data_5GID
#
_model_server_result.job_id            s83XZwxTC0HB-CcpcBt1xg 
_model_server_result.datetime_utc      '2024-11-22 03:18:26' 
_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          5gid 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    5GID 
#
_exptl.entry_id    5GID 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              575.821 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-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          96.46 
_cell.angle_gamma         90 
_cell.entry_id            5GID 
_cell.length_a            154.51 
_cell.length_b            42.345 
_cell.length_c            42.32 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GID 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
_chem_comp.formula           'C37 H53 N O4' 
_chem_comp.formula_weight    575.821 
_chem_comp.id                VDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one 
_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
C37 C36 VDP doub 376 n y 
C37 C32 VDP sing 377 n y 
C36 C35 VDP sing 378 n y 
C30 C31 VDP sing 379 n n 
C30 C29 VDP sing 380 n n 
C31 C32 VDP sing 381 n n 
C32 C33 VDP doub 382 n y 
C35 C34 VDP doub 383 n y 
C29 C28 VDP sing 384 n n 
C33 C34 VDP sing 385 n y 
C28 N28 VDP sing 386 n n 
N28 C25 VDP sing 387 n n 
N28 C23 VDP sing 388 n n 
O3 C25 VDP doub 389 n n 
C25 C26 VDP sing 390 n n 
C23 C22 VDP sing 391 n n 
C23 C27 VDP sing 392 n n 
C21 C20 VDP sing 393 n n 
C22 C20 VDP sing 394 n n 
C20 C16 VDP sing 395 n n 
C12 C13 VDP sing 396 n n 
C12 C11 VDP sing 397 n n 
C24 C26 VDP sing 398 n n 
C16 C11 VDP sing 399 n n 
C16 C17 VDP sing 400 n n 
C26 C27 VDP sing 401 n n 
C26 O4 VDP sing 402 n n 
C13 C14 VDP sing 403 n n 
C11 C9 VDP sing 404 n n 
C11 C18 VDP sing 405 n n 
C17 C15 VDP sing 406 n n 
C9 C15 VDP sing 407 n n 
C9 C8 VDP sing 408 n n 
C14 C8 VDP sing 409 n n 
C8 C7 VDP doub 410 e n 
C7 C6 VDP sing 411 n n 
C6 C5 VDP doub 412 z n 
C5 C4 VDP sing 413 n n 
C5 C10 VDP sing 414 n n 
C4 C3 VDP sing 415 n n 
C19 C10 VDP doub 416 n n 
C10 C1 VDP sing 417 n n 
C3 O2 VDP sing 418 n n 
C3 C2 VDP sing 419 n n 
C1 C2 VDP sing 420 n n 
C1 O1 VDP sing 421 n n 
O4 H1 VDP sing 422 n n 
C24 H2 VDP sing 423 n n 
C24 H3 VDP sing 424 n n 
C24 H4 VDP sing 425 n n 
C27 H5 VDP sing 426 n n 
C27 H6 VDP sing 427 n n 
C23 H7 VDP sing 428 n n 
C28 H8 VDP sing 429 n n 
C28 H9 VDP sing 430 n n 
C29 H10 VDP sing 431 n n 
C29 H11 VDP sing 432 n n 
C30 H12 VDP sing 433 n n 
C30 H13 VDP sing 434 n n 
C31 H14 VDP sing 435 n n 
C31 H15 VDP sing 436 n n 
C33 H16 VDP sing 437 n n 
C34 H17 VDP sing 438 n n 
C35 H18 VDP sing 439 n n 
C36 H19 VDP sing 440 n n 
C37 H20 VDP sing 441 n n 
C22 H21 VDP sing 442 n n 
C22 H22 VDP sing 443 n n 
C20 H23 VDP sing 444 n n 
C21 H24 VDP sing 445 n n 
C21 H25 VDP sing 446 n n 
C21 H26 VDP sing 447 n n 
C16 H27 VDP sing 448 n n 
C18 H28 VDP sing 449 n n 
C18 H29 VDP sing 450 n n 
C18 H30 VDP sing 451 n n 
C9 H31 VDP sing 452 n n 
C15 H32 VDP sing 453 n n 
C15 H33 VDP sing 454 n n 
C17 H34 VDP sing 455 n n 
C17 H35 VDP sing 456 n n 
C12 H36 VDP sing 457 n n 
C12 H37 VDP sing 458 n n 
C13 H38 VDP sing 459 n n 
C13 H39 VDP sing 460 n n 
C14 H40 VDP sing 461 n n 
C14 H41 VDP sing 462 n n 
C7 H42 VDP sing 463 n n 
C6 H43 VDP sing 464 n n 
C4 H44 VDP sing 465 n n 
C4 H45 VDP sing 466 n n 
C3 H46 VDP sing 467 n n 
O2 H47 VDP sing 468 n n 
C2 H48 VDP sing 469 n n 
C2 H49 VDP sing 470 n n 
C1 H50 VDP sing 471 n n 
O1 H51 VDP sing 472 n n 
C19 H52 VDP sing 473 n n 
C19 H53 VDP sing 474 n n 
#
_atom_sites.entry_id                     5GID 
_atom_sites.fract_transf_matrix[1][1]    0.006472 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000732 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023616 
_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]    0.02378 
_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 3 VDP A 1 501 1 VDP DpL . 
D 4 HOH A 1 601 43 HOH HOH . 
D 4 HOH A 2 602 18 HOH HOH . 
D 4 HOH A 3 603 13 HOH HOH . 
D 4 HOH A 4 604 19 HOH HOH . 
D 4 HOH A 5 605 21 HOH HOH . 
D 4 HOH A 6 606 9 HOH HOH . 
D 4 HOH A 7 607 22 HOH HOH . 
D 4 HOH A 8 608 2 HOH HOH . 
D 4 HOH A 9 609 11 HOH HOH . 
D 4 HOH A 10 610 29 HOH HOH . 
D 4 HOH A 11 611 17 HOH HOH . 
D 4 HOH A 12 612 30 HOH HOH . 
D 4 HOH A 13 613 5 HOH HOH . 
D 4 HOH A 14 614 10 HOH HOH . 
D 4 HOH A 15 615 20 HOH HOH . 
D 4 HOH A 16 616 3 HOH HOH . 
D 4 HOH A 17 617 24 HOH HOH . 
D 4 HOH A 18 618 1 HOH HOH . 
D 4 HOH A 19 619 41 HOH HOH . 
D 4 HOH A 20 620 6 HOH HOH . 
D 4 HOH A 21 621 26 HOH HOH . 
D 4 HOH A 22 622 7 HOH HOH . 
D 4 HOH A 23 623 14 HOH HOH . 
D 4 HOH A 24 624 38 HOH HOH . 
D 4 HOH A 25 625 16 HOH HOH . 
D 4 HOH A 26 626 39 HOH HOH . 
D 4 HOH A 27 627 45 HOH HOH . 
D 4 HOH A 28 628 44 HOH HOH . 
D 4 HOH A 29 629 15 HOH HOH . 
D 4 HOH A 30 630 31 HOH HOH . 
D 4 HOH A 31 631 46 HOH HOH . 
D 4 HOH A 32 632 27 HOH HOH . 
D 4 HOH A 33 633 36 HOH HOH . 
D 4 HOH A 34 634 4 HOH HOH . 
D 4 HOH A 35 635 32 HOH HOH . 
E 4 HOH C 1 701 25 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 O O3 VDP . . . C 3 -11.726 -1.974 -8.142 1 55.77 ? O3 VDP 501 A 1 
HETATM 2 C C25 VDP . . . C 3 -11.98 -0.884 -7.651 1 55.84 ? C25 VDP 501 A 1 
HETATM 3 C C26 VDP . . . C 3 -11.419 -0.448 -6.333 1 54.1 ? C26 VDP 501 A 1 
HETATM 4 O O4 VDP . . . C 3 -11.756 -1.397 -5.319 1 54.27 ? O4 VDP 501 A 1 
HETATM 5 C C24 VDP . . . C 3 -9.908 -0.282 -6.448 1 58.41 ? C24 VDP 501 A 1 
HETATM 6 C C27 VDP . . . C 3 -12.095 0.888 -6.065 1 53.12 ? C27 VDP 501 A 1 
HETATM 7 C C23 VDP . . . C 3 -12.812 1.298 -7.352 1 55.7 ? C23 VDP 501 A 1 
HETATM 8 N N28 VDP . . . C 3 -12.762 0.07 -8.15 1 56.29 ? N28 VDP 501 A 1 
HETATM 9 C C28 VDP . . . C 3 -13.55 0.083 -9.375 1 52.82 ? C28 VDP 501 A 1 
HETATM 10 C C29 VDP . . . C 3 -12.539 -0.05 -10.512 1 53.18 ? C29 VDP 501 A 1 
HETATM 11 C C30 VDP . . . C 3 -11.972 1.313 -10.9 1 55.83 ? C30 VDP 501 A 1 
HETATM 12 C C31 VDP . . . C 3 -10.443 1.353 -10.915 1 57.59 ? C31 VDP 501 A 1 
HETATM 13 C C32 VDP . . . C 3 -10.029 2.802 -11.065 1 59.16 ? C32 VDP 501 A 1 
HETATM 14 C C33 VDP . . . C 3 -10.011 3.398 -12.322 1 60.78 ? C33 VDP 501 A 1 
HETATM 15 C C34 VDP . . . C 3 -9.644 4.733 -12.463 1 61.04 ? C34 VDP 501 A 1 
HETATM 16 C C35 VDP . . . C 3 -9.299 5.479 -11.342 1 62.81 ? C35 VDP 501 A 1 
HETATM 17 C C36 VDP . . . C 3 -9.323 4.888 -10.082 1 62.36 ? C36 VDP 501 A 1 
HETATM 18 C C37 VDP . . . C 3 -9.69 3.552 -9.943 1 59.9 ? C37 VDP 501 A 1 
HETATM 19 C C22 VDP . . . C 3 -14.24 1.744 -7.017 1 55.16 ? C22 VDP 501 A 1 
HETATM 20 C C20 VDP . . . C 3 -14.128 3.193 -6.526 1 53.19 ? C20 VDP 501 A 1 
HETATM 21 C C21 VDP . . . C 3 -13.254 3.945 -7.537 1 54.7 ? C21 VDP 501 A 1 
HETATM 22 C C16 VDP . . . C 3 -15.471 3.858 -6.156 1 50.01 ? C16 VDP 501 A 1 
HETATM 23 C C11 VDP . . . C 3 -15.434 5.331 -5.716 1 50.84 ? C11 VDP 501 A 1 
HETATM 24 C C18 VDP . . . C 3 -14.293 5.565 -4.722 1 51.67 ? C18 VDP 501 A 1 
HETATM 25 C C9 VDP . . . C 3 -16.753 5.492 -4.975 1 49.72 ? C9 VDP 501 A 1 
HETATM 26 C C15 VDP . . . C 3 -16.841 4.235 -4.115 1 50.83 ? C15 VDP 501 A 1 
HETATM 27 C C17 VDP . . . C 3 -16.206 3.154 -5.007 1 49.89 ? C17 VDP 501 A 1 
HETATM 28 C C12 VDP . . . C 3 -15.394 6.354 -6.856 1 51.75 ? C12 VDP 501 A 1 
HETATM 29 C C13 VDP . . . C 3 -15.604 7.786 -6.366 1 51.89 ? C13 VDP 501 A 1 
HETATM 30 C C14 VDP . . . C 3 -16.866 7.934 -5.525 1 52.01 ? C14 VDP 501 A 1 
HETATM 31 C C8 VDP . . . C 3 -16.814 6.906 -4.431 1 50.1 ? C8 VDP 501 A 1 
HETATM 32 C C7 VDP . . . C 3 -16.819 7.405 -3.176 1 49.47 ? C7 VDP 501 A 1 
HETATM 33 C C6 VDP . . . C 3 -16.758 6.706 -1.902 1 50.8 ? C6 VDP 501 A 1 
HETATM 34 C C5 VDP . . . C 3 -16.749 7.401 -0.748 1 47.79 ? C5 VDP 501 A 1 
HETATM 35 C C4 VDP . . . C 3 -16.798 8.918 -0.714 1 43.69 ? C4 VDP 501 A 1 
HETATM 36 C C3 VDP . . . C 3 -17.107 9.491 0.68 1 41.95 ? C3 VDP 501 A 1 
HETATM 37 O O2 VDP . . . C 3 -18.521 9.536 0.923 1 40.7 ? O2 VDP 501 A 1 
HETATM 38 C C2 VDP . . . C 3 -16.459 8.667 1.787 1 41.55 ? C2 VDP 501 A 1 
HETATM 39 C C1 VDP . . . C 3 -17.071 7.277 1.778 1 42.79 ? C1 VDP 501 A 1 
HETATM 40 O O1 VDP . . . C 3 -16.591 6.491 2.872 1 44.7 ? O1 VDP 501 A 1 
HETATM 41 C C10 VDP . . . C 3 -16.67 6.645 0.489 1 45.5 ? C10 VDP 501 A 1 
HETATM 42 C C19 VDP . . . C 3 -16.221 5.412 0.461 1 49.6 ? C19 VDP 501 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           842 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           42 
#