data_4RMZ # _model_server_result.job_id '_X5XviEpzMLm2oW4ZglNzA' _model_server_result.datetime_utc '2024-12-27 09:29:04' _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 4rmz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 4RMZ # _exptl.entry_id 4RMZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 455.508 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-nitro-N-[1-phenyl-5-(piperidin-1-ylmethyl)-1H-benzimidazol-2-yl]benzamide _entity.pdbx_number_of_molecules 2 _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 4RMZ _cell.length_a 87.73 _cell.length_b 116.81 _cell.length_c 140.92 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RMZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 covale ? covale1 A C GLN 188 A GLN 341 1_555 A N TPO 189 A TPO 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C TPO 189 A TPO 342 1_555 A N VAL 190 A VAL 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C MET 191 A MET 344 1_555 A N TPO 192 A TPO 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C TPO 192 A TPO 345 1_555 A N SEP 193 A SEP 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C SEP 193 A SEP 346 1_555 A N ARG 194 A ARG 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale6 B C MET 191 B MET 344 1_555 B N TPO 192 B TPO 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale7 B C TPO 192 B TPO 345 1_555 B N SEP 193 B SEP 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 B C SEP 193 B SEP 346 1_555 B N ARG 194 B ARG 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? # _chem_comp.formula 'C26 H25 N5 O3' _chem_comp.formula_weight 455.508 _chem_comp.id T20 _chem_comp.mon_nstd_flag . _chem_comp.name 3-nitro-N-[1-phenyl-5-(piperidin-1-ylmethyl)-1H-benzimidazol-2-yl]benzamide _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 C3 C4 T20 doub 308 n y C3 C2 T20 sing 309 n y C4 C5 T20 sing 310 n y C2 C1 T20 doub 311 n y O27 N26 T20 doub 312 n n O28 N26 T20 doub 313 n n C5 C6 T20 doub 314 n y N26 C16 T20 sing 315 n n C1 C6 T20 sing 316 n y C6 N19 T20 sing 317 n n C16 C17 T20 doub 318 n y C16 C15 T20 sing 319 n y C17 C18 T20 sing 320 n y N19 C8 T20 sing 321 n y N19 C20 T20 sing 322 n y C15 C14 T20 doub 323 n y C7 C8 T20 doub 324 n y C7 C12 T20 sing 325 n y N23 C20 T20 sing 326 n n N23 C24 T20 sing 327 n n C8 C9 T20 sing 328 n y C20 N21 T20 doub 329 n y C18 C24 T20 sing 330 n n C18 C13 T20 doub 331 n y C12 C11 T20 doub 332 n y C14 C13 T20 sing 333 n y C24 O25 T20 doub 334 n n C9 N21 T20 sing 335 n y C9 C10 T20 doub 336 n y C11 C10 T20 sing 337 n y C11 C22 T20 sing 338 n n C34 C33 T20 sing 339 n n C34 N35 T20 sing 340 n n C33 C32 T20 sing 341 n n C22 N35 T20 sing 342 n n N35 C30 T20 sing 343 n n C32 C31 T20 sing 344 n n C30 C31 T20 sing 345 n n C1 H1 T20 sing 346 n n C2 H2 T20 sing 347 n n C3 H3 T20 sing 348 n n C4 H4 T20 sing 349 n n C5 H5 T20 sing 350 n n C7 H6 T20 sing 351 n n C10 H7 T20 sing 352 n n C12 H8 T20 sing 353 n n C13 H9 T20 sing 354 n n C14 H10 T20 sing 355 n n C15 H11 T20 sing 356 n n C17 H12 T20 sing 357 n n C22 H13 T20 sing 358 n n C22 H14 T20 sing 359 n n N23 H15 T20 sing 360 n n C30 H16 T20 sing 361 n n C30 H17 T20 sing 362 n n C31 H18 T20 sing 363 n n C31 H19 T20 sing 364 n n C32 H20 T20 sing 365 n n C32 H21 T20 sing 366 n n C33 H22 T20 sing 367 n n C33 H23 T20 sing 368 n n C34 H24 T20 sing 369 n n C34 H25 T20 sing 370 n n # _atom_sites.entry_id 4RMZ _atom_sites.fract_transf_matrix[1][1] 0.011399 _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] 0.008561 _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] 0.007096 _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 2 T20 A 1 501 1 T20 UNL . D 2 T20 B 1 501 2 T20 UNL . E 3 HOH A 1 601 27 HOH HOH . E 3 HOH A 2 602 28 HOH HOH . E 3 HOH A 3 603 53 HOH HOH . E 3 HOH A 4 604 54 HOH HOH . E 3 HOH A 5 605 55 HOH HOH . E 3 HOH A 6 606 56 HOH HOH . E 3 HOH A 7 607 57 HOH HOH . E 3 HOH A 8 608 58 HOH HOH . E 3 HOH A 9 609 59 HOH HOH . E 3 HOH A 10 610 60 HOH HOH . E 3 HOH A 11 611 61 HOH HOH . E 3 HOH A 12 612 62 HOH HOH . E 3 HOH A 13 613 63 HOH HOH . E 3 HOH A 14 614 64 HOH HOH . E 3 HOH A 15 615 65 HOH HOH . E 3 HOH A 16 616 66 HOH HOH . E 3 HOH A 17 617 67 HOH HOH . E 3 HOH A 18 618 68 HOH HOH . E 3 HOH A 19 619 69 HOH HOH . E 3 HOH A 20 620 70 HOH HOH . E 3 HOH A 21 621 72 HOH HOH . E 3 HOH A 22 622 73 HOH HOH . E 3 HOH A 23 623 74 HOH HOH . E 3 HOH A 24 624 75 HOH HOH . E 3 HOH A 25 625 76 HOH HOH . E 3 HOH A 26 626 77 HOH HOH . E 3 HOH A 27 627 78 HOH HOH . E 3 HOH A 28 628 79 HOH HOH . E 3 HOH A 29 629 80 HOH HOH . E 3 HOH A 30 630 81 HOH HOH . E 3 HOH A 31 631 82 HOH HOH . E 3 HOH A 32 632 83 HOH HOH . E 3 HOH A 33 633 84 HOH HOH . E 3 HOH A 34 634 85 HOH HOH . E 3 HOH A 35 635 87 HOH HOH . E 3 HOH A 36 636 88 HOH HOH . E 3 HOH A 37 637 89 HOH HOH . E 3 HOH A 38 638 90 HOH HOH . E 3 HOH A 39 639 91 HOH HOH . E 3 HOH A 40 640 92 HOH HOH . E 3 HOH A 41 641 93 HOH HOH . E 3 HOH A 42 642 94 HOH HOH . E 3 HOH A 43 643 95 HOH HOH . E 3 HOH A 44 644 96 HOH HOH . E 3 HOH A 45 645 97 HOH HOH . E 3 HOH A 46 646 98 HOH HOH . E 3 HOH A 47 647 99 HOH HOH . E 3 HOH A 48 648 100 HOH HOH . E 3 HOH A 49 649 101 HOH HOH . E 3 HOH A 50 650 102 HOH HOH . E 3 HOH A 51 651 103 HOH HOH . E 3 HOH A 52 652 104 HOH HOH . E 3 HOH A 53 653 105 HOH HOH . E 3 HOH A 54 654 106 HOH HOH . E 3 HOH A 55 655 107 HOH HOH . E 3 HOH A 56 656 108 HOH HOH . E 3 HOH A 57 657 109 HOH HOH . E 3 HOH A 58 658 110 HOH HOH . E 3 HOH A 59 659 125 HOH HOH . E 3 HOH A 60 660 134 HOH HOH . E 3 HOH A 61 661 135 HOH HOH . E 3 HOH A 62 662 136 HOH HOH . E 3 HOH A 63 663 137 HOH HOH . E 3 HOH A 64 664 138 HOH HOH . E 3 HOH A 65 665 139 HOH HOH . E 3 HOH A 66 666 140 HOH HOH . E 3 HOH A 67 667 141 HOH HOH . E 3 HOH A 68 668 142 HOH HOH . E 3 HOH A 69 669 143 HOH HOH . E 3 HOH A 70 670 144 HOH HOH . E 3 HOH A 71 671 145 HOH HOH . E 3 HOH A 72 672 146 HOH HOH . F 3 HOH B 1 601 1 HOH HOH . F 3 HOH B 2 602 2 HOH HOH . F 3 HOH B 3 603 3 HOH HOH . F 3 HOH B 4 604 4 HOH HOH . F 3 HOH B 5 605 5 HOH HOH . F 3 HOH B 6 606 6 HOH HOH . F 3 HOH B 7 607 7 HOH HOH . F 3 HOH B 8 608 8 HOH HOH . F 3 HOH B 9 609 9 HOH HOH . F 3 HOH B 10 610 10 HOH HOH . F 3 HOH B 11 611 11 HOH HOH . F 3 HOH B 12 612 12 HOH HOH . F 3 HOH B 13 613 13 HOH HOH . F 3 HOH B 14 614 14 HOH HOH . F 3 HOH B 15 615 15 HOH HOH . F 3 HOH B 16 616 16 HOH HOH . F 3 HOH B 17 617 17 HOH HOH . F 3 HOH B 18 618 18 HOH HOH . F 3 HOH B 19 619 19 HOH HOH . F 3 HOH B 20 620 20 HOH HOH . F 3 HOH B 21 621 21 HOH HOH . F 3 HOH B 22 622 22 HOH HOH . F 3 HOH B 23 623 23 HOH HOH . F 3 HOH B 24 624 24 HOH HOH . F 3 HOH B 25 625 25 HOH HOH . F 3 HOH B 26 626 26 HOH HOH . F 3 HOH B 27 627 29 HOH HOH . F 3 HOH B 28 628 30 HOH HOH . F 3 HOH B 29 629 31 HOH HOH . F 3 HOH B 30 630 32 HOH HOH . F 3 HOH B 31 631 33 HOH HOH . F 3 HOH B 32 632 34 HOH HOH . F 3 HOH B 33 633 35 HOH HOH . F 3 HOH B 34 634 36 HOH HOH . F 3 HOH B 35 635 37 HOH HOH . F 3 HOH B 36 636 38 HOH HOH . F 3 HOH B 37 637 39 HOH HOH . F 3 HOH B 38 638 40 HOH HOH . F 3 HOH B 39 639 41 HOH HOH . F 3 HOH B 40 640 42 HOH HOH . F 3 HOH B 41 641 43 HOH HOH . F 3 HOH B 42 642 44 HOH HOH . F 3 HOH B 43 643 45 HOH HOH . F 3 HOH B 44 644 46 HOH HOH . F 3 HOH B 45 645 47 HOH HOH . F 3 HOH B 46 646 48 HOH HOH . F 3 HOH B 47 647 49 HOH HOH . F 3 HOH B 48 648 50 HOH HOH . F 3 HOH B 49 649 51 HOH HOH . F 3 HOH B 50 650 52 HOH HOH . F 3 HOH B 51 651 86 HOH HOH . F 3 HOH B 52 652 111 HOH HOH . F 3 HOH B 53 653 112 HOH HOH . F 3 HOH B 54 654 113 HOH HOH . F 3 HOH B 55 655 114 HOH HOH . F 3 HOH B 56 656 115 HOH HOH . F 3 HOH B 57 657 116 HOH HOH . F 3 HOH B 58 658 117 HOH HOH . F 3 HOH B 59 659 118 HOH HOH . F 3 HOH B 60 660 119 HOH HOH . F 3 HOH B 61 661 120 HOH HOH . F 3 HOH B 62 662 121 HOH HOH . F 3 HOH B 63 663 122 HOH HOH . F 3 HOH B 64 664 123 HOH HOH . F 3 HOH B 65 665 124 HOH HOH . F 3 HOH B 66 666 126 HOH HOH . F 3 HOH B 67 667 127 HOH HOH . F 3 HOH B 68 668 128 HOH HOH . F 3 HOH B 69 669 129 HOH HOH . F 3 HOH B 70 670 130 HOH HOH . F 3 HOH B 71 671 131 HOH HOH . F 3 HOH B 72 672 132 HOH HOH . F 3 HOH B 73 673 133 HOH HOH . F 3 HOH B 74 674 147 HOH HOH . F 3 HOH B 75 675 148 HOH HOH . F 3 HOH B 76 676 149 HOH HOH . F 3 HOH B 77 677 150 HOH HOH . F 3 HOH B 78 678 151 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 C1 T20 . . . D 2 21.272 134.688 10.375 1 34.96 ? C1 T20 501 B 1 HETATM 2 C C2 T20 . . . D 2 21.117 134.479 11.77 1 37.36 ? C2 T20 501 B 1 HETATM 3 C C3 T20 . . . D 2 21.624 135.426 12.712 1 36.31 ? C3 T20 501 B 1 HETATM 4 C C4 T20 . . . D 2 22.31 136.567 12.241 1 35.24 ? C4 T20 501 B 1 HETATM 5 C C5 T20 . . . D 2 22.457 136.761 10.903 1 34.62 ? C5 T20 501 B 1 HETATM 6 C C6 T20 . . . D 2 21.935 135.789 9.925 1 32.31 ? C6 T20 501 B 1 HETATM 7 C C7 T20 . . . D 2 24.679 136.032 8.18 1 30.12 ? C7 T20 501 B 1 HETATM 8 C C8 T20 . . . D 2 23.297 136.184 7.813 1 28.91 ? C8 T20 501 B 1 HETATM 9 C C9 T20 . . . D 2 22.974 136.514 6.482 1 28.42 ? C9 T20 501 B 1 HETATM 10 C C10 T20 . . . D 2 23.99 136.682 5.506 1 28.61 ? C10 T20 501 B 1 HETATM 11 C C11 T20 . . . D 2 25.324 136.549 5.858 1 31.08 ? C11 T20 501 B 1 HETATM 12 C C12 T20 . . . D 2 25.658 136.215 7.243 1 30.42 ? C12 T20 501 B 1 HETATM 13 C C13 T20 . . . D 2 16.041 136.845 6.915 1 34.06 ? C13 T20 501 B 1 HETATM 14 C C14 T20 . . . D 2 14.781 136.812 7.583 1 33.92 ? C14 T20 501 B 1 HETATM 15 C C15 T20 . . . D 2 14.684 136.358 8.915 1 35.23 ? C15 T20 501 B 1 HETATM 16 C C16 T20 . . . D 2 15.826 135.98 9.556 1 39.31 ? C16 T20 501 B 1 HETATM 17 C C17 T20 . . . D 2 17.077 136.012 8.904 1 34.68 ? C17 T20 501 B 1 HETATM 18 C C18 T20 . . . D 2 17.176 136.421 7.598 1 32.49 ? C18 T20 501 B 1 HETATM 19 N N19 T20 . . . D 2 22.104 136.063 8.497 1 30.12 ? N19 T20 501 B 1 HETATM 20 C C20 T20 . . . D 2 21.063 136.315 7.613 1 28.24 ? C20 T20 501 B 1 HETATM 21 N N21 T20 . . . D 2 21.556 136.583 6.395 1 27.43 ? N21 T20 501 B 1 HETATM 22 C C22 T20 . . . D 2 26.441 136.732 4.791 1 32.82 ? C22 T20 501 B 1 HETATM 23 N N23 T20 . . . D 2 19.653 136.294 8 1 29.1 ? N23 T20 501 B 1 HETATM 24 C C24 T20 . . . D 2 18.579 136.44 7.03 1 30.52 ? C24 T20 501 B 1 HETATM 25 O O25 T20 . . . D 2 18.827 136.619 5.791 1 33.12 ? O25 T20 501 B 1 HETATM 26 N N26 T20 . . . D 2 15.84 135.54 10.926 1 46.65 ? N26 T20 501 B 1 HETATM 27 O O27 T20 . . . D 2 16.574 136.193 11.822 1 56.86 ? O27 T20 501 B 1 HETATM 28 O O28 T20 . . . D 2 15.139 134.473 11.282 1 56.83 ? O28 T20 501 B 1 HETATM 29 C C30 T20 . . . D 2 27.575 138.173 3.434 1 36.39 ? C30 T20 501 B 1 HETATM 30 C C31 T20 . . . D 2 28.091 139.522 3.025 1 38.29 ? C31 T20 501 B 1 HETATM 31 C C32 T20 . . . D 2 28.861 140.189 4.091 1 35.62 ? C32 T20 501 B 1 HETATM 32 C C33 T20 . . . D 2 28.088 140.199 5.318 1 36.43 ? C33 T20 501 B 1 HETATM 33 C C34 T20 . . . D 2 27.675 138.833 5.764 1 35.82 ? C34 T20 501 B 1 HETATM 34 N N35 T20 . . . D 2 26.909 138.109 4.734 1 36.5 ? N35 T20 501 B 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #