data_5R54 # _model_server_result.job_id uFLkpzpV5ahr-g1T7cfiiQ _model_server_result.datetime_utc '2024-11-14 19:16:34' _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 5r54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5R54 # _exptl.entry_id 5R54 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 233.268 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-(benzimidazol-1-ylmethyl)benzenecarbonitrile _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 5R54 _cell.length_a 49.58 _cell.length_b 52.34 _cell.length_c 101.61 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5R54 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,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 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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H11 N3' _chem_comp.formula_weight 233.268 _chem_comp.id RYM _chem_comp.mon_nstd_flag . _chem_comp.name 4-(benzimidazol-1-ylmethyl)benzenecarbonitrile _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 C6 RYM doub 286 n y C1 C2 RYM sing 287 n y C6 C5 RYM sing 288 n y C2 C3 RYM doub 289 n y C5 N1 RYM sing 290 n y C5 C4 RYM doub 291 n y N1 C7 RYM doub 292 n y C3 C4 RYM sing 293 n y C4 N2 RYM sing 294 n y C7 N2 RYM sing 295 n y N2 C8 RYM sing 296 n n C8 C9 RYM sing 297 n n C10 C9 RYM doub 298 n y C10 C11 RYM sing 299 n y C9 C14 RYM sing 300 n y C11 C12 RYM doub 301 n y C14 C13 RYM doub 302 n y C12 C13 RYM sing 303 n y C12 C15 RYM sing 304 n n C15 N3 RYM trip 305 n n C6 H1 RYM sing 306 n n C7 H2 RYM sing 307 n n C8 H3 RYM sing 308 n n C8 H4 RYM sing 309 n n C10 H5 RYM sing 310 n n C13 H6 RYM sing 311 n n C1 H7 RYM sing 312 n n C11 H8 RYM sing 313 n n C14 H9 RYM sing 314 n n C2 H10 RYM sing 315 n n C3 H11 RYM sing 316 n n # _atom_sites.entry_id 5R54 _atom_sites.fract_transf_matrix[1][1] 0.020169 _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] 0.019106 _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] 0.009842 _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 RYM A 1 401 401 RYM LIG . C 3 DMS A 1 402 1 DMS DMS . D 3 DMS A 1 403 2 DMS DMS . E 3 DMS A 1 404 3 DMS DMS . F 3 DMS A 1 405 4 DMS DMS . G 4 HOH A 1 501 147 HOH HOH . G 4 HOH A 2 502 158 HOH HOH . G 4 HOH A 3 503 65 HOH HOH . G 4 HOH A 4 504 117 HOH HOH . G 4 HOH A 5 505 141 HOH HOH . G 4 HOH A 6 506 75 HOH HOH . G 4 HOH A 7 507 113 HOH HOH . G 4 HOH A 8 508 156 HOH HOH . G 4 HOH A 9 509 37 HOH HOH . G 4 HOH A 10 510 131 HOH HOH . G 4 HOH A 11 511 93 HOH HOH . G 4 HOH A 12 512 112 HOH HOH . G 4 HOH A 13 513 56 HOH HOH . G 4 HOH A 14 514 116 HOH HOH . G 4 HOH A 15 515 62 HOH HOH . G 4 HOH A 16 516 57 HOH HOH . G 4 HOH A 17 517 58 HOH HOH . G 4 HOH A 18 518 82 HOH HOH . G 4 HOH A 19 519 146 HOH HOH . G 4 HOH A 20 520 145 HOH HOH . G 4 HOH A 21 521 50 HOH HOH . G 4 HOH A 22 522 91 HOH HOH . G 4 HOH A 23 523 45 HOH HOH . G 4 HOH A 24 524 87 HOH HOH . G 4 HOH A 25 525 61 HOH HOH . G 4 HOH A 26 526 99 HOH HOH . G 4 HOH A 27 527 157 HOH HOH . G 4 HOH A 28 528 121 HOH HOH . G 4 HOH A 29 529 125 HOH HOH . G 4 HOH A 30 530 71 HOH HOH . G 4 HOH A 31 531 40 HOH HOH . G 4 HOH A 32 532 34 HOH HOH . G 4 HOH A 33 533 139 HOH HOH . G 4 HOH A 34 534 136 HOH HOH . G 4 HOH A 35 535 1 HOH HOH . G 4 HOH A 36 536 115 HOH HOH . G 4 HOH A 37 537 129 HOH HOH . G 4 HOH A 38 538 13 HOH HOH . G 4 HOH A 39 539 55 HOH HOH . G 4 HOH A 40 540 83 HOH HOH . G 4 HOH A 41 541 153 HOH HOH . G 4 HOH A 42 542 120 HOH HOH . G 4 HOH A 43 543 160 HOH HOH . G 4 HOH A 44 544 80 HOH HOH . G 4 HOH A 45 545 47 HOH HOH . G 4 HOH A 46 546 88 HOH HOH . G 4 HOH A 47 547 148 HOH HOH . G 4 HOH A 48 548 46 HOH HOH . G 4 HOH A 49 549 63 HOH HOH . G 4 HOH A 50 550 2 HOH HOH . G 4 HOH A 51 551 102 HOH HOH . G 4 HOH A 52 552 38 HOH HOH . G 4 HOH A 53 553 107 HOH HOH . G 4 HOH A 54 554 138 HOH HOH . G 4 HOH A 55 555 132 HOH HOH . G 4 HOH A 56 556 20 HOH HOH . G 4 HOH A 57 557 41 HOH HOH . G 4 HOH A 58 558 3 HOH HOH . G 4 HOH A 59 559 27 HOH HOH . G 4 HOH A 60 560 42 HOH HOH . G 4 HOH A 61 561 39 HOH HOH . G 4 HOH A 62 562 84 HOH HOH . G 4 HOH A 63 563 94 HOH HOH . G 4 HOH A 64 564 85 HOH HOH . G 4 HOH A 65 565 16 HOH HOH . G 4 HOH A 66 566 19 HOH HOH . G 4 HOH A 67 567 111 HOH HOH . G 4 HOH A 68 568 29 HOH HOH . G 4 HOH A 69 569 35 HOH HOH . G 4 HOH A 70 570 49 HOH HOH . G 4 HOH A 71 571 90 HOH HOH . G 4 HOH A 72 572 137 HOH HOH . G 4 HOH A 73 573 143 HOH HOH . G 4 HOH A 74 574 73 HOH HOH . G 4 HOH A 75 575 6 HOH HOH . G 4 HOH A 76 576 144 HOH HOH . G 4 HOH A 77 577 59 HOH HOH . G 4 HOH A 78 578 21 HOH HOH . G 4 HOH A 79 579 10 HOH HOH . G 4 HOH A 80 580 103 HOH HOH . G 4 HOH A 81 581 70 HOH HOH . G 4 HOH A 82 582 24 HOH HOH . G 4 HOH A 83 583 98 HOH HOH . G 4 HOH A 84 584 43 HOH HOH . G 4 HOH A 85 585 66 HOH HOH . G 4 HOH A 86 586 30 HOH HOH . G 4 HOH A 87 587 18 HOH HOH . G 4 HOH A 88 588 152 HOH HOH . G 4 HOH A 89 589 9 HOH HOH . G 4 HOH A 90 590 5 HOH HOH . G 4 HOH A 91 591 28 HOH HOH . G 4 HOH A 92 592 14 HOH HOH . G 4 HOH A 93 593 15 HOH HOH . G 4 HOH A 94 594 100 HOH HOH . G 4 HOH A 95 595 86 HOH HOH . G 4 HOH A 96 596 114 HOH HOH . G 4 HOH A 97 597 101 HOH HOH . G 4 HOH A 98 598 60 HOH HOH . G 4 HOH A 99 599 22 HOH HOH . G 4 HOH A 100 600 72 HOH HOH . G 4 HOH A 101 601 51 HOH HOH . G 4 HOH A 102 602 4 HOH HOH . G 4 HOH A 103 603 69 HOH HOH . G 4 HOH A 104 604 8 HOH HOH . G 4 HOH A 105 605 133 HOH HOH . G 4 HOH A 106 606 97 HOH HOH . G 4 HOH A 107 607 127 HOH HOH . G 4 HOH A 108 608 31 HOH HOH . G 4 HOH A 109 609 23 HOH HOH . G 4 HOH A 110 610 118 HOH HOH . G 4 HOH A 111 611 105 HOH HOH . G 4 HOH A 112 612 12 HOH HOH . G 4 HOH A 113 613 135 HOH HOH . G 4 HOH A 114 614 128 HOH HOH . G 4 HOH A 115 615 154 HOH HOH . G 4 HOH A 116 616 44 HOH HOH . G 4 HOH A 117 617 67 HOH HOH . G 4 HOH A 118 618 150 HOH HOH . G 4 HOH A 119 619 11 HOH HOH . G 4 HOH A 120 620 36 HOH HOH . G 4 HOH A 121 621 134 HOH HOH . G 4 HOH A 122 622 123 HOH HOH . G 4 HOH A 123 623 54 HOH HOH . G 4 HOH A 124 624 25 HOH HOH . G 4 HOH A 125 625 106 HOH HOH . G 4 HOH A 126 626 96 HOH HOH . G 4 HOH A 127 627 74 HOH HOH . G 4 HOH A 128 628 26 HOH HOH . G 4 HOH A 129 629 33 HOH HOH . G 4 HOH A 130 630 104 HOH HOH . G 4 HOH A 131 631 76 HOH HOH . G 4 HOH A 132 632 7 HOH HOH . G 4 HOH A 133 633 77 HOH HOH . G 4 HOH A 134 634 78 HOH HOH . G 4 HOH A 135 635 155 HOH HOH . G 4 HOH A 136 636 130 HOH HOH . G 4 HOH A 137 637 92 HOH HOH . G 4 HOH A 138 638 126 HOH HOH . G 4 HOH A 139 639 124 HOH HOH . G 4 HOH A 140 640 32 HOH HOH . G 4 HOH A 141 641 122 HOH HOH . G 4 HOH A 142 642 119 HOH HOH . G 4 HOH A 143 643 95 HOH HOH . G 4 HOH A 144 644 68 HOH HOH . G 4 HOH A 145 645 89 HOH HOH . G 4 HOH A 146 646 64 HOH HOH . G 4 HOH A 147 647 108 HOH HOH . G 4 HOH A 148 648 17 HOH HOH . G 4 HOH A 149 649 48 HOH HOH . G 4 HOH A 150 650 142 HOH HOH . G 4 HOH A 151 651 151 HOH HOH . G 4 HOH A 152 652 159 HOH HOH . G 4 HOH A 153 653 79 HOH HOH . G 4 HOH A 154 654 140 HOH HOH . G 4 HOH A 155 655 81 HOH HOH . G 4 HOH A 156 656 162 HOH HOH . G 4 HOH A 157 657 149 HOH HOH . G 4 HOH A 158 658 109 HOH HOH . G 4 HOH A 159 659 53 HOH HOH . G 4 HOH A 160 660 110 HOH HOH . G 4 HOH A 161 661 52 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 N N1 RYM . . . B 2 14.063 23.25 -1.47 0.54 42.01 ? N1 RYM 401 A 1 HETATM 2 N N3 RYM . . . B 2 8.197 27.358 2.794 0.54 33.56 ? N3 RYM 401 A 1 HETATM 3 C C4 RYM . . . B 2 12.214 22.107 -0.809 0.54 42.79 ? C4 RYM 401 A 1 HETATM 4 C C5 RYM . . . B 2 12.918 22.593 -1.911 0.54 43.25 ? C5 RYM 401 A 1 HETATM 5 C C6 RYM . . . B 2 12.429 22.378 -3.196 0.54 42.99 ? C6 RYM 401 A 1 HETATM 6 C C7 RYM . . . B 2 14.03 23.166 -0.163 0.54 41.62 ? C7 RYM 401 A 1 HETATM 7 C C8 RYM . . . B 2 12.6 22.246 1.692 0.54 40.8 ? C8 RYM 401 A 1 HETATM 8 C C10 RYM . . . B 2 10.262 23.113 1.94 0.54 37.51 ? C10 RYM 401 A 1 HETATM 9 C C13 RYM . . . B 2 11.197 25.626 2.619 0.54 36.06 ? C13 RYM 401 A 1 HETATM 10 C C15 RYM . . . B 2 8.906 26.46 2.774 0.54 33.58 ? C15 RYM 401 A 1 HETATM 11 C C1 RYM . . . B 2 11.244 21.687 -3.332 0.54 43.91 ? C1 RYM 401 A 1 HETATM 12 C C11 RYM . . . B 2 9.363 24.129 2.204 0.54 36.74 ? C11 RYM 401 A 1 HETATM 13 C C12 RYM . . . B 2 9.833 25.387 2.55 0.54 35.86 ? C12 RYM 401 A 1 HETATM 14 C C14 RYM . . . B 2 12.083 24.597 2.364 0.54 36.73 ? C14 RYM 401 A 1 HETATM 15 C C2 RYM . . . B 2 10.551 21.203 -2.22 0.54 43.07 ? C2 RYM 401 A 1 HETATM 16 C C3 RYM . . . B 2 11.023 21.404 -0.944 0.54 42.39 ? C3 RYM 401 A 1 HETATM 17 C C9 RYM . . . B 2 11.622 23.328 2.065 0.54 38.28 ? C9 RYM 401 A 1 HETATM 18 N N2 RYM . . . B 2 12.967 22.461 0.296 0.54 42.89 ? N2 RYM 401 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 18 #