data_8GDM # _model_server_result.job_id fDM2VT-FnIHetQfSfvzA2A _model_server_result.datetime_utc '2024-12-23 06:42:24' _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 8gdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8GDM # _exptl.entry_id 8GDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 389.513 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1S)-N-{[3-(diphenylmethyl)-1,2,4-oxadiazol-5-yl]methyl}-N-methyl-1-(thiophen-2-yl)ethan-1-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 90 _cell.entry_id 8GDM _cell.length_a 37.349 _cell.length_b 39.015 _cell.length_c 94.027 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 'C23 H23 N3 O S' _chem_comp.formula_weight 389.513 _chem_comp.id ZA6 _chem_comp.mon_nstd_flag . _chem_comp.name (1S)-N-{[3-(diphenylmethyl)-1,2,4-oxadiazol-5-yl]methyl}-N-methyl-1-(thiophen-2-yl)ethan-1-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 C21 C22 ZA6 doub 376 n y C21 S01 ZA6 sing 377 n y C22 C23 ZA6 sing 378 n y S01 C20 ZA6 sing 379 n y C23 C20 ZA6 doub 380 n y C20 C18 ZA6 sing 381 n n C18 C19 ZA6 sing 382 n n C18 N03 ZA6 sing 383 n n O01 N01 ZA6 sing 384 n y O01 C15 ZA6 sing 385 n y N01 C09 ZA6 doub 386 n y C06 C05 ZA6 doub 387 n y C06 C01 ZA6 sing 388 n y N03 C16 ZA6 sing 389 n n N03 C17 ZA6 sing 390 n n C05 C04 ZA6 sing 391 n y C01 C02 ZA6 doub 392 n y C15 C16 ZA6 sing 393 n n C15 N02 ZA6 doub 394 n y C09 C07 ZA6 sing 395 n n C09 N02 ZA6 sing 396 n y C04 C03 ZA6 doub 397 n y C04 C07 ZA6 sing 398 n n C02 C03 ZA6 sing 399 n y C07 C08 ZA6 sing 400 n n C08 C13 ZA6 doub 401 n y C08 C10 ZA6 sing 402 n y C13 C12 ZA6 sing 403 n y C10 C14 ZA6 doub 404 n y C12 C11 ZA6 doub 405 n y C14 C11 ZA6 sing 406 n y C01 H1 ZA6 sing 407 n n C02 H2 ZA6 sing 408 n n C03 H3 ZA6 sing 409 n n C05 H4 ZA6 sing 410 n n C06 H5 ZA6 sing 411 n n C07 H6 ZA6 sing 412 n n C10 H7 ZA6 sing 413 n n C11 H8 ZA6 sing 414 n n C12 H9 ZA6 sing 415 n n C13 H10 ZA6 sing 416 n n C14 H11 ZA6 sing 417 n n C16 H12 ZA6 sing 418 n n C16 H13 ZA6 sing 419 n n C17 H14 ZA6 sing 420 n n C17 H15 ZA6 sing 421 n n C17 H16 ZA6 sing 422 n n C18 H17 ZA6 sing 423 n n C19 H18 ZA6 sing 424 n n C19 H19 ZA6 sing 425 n n C19 H20 ZA6 sing 426 n n C21 H21 ZA6 sing 427 n n C22 H22 ZA6 sing 428 n n C23 H23 ZA6 sing 429 n n # _atom_sites.entry_id 8GDM _atom_sites.fract_transf_matrix[1][1] 0.026774 _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] 0.025631 _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] 0.010635 _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 ZA6 A 1 201 201 ZA6 UNL . C 3 HOH A 1 301 148 HOH HOH . C 3 HOH A 2 302 46 HOH HOH . C 3 HOH A 3 303 24 HOH HOH . C 3 HOH A 4 304 10 HOH HOH . C 3 HOH A 5 305 94 HOH HOH . C 3 HOH A 6 306 116 HOH HOH . C 3 HOH A 7 307 31 HOH HOH . C 3 HOH A 8 308 95 HOH HOH . C 3 HOH A 9 309 76 HOH HOH . C 3 HOH A 10 310 151 HOH HOH . C 3 HOH A 11 311 137 HOH HOH . C 3 HOH A 12 312 81 HOH HOH . C 3 HOH A 13 313 110 HOH HOH . C 3 HOH A 14 314 78 HOH HOH . C 3 HOH A 15 315 122 HOH HOH . C 3 HOH A 16 316 45 HOH HOH . C 3 HOH A 17 317 25 HOH HOH . C 3 HOH A 18 318 34 HOH HOH . C 3 HOH A 19 319 64 HOH HOH . C 3 HOH A 20 320 6 HOH HOH . C 3 HOH A 21 321 4 HOH HOH . C 3 HOH A 22 322 55 HOH HOH . C 3 HOH A 23 323 7 HOH HOH . C 3 HOH A 24 324 150 HOH HOH . C 3 HOH A 25 325 37 HOH HOH . C 3 HOH A 26 326 118 HOH HOH . C 3 HOH A 27 327 12 HOH HOH . C 3 HOH A 28 328 130 HOH HOH . C 3 HOH A 29 329 138 HOH HOH . C 3 HOH A 30 330 101 HOH HOH . C 3 HOH A 31 331 41 HOH HOH . C 3 HOH A 32 332 16 HOH HOH . C 3 HOH A 33 333 59 HOH HOH . C 3 HOH A 34 334 27 HOH HOH . C 3 HOH A 35 335 2 HOH HOH . C 3 HOH A 36 336 61 HOH HOH . C 3 HOH A 37 337 42 HOH HOH . C 3 HOH A 38 338 133 HOH HOH . C 3 HOH A 39 339 1 HOH HOH . C 3 HOH A 40 340 89 HOH HOH . C 3 HOH A 41 341 28 HOH HOH . C 3 HOH A 42 342 126 HOH HOH . C 3 HOH A 43 343 18 HOH HOH . C 3 HOH A 44 344 19 HOH HOH . C 3 HOH A 45 345 108 HOH HOH . C 3 HOH A 46 346 70 HOH HOH . C 3 HOH A 47 347 20 HOH HOH . C 3 HOH A 48 348 87 HOH HOH . C 3 HOH A 49 349 5 HOH HOH . C 3 HOH A 50 350 54 HOH HOH . C 3 HOH A 51 351 152 HOH HOH . C 3 HOH A 52 352 63 HOH HOH . C 3 HOH A 53 353 51 HOH HOH . C 3 HOH A 54 354 48 HOH HOH . C 3 HOH A 55 355 98 HOH HOH . C 3 HOH A 56 356 145 HOH HOH . C 3 HOH A 57 357 32 HOH HOH . C 3 HOH A 58 358 29 HOH HOH . C 3 HOH A 59 359 109 HOH HOH . C 3 HOH A 60 360 117 HOH HOH . C 3 HOH A 61 361 8 HOH HOH . C 3 HOH A 62 362 57 HOH HOH . C 3 HOH A 63 363 9 HOH HOH . C 3 HOH A 64 364 99 HOH HOH . C 3 HOH A 65 365 72 HOH HOH . C 3 HOH A 66 366 22 HOH HOH . C 3 HOH A 67 367 56 HOH HOH . C 3 HOH A 68 368 102 HOH HOH . C 3 HOH A 69 369 132 HOH HOH . C 3 HOH A 70 370 21 HOH HOH . C 3 HOH A 71 371 3 HOH HOH . C 3 HOH A 72 372 15 HOH HOH . C 3 HOH A 73 373 91 HOH HOH . C 3 HOH A 74 374 86 HOH HOH . C 3 HOH A 75 375 90 HOH HOH . C 3 HOH A 76 376 73 HOH HOH . C 3 HOH A 77 377 49 HOH HOH . C 3 HOH A 78 378 127 HOH HOH . C 3 HOH A 79 379 100 HOH HOH . C 3 HOH A 80 380 68 HOH HOH . C 3 HOH A 81 381 75 HOH HOH . C 3 HOH A 82 382 52 HOH HOH . C 3 HOH A 83 383 146 HOH HOH . C 3 HOH A 84 384 69 HOH HOH . C 3 HOH A 85 385 17 HOH HOH . C 3 HOH A 86 386 43 HOH HOH . C 3 HOH A 87 387 62 HOH HOH . C 3 HOH A 88 388 40 HOH HOH . C 3 HOH A 89 389 14 HOH HOH . C 3 HOH A 90 390 112 HOH HOH . C 3 HOH A 91 391 144 HOH HOH . C 3 HOH A 92 392 113 HOH HOH . C 3 HOH A 93 393 93 HOH HOH . C 3 HOH A 94 394 47 HOH HOH . C 3 HOH A 95 395 23 HOH HOH . C 3 HOH A 96 396 65 HOH HOH . C 3 HOH A 97 397 140 HOH HOH . C 3 HOH A 98 398 35 HOH HOH . C 3 HOH A 99 399 74 HOH HOH . C 3 HOH A 100 400 11 HOH HOH . C 3 HOH A 101 401 50 HOH HOH . C 3 HOH A 102 402 38 HOH HOH . C 3 HOH A 103 403 82 HOH HOH . C 3 HOH A 104 404 123 HOH HOH . C 3 HOH A 105 405 142 HOH HOH . C 3 HOH A 106 406 30 HOH HOH . C 3 HOH A 107 407 80 HOH HOH . C 3 HOH A 108 408 84 HOH HOH . C 3 HOH A 109 409 125 HOH HOH . C 3 HOH A 110 410 104 HOH HOH . C 3 HOH A 111 411 39 HOH HOH . C 3 HOH A 112 412 107 HOH HOH . C 3 HOH A 113 413 128 HOH HOH . C 3 HOH A 114 414 115 HOH HOH . C 3 HOH A 115 415 88 HOH HOH . C 3 HOH A 116 416 97 HOH HOH . C 3 HOH A 117 417 103 HOH HOH . C 3 HOH A 118 418 131 HOH HOH . C 3 HOH A 119 419 77 HOH HOH . C 3 HOH A 120 420 83 HOH HOH . C 3 HOH A 121 421 106 HOH HOH . C 3 HOH A 122 422 141 HOH HOH . C 3 HOH A 123 423 153 HOH HOH . C 3 HOH A 124 424 85 HOH HOH . C 3 HOH A 125 425 92 HOH HOH . C 3 HOH A 126 426 129 HOH HOH . C 3 HOH A 127 427 149 HOH HOH . C 3 HOH A 128 428 58 HOH HOH . C 3 HOH A 129 429 119 HOH HOH . C 3 HOH A 130 430 134 HOH HOH . C 3 HOH A 131 431 135 HOH HOH . C 3 HOH A 132 432 111 HOH HOH . C 3 HOH A 133 433 53 HOH HOH . C 3 HOH A 134 434 13 HOH HOH . C 3 HOH A 135 435 26 HOH HOH . C 3 HOH A 136 436 143 HOH HOH . C 3 HOH A 137 437 156 HOH HOH . C 3 HOH A 138 438 79 HOH HOH . C 3 HOH A 139 439 67 HOH HOH . C 3 HOH A 140 440 147 HOH HOH . C 3 HOH A 141 441 44 HOH HOH . C 3 HOH A 142 442 66 HOH HOH . C 3 HOH A 143 443 60 HOH HOH . C 3 HOH A 144 444 71 HOH HOH . C 3 HOH A 145 445 114 HOH HOH . C 3 HOH A 146 446 124 HOH HOH . C 3 HOH A 147 447 155 HOH HOH . C 3 HOH A 148 448 139 HOH HOH . C 3 HOH A 149 449 157 HOH HOH . C 3 HOH A 150 450 154 HOH HOH . C 3 HOH A 151 451 121 HOH HOH . C 3 HOH A 152 452 120 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 ZA6 . . . B 2 -15.854 -8.417 14.712 1 43.62 ? C01 ZA6 201 A 1 HETATM 2 C C02 ZA6 . . . B 2 -16.187 -7.227 15.339 1 44.33 ? C02 ZA6 201 A 1 HETATM 3 C C03 ZA6 . . . B 2 -15.206 -6.297 15.652 1 43.68 ? C03 ZA6 201 A 1 HETATM 4 C C04 ZA6 . . . B 2 -13.88 -6.565 15.334 1 43 ? C04 ZA6 201 A 1 HETATM 5 C C05 ZA6 . . . B 2 -13.545 -7.753 14.705 1 43.44 ? C05 ZA6 201 A 1 HETATM 6 C C06 ZA6 . . . B 2 -14.53 -8.682 14.398 1 50.89 ? C06 ZA6 201 A 1 HETATM 7 C C07 ZA6 . . . B 2 -12.78 -5.559 15.66 1 48.14 ? C07 ZA6 201 A 1 HETATM 8 C C08 ZA6 . . . B 2 -12.464 -5.504 17.164 1 51.45 ? C08 ZA6 201 A 1 HETATM 9 C C09 ZA6 . . . B 2 -13.163 -4.157 15.155 1 58.77 ? C09 ZA6 201 A 1 HETATM 10 C C10 ZA6 . . . B 2 -12.848 -6.526 18.033 1 55.3 ? C10 ZA6 201 A 1 HETATM 11 C C11 ZA6 . . . B 2 -11.852 -5.356 19.877 1 44.93 ? C11 ZA6 201 A 1 HETATM 12 C C12 ZA6 . . . B 2 -11.465 -4.342 19.037 1 40.11 ? C12 ZA6 201 A 1 HETATM 13 C C13 ZA6 . . . B 2 -11.77 -4.41 17.688 1 38.3 ? C13 ZA6 201 A 1 HETATM 14 C C14 ZA6 . . . B 2 -12.541 -6.442 19.383 1 52.97 ? C14 ZA6 201 A 1 HETATM 15 C C15 ZA6 . . . B 2 -14.129 -2.205 14.984 1 55.94 ? C15 ZA6 201 A 1 HETATM 16 C C16 ZA6 . . . B 2 -15.042 -0.984 15.215 1 57.77 ? C16 ZA6 201 A 1 HETATM 17 C C17 ZA6 . . . B 2 -17.213 -1.94 15.527 1 53.86 ? C17 ZA6 201 A 1 HETATM 18 C C18 ZA6 . . . B 2 -16.207 -1.989 13.364 1 60.34 ? C18 ZA6 201 A 1 HETATM 19 C C19 ZA6 . . . B 2 -16.58 -3.447 13.579 1 52.04 ? C19 ZA6 201 A 1 HETATM 20 C C20 ZA6 . . . B 2 -17.156 -1.409 12.317 1 46.25 ? C20 ZA6 201 A 1 HETATM 21 C C21 ZA6 . . . B 2 -18.18 0.112 10.5 1 41.2 ? C21 ZA6 201 A 1 HETATM 22 C C22 ZA6 . . . B 2 -19.12 -0.986 10.772 1 36.24 ? C22 ZA6 201 A 1 HETATM 23 C C23 ZA6 . . . B 2 -18.471 -1.965 11.932 1 29.82 ? C23 ZA6 201 A 1 HETATM 24 N N01 ZA6 . . . B 2 -12.604 -3.563 14.113 1 58.75 ? N01 ZA6 201 A 1 HETATM 25 N N02 ZA6 . . . B 2 -14.105 -3.347 15.712 1 51.5 ? N02 ZA6 201 A 1 HETATM 26 N N03 ZA6 . . . B 2 -16.348 -1.224 14.599 1 57.14 ? N03 ZA6 201 A 1 HETATM 27 O O01 ZA6 . . . B 2 -13.195 -2.33 13.974 1 62.56 ? O01 ZA6 201 A 1 HETATM 28 S S01 ZA6 . . . B 2 -16.904 -0.083 11.452 1 56.77 ? S01 ZA6 201 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #