data_5R0L # _model_server_result.job_id D2tTKtc2zGNQmN5H4mJMtw _model_server_result.datetime_utc '2024-11-13 08:13:59' _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 5r0l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2501}' # _entry.id 5R0L # _exptl.entry_id 5R0L _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 107.93 _cell.angle_gamma 90 _cell.entry_id 5R0L _cell.length_a 88.239 _cell.length_b 81.981 _cell.length_c 93.362 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5R0L _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 _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 290 n n C C4 TBJ sing 291 n n C C1 TBJ sing 292 n n C4 C3 TBJ sing 293 n n C1 C2 TBJ sing 294 n n C3 C2 TBJ sing 295 n n C3 N TBJ sing 296 n n C5 N TBJ sing 297 n n C5 N1 TBJ sing 298 n n C6 N1 TBJ sing 299 n n C6 C7 TBJ sing 300 n n O1 C10 TBJ sing 301 n n O1 C7 TBJ sing 302 n n C10 C9 TBJ sing 303 n n C7 C8 TBJ sing 304 n n C9 C8 TBJ sing 305 n n C4 H1 TBJ sing 306 n n C4 H2 TBJ sing 307 n n C6 H3 TBJ sing 308 n n C6 H4 TBJ sing 309 n n N1 H5 TBJ sing 310 n n C7 H6 TBJ sing 311 n n C8 H7 TBJ sing 312 n n C8 H8 TBJ sing 313 n n C9 H9 TBJ sing 314 n n C9 H10 TBJ sing 315 n n C10 H11 TBJ sing 316 n n C10 H12 TBJ sing 317 n n N H13 TBJ sing 318 n n C3 H14 TBJ sing 319 n n C2 H15 TBJ sing 320 n n C2 H16 TBJ sing 321 n n C1 H17 TBJ sing 322 n n C1 H18 TBJ sing 323 n n C H19 TBJ sing 324 n n C H20 TBJ sing 325 n n # _atom_sites.entry_id 5R0L _atom_sites.fract_transf_matrix[1][1] 0.011333 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003668 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012198 _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] 0.011258 _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 2501 2501 TBJ XXX . D 4 HOH A 1 2601 118 HOH HOH . D 4 HOH A 2 2602 126 HOH HOH . D 4 HOH A 3 2603 68 HOH HOH . D 4 HOH A 4 2604 111 HOH HOH . D 4 HOH A 5 2605 128 HOH HOH . D 4 HOH A 6 2606 37 HOH HOH . D 4 HOH A 7 2607 100 HOH HOH . D 4 HOH A 8 2608 18 HOH HOH . D 4 HOH A 9 2609 20 HOH HOH . D 4 HOH A 10 2610 66 HOH HOH . D 4 HOH A 11 2611 53 HOH HOH . D 4 HOH A 12 2612 2 HOH HOH . D 4 HOH A 13 2613 6 HOH HOH . D 4 HOH A 14 2614 63 HOH HOH . D 4 HOH A 15 2615 116 HOH HOH . D 4 HOH A 16 2616 113 HOH HOH . D 4 HOH A 17 2617 90 HOH HOH . D 4 HOH A 18 2618 32 HOH HOH . D 4 HOH A 19 2619 16 HOH HOH . D 4 HOH A 20 2620 3 HOH HOH . D 4 HOH A 21 2621 9 HOH HOH . D 4 HOH A 22 2622 24 HOH HOH . D 4 HOH A 23 2623 11 HOH HOH . D 4 HOH A 24 2624 28 HOH HOH . D 4 HOH A 25 2625 91 HOH HOH . D 4 HOH A 26 2626 88 HOH HOH . D 4 HOH A 27 2627 23 HOH HOH . D 4 HOH A 28 2628 46 HOH HOH . D 4 HOH A 29 2629 7 HOH HOH . D 4 HOH A 30 2630 64 HOH HOH . D 4 HOH A 31 2631 98 HOH HOH . D 4 HOH A 32 2632 60 HOH HOH . D 4 HOH A 33 2633 67 HOH HOH . D 4 HOH A 34 2634 89 HOH HOH . D 4 HOH A 35 2635 56 HOH HOH . D 4 HOH A 36 2636 77 HOH HOH . D 4 HOH A 37 2637 62 HOH HOH . D 4 HOH A 38 2638 103 HOH HOH . D 4 HOH A 39 2639 8 HOH HOH . D 4 HOH A 40 2640 58 HOH HOH . D 4 HOH A 41 2641 10 HOH HOH . D 4 HOH A 42 2642 21 HOH HOH . D 4 HOH A 43 2643 80 HOH HOH . D 4 HOH A 44 2644 5 HOH HOH . D 4 HOH A 45 2645 27 HOH HOH . D 4 HOH A 46 2646 72 HOH HOH . D 4 HOH A 47 2647 26 HOH HOH . D 4 HOH A 48 2648 123 HOH HOH . D 4 HOH A 49 2649 43 HOH HOH . D 4 HOH A 50 2650 4 HOH HOH . D 4 HOH A 51 2651 25 HOH HOH . D 4 HOH A 52 2652 39 HOH HOH . D 4 HOH A 53 2653 34 HOH HOH . D 4 HOH A 54 2654 73 HOH HOH . D 4 HOH A 55 2655 104 HOH HOH . D 4 HOH A 56 2656 119 HOH HOH . D 4 HOH A 57 2657 110 HOH HOH . D 4 HOH A 58 2658 93 HOH HOH . D 4 HOH A 59 2659 14 HOH HOH . D 4 HOH A 60 2660 75 HOH HOH . D 4 HOH A 61 2661 54 HOH HOH . D 4 HOH A 62 2662 52 HOH HOH . D 4 HOH A 63 2663 79 HOH HOH . D 4 HOH A 64 2664 44 HOH HOH . D 4 HOH A 65 2665 83 HOH HOH . D 4 HOH A 66 2666 74 HOH HOH . D 4 HOH A 67 2667 31 HOH HOH . D 4 HOH A 68 2668 105 HOH HOH . D 4 HOH A 69 2669 106 HOH HOH . D 4 HOH A 70 2670 99 HOH HOH . D 4 HOH A 71 2671 108 HOH HOH . D 4 HOH A 72 2672 50 HOH HOH . D 4 HOH A 73 2673 127 HOH HOH . E 4 HOH B 1 401 120 HOH HOH . E 4 HOH B 2 402 109 HOH HOH . E 4 HOH B 3 403 55 HOH HOH . E 4 HOH B 4 404 86 HOH HOH . E 4 HOH B 5 405 19 HOH HOH . E 4 HOH B 6 406 121 HOH HOH . E 4 HOH B 7 407 35 HOH HOH . E 4 HOH B 8 408 22 HOH HOH . E 4 HOH B 9 409 81 HOH HOH . E 4 HOH B 10 410 13 HOH HOH . E 4 HOH B 11 411 95 HOH HOH . E 4 HOH B 12 412 47 HOH HOH . E 4 HOH B 13 413 15 HOH HOH . E 4 HOH B 14 414 42 HOH HOH . E 4 HOH B 15 415 124 HOH HOH . E 4 HOH B 16 416 29 HOH HOH . E 4 HOH B 17 417 87 HOH HOH . E 4 HOH B 18 418 69 HOH HOH . E 4 HOH B 19 419 70 HOH HOH . E 4 HOH B 20 420 97 HOH HOH . E 4 HOH B 21 421 122 HOH HOH . E 4 HOH B 22 422 41 HOH HOH . E 4 HOH B 23 423 78 HOH HOH . E 4 HOH B 24 424 51 HOH HOH . E 4 HOH B 25 425 96 HOH HOH . E 4 HOH B 26 426 17 HOH HOH . E 4 HOH B 27 427 57 HOH HOH . E 4 HOH B 28 428 59 HOH HOH . E 4 HOH B 29 429 36 HOH HOH . E 4 HOH B 30 430 125 HOH HOH . E 4 HOH B 31 431 94 HOH HOH . E 4 HOH B 32 432 38 HOH HOH . E 4 HOH B 33 433 92 HOH HOH . E 4 HOH B 34 434 45 HOH HOH . E 4 HOH B 35 435 71 HOH HOH . E 4 HOH B 36 436 102 HOH HOH . E 4 HOH B 37 437 61 HOH HOH . E 4 HOH B 38 438 107 HOH HOH . E 4 HOH B 39 439 30 HOH HOH . E 4 HOH B 40 440 40 HOH HOH . E 4 HOH B 41 441 49 HOH HOH . E 4 HOH B 42 442 12 HOH HOH . E 4 HOH B 43 443 115 HOH HOH . E 4 HOH B 44 444 76 HOH HOH . E 4 HOH B 45 445 48 HOH HOH . E 4 HOH B 46 446 82 HOH HOH . E 4 HOH B 47 447 112 HOH HOH . E 4 HOH B 48 448 101 HOH HOH . E 4 HOH B 49 449 117 HOH HOH . E 4 HOH B 50 450 84 HOH HOH . E 4 HOH B 51 451 65 HOH HOH . E 4 HOH B 52 452 33 HOH HOH . E 4 HOH B 53 453 114 HOH HOH . E 4 HOH B 54 454 85 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 . . . C 3 30.986 15.175 48.454 0.48 20 ? C4 TBJ 2501 A 1 HETATM 2 C C5 TBJ . . . C 3 32.262 14.451 45.477 0.48 20 ? C5 TBJ 2501 A 1 HETATM 3 C C6 TBJ . . . C 3 33.48 13.614 43.592 0.48 20 ? C6 TBJ 2501 A 1 HETATM 4 N N1 TBJ . . . C 3 33.27 14.61 44.622 0.48 20 ? N1 TBJ 2501 A 1 HETATM 5 C C7 TBJ . . . C 3 34.758 12.826 43.755 0.48 20 ? C7 TBJ 2501 A 1 HETATM 6 C C8 TBJ . . . C 3 35.147 12.602 45.181 0.48 20 ? C8 TBJ 2501 A 1 HETATM 7 C C9 TBJ . . . C 3 36.565 12.727 45.127 0.48 20 ? C9 TBJ 2501 A 1 HETATM 8 C C10 TBJ . . . C 3 36.74 13.825 44.185 0.48 20 ? C10 TBJ 2501 A 1 HETATM 9 O O TBJ . . . C 3 31.813 13.366 45.683 0.48 20 ? O TBJ 2501 A 1 HETATM 10 N N TBJ . . . C 3 31.828 15.513 46.132 0.48 20 ? N TBJ 2501 A 1 HETATM 11 C C3 TBJ . . . C 3 30.662 15.419 46.995 0.48 20 ? C3 TBJ 2501 A 1 HETATM 12 C C2 TBJ . . . C 3 29.923 16.66 47.02 0.48 20 ? C2 TBJ 2501 A 1 HETATM 13 C C1 TBJ . . . C 3 30.58 17.463 48.071 0.48 20 ? C1 TBJ 2501 A 1 HETATM 14 C C TBJ . . . C 3 30.835 16.533 49.131 0.48 20 ? C TBJ 2501 A 1 HETATM 15 O O1 TBJ . . . C 3 35.803 13.598 43.183 0.48 20 ? O1 TBJ 2501 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 215 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 15 #