data_6VCB
#
_model_server_result.job_id            ap9LZnq_5L_m0r_AkKGzUw 
_model_server_result.datetime_utc      '2025-08-31 01:34:16' 
_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          6vcb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":501}' 
#
_entry.id    6VCB 
#
_exptl.entry_id    6VCB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              480.429 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-[(1R)-1-(2,6-dichloro-3-methoxyphenyl)ethyl]-6-{2-[(2R)-piperidin-2-yl]phenyl}-1H-benzimidazole 
_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            6VCB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VCB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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    ? 
_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                      7 
_struct_asym.id                             G 
_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
disulf ? disulf1 A SG CYS 69 R CYS 46 1_555 A SG CYS 94 R CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 A SG CYS 85 R CYS 62 1_555 A SG CYS 127 R CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 A SG CYS 108 R CYS 85 1_555 A SG CYS 149 R CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 A SG CYS 249 R CYS 226 1_555 A SG CYS 319 R CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf5 F SG CYS 44 N CYS 22 1_555 F SG CYS 118 N CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 F SG CYS 121 N CYS 99 1_555 F SG CYS 129 N CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
#
_chem_comp.formula           'C27 H27 Cl2 N3 O' 
_chem_comp.formula_weight    480.429 
_chem_comp.id                QW7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-[(1R)-1-(2,6-dichloro-3-methoxyphenyl)ethyl]-6-{2-[(2R)-piperidin-2-yl]phenyl}-1H-benzimidazole 
_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
CL07 C06 QW7 sing 275 n n 
C05 C06 QW7 doub 276 n y 
C05 C04 QW7 sing 277 n y 
C06 C08 QW7 sing 278 n y 
C04 C03 QW7 doub 279 n y 
C10 C09 QW7 sing 280 n n 
C08 C09 QW7 sing 281 n n 
C08 C32 QW7 doub 282 n y 
C09 N11 QW7 sing 283 n n 
C03 C32 QW7 sing 284 n y 
C03 O02 QW7 sing 285 n n 
C32 CL33 QW7 sing 286 n n 
O02 C01 QW7 sing 287 n n 
N11 C12 QW7 sing 288 n y 
N11 C31 QW7 sing 289 n y 
C30 C31 QW7 doub 290 n y 
C30 C17 QW7 sing 291 n y 
C12 N13 QW7 doub 292 n y 
C31 C14 QW7 sing 293 n y 
C20 C21 QW7 doub 294 n y 
C20 C19 QW7 sing 295 n y 
C21 C22 QW7 sing 296 n y 
C19 C18 QW7 doub 297 n y 
C22 C23 QW7 doub 298 n y 
C18 C17 QW7 sing 299 n n 
C18 C23 QW7 sing 300 n y 
C25 C26 QW7 sing 301 n n 
C25 C24 QW7 sing 302 n n 
C17 C16 QW7 doub 303 n y 
C23 C24 QW7 sing 304 n n 
N13 C14 QW7 sing 305 n y 
C26 C27 QW7 sing 306 n n 
C14 C15 QW7 doub 307 n y 
C24 N29 QW7 sing 308 n n 
C16 C15 QW7 sing 309 n y 
C27 C28 QW7 sing 310 n n 
N29 C28 QW7 sing 311 n n 
C10 H1 QW7 sing 312 n n 
C10 H2 QW7 sing 313 n n 
C10 H3 QW7 sing 314 n n 
C15 H4 QW7 sing 315 n n 
C16 H5 QW7 sing 316 n n 
C19 H6 QW7 sing 317 n n 
C24 H7 QW7 sing 318 n n 
C25 H8 QW7 sing 319 n n 
C25 H9 QW7 sing 320 n n 
C26 H10 QW7 sing 321 n n 
C26 H11 QW7 sing 322 n n 
C27 H12 QW7 sing 323 n n 
C27 H13 QW7 sing 324 n n 
C28 H14 QW7 sing 325 n n 
C28 H15 QW7 sing 326 n n 
C01 H16 QW7 sing 327 n n 
C01 H17 QW7 sing 328 n n 
C01 H18 QW7 sing 329 n n 
C04 H19 QW7 sing 330 n n 
C05 H20 QW7 sing 331 n n 
C09 H21 QW7 sing 332 n n 
C12 H22 QW7 sing 333 n n 
C20 H23 QW7 sing 334 n n 
C21 H24 QW7 sing 335 n n 
C22 H25 QW7 sing 336 n n 
C30 H26 QW7 sing 337 n n 
N29 H27 QW7 sing 338 n n 
#
_atom_sites.entry_id                     6VCB 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          G 
_pdbx_nonpoly_scheme.entity_id        7 
_pdbx_nonpoly_scheme.mon_id           QW7 
_pdbx_nonpoly_scheme.pdb_strand_id    R 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      501 
_pdbx_nonpoly_scheme.auth_seq_num     1 
_pdbx_nonpoly_scheme.pdb_mon_id       QW7 
_pdbx_nonpoly_scheme.auth_mon_id      PM1 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 C10 QW7 . . . G 7 151.854 143.985 123.819 1 82.63 ? C10 QW7 501 R 1 
HETATM 2 C C14 QW7 . . . G 7 150.374 145.558 127.826 1 82.63 ? C14 QW7 501 R 1 
HETATM 3 C C15 QW7 . . . G 7 149.908 146.337 128.923 1 82.63 ? C15 QW7 501 R 1 
HETATM 4 C C16 QW7 . . . G 7 149.578 147.677 128.732 1 82.63 ? C16 QW7 501 R 1 
HETATM 5 C C17 QW7 . . . G 7 149.706 148.255 127.463 1 82.63 ? C17 QW7 501 R 1 
HETATM 6 C C18 QW7 . . . G 7 149.376 149.593 127.272 1 82.63 ? C18 QW7 501 R 1 
HETATM 7 C C19 QW7 . . . G 7 148.09 149.937 126.89 1 82.63 ? C19 QW7 501 R 1 
HETATM 8 C C23 QW7 . . . G 7 150.331 150.585 127.463 1 82.63 ? C23 QW7 501 R 1 
HETATM 9 C C24 QW7 . . . G 7 151.751 150.211 127.885 1 82.63 ? C24 QW7 501 R 1 
HETATM 10 C C25 QW7 . . . G 7 152.725 151.235 127.304 1 82.63 ? C25 QW7 501 R 1 
HETATM 11 C C26 QW7 . . . G 7 154.11 151.026 127.796 1 82.63 ? C26 QW7 501 R 1 
HETATM 12 C C27 QW7 . . . G 7 154.172 150.975 129.277 1 82.63 ? C27 QW7 501 R 1 
HETATM 13 C C28 QW7 . . . G 7 153.196 149.954 129.857 1 82.63 ? C28 QW7 501 R 1 
HETATM 14 C C01 QW7 . . . G 7 155.811 148.791 125.895 1 82.63 ? C01 QW7 501 R 1 
HETATM 15 C C03 QW7 . . . G 7 154.309 147.515 124.625 1 82.63 ? C03 QW7 501 R 1 
HETATM 16 C C04 QW7 . . . G 7 153.995 148.53 123.735 1 82.63 ? C04 QW7 501 R 1 
HETATM 17 C C05 QW7 . . . G 7 152.794 148.497 123.042 1 82.63 ? C05 QW7 501 R 1 
HETATM 18 C C06 QW7 . . . G 7 151.907 147.45 123.239 1 82.63 ? C06 QW7 501 R 1 
HETATM 19 C C08 QW7 . . . G 7 152.221 146.435 124.129 1 82.63 ? C08 QW7 501 R 1 
HETATM 20 C C09 QW7 . . . G 7 151.241 145.28 124.346 1 82.63 ? C09 QW7 501 R 1 
HETATM 21 C C12 QW7 . . . G 7 151.104 144.033 126.479 1 82.63 ? C12 QW7 501 R 1 
HETATM 22 C C20 QW7 . . . G 7 147.755 151.268 126.698 1 82.63 ? C20 QW7 501 R 1 
HETATM 23 C C21 QW7 . . . G 7 148.708 152.257 126.888 1 82.63 ? C21 QW7 501 R 1 
HETATM 24 C C22 QW7 . . . G 7 149.995 151.914 127.271 1 82.63 ? C22 QW7 501 R 1 
HETATM 25 C C30 QW7 . . . G 7 150.162 147.491 126.39 1 82.63 ? C30 QW7 501 R 1 
HETATM 26 C C31 QW7 . . . G 7 150.498 146.123 126.587 1 82.63 ? C31 QW7 501 R 1 
HETATM 27 C C32 QW7 . . . G 7 153.424 146.467 124.823 1 82.63 ? C32 QW7 501 R 1 
HETATM 28 N N11 QW7 . . . G 7 150.959 145.14 125.763 1 82.63 ? N11 QW7 501 R 1 
HETATM 29 N N13 QW7 . . . G 7 150.756 144.254 127.74 1 82.63 ? N13 QW7 501 R 1 
HETATM 30 N N29 QW7 . . . G 7 151.814 150.16 129.363 1 82.63 ? N29 QW7 501 R 1 
HETATM 31 O O02 QW7 . . . G 7 155.522 147.549 125.324 1 82.63 ? O02 QW7 501 R 1 
HETATM 32 CL CL07 QW7 . . . G 7 150.362 147.409 122.347 1 82.63 ? CL07 QW7 501 R 1 
HETATM 33 CL CL33 QW7 . . . G 7 153.83 145.161 125.97 1 82.63 ? CL33 QW7 501 R 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           59 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           506 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           33 
#