data_8I6D
#
_model_server_result.job_id            DLhZJnWEJJcV6eEN2cpm7g 
_model_server_result.datetime_utc      '2024-11-08 09:10:43' 
_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          8i6d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    8I6D 
#
_exptl.entry_id    8I6D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              128.086 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-oxidanyl-1~{H}-pyrimidine-2,4-dione 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          102.02 
_cell.angle_gamma         90 
_cell.entry_id            8I6D 
_cell.length_a            45.98 
_cell.length_b            77.99 
_cell.length_c            59.37 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8I6D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,H 1 1 
B,F,G,I 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
? 2 F N N 
#
_chem_comp.formula           'C4 H4 N2 O3' 
_chem_comp.formula_weight    128.086 
_chem_comp.id                ODF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-oxidanyl-1~{H}-pyrimidine-2,4-dione 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     5-Hydroxy-2,4(1H,3H)-pyrimidinedion 
#
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
O1 C1 ODF sing 246 n n 
O2 C2 ODF doub 247 n n 
C1 C2 ODF sing 248 n n 
C1 C3 ODF doub 249 n n 
C2 N1 ODF sing 250 n n 
C3 N2 ODF sing 251 n n 
N1 C4 ODF sing 252 n n 
N2 C4 ODF sing 253 n n 
C4 O3 ODF doub 254 n n 
N1 H1 ODF sing 255 n n 
C3 H2 ODF sing 256 n n 
O1 H4 ODF sing 257 n n 
N2 H5 ODF sing 258 n n 
#
_atom_sites.entry_id                     8I6D 
_atom_sites.fract_transf_matrix[1][1]    0.021749 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004631 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012822 
_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]    0.017221 
_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 ODF A 1 301 301 ODF UNL . 
D 2 ODF A 1 302 401 ODF UNL . 
E 3 EDO A 1 303 501 EDO EDO . 
F 2 ODF B 1 301 301 ODF UNL . 
G 4 PEG B 1 302 401 PEG PEG . 
H 5 HOH A 1 401 21 HOH HOH . 
H 5 HOH A 2 402 133 HOH HOH . 
H 5 HOH A 3 403 65 HOH HOH . 
H 5 HOH A 4 404 121 HOH HOH . 
H 5 HOH A 5 405 117 HOH HOH . 
H 5 HOH A 6 406 118 HOH HOH . 
H 5 HOH A 7 407 71 HOH HOH . 
H 5 HOH A 8 408 46 HOH HOH . 
H 5 HOH A 9 409 37 HOH HOH . 
H 5 HOH A 10 410 124 HOH HOH . 
H 5 HOH A 11 411 82 HOH HOH . 
H 5 HOH A 12 412 9 HOH HOH . 
H 5 HOH A 13 413 3 HOH HOH . 
H 5 HOH A 14 414 123 HOH HOH . 
H 5 HOH A 15 415 16 HOH HOH . 
H 5 HOH A 16 416 15 HOH HOH . 
H 5 HOH A 17 417 43 HOH HOH . 
H 5 HOH A 18 418 31 HOH HOH . 
H 5 HOH A 19 419 92 HOH HOH . 
H 5 HOH A 20 420 137 HOH HOH . 
H 5 HOH A 21 421 98 HOH HOH . 
H 5 HOH A 22 422 8 HOH HOH . 
H 5 HOH A 23 423 50 HOH HOH . 
H 5 HOH A 24 424 33 HOH HOH . 
H 5 HOH A 25 425 94 HOH HOH . 
H 5 HOH A 26 426 7 HOH HOH . 
H 5 HOH A 27 427 130 HOH HOH . 
H 5 HOH A 28 428 30 HOH HOH . 
H 5 HOH A 29 429 68 HOH HOH . 
H 5 HOH A 30 430 88 HOH HOH . 
H 5 HOH A 31 431 5 HOH HOH . 
H 5 HOH A 32 432 97 HOH HOH . 
H 5 HOH A 33 433 141 HOH HOH . 
H 5 HOH A 34 434 38 HOH HOH . 
H 5 HOH A 35 435 87 HOH HOH . 
H 5 HOH A 36 436 128 HOH HOH . 
H 5 HOH A 37 437 90 HOH HOH . 
H 5 HOH A 38 438 1 HOH HOH . 
H 5 HOH A 39 439 39 HOH HOH . 
H 5 HOH A 40 440 12 HOH HOH . 
H 5 HOH A 41 441 89 HOH HOH . 
H 5 HOH A 42 442 47 HOH HOH . 
H 5 HOH A 43 443 113 HOH HOH . 
H 5 HOH A 44 444 80 HOH HOH . 
H 5 HOH A 45 445 61 HOH HOH . 
H 5 HOH A 46 446 55 HOH HOH . 
H 5 HOH A 47 447 34 HOH HOH . 
H 5 HOH A 48 448 53 HOH HOH . 
H 5 HOH A 49 449 84 HOH HOH . 
H 5 HOH A 50 450 42 HOH HOH . 
H 5 HOH A 51 451 73 HOH HOH . 
H 5 HOH A 52 452 91 HOH HOH . 
H 5 HOH A 53 453 48 HOH HOH . 
H 5 HOH A 54 454 70 HOH HOH . 
H 5 HOH A 55 455 85 HOH HOH . 
H 5 HOH A 56 456 14 HOH HOH . 
H 5 HOH A 57 457 134 HOH HOH . 
H 5 HOH A 58 458 56 HOH HOH . 
H 5 HOH A 59 459 25 HOH HOH . 
H 5 HOH A 60 460 11 HOH HOH . 
H 5 HOH A 61 461 127 HOH HOH . 
H 5 HOH A 62 462 32 HOH HOH . 
H 5 HOH A 63 463 27 HOH HOH . 
H 5 HOH A 64 464 72 HOH HOH . 
H 5 HOH A 65 465 13 HOH HOH . 
H 5 HOH A 66 466 18 HOH HOH . 
H 5 HOH A 67 467 66 HOH HOH . 
H 5 HOH A 68 468 81 HOH HOH . 
H 5 HOH A 69 469 45 HOH HOH . 
H 5 HOH A 70 470 52 HOH HOH . 
H 5 HOH A 71 471 107 HOH HOH . 
H 5 HOH A 72 472 57 HOH HOH . 
H 5 HOH A 73 473 105 HOH HOH . 
H 5 HOH A 74 474 24 HOH HOH . 
H 5 HOH A 75 475 69 HOH HOH . 
H 5 HOH A 76 476 104 HOH HOH . 
H 5 HOH A 77 477 2 HOH HOH . 
H 5 HOH A 78 478 140 HOH HOH . 
H 5 HOH A 79 479 136 HOH HOH . 
H 5 HOH A 80 480 106 HOH HOH . 
I 5 HOH B 1 401 125 HOH HOH . 
I 5 HOH B 2 402 131 HOH HOH . 
I 5 HOH B 3 403 63 HOH HOH . 
I 5 HOH B 4 404 112 HOH HOH . 
I 5 HOH B 5 405 126 HOH HOH . 
I 5 HOH B 6 406 77 HOH HOH . 
I 5 HOH B 7 407 114 HOH HOH . 
I 5 HOH B 8 408 40 HOH HOH . 
I 5 HOH B 9 409 62 HOH HOH . 
I 5 HOH B 10 410 144 HOH HOH . 
I 5 HOH B 11 411 44 HOH HOH . 
I 5 HOH B 12 412 26 HOH HOH . 
I 5 HOH B 13 413 76 HOH HOH . 
I 5 HOH B 14 414 119 HOH HOH . 
I 5 HOH B 15 415 120 HOH HOH . 
I 5 HOH B 16 416 86 HOH HOH . 
I 5 HOH B 17 417 74 HOH HOH . 
I 5 HOH B 18 418 146 HOH HOH . 
I 5 HOH B 19 419 58 HOH HOH . 
I 5 HOH B 20 420 135 HOH HOH . 
I 5 HOH B 21 421 41 HOH HOH . 
I 5 HOH B 22 422 129 HOH HOH . 
I 5 HOH B 23 423 49 HOH HOH . 
I 5 HOH B 24 424 20 HOH HOH . 
I 5 HOH B 25 425 4 HOH HOH . 
I 5 HOH B 26 426 116 HOH HOH . 
I 5 HOH B 27 427 142 HOH HOH . 
I 5 HOH B 28 428 60 HOH HOH . 
I 5 HOH B 29 429 75 HOH HOH . 
I 5 HOH B 30 430 110 HOH HOH . 
I 5 HOH B 31 431 28 HOH HOH . 
I 5 HOH B 32 432 109 HOH HOH . 
I 5 HOH B 33 433 6 HOH HOH . 
I 5 HOH B 34 434 29 HOH HOH . 
I 5 HOH B 35 435 36 HOH HOH . 
I 5 HOH B 36 436 122 HOH HOH . 
I 5 HOH B 37 437 138 HOH HOH . 
I 5 HOH B 38 438 35 HOH HOH . 
I 5 HOH B 39 439 99 HOH HOH . 
I 5 HOH B 40 440 115 HOH HOH . 
I 5 HOH B 41 441 96 HOH HOH . 
I 5 HOH B 42 442 19 HOH HOH . 
I 5 HOH B 43 443 143 HOH HOH . 
I 5 HOH B 44 444 83 HOH HOH . 
I 5 HOH B 45 445 132 HOH HOH . 
I 5 HOH B 46 446 145 HOH HOH . 
I 5 HOH B 47 447 111 HOH HOH . 
I 5 HOH B 48 448 78 HOH HOH . 
I 5 HOH B 49 449 59 HOH HOH . 
I 5 HOH B 50 450 64 HOH HOH . 
I 5 HOH B 51 451 79 HOH HOH . 
I 5 HOH B 52 452 139 HOH HOH . 
I 5 HOH B 53 453 51 HOH HOH . 
I 5 HOH B 54 454 22 HOH HOH . 
I 5 HOH B 55 455 103 HOH HOH . 
I 5 HOH B 56 456 95 HOH HOH . 
I 5 HOH B 57 457 10 HOH HOH . 
I 5 HOH B 58 458 17 HOH HOH . 
I 5 HOH B 59 459 54 HOH HOH . 
I 5 HOH B 60 460 100 HOH HOH . 
I 5 HOH B 61 461 102 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 O O3 ODF . . . C 2 -8.68 -18.247 -23.499 1 28.58 ? O3 ODF 301 A 1 
HETATM 2 C C4 ODF . . . C 2 -9.034 -18.45 -22.388 1 29.17 ? C4 ODF 301 A 1 
HETATM 3 N N1 ODF . . . C 2 -9.828 -17.516 -21.678 1 29.16 ? N1 ODF 301 A 1 
HETATM 4 C C2 ODF . . . C 2 -10.243 -17.781 -20.341 1 28.63 ? C2 ODF 301 A 1 
HETATM 5 O O2 ODF . . . C 2 -10.915 -16.989 -19.759 1 26.18 ? O2 ODF 301 A 1 
HETATM 6 N N2 ODF . . . C 2 -8.627 -19.669 -21.73 1 29.37 ? N2 ODF 301 A 1 
HETATM 7 C C3 ODF . . . C 2 -9.055 -19.949 -20.343 1 29.03 ? C3 ODF 301 A 1 
HETATM 8 C C1 ODF . . . C 2 -9.819 -19.086 -19.673 1 29.28 ? C1 ODF 301 A 1 
HETATM 9 O O1 ODF . . . C 2 -10.196 -19.4 -18.354 1 32.33 ? O1 ODF 301 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           338 
_model_server_stats.encode_time_ms          19 
_model_server_stats.element_count           9 
#