C03 H032 A1D49 sing 34 n n 
C03 H031 A1D49 sing 35 n n 
C06 H061 A1D49 sing 36 n n 
C07 H071 A1D49 sing 37 n n 
C09 H091 A1D49 sing 38 n n 
C10 H101 A1D49 sing 39 n n 
C11 H111 A1D49 sing 40 n n 
C12 H121 A1D49 sing 41 n n 
C12 H122 A1D49 sing 42 n n 
N13 H131 A1D49 sing 43 n n 
C18 H181 A1D49 sing 44 n n 
C19 H191 A1D49 sing 45 n n 
C22 H221 A1D49 sing 46 n n 
N23 H231 A1D49 sing 47 n n 
C25 H251 A1D49 sing 48 n n 
#
_atom_sites.entry_id                     8XGB 
_atom_sites.fract_transf_matrix[1][1]    0.006393 
_atom_sites.fract_transf_matrix[1][2]    0.003691 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007382 
_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]    0.012356 
_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
B 2 ZN B 1 401 1 ZN ZN . 
C 3 A1D49 B 1 402 1 A1D49 912 . 
D 4 HOH B 1 501 6 HOH HOH . 
D 4 HOH B 2 502 2 HOH HOH . 
D 4 HOH B 3 503 4 HOH HOH . 
D 4 HOH B 4 504 1 HOH HOH . 
D 4 HOH B 5 505 5 HOH HOH . 
D 4 HOH B 6 506 3 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 C01 A1D49 . . . C 3 -15.317 -4.188 41.616 1 23.72 ? C01 A1D49 402 B 1 
HETATM 2 C C02 A1D49 . . . C 3 -14.2 -4.582 40.69 1 14.18 ? C02 A1D49 402 B 1 
HETATM 3 C C03 A1D49 . . . C 3 -14.571 -4.113 39.324 1 37.15 ? C03 A1D49 402 B 1 
HETATM 4 O O04 A1D49 . . . C 3 -13.41 -3.988 38.574 1 37.42 ? O04 A1D49 402 B 1 
HETATM 5 C C05 A1D49 . . . C 3 -13.375 -4.638 37.366 1 25.87 ? C05 A1D49 402 B 1 
HETATM 6 C C06 A1D49 . . . C 3 -12.446 -5.589 37.174 1 29.89 ? C06 A1D49 402 B 1 
HETATM 7 C C07 A1D49 . . . C 3 -12.376 -6.285 36.019 1 34.56 ? C07 A1D49 402 B 1 
HETATM 8 C C08 A1D49 . . . C 3 -13.243 -6.016 35.016 1 46.23 ? C08 A1D49 402 B 1 
HETATM 9 C C09 A1D49 . . . C 3 -14.219 -5.062 35.217 1 34.07 ? C09 A1D49 402 B 1 
HETATM 10 C C10 A1D49 . . . C 3 -14.275 -4.364 36.397 1 32.99 ? C10 A1D49 402 B 1 
HETATM 11 C C11 A1D49 . . . C 3 -13.17 -6.849 33.726 1 50.54 ? C11 A1D49 402 B 1 
HETATM 12 C C12 A1D49 . . . C 3 -13.965 -6.224 32.628 1 39.3 ? C12 A1D49 402 B 1 
HETATM 13 N N13 A1D49 . . . C 3 -13.176 -6.266 31.453 1 40.69 ? N13 A1D49 402 B 1 
HETATM 14 C C14 A1D49 . . . C 3 -11.902 -6.836 31.849 1 43.94 ? C14 A1D49 402 B 1 
HETATM 15 O O15 A1D49 . . . C 3 -11.032 -6.986 31.111 1 55 ? O15 A1D49 402 B 1 
HETATM 16 N N16 A1D49 . . . C 3 -11.844 -7.162 33.258 1 36.4 ? N16 A1D49 402 B 1 
HETATM 17 C C17 A1D49 . . . C 3 -10.753 -7.865 33.931 1 34.13 ? C17 A1D49 402 B 1 
HETATM 18 C C18 A1D49 . . . C 3 -9.484 -7.412 34.204 1 30.84 ? C18 A1D49 402 B 1 
HETATM 19 C C19 A1D49 . . . C 3 -8.565 -8.241 34.84 1 33.67 ? C19 A1D49 402 B 1 
HETATM 20 C C20 A1D49 . . . C 3 -8.893 -9.571 35.236 1 44.78 ? C20 A1D49 402 B 1 
HETATM 21 N N21 A1D49 . . . C 3 -8.215 -10.59 35.872 1 36.79 ? N21 A1D49 402 B 1 
HETATM 22 C C22 A1D49 . . . C 3 -9.011 -11.618 35.973 1 30.63 ? C22 A1D49 402 B 1 
HETATM 23 N N23 A1D49 . . . C 3 -10.164 -11.315 35.443 1 26.74 ? N23 A1D49 402 B 1 
HETATM 24 C C24 A1D49 . . . C 3 -10.125 -10.036 34.978 1 37.51 ? C24 A1D49 402 B 1 
HETATM 25 C C25 A1D49 . . . C 3 -11.041 -9.166 34.316 1 43.1 ? C25 A1D49 402 B 1 
HETATM 26 H H011 A1D49 . . . C 3 -15.1 -4.435 42.495 1 28.46 ? H011 A1D49 402 B 1 
HETATM 27 H H012 A1D49 . . . C 3 -16.106 -4.611 41.345 1 28.46 ? H012 A1D49 402 B 1 
HETATM 28 H H013 A1D49 . . . C 3 -15.439 -3.263 41.568 1 28.46 ? H013 A1D49 402 B 1 
HETATM 29 H H022 A1D49 . . . C 3 -13.402 -4.182 40.959 1 17.01 ? H022 A1D49 402 B 1 
HETATM 30 H H021 A1D49 . . . C 3 -14.101 -5.511 40.682 1 17.01 ? H021 A1D49 402 B 1 
HETATM 31 H H032 A1D49 . . . C 3 -15.191 -4.717 38.966 1 44.57 ? H032 A1D49 402 B 1 
HETATM 32 H H031 A1D49 . . . C 3 -14.974 -3.273 39.39 1 44.57 ? H031 A1D49 402 B 1 
HETATM 33 H H061 A1D49 . . . C 3 -11.839 -5.769 37.847 1 35.87 ? H061 A1D49 402 B 1 
HETATM 34 H H071 A1D49 . . . C 3 -11.727 -6.924 35.935 1 41.48 ? H071 A1D49 402 B 1 
HETATM 35 H H091 A1D49 . . . C 3 -14.828 -4.88 34.54 1 40.88 ? H091 A1D49 402 B 1 
HETATM 36 H H101 A1D49 . . . C 3 -14.919 -3.712 36.53 1 39.59 ? H101 A1D49 402 B 1 
HETATM 37 H H111 A1D49 . . . C 3 -13.574 -7.672 33.912 1 60.65 ? H111 A1D49 402 B 1 
HETATM 38 H H121 A1D49 . . . C 3 -14.69 -6.79 32.473 1 47.16 ? H121 A1D49 402 B 1 
HETATM 39 H H122 A1D49 . . . C 3 -14.06 -5.316 32.812 1 47.16 ? H122 A1D49 402 B 1 
HETATM 40 H H131 A1D49 . . . C 3 -13.389 -5.964 30.67 1 48.82 ? H131 A1D49 402 B 1 
HETATM 41 H H181 A1D49 . . . C 3 -9.242 -6.554 33.96 1 37.01 ? H181 A1D49 402 B 1 
HETATM 42 H H191 A1D49 . . . C 3 -7.718 -7.914 35.021 1 40.4 ? H191 A1D49 402 B 1 
HETATM 43 H H221 A1D49 . . . C 3 -8.785 -12.423 36.363 1 36.75 ? H221 A1D49 402 B 1 
HETATM 44 H H231 A1D49 . . . C 3 -10.845 -11.842 35.405 1 32.09 ? H231 A1D49 402 B 1 
HETATM 45 H H251 A1D49 . . . C 3 -11.893 -9.487 34.133 1 51.72 ? H251 A1D49 402 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           45 
#