data_5QYJ # _model_server_result.job_id uOdiTgRD7TRV3v5_-VDxNg _model_server_result.datetime_utc '2025-07-17 12:29:20' _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 5qyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2101}' # _entry.id 5QYJ # _exptl.entry_id 5QYJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 212.289 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "N-cyclopentyl-N'-{[(2R)-oxolan-2-yl]methyl}urea" _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 108.34 _cell.angle_gamma 90 _cell.entry_id 5QYJ _cell.length_a 88.93 _cell.length_b 81.721 _cell.length_c 93.471 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H20 N2 O2' _chem_comp.formula_weight 212.289 _chem_comp.id TBJ _chem_comp.mon_nstd_flag . _chem_comp.name "N-cyclopentyl-N'-{[(2R)-oxolan-2-yl]methyl}urea" _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 O C5 TBJ doub 306 n n C C4 TBJ sing 307 n n C C1 TBJ sing 308 n n C4 C3 TBJ sing 309 n n C1 C2 TBJ sing 310 n n C3 C2 TBJ sing 311 n n C3 N TBJ sing 312 n n C5 N TBJ sing 313 n n C5 N1 TBJ sing 314 n n C6 N1 TBJ sing 315 n n C6 C7 TBJ sing 316 n n O1 C10 TBJ sing 317 n n O1 C7 TBJ sing 318 n n C10 C9 TBJ sing 319 n n C7 C8 TBJ sing 320 n n C9 C8 TBJ sing 321 n n C4 H1 TBJ sing 322 n n C4 H2 TBJ sing 323 n n C6 H3 TBJ sing 324 n n C6 H4 TBJ sing 325 n n N1 H5 TBJ sing 326 n n C7 H6 TBJ sing 327 n n C8 H7 TBJ sing 328 n n C8 H8 TBJ sing 329 n n C9 H9 TBJ sing 330 n n C9 H10 TBJ sing 331 n n C10 H11 TBJ sing 332 n n C10 H12 TBJ sing 333 n n N H13 TBJ sing 334 n n C3 H14 TBJ sing 335 n n C2 H15 TBJ sing 336 n n C2 H16 TBJ sing 337 n n C1 H17 TBJ sing 338 n n C1 H18 TBJ sing 339 n n C H19 TBJ sing 340 n n C H20 TBJ sing 341 n n # _atom_sites.entry_id 5QYJ _atom_sites.fract_transf_matrix[1][1] 0.011245 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003728 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012237 _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] 0.011271 _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 3 TBJ A 1 2101 2101 TBJ XXX . D 4 SO4 A 1 2102 2201 SO4 SO4 . E 4 SO4 A 1 2103 2301 SO4 SO4 . F 5 PGR A 1 2104 2401 PGR PGR . G 5 PGR A 1 2105 2501 PGR PGR . H 5 PGR A 1 2106 2601 PGR PGR . I 6 HOH A 1 2201 158 HOH HOH . I 6 HOH A 2 2202 105 HOH HOH . I 6 HOH A 3 2203 22 HOH HOH . I 6 HOH A 4 2204 45 HOH HOH . I 6 HOH A 5 2205 90 HOH HOH . I 6 HOH A 6 2206 131 HOH HOH . I 6 HOH A 7 2207 52 HOH HOH . I 6 HOH A 8 2208 96 HOH HOH . I 6 HOH A 9 2209 111 HOH HOH . I 6 HOH A 10 2210 103 HOH HOH . I 6 HOH A 11 2211 146 HOH HOH . I 6 HOH A 12 2212 135 HOH HOH . I 6 HOH A 13 2213 66 HOH HOH . I 6 HOH A 14 2214 155 HOH HOH . I 6 HOH A 15 2215 2 HOH HOH . I 6 HOH A 16 2216 97 HOH HOH . I 6 HOH A 17 2217 81 HOH HOH . I 6 HOH A 18 2218 86 HOH HOH . I 6 HOH A 19 2219 125 HOH HOH . I 6 HOH A 20 2220 36 HOH HOH . I 6 HOH A 21 2221 110 HOH HOH . I 6 HOH A 22 2222 57 HOH HOH . I 6 HOH A 23 2223 51 HOH HOH . I 6 HOH A 24 2224 88 HOH HOH . I 6 HOH A 25 2225 25 HOH HOH . I 6 HOH A 26 2226 121 HOH HOH . I 6 HOH A 27 2227 4 HOH HOH . I 6 HOH A 28 2228 20 HOH HOH . I 6 HOH A 29 2229 17 HOH HOH . I 6 HOH A 30 2230 13 HOH HOH . I 6 HOH A 31 2231 129 HOH HOH . I 6 HOH A 32 2232 43 HOH HOH . I 6 HOH A 33 2233 32 HOH HOH . I 6 HOH A 34 2234 78 HOH HOH . I 6 HOH A 35 2235 104 HOH HOH . I 6 HOH A 36 2236 93 HOH HOH . I 6 HOH A 37 2237 10 HOH HOH . I 6 HOH A 38 2238 23 HOH HOH . I 6 HOH A 39 2239 19 HOH HOH . I 6 HOH A 40 2240 108 HOH HOH . I 6 HOH A 41 2241 140 HOH HOH . I 6 HOH A 42 2242 92 HOH HOH . I 6 HOH A 43 2243 79 HOH HOH . I 6 HOH A 44 2244 114 HOH HOH . I 6 HOH A 45 2245 132 HOH HOH . I 6 HOH A 46 2246 59 HOH HOH . I 6 HOH A 47 2247 34 HOH HOH . I 6 HOH A 48 2248 95 HOH HOH . I 6 HOH A 49 2249 87 HOH HOH . I 6 HOH A 50 2250 14 HOH HOH . I 6 HOH A 51 2251 60 HOH HOH . I 6 HOH A 52 2252 41 HOH HOH . I 6 HOH A 53 2253 77 HOH HOH . I 6 HOH A 54 2254 116 HOH HOH . I 6 HOH A 55 2255 124 HOH HOH . I 6 HOH A 56 2256 62 HOH HOH . I 6 HOH A 57 2257 115 HOH HOH . I 6 HOH A 58 2258 7 HOH HOH . I 6 HOH A 59 2259 73 HOH HOH . I 6 HOH A 60 2260 18 HOH HOH . I 6 HOH A 61 2261 117 HOH HOH . I 6 HOH A 62 2262 99 HOH HOH . I 6 HOH A 63 2263 5 HOH HOH . I 6 HOH A 64 2264 27 HOH HOH . I 6 HOH A 65 2265 118 HOH HOH . I 6 HOH A 66 2266 154 HOH HOH . I 6 HOH A 67 2267 65 HOH HOH . I 6 HOH A 68 2268 6 HOH HOH . I 6 HOH A 69 2269 53 HOH HOH . I 6 HOH A 70 2270 37 HOH HOH . I 6 HOH A 71 2271 56 HOH HOH . I 6 HOH A 72 2272 3 HOH HOH . I 6 HOH A 73 2273 113 HOH HOH . I 6 HOH A 74 2274 120 HOH HOH . I 6 HOH A 75 2275 69 HOH HOH . I 6 HOH A 76 2276 49 HOH HOH . I 6 HOH A 77 2277 123 HOH HOH . I 6 HOH A 78 2278 40 HOH HOH . I 6 HOH A 79 2279 112 HOH HOH . I 6 HOH A 80 2280 119 HOH HOH . I 6 HOH A 81 2281 157 HOH HOH . I 6 HOH A 82 2282 100 HOH HOH . I 6 HOH A 83 2283 122 HOH HOH . I 6 HOH A 84 2284 160 HOH HOH . I 6 HOH A 85 2285 58 HOH HOH . I 6 HOH A 86 2286 153 HOH HOH . J 6 HOH B 1 401 152 HOH HOH . J 6 HOH B 2 402 156 HOH HOH . J 6 HOH B 3 403 107 HOH HOH . J 6 HOH B 4 404 84 HOH HOH . J 6 HOH B 5 405 16 HOH HOH . J 6 HOH B 6 406 109 HOH HOH . J 6 HOH B 7 407 72 HOH HOH . J 6 HOH B 8 408 47 HOH HOH . J 6 HOH B 9 409 148 HOH HOH . J 6 HOH B 10 410 28 HOH HOH . J 6 HOH B 11 411 91 HOH HOH . J 6 HOH B 12 412 145 HOH HOH . J 6 HOH B 13 413 80 HOH HOH . J 6 HOH B 14 414 64 HOH HOH . J 6 HOH B 15 415 68 HOH HOH . J 6 HOH B 16 416 136 HOH HOH . J 6 HOH B 17 417 44 HOH HOH . J 6 HOH B 18 418 159 HOH HOH . J 6 HOH B 19 419 12 HOH HOH . J 6 HOH B 20 420 143 HOH HOH . J 6 HOH B 21 421 71 HOH HOH . J 6 HOH B 22 422 128 HOH HOH . J 6 HOH B 23 423 11 HOH HOH . J 6 HOH B 24 424 55 HOH HOH . J 6 HOH B 25 425 9 HOH HOH . J 6 HOH B 26 426 48 HOH HOH . J 6 HOH B 27 427 74 HOH HOH . J 6 HOH B 28 428 26 HOH HOH . J 6 HOH B 29 429 70 HOH HOH . J 6 HOH B 30 430 151 HOH HOH . J 6 HOH B 31 431 98 HOH HOH . J 6 HOH B 32 432 83 HOH HOH . J 6 HOH B 33 433 76 HOH HOH . J 6 HOH B 34 434 38 HOH HOH . J 6 HOH B 35 435 24 HOH HOH . J 6 HOH B 36 436 29 HOH HOH . J 6 HOH B 37 437 94 HOH HOH . J 6 HOH B 38 438 21 HOH HOH . J 6 HOH B 39 439 54 HOH HOH . J 6 HOH B 40 440 82 HOH HOH . J 6 HOH B 41 441 63 HOH HOH . J 6 HOH B 42 442 144 HOH HOH . J 6 HOH B 43 443 133 HOH HOH . J 6 HOH B 44 444 50 HOH HOH . J 6 HOH B 45 445 67 HOH HOH . J 6 HOH B 46 446 102 HOH HOH . J 6 HOH B 47 447 89 HOH HOH . J 6 HOH B 48 448 15 HOH HOH . J 6 HOH B 49 449 101 HOH HOH . J 6 HOH B 50 450 61 HOH HOH . J 6 HOH B 51 451 42 HOH HOH . J 6 HOH B 52 452 106 HOH HOH . J 6 HOH B 53 453 141 HOH HOH . J 6 HOH B 54 454 35 HOH HOH . J 6 HOH B 55 455 39 HOH HOH . J 6 HOH B 56 456 149 HOH HOH . J 6 HOH B 57 457 30 HOH HOH . J 6 HOH B 58 458 46 HOH HOH . J 6 HOH B 59 459 8 HOH HOH . J 6 HOH B 60 460 85 HOH HOH . J 6 HOH B 61 461 33 HOH HOH . J 6 HOH B 62 462 126 HOH HOH . J 6 HOH B 63 463 137 HOH HOH . J 6 HOH B 64 464 150 HOH HOH . J 6 HOH B 65 465 127 HOH HOH . J 6 HOH B 66 466 31 HOH HOH . J 6 HOH B 67 467 75 HOH HOH . J 6 HOH B 68 468 134 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 C4 TBJ . D . C 3 31.512 15.611 48.339 0.18 47.44 ? C4 TBJ 2101 A 1 HETATM 2 C C4 TBJ . E . C 3 31.51 15.611 48.34 0.18 47.43 ? C4 TBJ 2101 A 1 HETATM 3 C C4 TBJ . F . C 3 31.51 15.611 48.34 0.18 47.43 ? C4 TBJ 2101 A 1 HETATM 4 C C5 TBJ . D . C 3 32.64 14.032 45.498 0.18 52.75 ? C5 TBJ 2101 A 1 HETATM 5 C C5 TBJ . E . C 3 32.639 14.032 45.498 0.18 52.73 ? C5 TBJ 2101 A 1 HETATM 6 C C5 TBJ . F . C 3 32.639 14.032 45.498 0.18 52.73 ? C5 TBJ 2101 A 1 HETATM 7 C C6 TBJ . D . C 3 34.322 13.181 43.841 0.18 52.22 ? C6 TBJ 2101 A 1 HETATM 8 C C6 TBJ . E . C 3 34.32 13.182 43.841 0.18 52.2 ? C6 TBJ 2101 A 1 HETATM 9 C C6 TBJ . F . C 3 34.32 13.182 43.841 0.18 52.2 ? C6 TBJ 2101 A 1 HETATM 10 N N1 TBJ . D . C 3 33.529 14.21 44.514 0.18 52.79 ? N1 TBJ 2101 A 1 HETATM 11 N N1 TBJ . E . C 3 33.529 14.211 44.516 0.18 52.78 ? N1 TBJ 2101 A 1 HETATM 12 N N1 TBJ . F . C 3 33.529 14.211 44.516 0.18 52.78 ? N1 TBJ 2101 A 1 HETATM 13 C C7 TBJ . D . C 3 35.429 12.771 44.81 0.18 51.35 ? C7 TBJ 2101 A 1 HETATM 14 C C7 TBJ . E . C 3 35.428 12.769 44.809 0.18 51.34 ? C7 TBJ 2101 A 1 HETATM 15 C C7 TBJ . F . C 3 35.428 12.769 44.809 0.18 51.34 ? C7 TBJ 2101 A 1 HETATM 16 C C8 TBJ . D . C 3 35.766 11.293 44.685 0.18 51.08 ? C8 TBJ 2101 A 1 HETATM 17 C C8 TBJ . E . C 3 35.765 11.292 44.682 0.18 51.06 ? C8 TBJ 2101 A 1 HETATM 18 C C8 TBJ . F . C 3 35.765 11.292 44.682 0.18 51.06 ? C8 TBJ 2101 A 1 HETATM 19 C C9 TBJ . D . C 3 37.279 11.22 44.815 0.18 50.18 ? C9 TBJ 2101 A 1 HETATM 20 C C9 TBJ . E . C 3 37.278 11.22 44.813 0.18 50.16 ? C9 TBJ 2101 A 1 HETATM 21 C C9 TBJ . F . C 3 37.278 11.22 44.813 0.18 50.16 ? C9 TBJ 2101 A 1 HETATM 22 C C10 TBJ . D . C 3 37.772 12.638 44.587 0.18 49.47 ? C10 TBJ 2101 A 1 HETATM 23 C C10 TBJ . E . C 3 37.771 12.638 44.587 0.18 49.45 ? C10 TBJ 2101 A 1 HETATM 24 C C10 TBJ . F . C 3 37.771 12.638 44.587 0.18 49.45 ? C10 TBJ 2101 A 1 HETATM 25 O O TBJ . D . C 3 32.42 12.911 45.93 0.18 54.28 ? O TBJ 2101 A 1 HETATM 26 O O TBJ . E . C 3 32.415 12.911 45.927 0.18 54.27 ? O TBJ 2101 A 1 HETATM 27 O O TBJ . F . C 3 32.415 12.911 45.927 0.18 54.27 ? O TBJ 2101 A 1 HETATM 28 N N TBJ . D . C 3 32 15.088 46.013 0.18 49.64 ? N TBJ 2101 A 1 HETATM 29 N N TBJ . E . C 3 32.001 15.089 46.014 0.18 49.63 ? N TBJ 2101 A 1 HETATM 30 N N TBJ . F . C 3 32.001 15.089 46.014 0.18 49.63 ? N TBJ 2101 A 1 HETATM 31 C C3 TBJ . D . C 3 31.016 14.912 47.082 0.18 47.79 ? C3 TBJ 2101 A 1 HETATM 32 C C3 TBJ . E . C 3 31.015 14.913 47.081 0.18 47.77 ? C3 TBJ 2101 A 1 HETATM 33 C C3 TBJ . F . C 3 31.015 14.913 47.081 0.18 47.77 ? C3 TBJ 2101 A 1 HETATM 34 C C2 TBJ . D . C 3 29.728 15.607 46.645 0.18 46.85 ? C2 TBJ 2101 A 1 HETATM 35 C C2 TBJ . E . C 3 29.728 15.609 46.643 0.18 46.84 ? C2 TBJ 2101 A 1 HETATM 36 C C2 TBJ . F . C 3 29.728 15.609 46.643 0.18 46.84 ? C2 TBJ 2101 A 1 HETATM 37 C C1 TBJ . D . C 3 29.307 16.543 47.764 0.18 46.38 ? C1 TBJ 2101 A 1 HETATM 38 C C1 TBJ . E . C 3 29.306 16.545 47.763 0.18 46.37 ? C1 TBJ 2101 A 1 HETATM 39 C C1 TBJ . F . C 3 29.306 16.545 47.763 0.18 46.37 ? C1 TBJ 2101 A 1 HETATM 40 C C TBJ . D . C 3 30.374 16.49 48.845 0.18 46.49 ? C TBJ 2101 A 1 HETATM 41 C C TBJ . E . C 3 30.372 16.491 48.845 0.18 46.48 ? C TBJ 2101 A 1 HETATM 42 C C TBJ . F . C 3 30.372 16.491 48.845 0.18 46.48 ? C TBJ 2101 A 1 HETATM 43 O O1 TBJ . D . C 3 36.631 13.49 44.539 0.18 49.87 ? O1 TBJ 2101 A 1 HETATM 44 O O1 TBJ . E . C 3 36.63 13.489 44.539 0.18 49.85 ? O1 TBJ 2101 A 1 HETATM 45 O O1 TBJ . F . C 3 36.63 13.489 44.539 0.18 49.85 ? O1 TBJ 2101 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 45 #