data_8X5Y
#
_model_server_result.job_id            aZWeK66ghRZx5L0v5xtEXg 
_model_server_result.datetime_utc      '2025-03-01 03:38:10' 
_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          8x5y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
#
_entry.id    8X5Y 
#
_exptl.entry_id    8X5Y 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              458.57 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine 
_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            8X5Y 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8X5Y 
_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    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 
_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                      2 
_struct_asym.id                             B 
_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 89 B CYS 100 1_555 A SG CYS 169 B CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 346 B CYS 441 1_555 A SG CYS 349 B CYS 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
#
_chem_comp.formula           'C28 H31 F N4 O' 
_chem_comp.formula_weight    458.57 
_chem_comp.id                XB7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine 
_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
C1 O1 XB7 sing 374 n n 
O1 C2 XB7 sing 375 n n 
C3 C2 XB7 doub 376 n y 
C3 C4 XB7 sing 377 n y 
C2 C28 XB7 sing 378 n y 
C4 C5 XB7 doub 379 n y 
C28 C27 XB7 doub 380 n y 
C5 C27 XB7 sing 381 n y 
C5 C6 XB7 sing 382 n n 
C7 C6 XB7 sing 383 n n 
C7 N1 XB7 sing 384 n n 
C12 N1 XB7 sing 385 n n 
C12 C11 XB7 sing 386 n n 
N1 C8 XB7 sing 387 n n 
C11 C10 XB7 sing 388 n n 
C8 C9 XB7 sing 389 n n 
F1 C24 XB7 sing 390 n n 
C10 C9 XB7 sing 391 n n 
C10 N2 XB7 sing 392 n n 
C24 C23 XB7 doub 393 n y 
C24 C25 XB7 sing 394 n y 
C23 C22 XB7 sing 395 n y 
N3 C13 XB7 doub 396 n y 
N3 C14 XB7 sing 397 n y 
C25 C26 XB7 doub 398 n y 
N2 C13 XB7 sing 399 n n 
C13 N4 XB7 sing 400 n y 
C15 C14 XB7 doub 401 n y 
C15 C16 XB7 sing 402 n y 
C22 C21 XB7 doub 403 n y 
C14 C19 XB7 sing 404 n y 
C26 C21 XB7 sing 405 n y 
C21 C20 XB7 sing 406 n n 
C16 C17 XB7 doub 407 n y 
N4 C19 XB7 sing 408 n y 
N4 C20 XB7 sing 409 n n 
C19 C18 XB7 doub 410 n y 
C17 C18 XB7 sing 411 n y 
C1 H1 XB7 sing 412 n n 
C1 H2 XB7 sing 413 n n 
C1 H3 XB7 sing 414 n n 
C10 H4 XB7 sing 415 n n 
C11 H5 XB7 sing 416 n n 
C11 H6 XB7 sing 417 n n 
C12 H7 XB7 sing 418 n n 
C12 H8 XB7 sing 419 n n 
C15 H9 XB7 sing 420 n n 
C16 H10 XB7 sing 421 n n 
C17 H11 XB7 sing 422 n n 
C18 H12 XB7 sing 423 n n 
C20 H13 XB7 sing 424 n n 
C20 H14 XB7 sing 425 n n 
C22 H15 XB7 sing 426 n n 
C23 H16 XB7 sing 427 n n 
C25 H17 XB7 sing 428 n n 
C26 H18 XB7 sing 429 n n 
C27 H19 XB7 sing 430 n n 
C28 H20 XB7 sing 431 n n 
C3 H21 XB7 sing 432 n n 
C4 H22 XB7 sing 433 n n 
C6 H23 XB7 sing 434 n n 
C6 H24 XB7 sing 435 n n 
C7 H25 XB7 sing 436 n n 
C7 H26 XB7 sing 437 n n 
C8 H27 XB7 sing 438 n n 
C8 H28 XB7 sing 439 n n 
C9 H29 XB7 sing 440 n n 
C9 H30 XB7 sing 441 n n 
N2 H32 XB7 sing 442 n n 
#
_atom_sites.entry_id                     8X5Y 
_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          B 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           XB7 
_pdbx_nonpoly_scheme.pdb_strand_id    B 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      601 
_pdbx_nonpoly_scheme.auth_seq_num     501 
_pdbx_nonpoly_scheme.pdb_mon_id       XB7 
_pdbx_nonpoly_scheme.auth_mon_id      XB7 
_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 C1 XB7 . . . B 2 182.446 158.638 138.497 1 101.8 ? C1 XB7 601 B 1 
HETATM 2 C C10 XB7 . . . B 2 179.031 169.14 138.572 1 101.8 ? C10 XB7 601 B 1 
HETATM 3 C C11 XB7 . . . B 2 179.263 168.529 139.969 1 101.8 ? C11 XB7 601 B 1 
HETATM 4 C C12 XB7 . . . B 2 179.856 167.04 139.795 1 101.8 ? C12 XB7 601 B 1 
HETATM 5 C C13 XB7 . . . B 2 177.911 171.191 137.532 1 101.8 ? C13 XB7 601 B 1 
HETATM 6 C C14 XB7 . . . B 2 177.718 172.195 135.519 1 101.8 ? C14 XB7 601 B 1 
HETATM 7 C C15 XB7 . . . B 2 177.714 172.657 134.183 1 101.8 ? C15 XB7 601 B 1 
HETATM 8 C C16 XB7 . . . B 2 177.039 173.882 133.901 1 101.8 ? C16 XB7 601 B 1 
HETATM 9 C C17 XB7 . . . B 2 176.399 174.609 134.908 1 101.8 ? C17 XB7 601 B 1 
HETATM 10 C C18 XB7 . . . B 2 176.404 174.154 136.216 1 101.8 ? C18 XB7 601 B 1 
HETATM 11 C C19 XB7 . . . B 2 177.046 172.978 136.523 1 101.8 ? C19 XB7 601 B 1 
HETATM 12 C C2 XB7 . . . B 2 181.428 160.523 137.433 1 101.8 ? C2 XB7 601 B 1 
HETATM 13 C C20 XB7 . . . B 2 176.717 172.733 138.863 1 101.8 ? C20 XB7 601 B 1 
HETATM 14 C C21 XB7 . . . B 2 177.669 173.808 139.47 1 101.8 ? C21 XB7 601 B 1 
HETATM 15 C C22 XB7 . . . B 2 177.27 175.056 139.574 1 101.8 ? C22 XB7 601 B 1 
HETATM 16 C C23 XB7 . . . B 2 178.216 176.124 140.177 1 101.8 ? C23 XB7 601 B 1 
HETATM 17 C C24 XB7 . . . B 2 179.431 175.779 140.586 1 101.8 ? C24 XB7 601 B 1 
HETATM 18 C C25 XB7 . . . B 2 179.898 174.324 140.465 1 101.8 ? C25 XB7 601 B 1 
HETATM 19 C C26 XB7 . . . B 2 179.09 173.408 139.947 1 101.8 ? C26 XB7 601 B 1 
HETATM 20 C C27 XB7 . . . B 2 180.127 162.135 138.782 1 101.8 ? C27 XB7 601 B 1 
HETATM 21 C C28 XB7 . . . B 2 180.996 160.882 138.621 1 101.8 ? C28 XB7 601 B 1 
HETATM 22 C C3 XB7 . . . B 2 181.063 161.356 136.213 1 101.8 ? C3 XB7 601 B 1 
HETATM 23 C C4 XB7 . . . B 2 180.311 162.44 136.35 1 101.8 ? C4 XB7 601 B 1 
HETATM 24 C C5 XB7 . . . B 2 179.811 162.85 137.731 1 101.8 ? C5 XB7 601 B 1 
HETATM 25 C C6 XB7 . . . B 2 178.93 164.126 137.912 1 101.8 ? C6 XB7 601 B 1 
HETATM 26 C C7 XB7 . . . B 2 179.75 165.13 138.778 1 101.8 ? C7 XB7 601 B 1 
HETATM 27 C C8 XB7 . . . B 2 179.144 166.873 137.728 1 101.8 ? C8 XB7 601 B 1 
HETATM 28 C C9 XB7 . . . B 2 178.365 168.132 137.731 1 101.8 ? C9 XB7 601 B 1 
HETATM 29 F F1 XB7 . . . B 2 180.268 176.72 141.119 1 101.8 ? F1 XB7 601 B 1 
HETATM 30 N N1 XB7 . . . B 2 179.149 166.297 138.882 1 101.8 ? N1 XB7 601 B 1 
HETATM 31 N N2 XB7 . . . B 2 178.181 170.335 138.704 1 101.8 ? N2 XB7 601 B 1 
HETATM 32 N N3 XB7 . . . B 2 178.319 170.946 136.245 1 101.8 ? N3 XB7 601 B 1 
HETATM 33 N N4 XB7 . . . B 2 177.256 172.271 137.561 1 101.8 ? N4 XB7 601 B 1 
HETATM 34 O O1 XB7 . . . B 2 182.237 159.354 137.291 1 101.8 ? O1 XB7 601 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           247 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           34 
#