data_5QEK # _model_server_result.job_id VV8cJgy9W6WtVDUK6Hlobw _model_server_result.datetime_utc '2024-11-22 00:22:47' _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 5qek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5QEK # _exptl.entry_id 5QEK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.177 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-methyl-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 120 _cell.entry_id 5QEK _cell.length_a 89.839 _cell.length_b 89.839 _cell.length_c 106.671 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QEK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 'C8 H9 N3' _chem_comp.formula_weight 147.177 _chem_comp.id ES7 _chem_comp.mon_nstd_flag . _chem_comp.name 1-methyl-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 C10 N02 ES7 sing 83 n y C10 N09 ES7 doub 84 n y C10 N11 ES7 sing 85 n n C01 N02 ES7 sing 86 n n N02 C03 ES7 sing 87 n y C03 C04 ES7 doub 88 n y C03 C08 ES7 sing 89 n y C04 C05 ES7 sing 90 n y C05 C06 ES7 doub 91 n y C06 C07 ES7 sing 92 n y C07 C08 ES7 doub 93 n y C08 N09 ES7 sing 94 n y C01 H01 ES7 sing 95 n n C01 H01A ES7 sing 96 n n C01 H01B ES7 sing 97 n n C04 H04 ES7 sing 98 n n C05 H05 ES7 sing 99 n n C06 H06 ES7 sing 100 n n C07 H07 ES7 sing 101 n n N11 HN11 ES7 sing 102 n n N11 HN1A ES7 sing 103 n n # _atom_sites.entry_id 5QEK _atom_sites.fract_transf_matrix[1][1] 0.011131 _atom_sites.fract_transf_matrix[1][2] 0.006426 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012853 _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] 0.009375 _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 ES7 A 1 401 1 ES7 LIG . C 3 TRS A 1 402 500 TRS TRS . D 4 HOH A 1 501 36 HOH HOH . D 4 HOH A 2 502 164 HOH HOH . D 4 HOH A 3 503 19 HOH HOH . D 4 HOH A 4 504 53 HOH HOH . D 4 HOH A 5 505 115 HOH HOH . D 4 HOH A 6 506 179 HOH HOH . D 4 HOH A 7 507 131 HOH HOH . D 4 HOH A 8 508 113 HOH HOH . D 4 HOH A 9 509 145 HOH HOH . D 4 HOH A 10 510 22 HOH HOH . D 4 HOH A 11 511 37 HOH HOH . D 4 HOH A 12 512 141 HOH HOH . D 4 HOH A 13 513 114 HOH HOH . D 4 HOH A 14 514 130 HOH HOH . D 4 HOH A 15 515 138 HOH HOH . D 4 HOH A 16 516 58 HOH HOH . D 4 HOH A 17 517 85 HOH HOH . D 4 HOH A 18 518 54 HOH HOH . D 4 HOH A 19 519 3 HOH HOH . D 4 HOH A 20 520 5 HOH HOH . D 4 HOH A 21 521 64 HOH HOH . D 4 HOH A 22 522 14 HOH HOH . D 4 HOH A 23 523 7 HOH HOH . D 4 HOH A 24 524 123 HOH HOH . D 4 HOH A 25 525 157 HOH HOH . D 4 HOH A 26 526 17 HOH HOH . D 4 HOH A 27 527 4 HOH HOH . D 4 HOH A 28 528 52 HOH HOH . D 4 HOH A 29 529 87 HOH HOH . D 4 HOH A 30 530 102 HOH HOH . D 4 HOH A 31 531 129 HOH HOH . D 4 HOH A 32 532 29 HOH HOH . D 4 HOH A 33 533 20 HOH HOH . D 4 HOH A 34 534 189 HOH HOH . D 4 HOH A 35 535 112 HOH HOH . D 4 HOH A 36 536 158 HOH HOH . D 4 HOH A 37 537 118 HOH HOH . D 4 HOH A 38 538 91 HOH HOH . D 4 HOH A 39 539 111 HOH HOH . D 4 HOH A 40 540 11 HOH HOH . D 4 HOH A 41 541 6 HOH HOH . D 4 HOH A 42 542 226 HOH HOH . D 4 HOH A 43 543 70 HOH HOH . D 4 HOH A 44 544 127 HOH HOH . D 4 HOH A 45 545 10 HOH HOH . D 4 HOH A 46 546 182 HOH HOH . D 4 HOH A 47 547 170 HOH HOH . D 4 HOH A 48 548 56 HOH HOH . D 4 HOH A 49 549 78 HOH HOH . D 4 HOH A 50 550 156 HOH HOH . D 4 HOH A 51 551 152 HOH HOH . D 4 HOH A 52 552 73 HOH HOH . D 4 HOH A 53 553 86 HOH HOH . D 4 HOH A 54 554 13 HOH HOH . D 4 HOH A 55 555 76 HOH HOH . D 4 HOH A 56 556 101 HOH HOH . D 4 HOH A 57 557 103 HOH HOH . D 4 HOH A 58 558 180 HOH HOH . D 4 HOH A 59 559 48 HOH HOH . D 4 HOH A 60 560 174 HOH HOH . D 4 HOH A 61 561 212 HOH HOH . D 4 HOH A 62 562 1 HOH HOH . D 4 HOH A 63 563 38 HOH HOH . D 4 HOH A 64 564 23 HOH HOH . D 4 HOH A 65 565 106 HOH HOH . D 4 HOH A 66 566 2 HOH HOH . D 4 HOH A 67 567 26 HOH HOH . D 4 HOH A 68 568 55 HOH HOH . D 4 HOH A 69 569 18 HOH HOH . D 4 HOH A 70 570 79 HOH HOH . D 4 HOH A 71 571 8 HOH HOH . D 4 HOH A 72 572 25 HOH HOH . D 4 HOH A 73 573 31 HOH HOH . D 4 HOH A 74 574 205 HOH HOH . D 4 HOH A 75 575 47 HOH HOH . D 4 HOH A 76 576 41 HOH HOH . D 4 HOH A 77 577 60 HOH HOH . D 4 HOH A 78 578 95 HOH HOH . D 4 HOH A 79 579 146 HOH HOH . D 4 HOH A 80 580 9 HOH HOH . D 4 HOH A 81 581 82 HOH HOH . D 4 HOH A 82 582 28 HOH HOH . D 4 HOH A 83 583 49 HOH HOH . D 4 HOH A 84 584 120 HOH HOH . D 4 HOH A 85 585 172 HOH HOH . D 4 HOH A 86 586 186 HOH HOH . D 4 HOH A 87 587 71 HOH HOH . D 4 HOH A 88 588 108 HOH HOH . D 4 HOH A 89 589 12 HOH HOH . D 4 HOH A 90 590 209 HOH HOH . D 4 HOH A 91 591 194 HOH HOH . D 4 HOH A 92 592 39 HOH HOH . D 4 HOH A 93 593 67 HOH HOH . D 4 HOH A 94 594 32 HOH HOH . D 4 HOH A 95 595 162 HOH HOH . D 4 HOH A 96 596 213 HOH HOH . D 4 HOH A 97 597 15 HOH HOH . D 4 HOH A 98 598 30 HOH HOH . D 4 HOH A 99 599 24 HOH HOH . D 4 HOH A 100 600 137 HOH HOH . D 4 HOH A 101 601 202 HOH HOH . D 4 HOH A 102 602 33 HOH HOH . D 4 HOH A 103 603 121 HOH HOH . D 4 HOH A 104 604 21 HOH HOH . D 4 HOH A 105 605 42 HOH HOH . D 4 HOH A 106 606 83 HOH HOH . D 4 HOH A 107 607 139 HOH HOH . D 4 HOH A 108 608 132 HOH HOH . D 4 HOH A 109 609 16 HOH HOH . D 4 HOH A 110 610 63 HOH HOH . D 4 HOH A 111 611 100 HOH HOH . D 4 HOH A 112 612 184 HOH HOH . D 4 HOH A 113 613 51 HOH HOH . D 4 HOH A 114 614 198 HOH HOH . D 4 HOH A 115 615 97 HOH HOH . D 4 HOH A 116 616 94 HOH HOH . D 4 HOH A 117 617 217 HOH HOH . D 4 HOH A 118 618 81 HOH HOH . D 4 HOH A 119 619 96 HOH HOH . D 4 HOH A 120 620 104 HOH HOH . D 4 HOH A 121 621 153 HOH HOH . D 4 HOH A 122 622 188 HOH HOH . D 4 HOH A 123 623 223 HOH HOH . D 4 HOH A 124 624 84 HOH HOH . D 4 HOH A 125 625 192 HOH HOH . D 4 HOH A 126 626 44 HOH HOH . D 4 HOH A 127 627 150 HOH HOH . D 4 HOH A 128 628 75 HOH HOH . D 4 HOH A 129 629 133 HOH HOH . D 4 HOH A 130 630 166 HOH HOH . D 4 HOH A 131 631 107 HOH HOH . D 4 HOH A 132 632 62 HOH HOH . D 4 HOH A 133 633 134 HOH HOH . D 4 HOH A 134 634 109 HOH HOH . D 4 HOH A 135 635 90 HOH HOH . D 4 HOH A 136 636 61 HOH HOH . D 4 HOH A 137 637 200 HOH HOH . D 4 HOH A 138 638 92 HOH HOH . D 4 HOH A 139 639 46 HOH HOH . D 4 HOH A 140 640 124 HOH HOH . D 4 HOH A 141 641 151 HOH HOH . D 4 HOH A 142 642 93 HOH HOH . D 4 HOH A 143 643 66 HOH HOH . D 4 HOH A 144 644 45 HOH HOH . D 4 HOH A 145 645 175 HOH HOH . D 4 HOH A 146 646 34 HOH HOH . D 4 HOH A 147 647 185 HOH HOH . D 4 HOH A 148 648 99 HOH HOH . D 4 HOH A 149 649 190 HOH HOH . D 4 HOH A 150 650 116 HOH HOH . D 4 HOH A 151 651 72 HOH HOH . D 4 HOH A 152 652 149 HOH HOH . D 4 HOH A 153 653 35 HOH HOH . D 4 HOH A 154 654 27 HOH HOH . D 4 HOH A 155 655 57 HOH HOH . D 4 HOH A 156 656 40 HOH HOH . D 4 HOH A 157 657 183 HOH HOH . D 4 HOH A 158 658 206 HOH HOH . D 4 HOH A 159 659 69 HOH HOH . D 4 HOH A 160 660 98 HOH HOH . D 4 HOH A 161 661 173 HOH HOH . D 4 HOH A 162 662 65 HOH HOH . D 4 HOH A 163 663 171 HOH HOH . D 4 HOH A 164 664 208 HOH HOH . D 4 HOH A 165 665 178 HOH HOH . D 4 HOH A 166 666 215 HOH HOH . D 4 HOH A 167 667 110 HOH HOH . D 4 HOH A 168 668 74 HOH HOH . D 4 HOH A 169 669 117 HOH HOH . D 4 HOH A 170 670 135 HOH HOH . D 4 HOH A 171 671 88 HOH HOH . D 4 HOH A 172 672 159 HOH HOH . D 4 HOH A 173 673 220 HOH HOH . D 4 HOH A 174 674 165 HOH HOH . D 4 HOH A 175 675 142 HOH HOH . D 4 HOH A 176 676 211 HOH HOH . D 4 HOH A 177 677 119 HOH HOH . D 4 HOH A 178 678 219 HOH HOH . D 4 HOH A 179 679 50 HOH HOH . D 4 HOH A 180 680 43 HOH HOH . D 4 HOH A 181 681 136 HOH HOH . D 4 HOH A 182 682 177 HOH HOH . D 4 HOH A 183 683 204 HOH HOH . D 4 HOH A 184 684 216 HOH HOH . D 4 HOH A 185 685 193 HOH HOH . D 4 HOH A 186 686 176 HOH HOH . D 4 HOH A 187 687 197 HOH HOH . D 4 HOH A 188 688 105 HOH HOH . D 4 HOH A 189 689 68 HOH HOH . D 4 HOH A 190 690 224 HOH HOH . D 4 HOH A 191 691 203 HOH HOH . D 4 HOH A 192 692 207 HOH HOH . D 4 HOH A 193 693 125 HOH HOH . D 4 HOH A 194 694 126 HOH HOH . D 4 HOH A 195 695 191 HOH HOH . D 4 HOH A 196 696 201 HOH HOH . D 4 HOH A 197 697 221 HOH HOH . D 4 HOH A 198 698 169 HOH HOH . D 4 HOH A 199 699 181 HOH HOH . D 4 HOH A 200 700 148 HOH HOH . D 4 HOH A 201 701 128 HOH HOH . D 4 HOH A 202 702 196 HOH HOH . D 4 HOH A 203 703 89 HOH HOH . D 4 HOH A 204 704 199 HOH HOH . D 4 HOH A 205 705 214 HOH HOH . D 4 HOH A 206 706 161 HOH HOH . D 4 HOH A 207 707 163 HOH HOH . D 4 HOH A 208 708 147 HOH HOH . D 4 HOH A 209 709 59 HOH HOH . D 4 HOH A 210 710 225 HOH HOH . D 4 HOH A 211 711 154 HOH HOH . D 4 HOH A 212 712 77 HOH HOH . D 4 HOH A 213 713 155 HOH HOH . D 4 HOH A 214 714 122 HOH HOH . D 4 HOH A 215 715 80 HOH HOH . D 4 HOH A 216 716 187 HOH HOH . D 4 HOH A 217 717 167 HOH HOH . D 4 HOH A 218 718 144 HOH HOH . D 4 HOH A 219 719 195 HOH HOH . D 4 HOH A 220 720 143 HOH HOH . D 4 HOH A 221 721 210 HOH HOH . D 4 HOH A 222 722 160 HOH HOH . D 4 HOH A 223 723 168 HOH HOH . D 4 HOH A 224 724 218 HOH HOH . D 4 HOH A 225 725 140 HOH HOH . D 4 HOH A 226 726 222 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 C10 ES7 . C . B 2 39.659 -41.27 1.389 0.2 37.7 ? C10 ES7 401 A 1 HETATM 2 C C10 ES7 . D . B 2 39.659 -41.27 1.389 0.2 37.7 ? C10 ES7 401 A 1 HETATM 3 C C01 ES7 . C . B 2 37.325 -41.269 0.837 0.2 39.47 ? C01 ES7 401 A 1 HETATM 4 C C01 ES7 . D . B 2 37.325 -41.269 0.837 0.2 39.47 ? C01 ES7 401 A 1 HETATM 5 N N02 ES7 . C . B 2 38.656 -41.855 1.011 0.2 33.69 ? N02 ES7 401 A 1 HETATM 6 N N02 ES7 . D . B 2 38.656 -41.855 1.011 0.2 33.69 ? N02 ES7 401 A 1 HETATM 7 C C03 ES7 . C . B 2 39.121 -43.033 0.782 0.2 41.04 ? C03 ES7 401 A 1 HETATM 8 C C03 ES7 . D . B 2 39.121 -43.033 0.782 0.2 41.04 ? C03 ES7 401 A 1 HETATM 9 C C04 ES7 . C . B 2 38.423 -44.204 0.277 0.2 34.3 ? C04 ES7 401 A 1 HETATM 10 C C04 ES7 . D . B 2 38.423 -44.204 0.277 0.2 34.3 ? C04 ES7 401 A 1 HETATM 11 C C05 ES7 . C . B 2 39.159 -45.292 0.091 0.2 33.37 ? C05 ES7 401 A 1 HETATM 12 C C05 ES7 . D . B 2 39.159 -45.292 0.091 0.2 33.37 ? C05 ES7 401 A 1 HETATM 13 C C06 ES7 . C . B 2 40.44 -45.351 0.401 0.2 38.02 ? C06 ES7 401 A 1 HETATM 14 C C06 ES7 . D . B 2 40.44 -45.351 0.401 0.2 38.02 ? C06 ES7 401 A 1 HETATM 15 C C07 ES7 . C . B 2 41.117 -44.242 0.885 0.2 37.35 ? C07 ES7 401 A 1 HETATM 16 C C07 ES7 . D . B 2 41.117 -44.242 0.885 0.2 37.35 ? C07 ES7 401 A 1 HETATM 17 C C08 ES7 . C . B 2 40.371 -43.081 1.019 0.2 27.22 ? C08 ES7 401 A 1 HETATM 18 C C08 ES7 . D . B 2 40.371 -43.081 1.019 0.2 27.22 ? C08 ES7 401 A 1 HETATM 19 N N09 ES7 . C . B 2 40.728 -41.99 1.44 0.2 30.12 ? N09 ES7 401 A 1 HETATM 20 N N09 ES7 . D . B 2 40.728 -41.99 1.44 0.2 30.12 ? N09 ES7 401 A 1 HETATM 21 N N11 ES7 . C . B 2 39.484 -39.942 1.714 0.2 39.9 ? N11 ES7 401 A 1 HETATM 22 N N11 ES7 . D . B 2 39.484 -39.942 1.714 0.2 39.9 ? N11 ES7 401 A 1 HETATM 23 H H01 ES7 . C . B 2 36.602 -41.985 0.435 0.2 47.36 ? H01 ES7 401 A 1 HETATM 24 H H01 ES7 . D . B 2 36.602 -41.985 0.435 0.2 47.36 ? H01 ES7 401 A 1 HETATM 25 H H01A ES7 . C . B 2 37.374 -40.411 0.134 0.2 47.36 ? H01A ES7 401 A 1 HETATM 26 H H01A ES7 . D . B 2 37.374 -40.411 0.134 0.2 47.36 ? H01A ES7 401 A 1 HETATM 27 H H01B ES7 . C . B 2 36.935 -40.912 1.802 0.2 47.36 ? H01B ES7 401 A 1 HETATM 28 H H01B ES7 . D . B 2 36.935 -40.912 1.802 0.2 47.36 ? H01B ES7 401 A 1 HETATM 29 H H04 ES7 . C . B 2 37.397 -44.19 0.075 0.2 41.16 ? H04 ES7 401 A 1 HETATM 30 H H04 ES7 . D . B 2 37.397 -44.19 0.075 0.2 41.16 ? H04 ES7 401 A 1 HETATM 31 H H05 ES7 . C . B 2 38.729 -46.21 -0.337 0.2 40.05 ? H05 ES7 401 A 1 HETATM 32 H H05 ES7 . D . B 2 38.729 -46.21 -0.337 0.2 40.05 ? H05 ES7 401 A 1 HETATM 33 H H06 ES7 . C . B 2 41.009 -46.282 0.226 0.2 45.63 ? H06 ES7 401 A 1 HETATM 34 H H06 ES7 . D . B 2 41.009 -46.282 0.226 0.2 45.63 ? H06 ES7 401 A 1 HETATM 35 H H07 ES7 . C . B 2 42.145 -44.295 1.132 0.2 44.82 ? H07 ES7 401 A 1 HETATM 36 H H07 ES7 . D . B 2 42.145 -44.295 1.132 0.2 44.82 ? H07 ES7 401 A 1 HETATM 37 H HN11 ES7 . C . B 2 38.572 -39.569 1.604 0.2 47.88 ? HN11 ES7 401 A 1 HETATM 38 H HN11 ES7 . D . B 2 38.572 -39.569 1.604 0.2 47.88 ? HN11 ES7 401 A 1 HETATM 39 H HN1A ES7 . C . B 2 40.257 -39.427 2.036 0.2 47.88 ? HN1A ES7 401 A 1 HETATM 40 H HN1A ES7 . D . B 2 40.257 -39.427 2.036 0.2 47.88 ? HN1A ES7 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 393 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #