data_5D2T # _model_server_result.job_id 6G8THLTy1Vuoqooreug3FQ _model_server_result.datetime_utc '2024-10-15 11:25:11' _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 5d2t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5D2T # _exptl.entry_id 5D2T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 164.118 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-nitro-2-oxidanyl-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 120 _cell.entry_id 5D2T _cell.length_a 96.338 _cell.length_b 96.338 _cell.length_c 155.323 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D2T _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 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 # 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 CA HIS 261 A HIS 263 1_555 B NAL 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A CB HIS 261 A HIS 263 1_555 B OAD 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.11 ? covale ? covale3 A CG HIS 261 A HIS 263 1_555 B CAH 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.269 ? covale ? covale4 A CD2 HIS 261 A HIS 263 1_555 B CAJ 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? covale ? covale5 A CD2 HIS 261 A HIS 263 1_555 B CAK 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? covale ? covale6 A CE1 HIS 261 A HIS 263 1_555 B CAI 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.092 ? covale ? covale7 A CE1 HIS 261 A HIS 263 1_555 B CAF 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.087 ? covale ? covale8 A CE1 HIS 261 A HIS 263 1_555 B CAG 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale9 A CE1 HIS 261 A HIS 263 1_555 B CAJ 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.512 ? covale ? covale10 A NE2 HIS 261 A HIS 263 1_555 B CAI 6VP . A 6VP 301 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? # _chem_comp.formula 'C7 H4 N2 O3' _chem_comp.formula_weight 164.118 _chem_comp.id 6VP _chem_comp.mon_nstd_flag . _chem_comp.name 5-nitro-2-oxidanyl-benzenecarbonitrile _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-hydroxy-5-nitrobenzonitrile # 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 NAA CAE 6VP trip 1 n n CAE CAJ 6VP sing 2 n n OAB CAI 6VP sing 3 n n CAJ CAI 6VP doub 4 n y CAJ CAH 6VP sing 5 n y CAI CAF 6VP sing 6 n y CAF CAG 6VP doub 7 n y CAH CAK 6VP doub 8 n y CAG CAK 6VP sing 9 n y CAK NAL 6VP sing 10 n n NAL OAD 6VP doub 11 n n NAL OAC 6VP sing 12 n n CAH H1 6VP sing 13 n n OAB H2 6VP sing 14 n n CAF H3 6VP sing 15 n n CAG H4 6VP sing 16 n n # _atom_sites.entry_id 5D2T _atom_sites.fract_transf_matrix[1][1] 0.01038 _atom_sites.fract_transf_matrix[1][2] 0.005993 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011986 _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] 0.006438 _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 6VP A 1 301 1 6VP DRG . C 3 HOH A 1 401 253 HOH HOH . C 3 HOH A 2 402 122 HOH HOH . C 3 HOH A 3 403 84 HOH HOH . C 3 HOH A 4 404 186 HOH HOH . C 3 HOH A 5 405 210 HOH HOH . C 3 HOH A 6 406 69 HOH HOH . C 3 HOH A 7 407 221 HOH HOH . C 3 HOH A 8 408 91 HOH HOH . C 3 HOH A 9 409 225 HOH HOH . C 3 HOH A 10 410 215 HOH HOH . C 3 HOH A 11 411 83 HOH HOH . C 3 HOH A 12 412 153 HOH HOH . C 3 HOH A 13 413 107 HOH HOH . C 3 HOH A 14 414 13 HOH HOH . C 3 HOH A 15 415 184 HOH HOH . C 3 HOH A 16 416 146 HOH HOH . C 3 HOH A 17 417 12 HOH HOH . C 3 HOH A 18 418 118 HOH HOH . C 3 HOH A 19 419 213 HOH HOH . C 3 HOH A 20 420 220 HOH HOH . C 3 HOH A 21 421 77 HOH HOH . C 3 HOH A 22 422 54 HOH HOH . C 3 HOH A 23 423 5 HOH HOH . C 3 HOH A 24 424 242 HOH HOH . C 3 HOH A 25 425 255 HOH HOH . C 3 HOH A 26 426 235 HOH HOH . C 3 HOH A 27 427 105 HOH HOH . C 3 HOH A 28 428 19 HOH HOH . C 3 HOH A 29 429 133 HOH HOH . C 3 HOH A 30 430 194 HOH HOH . C 3 HOH A 31 431 67 HOH HOH . C 3 HOH A 32 432 66 HOH HOH . C 3 HOH A 33 433 256 HOH HOH . C 3 HOH A 34 434 52 HOH HOH . C 3 HOH A 35 435 25 HOH HOH . C 3 HOH A 36 436 191 HOH HOH . C 3 HOH A 37 437 92 HOH HOH . C 3 HOH A 38 438 70 HOH HOH . C 3 HOH A 39 439 197 HOH HOH . C 3 HOH A 40 440 39 HOH HOH . C 3 HOH A 41 441 63 HOH HOH . C 3 HOH A 42 442 167 HOH HOH . C 3 HOH A 43 443 65 HOH HOH . C 3 HOH A 44 444 123 HOH HOH . C 3 HOH A 45 445 130 HOH HOH . C 3 HOH A 46 446 176 HOH HOH . C 3 HOH A 47 447 3 HOH HOH . C 3 HOH A 48 448 188 HOH HOH . C 3 HOH A 49 449 257 HOH HOH . C 3 HOH A 50 450 75 HOH HOH . C 3 HOH A 51 451 30 HOH HOH . C 3 HOH A 52 452 82 HOH HOH . C 3 HOH A 53 453 24 HOH HOH . C 3 HOH A 54 454 14 HOH HOH . C 3 HOH A 55 455 74 HOH HOH . C 3 HOH A 56 456 44 HOH HOH . C 3 HOH A 57 457 50 HOH HOH . C 3 HOH A 58 458 59 HOH HOH . C 3 HOH A 59 459 94 HOH HOH . C 3 HOH A 60 460 154 HOH HOH . C 3 HOH A 61 461 10 HOH HOH . C 3 HOH A 62 462 4 HOH HOH . C 3 HOH A 63 463 78 HOH HOH . C 3 HOH A 64 464 29 HOH HOH . C 3 HOH A 65 465 161 HOH HOH . C 3 HOH A 66 466 207 HOH HOH . C 3 HOH A 67 467 97 HOH HOH . C 3 HOH A 68 468 47 HOH HOH . C 3 HOH A 69 469 11 HOH HOH . C 3 HOH A 70 470 1 HOH HOH . C 3 HOH A 71 471 2 HOH HOH . C 3 HOH A 72 472 117 HOH HOH . C 3 HOH A 73 473 119 HOH HOH . C 3 HOH A 74 474 43 HOH HOH . C 3 HOH A 75 475 112 HOH HOH . C 3 HOH A 76 476 17 HOH HOH . C 3 HOH A 77 477 90 HOH HOH . C 3 HOH A 78 478 236 HOH HOH . C 3 HOH A 79 479 16 HOH HOH . C 3 HOH A 80 480 81 HOH HOH . C 3 HOH A 81 481 106 HOH HOH . C 3 HOH A 82 482 46 HOH HOH . C 3 HOH A 83 483 26 HOH HOH . C 3 HOH A 84 484 27 HOH HOH . C 3 HOH A 85 485 7 HOH HOH . C 3 HOH A 86 486 71 HOH HOH . C 3 HOH A 87 487 42 HOH HOH . C 3 HOH A 88 488 202 HOH HOH . C 3 HOH A 89 489 35 HOH HOH . C 3 HOH A 90 490 22 HOH HOH . C 3 HOH A 91 491 208 HOH HOH . C 3 HOH A 92 492 241 HOH HOH . C 3 HOH A 93 493 244 HOH HOH . C 3 HOH A 94 494 9 HOH HOH . C 3 HOH A 95 495 51 HOH HOH . C 3 HOH A 96 496 108 HOH HOH . C 3 HOH A 97 497 40 HOH HOH . C 3 HOH A 98 498 58 HOH HOH . C 3 HOH A 99 499 189 HOH HOH . C 3 HOH A 100 500 20 HOH HOH . C 3 HOH A 101 501 237 HOH HOH . C 3 HOH A 102 502 56 HOH HOH . C 3 HOH A 103 503 53 HOH HOH . C 3 HOH A 104 504 104 HOH HOH . C 3 HOH A 105 505 61 HOH HOH . C 3 HOH A 106 506 73 HOH HOH . C 3 HOH A 107 507 55 HOH HOH . C 3 HOH A 108 508 249 HOH HOH . C 3 HOH A 109 509 124 HOH HOH . C 3 HOH A 110 510 114 HOH HOH . C 3 HOH A 111 511 193 HOH HOH . C 3 HOH A 112 512 139 HOH HOH . C 3 HOH A 113 513 164 HOH HOH . C 3 HOH A 114 514 64 HOH HOH . C 3 HOH A 115 515 36 HOH HOH . C 3 HOH A 116 516 31 HOH HOH . C 3 HOH A 117 517 227 HOH HOH . C 3 HOH A 118 518 38 HOH HOH . C 3 HOH A 119 519 99 HOH HOH . C 3 HOH A 120 520 140 HOH HOH . C 3 HOH A 121 521 181 HOH HOH . C 3 HOH A 122 522 203 HOH HOH . C 3 HOH A 123 523 33 HOH HOH . C 3 HOH A 124 524 172 HOH HOH . C 3 HOH A 125 525 62 HOH HOH . C 3 HOH A 126 526 87 HOH HOH . C 3 HOH A 127 527 49 HOH HOH . C 3 HOH A 128 528 199 HOH HOH . C 3 HOH A 129 529 37 HOH HOH . C 3 HOH A 130 530 79 HOH HOH . C 3 HOH A 131 531 226 HOH HOH . C 3 HOH A 132 532 174 HOH HOH . C 3 HOH A 133 533 80 HOH HOH . C 3 HOH A 134 534 165 HOH HOH . C 3 HOH A 135 535 195 HOH HOH . C 3 HOH A 136 536 6 HOH HOH . C 3 HOH A 137 537 240 HOH HOH . C 3 HOH A 138 538 230 HOH HOH . C 3 HOH A 139 539 214 HOH HOH . C 3 HOH A 140 540 141 HOH HOH . C 3 HOH A 141 541 129 HOH HOH . C 3 HOH A 142 542 116 HOH HOH . C 3 HOH A 143 543 205 HOH HOH . C 3 HOH A 144 544 170 HOH HOH . C 3 HOH A 145 545 131 HOH HOH . C 3 HOH A 146 546 206 HOH HOH . C 3 HOH A 147 547 201 HOH HOH . C 3 HOH A 148 548 192 HOH HOH . C 3 HOH A 149 549 60 HOH HOH . C 3 HOH A 150 550 251 HOH HOH . C 3 HOH A 151 551 219 HOH HOH . C 3 HOH A 152 552 111 HOH HOH . C 3 HOH A 153 553 163 HOH HOH . C 3 HOH A 154 554 190 HOH HOH . C 3 HOH A 155 555 134 HOH HOH . C 3 HOH A 156 556 216 HOH HOH . C 3 HOH A 157 557 171 HOH HOH . C 3 HOH A 158 558 238 HOH HOH . C 3 HOH A 159 559 132 HOH HOH . C 3 HOH A 160 560 254 HOH HOH . C 3 HOH A 161 561 209 HOH HOH . C 3 HOH A 162 562 121 HOH HOH . C 3 HOH A 163 563 162 HOH HOH . C 3 HOH A 164 564 109 HOH HOH . C 3 HOH A 165 565 239 HOH HOH . C 3 HOH A 166 566 128 HOH HOH . C 3 HOH A 167 567 173 HOH HOH . C 3 HOH A 168 568 142 HOH HOH . C 3 HOH A 169 569 93 HOH HOH . C 3 HOH A 170 570 224 HOH HOH . C 3 HOH A 171 571 178 HOH HOH . C 3 HOH A 172 572 144 HOH HOH . C 3 HOH A 173 573 223 HOH HOH . C 3 HOH A 174 574 198 HOH HOH . C 3 HOH A 175 575 158 HOH HOH . C 3 HOH A 176 576 182 HOH HOH . C 3 HOH A 177 577 86 HOH HOH . C 3 HOH A 178 578 168 HOH HOH . C 3 HOH A 179 579 200 HOH HOH . C 3 HOH A 180 580 34 HOH HOH . C 3 HOH A 181 581 23 HOH HOH . C 3 HOH A 182 582 147 HOH HOH . C 3 HOH A 183 583 115 HOH HOH . C 3 HOH A 184 584 159 HOH HOH . C 3 HOH A 185 585 95 HOH HOH . C 3 HOH A 186 586 76 HOH HOH . C 3 HOH A 187 587 155 HOH HOH . C 3 HOH A 188 588 137 HOH HOH . C 3 HOH A 189 589 250 HOH HOH . C 3 HOH A 190 590 145 HOH HOH . C 3 HOH A 191 591 136 HOH HOH . C 3 HOH A 192 592 113 HOH HOH . C 3 HOH A 193 593 185 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 NAA 6VP . . . B 2 -13.096 -19.155 -11.036 0.3 32.08 ? NAA 6VP 301 A 1 HETATM 2 C CAE 6VP . . . B 2 -12.818 -19.651 -10.05 0.3 32.13 ? CAE 6VP 301 A 1 HETATM 3 C CAJ 6VP . . . B 2 -12.468 -20.274 -8.811 0.3 32.36 ? CAJ 6VP 301 A 1 HETATM 4 C CAH 6VP . . . B 2 -12.717 -19.628 -7.606 0.3 31.47 ? CAH 6VP 301 A 1 HETATM 5 C CAI 6VP . . . B 2 -11.876 -21.531 -8.801 0.3 31.26 ? CAI 6VP 301 A 1 HETATM 6 O OAB 6VP . . . B 2 -11.659 -22.111 -10.012 0.3 20.16 ? OAB 6VP 301 A 1 HETATM 7 C CAF 6VP . . . B 2 -11.529 -22.152 -7.609 0.3 35.5 ? CAF 6VP 301 A 1 HETATM 8 C CAG 6VP . . . B 2 -11.781 -21.501 -6.407 0.3 34.56 ? CAG 6VP 301 A 1 HETATM 9 C CAK 6VP . . . B 2 -12.373 -20.242 -6.406 0.3 32.7 ? CAK 6VP 301 A 1 HETATM 10 N NAL 6VP . . . B 2 -12.611 -19.623 -5.253 0.3 32.92 ? NAL 6VP 301 A 1 HETATM 11 O OAD 6VP . . . B 2 -13.188 -18.282 -5.242 0.3 35.37 ? OAD 6VP 301 A 1 HETATM 12 O OAC 6VP . . . B 2 -12.298 -20.278 -3.986 0.3 35.95 ? OAC 6VP 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 12 #