data_5V5N # _model_server_result.job_id BhUTXKjy-p2wxhd0f140Tw _model_server_result.datetime_utc '2024-11-22 17:16:40' _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 5v5n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5V5N # _exptl.entry_id 5V5N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.361 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N~1~-(1-propyl-1,3-dihydro-2H-benzimidazol-2-ylidene)benzene-1,3-dicarboxamide _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 5V5N _cell.length_a 58.34 _cell.length_b 134.227 _cell.length_c 143.385 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V5N _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _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 'C18 H18 N4 O2' _chem_comp.formula_weight 322.361 _chem_comp.id EDH _chem_comp.mon_nstd_flag . _chem_comp.name N~1~-(1-propyl-1,3-dihydro-2H-benzimidazol-2-ylidene)benzene-1,3-dicarboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms EDHS-206 # 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 C17 C16 EDH sing 83 n n C16 C15 EDH sing 84 n n C12 C11 EDH doub 85 n y C12 C13 EDH sing 86 n y C11 C10 EDH sing 87 n y C13 C14 EDH doub 88 n y C15 N04 EDH sing 89 n n C10 N04 EDH sing 90 n n C10 C09 EDH doub 91 n y N04 C08 EDH sing 92 n n C14 C09 EDH sing 93 n y C09 N03 EDH sing 94 n n C08 N03 EDH sing 95 n n C08 N02 EDH doub 96 n n N01 C01 EDH sing 97 n n N02 C07 EDH sing 98 n n C01 C02 EDH sing 99 n n C01 O02 EDH doub 100 n n C07 C06 EDH sing 101 n n C07 O01 EDH doub 102 n n C18 C02 EDH doub 103 n y C18 C06 EDH sing 104 n y C02 C03 EDH sing 105 n y C06 C05 EDH doub 106 n y C03 C04 EDH doub 107 n y C05 C04 EDH sing 108 n y C03 H03 EDH sing 109 n n C04 H04 EDH sing 110 n n C05 H05 EDH sing 111 n n C11 H06 EDH sing 112 n n C12 H07 EDH sing 113 n n C13 H08 EDH sing 114 n n C14 H09 EDH sing 115 n n C15 H10 EDH sing 116 n n C15 H11 EDH sing 117 n n C16 H12 EDH sing 118 n n C16 H13 EDH sing 119 n n C17 H18 EDH sing 120 n n C17 H16 EDH sing 121 n n C17 H17 EDH sing 122 n n C18 H14 EDH sing 123 n n N01 H01 EDH sing 124 n n N01 H02 EDH sing 125 n n N03 H15 EDH sing 126 n n # _atom_sites.entry_id 5V5N _atom_sites.fract_transf_matrix[1][1] 0.017141 _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] 0.00745 _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] 0.006974 _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 EDH A 1 501 1 EDH EDH . C 3 HOH A 1 601 3 HOH HOH . C 3 HOH A 2 602 91 HOH HOH . C 3 HOH A 3 603 43 HOH HOH . C 3 HOH A 4 604 38 HOH HOH . C 3 HOH A 5 605 112 HOH HOH . C 3 HOH A 6 606 17 HOH HOH . C 3 HOH A 7 607 25 HOH HOH . C 3 HOH A 8 608 4 HOH HOH . C 3 HOH A 9 609 51 HOH HOH . C 3 HOH A 10 610 1 HOH HOH . C 3 HOH A 11 611 72 HOH HOH . C 3 HOH A 12 612 37 HOH HOH . C 3 HOH A 13 613 42 HOH HOH . C 3 HOH A 14 614 83 HOH HOH . C 3 HOH A 15 615 97 HOH HOH . C 3 HOH A 16 616 19 HOH HOH . C 3 HOH A 17 617 113 HOH HOH . C 3 HOH A 18 618 2 HOH HOH . C 3 HOH A 19 619 59 HOH HOH . C 3 HOH A 20 620 60 HOH HOH . C 3 HOH A 21 621 87 HOH HOH . C 3 HOH A 22 622 44 HOH HOH . C 3 HOH A 23 623 71 HOH HOH . C 3 HOH A 24 624 57 HOH HOH . C 3 HOH A 25 625 65 HOH HOH . C 3 HOH A 26 626 80 HOH HOH . C 3 HOH A 27 627 23 HOH HOH . C 3 HOH A 28 628 8 HOH HOH . C 3 HOH A 29 629 101 HOH HOH . C 3 HOH A 30 630 16 HOH HOH . C 3 HOH A 31 631 33 HOH HOH . C 3 HOH A 32 632 74 HOH HOH . C 3 HOH A 33 633 102 HOH HOH . C 3 HOH A 34 634 109 HOH HOH . C 3 HOH A 35 635 86 HOH HOH . C 3 HOH A 36 636 90 HOH HOH . C 3 HOH A 37 637 50 HOH HOH . C 3 HOH A 38 638 10 HOH HOH . C 3 HOH A 39 639 32 HOH HOH . C 3 HOH A 40 640 13 HOH HOH . C 3 HOH A 41 641 70 HOH HOH . C 3 HOH A 42 642 115 HOH HOH . C 3 HOH A 43 643 111 HOH HOH . C 3 HOH A 44 644 24 HOH HOH . C 3 HOH A 45 645 82 HOH HOH . C 3 HOH A 46 646 40 HOH HOH . C 3 HOH A 47 647 12 HOH HOH . C 3 HOH A 48 648 68 HOH HOH . C 3 HOH A 49 649 108 HOH HOH . C 3 HOH A 50 650 14 HOH HOH . C 3 HOH A 51 651 61 HOH HOH . C 3 HOH A 52 652 93 HOH HOH . C 3 HOH A 53 653 47 HOH HOH . C 3 HOH A 54 654 88 HOH HOH . C 3 HOH A 55 655 100 HOH HOH . C 3 HOH A 56 656 66 HOH HOH . C 3 HOH A 57 657 15 HOH HOH . C 3 HOH A 58 658 63 HOH HOH . C 3 HOH A 59 659 29 HOH HOH . C 3 HOH A 60 660 27 HOH HOH . C 3 HOH A 61 661 30 HOH HOH . C 3 HOH A 62 662 45 HOH HOH . C 3 HOH A 63 663 77 HOH HOH . C 3 HOH A 64 664 107 HOH HOH . C 3 HOH A 65 665 73 HOH HOH . C 3 HOH A 66 666 69 HOH HOH . C 3 HOH A 67 667 7 HOH HOH . C 3 HOH A 68 668 9 HOH HOH . C 3 HOH A 69 669 5 HOH HOH . C 3 HOH A 70 670 31 HOH HOH . C 3 HOH A 71 671 18 HOH HOH . C 3 HOH A 72 672 35 HOH HOH . C 3 HOH A 73 673 78 HOH HOH . C 3 HOH A 74 674 67 HOH HOH . C 3 HOH A 75 675 94 HOH HOH . C 3 HOH A 76 676 49 HOH HOH . C 3 HOH A 77 677 84 HOH HOH . C 3 HOH A 78 678 55 HOH HOH . C 3 HOH A 79 679 41 HOH HOH . C 3 HOH A 80 680 22 HOH HOH . C 3 HOH A 81 681 39 HOH HOH . C 3 HOH A 82 682 46 HOH HOH . C 3 HOH A 83 683 6 HOH HOH . C 3 HOH A 84 684 11 HOH HOH . C 3 HOH A 85 685 48 HOH HOH . C 3 HOH A 86 686 36 HOH HOH . C 3 HOH A 87 687 21 HOH HOH . C 3 HOH A 88 688 52 HOH HOH . C 3 HOH A 89 689 114 HOH HOH . C 3 HOH A 90 690 53 HOH HOH . C 3 HOH A 91 691 105 HOH HOH . C 3 HOH A 92 692 92 HOH HOH . C 3 HOH A 93 693 106 HOH HOH . C 3 HOH A 94 694 34 HOH HOH . C 3 HOH A 95 695 58 HOH HOH . C 3 HOH A 96 696 76 HOH HOH . C 3 HOH A 97 697 99 HOH HOH . C 3 HOH A 98 698 54 HOH HOH . C 3 HOH A 99 699 26 HOH HOH . C 3 HOH A 100 700 96 HOH HOH . C 3 HOH A 101 701 64 HOH HOH . C 3 HOH A 102 702 110 HOH HOH . C 3 HOH A 103 703 85 HOH HOH . C 3 HOH A 104 704 75 HOH HOH . C 3 HOH A 105 705 81 HOH HOH . C 3 HOH A 106 706 89 HOH HOH . C 3 HOH A 107 707 20 HOH HOH . C 3 HOH A 108 708 103 HOH HOH . C 3 HOH A 109 709 62 HOH HOH . C 3 HOH A 110 710 56 HOH HOH . C 3 HOH A 111 711 95 HOH HOH . C 3 HOH A 112 712 79 HOH HOH . C 3 HOH A 113 713 28 HOH HOH . C 3 HOH A 114 714 98 HOH HOH . C 3 HOH A 115 715 104 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 C01 EDH . . . B 2 -10.029 -49.697 -15.025 1 55.5 ? C01 EDH 501 A 1 HETATM 2 C C02 EDH . . . B 2 -10.855 -48.485 -14.605 1 50.29 ? C02 EDH 501 A 1 HETATM 3 C C03 EDH . . . B 2 -10.267 -47.476 -13.867 1 60.11 ? C03 EDH 501 A 1 HETATM 4 C C04 EDH . . . B 2 -11.006 -46.356 -13.471 1 61.22 ? C04 EDH 501 A 1 HETATM 5 C C05 EDH . . . B 2 -12.358 -46.253 -13.828 1 52.04 ? C05 EDH 501 A 1 HETATM 6 C C06 EDH . . . B 2 -12.949 -47.264 -14.564 1 59.91 ? C06 EDH 501 A 1 HETATM 7 C C07 EDH . . . B 2 -14.443 -47.171 -14.98 1 57.57 ? C07 EDH 501 A 1 HETATM 8 C C08 EDH . . . B 2 -16.297 -48.164 -16.359 1 66.77 ? C08 EDH 501 A 1 HETATM 9 C C09 EDH . . . B 2 -18.403 -47.584 -16.787 1 75.28 ? C09 EDH 501 A 1 HETATM 10 C C10 EDH . . . B 2 -18.168 -48.816 -17.372 1 66 ? C10 EDH 501 A 1 HETATM 11 C C11 EDH . . . B 2 -19.207 -49.479 -18.095 1 62.68 ? C11 EDH 501 A 1 HETATM 12 C C12 EDH . . . B 2 -20.455 -48.882 -18.208 1 65.22 ? C12 EDH 501 A 1 HETATM 13 C C13 EDH . . . B 2 -20.697 -47.627 -17.613 1 66.88 ? C13 EDH 501 A 1 HETATM 14 C C14 EDH . . . B 2 -19.679 -46.975 -16.904 1 70.09 ? C14 EDH 501 A 1 HETATM 15 C C15 EDH . . . B 2 -16.177 -50.364 -17.514 1 62.01 ? C15 EDH 501 A 1 HETATM 16 C C16 EDH . . . B 2 -15.355 -50.101 -18.73 1 68.58 ? C16 EDH 501 A 1 HETATM 17 C C17 EDH . . . B 2 -14.506 -51.278 -19.111 1 82.38 ? C17 EDH 501 A 1 HETATM 18 C C18 EDH . . . B 2 -12.206 -48.381 -14.962 1 54.05 ? C18 EDH 501 A 1 HETATM 19 N N01 EDH . . . B 2 -10.556 -50.645 -15.965 1 57.23 ? N01 EDH 501 A 1 HETATM 20 N N02 EDH . . . B 2 -14.939 -48.17 -15.9 1 59.03 ? N02 EDH 501 A 1 HETATM 21 N N03 EDH . . . B 2 -17.21 -47.194 -16.159 1 64.43 ? N03 EDH 501 A 1 HETATM 22 N N04 EDH . . . B 2 -16.857 -49.152 -17.096 1 64.25 ? N04 EDH 501 A 1 HETATM 23 O O01 EDH . . . B 2 -15.163 -46.288 -14.554 1 63.74 ? O01 EDH 501 A 1 HETATM 24 O O02 EDH . . . B 2 -8.923 -49.862 -14.562 1 66.97 ? O02 EDH 501 A 1 HETATM 25 H H03 EDH . . . B 2 -9.371 -47.544 -13.628 1 72.13 ? H03 EDH 501 A 1 HETATM 26 H H04 EDH . . . B 2 -10.601 -45.683 -12.973 1 73.46 ? H04 EDH 501 A 1 HETATM 27 H H05 EDH . . . B 2 -12.854 -45.51 -13.568 1 62.45 ? H05 EDH 501 A 1 HETATM 28 H H06 EDH . . . B 2 -19.048 -50.308 -18.488 1 75.22 ? H06 EDH 501 A 1 HETATM 29 H H07 EDH . . . B 2 -21.134 -49.311 -18.677 1 78.27 ? H07 EDH 501 A 1 HETATM 30 H H08 EDH . . . B 2 -21.534 -47.23 -17.69 1 80.25 ? H08 EDH 501 A 1 HETATM 31 H H09 EDH . . . B 2 -19.839 -46.147 -16.511 1 84.11 ? H09 EDH 501 A 1 HETATM 32 H H10 EDH . . . B 2 -15.599 -50.671 -16.799 1 74.41 ? H10 EDH 501 A 1 HETATM 33 H H11 EDH . . . B 2 -16.835 -51.048 -17.713 1 74.41 ? H11 EDH 501 A 1 HETATM 34 H H12 EDH . . . B 2 -15.947 -49.889 -19.469 1 82.3 ? H12 EDH 501 A 1 HETATM 35 H H13 EDH . . . B 2 -14.779 -49.339 -18.562 1 82.3 ? H13 EDH 501 A 1 HETATM 36 H H18 EDH . . . B 2 -15.075 -52.039 -19.304 1 98.86 ? H18 EDH 501 A 1 HETATM 37 H H16 EDH . . . B 2 -13.91 -51.498 -18.378 1 98.86 ? H16 EDH 501 A 1 HETATM 38 H H17 EDH . . . B 2 -13.983 -51.059 -19.898 1 98.86 ? H17 EDH 501 A 1 HETATM 39 H H14 EDH . . . B 2 -12.609 -49.055 -15.46 1 64.86 ? H14 EDH 501 A 1 HETATM 40 H H01 EDH . . . B 2 -11.342 -50.532 -16.296 1 68.68 ? H01 EDH 501 A 1 HETATM 41 H H02 EDH . . . B 2 -10.086 -51.327 -16.198 1 68.68 ? H02 EDH 501 A 1 HETATM 42 H H15 EDH . . . B 2 -17.084 -46.465 -15.72 1 77.32 ? H15 EDH 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 42 #