data_7I1J # _model_server_result.job_id u3_9vMNvZRPgCSFPJRuSIg _model_server_result.datetime_utc '2025-08-24 04:54:32' _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 7i1j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 7I1J # _exptl.entry_id 7I1J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 212.289 _entity.id 3 _entity.src_method syn _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 90 _cell.angle_gamma 90 _cell.entry_id 7I1J _cell.length_a 68.28 _cell.length_b 98.8 _cell.length_c 104.47 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7I1J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 D _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 299 n n C C4 TBJ sing 300 n n C C1 TBJ sing 301 n n C4 C3 TBJ sing 302 n n C1 C2 TBJ sing 303 n n C3 C2 TBJ sing 304 n n C3 N TBJ sing 305 n n C5 N TBJ sing 306 n n C5 N1 TBJ sing 307 n n C6 N1 TBJ sing 308 n n C6 C7 TBJ sing 309 n n O1 C10 TBJ sing 310 n n O1 C7 TBJ sing 311 n n C10 C9 TBJ sing 312 n n C7 C8 TBJ sing 313 n n C9 C8 TBJ sing 314 n n C4 H1 TBJ sing 315 n n C4 H2 TBJ sing 316 n n C6 H3 TBJ sing 317 n n C6 H4 TBJ sing 318 n n N1 H5 TBJ sing 319 n n C7 H6 TBJ sing 320 n n C8 H7 TBJ sing 321 n n C8 H8 TBJ sing 322 n n C9 H9 TBJ sing 323 n n C9 H10 TBJ sing 324 n n C10 H11 TBJ sing 325 n n C10 H12 TBJ sing 326 n n N H13 TBJ sing 327 n n C3 H14 TBJ sing 328 n n C2 H15 TBJ sing 329 n n C2 H16 TBJ sing 330 n n C1 H17 TBJ sing 331 n n C1 H18 TBJ sing 332 n n C H19 TBJ sing 333 n n C H20 TBJ sing 334 n n # _atom_sites.entry_id 7I1J _atom_sites.fract_transf_matrix[1][1] 0.014646 _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] 0.010121 _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] 0.009572 _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 CL A 1 401 410 CL CL . D 3 TBJ A 1 402 501 TBJ LIG . E 4 DMS A 1 403 601 DMS DMS . F 4 DMS B 1 401 401 DMS DMS . G 5 HOH A 1 501 130 HOH HOH . G 5 HOH A 2 502 108 HOH HOH . G 5 HOH A 3 503 17 HOH HOH . G 5 HOH A 4 504 80 HOH HOH . G 5 HOH A 5 505 116 HOH HOH . G 5 HOH A 6 506 98 HOH HOH . G 5 HOH A 7 507 90 HOH HOH . G 5 HOH A 8 508 55 HOH HOH . G 5 HOH A 9 509 52 HOH HOH . G 5 HOH A 10 510 47 HOH HOH . G 5 HOH A 11 511 22 HOH HOH . G 5 HOH A 12 512 138 HOH HOH . G 5 HOH A 13 513 110 HOH HOH . G 5 HOH A 14 514 75 HOH HOH . G 5 HOH A 15 515 57 HOH HOH . G 5 HOH A 16 516 78 HOH HOH . G 5 HOH A 17 517 104 HOH HOH . G 5 HOH A 18 518 42 HOH HOH . G 5 HOH A 19 519 120 HOH HOH . G 5 HOH A 20 520 19 HOH HOH . G 5 HOH A 21 521 74 HOH HOH . G 5 HOH A 22 522 6 HOH HOH . G 5 HOH A 23 523 77 HOH HOH . G 5 HOH A 24 524 129 HOH HOH . G 5 HOH A 25 525 30 HOH HOH . G 5 HOH A 26 526 105 HOH HOH . G 5 HOH A 27 527 60 HOH HOH . G 5 HOH A 28 528 39 HOH HOH . G 5 HOH A 29 529 133 HOH HOH . G 5 HOH A 30 530 31 HOH HOH . G 5 HOH A 31 531 28 HOH HOH . G 5 HOH A 32 532 23 HOH HOH . G 5 HOH A 33 533 26 HOH HOH . G 5 HOH A 34 534 123 HOH HOH . G 5 HOH A 35 535 46 HOH HOH . G 5 HOH A 36 536 59 HOH HOH . G 5 HOH A 37 537 82 HOH HOH . G 5 HOH A 38 538 95 HOH HOH . G 5 HOH A 39 539 20 HOH HOH . G 5 HOH A 40 540 131 HOH HOH . G 5 HOH A 41 541 126 HOH HOH . G 5 HOH A 42 542 112 HOH HOH . G 5 HOH A 43 543 10 HOH HOH . G 5 HOH A 44 544 2 HOH HOH . G 5 HOH A 45 545 117 HOH HOH . G 5 HOH A 46 546 4 HOH HOH . G 5 HOH A 47 547 66 HOH HOH . G 5 HOH A 48 548 84 HOH HOH . G 5 HOH A 49 549 29 HOH HOH . G 5 HOH A 50 550 83 HOH HOH . G 5 HOH A 51 551 27 HOH HOH . G 5 HOH A 52 552 36 HOH HOH . G 5 HOH A 53 553 124 HOH HOH . G 5 HOH A 54 554 38 HOH HOH . G 5 HOH A 55 555 12 HOH HOH . G 5 HOH A 56 556 11 HOH HOH . G 5 HOH A 57 557 58 HOH HOH . G 5 HOH A 58 558 35 HOH HOH . G 5 HOH A 59 559 5 HOH HOH . G 5 HOH A 60 560 70 HOH HOH . G 5 HOH A 61 561 99 HOH HOH . G 5 HOH A 62 562 62 HOH HOH . G 5 HOH A 63 563 49 HOH HOH . G 5 HOH A 64 564 21 HOH HOH . G 5 HOH A 65 565 107 HOH HOH . G 5 HOH A 66 566 73 HOH HOH . G 5 HOH A 67 567 68 HOH HOH . G 5 HOH A 68 568 33 HOH HOH . G 5 HOH A 69 569 92 HOH HOH . G 5 HOH A 70 570 93 HOH HOH . G 5 HOH A 71 571 32 HOH HOH . G 5 HOH A 72 572 86 HOH HOH . G 5 HOH A 73 573 34 HOH HOH . G 5 HOH A 74 574 111 HOH HOH . G 5 HOH A 75 575 114 HOH HOH . G 5 HOH A 76 576 54 HOH HOH . G 5 HOH A 77 577 134 HOH HOH . G 5 HOH A 78 578 135 HOH HOH . G 5 HOH A 79 579 53 HOH HOH . G 5 HOH A 80 580 97 HOH HOH . G 5 HOH A 81 581 136 HOH HOH . G 5 HOH A 82 582 118 HOH HOH . G 5 HOH A 83 583 128 HOH HOH . G 5 HOH A 84 584 94 HOH HOH . G 5 HOH A 85 585 113 HOH HOH . H 5 HOH B 1 501 89 HOH HOH . H 5 HOH B 2 502 96 HOH HOH . H 5 HOH B 3 503 9 HOH HOH . H 5 HOH B 4 504 121 HOH HOH . H 5 HOH B 5 505 137 HOH HOH . H 5 HOH B 6 506 102 HOH HOH . H 5 HOH B 7 507 91 HOH HOH . H 5 HOH B 8 508 79 HOH HOH . H 5 HOH B 9 509 109 HOH HOH . H 5 HOH B 10 510 40 HOH HOH . H 5 HOH B 11 511 8 HOH HOH . H 5 HOH B 12 512 61 HOH HOH . H 5 HOH B 13 513 51 HOH HOH . H 5 HOH B 14 514 16 HOH HOH . H 5 HOH B 15 515 119 HOH HOH . H 5 HOH B 16 516 81 HOH HOH . H 5 HOH B 17 517 14 HOH HOH . H 5 HOH B 18 518 69 HOH HOH . H 5 HOH B 19 519 115 HOH HOH . H 5 HOH B 20 520 48 HOH HOH . H 5 HOH B 21 521 100 HOH HOH . H 5 HOH B 22 522 7 HOH HOH . H 5 HOH B 23 523 101 HOH HOH . H 5 HOH B 24 524 106 HOH HOH . H 5 HOH B 25 525 87 HOH HOH . H 5 HOH B 26 526 85 HOH HOH . H 5 HOH B 27 527 15 HOH HOH . H 5 HOH B 28 528 67 HOH HOH . H 5 HOH B 29 529 50 HOH HOH . H 5 HOH B 30 530 76 HOH HOH . H 5 HOH B 31 531 24 HOH HOH . H 5 HOH B 32 532 127 HOH HOH . H 5 HOH B 33 533 13 HOH HOH . H 5 HOH B 34 534 3 HOH HOH . H 5 HOH B 35 535 25 HOH HOH . H 5 HOH B 36 536 88 HOH HOH . H 5 HOH B 37 537 132 HOH HOH . H 5 HOH B 38 538 37 HOH HOH . H 5 HOH B 39 539 65 HOH HOH . H 5 HOH B 40 540 64 HOH HOH . H 5 HOH B 41 541 43 HOH HOH . H 5 HOH B 42 542 44 HOH HOH . H 5 HOH B 43 543 41 HOH HOH . H 5 HOH B 44 544 103 HOH HOH . H 5 HOH B 45 545 71 HOH HOH . H 5 HOH B 46 546 45 HOH HOH . H 5 HOH B 47 547 56 HOH HOH . H 5 HOH B 48 548 72 HOH HOH . H 5 HOH B 49 549 63 HOH HOH . H 5 HOH B 50 550 122 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 . D 3 1.57 -13.421 -32.386 0.36 38.68 ? C4 TBJ 402 A 1 HETATM 2 C C4 TBJ . D . D 3 1.57 -13.421 -32.386 0.36 38.68 ? C4 TBJ 402 A 1 HETATM 3 C C5 TBJ . C . D 3 1.12 -13.006 -36.164 0.36 43.19 ? C5 TBJ 402 A 1 HETATM 4 C C5 TBJ . D . D 3 1.12 -13.006 -36.164 0.36 43.19 ? C5 TBJ 402 A 1 HETATM 5 C C6 TBJ . C . D 3 2.441 -11.472 -37.739 0.36 43.68 ? C6 TBJ 402 A 1 HETATM 6 C C6 TBJ . D . D 3 2.441 -11.472 -37.739 0.36 43.68 ? C6 TBJ 402 A 1 HETATM 7 N N1 TBJ . C . D 3 1.959 -11.91 -36.408 0.36 40.85 ? N1 TBJ 402 A 1 HETATM 8 N N1 TBJ . D . D 3 1.959 -11.91 -36.408 0.36 40.85 ? N1 TBJ 402 A 1 HETATM 9 C C7 TBJ . C . D 3 1.286 -10.643 -38.492 0.36 45.03 ? C7 TBJ 402 A 1 HETATM 10 C C7 TBJ . D . D 3 1.286 -10.643 -38.492 0.36 45.03 ? C7 TBJ 402 A 1 HETATM 11 C C8 TBJ . C . D 3 0.712 -9.558 -37.529 0.36 46.62 ? C8 TBJ 402 A 1 HETATM 12 C C8 TBJ . D . D 3 0.712 -9.558 -37.529 0.36 46.62 ? C8 TBJ 402 A 1 HETATM 13 C C9 TBJ . C . D 3 0.802 -8.257 -38.309 0.36 45.48 ? C9 TBJ 402 A 1 HETATM 14 C C9 TBJ . D . D 3 0.802 -8.257 -38.309 0.36 45.48 ? C9 TBJ 402 A 1 HETATM 15 C C10 TBJ . C . D 3 1.032 -8.675 -39.764 0.36 44.9 ? C10 TBJ 402 A 1 HETATM 16 C C10 TBJ . D . D 3 1.032 -8.675 -39.764 0.36 44.9 ? C10 TBJ 402 A 1 HETATM 17 O O TBJ . C . D 3 0.777 -13.715 -37.107 0.36 43 ? O TBJ 402 A 1 HETATM 18 O O TBJ . D . D 3 0.777 -13.715 -37.107 0.36 43 ? O TBJ 402 A 1 HETATM 19 N N TBJ . C . D 3 0.661 -13.358 -34.86 0.36 44.98 ? N TBJ 402 A 1 HETATM 20 N N TBJ . D . D 3 0.661 -13.358 -34.86 0.36 44.98 ? N TBJ 402 A 1 HETATM 21 C C3 TBJ . C . D 3 0.912 -12.618 -33.591 0.36 41.23 ? C3 TBJ 402 A 1 HETATM 22 C C3 TBJ . D . D 3 0.912 -12.618 -33.591 0.36 41.23 ? C3 TBJ 402 A 1 HETATM 23 C C2 TBJ . C . D 3 -0.457 -12.188 -33.02 0.36 40.1 ? C2 TBJ 402 A 1 HETATM 24 C C2 TBJ . D . D 3 -0.457 -12.188 -33.02 0.36 40.1 ? C2 TBJ 402 A 1 HETATM 25 C C1 TBJ . C . D 3 -0.823 -13.295 -32.022 0.36 40.57 ? C1 TBJ 402 A 1 HETATM 26 C C1 TBJ . D . D 3 -0.823 -13.295 -32.022 0.36 40.57 ? C1 TBJ 402 A 1 HETATM 27 C C TBJ . C . D 3 0.49 -13.649 -31.303 0.36 37.75 ? C TBJ 402 A 1 HETATM 28 C C TBJ . D . D 3 0.49 -13.649 -31.303 0.36 37.75 ? C TBJ 402 A 1 HETATM 29 O O1 TBJ . C . D 3 1.713 -9.942 -39.638 0.36 46.4 ? O1 TBJ 402 A 1 HETATM 30 O O1 TBJ . D . D 3 1.713 -9.942 -39.638 0.36 46.4 ? O1 TBJ 402 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #