data_8DIO
#
_model_server_result.job_id            yBST5FJbgRJTHFH1o8XcZg 
_model_server_result.datetime_utc      '2024-10-22 18:01:48' 
_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          8dio 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1001}' 
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_entry.id    8DIO 
#
_exptl.entry_id    8DIO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              165.153 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-amino-7-methyl-1,7-dihydro-6H-purin-6-one 
_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          100.307 
_cell.angle_gamma         90 
_cell.entry_id            8DIO 
_cell.length_a            47.95 
_cell.length_b            59.702 
_cell.length_c            60.381 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DIO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_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,E 1 1 
B,D,F 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 
#
_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           'C6 H7 N5 O' 
_chem_comp.formula_weight    165.153 
_chem_comp.id                MY6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-amino-7-methyl-1,7-dihydro-6H-purin-6-one 
_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
N4 C1 MY6 sing 320 n n 
C1 H1 MY6 sing 321 n n 
C1 H1A MY6 sing 322 n n 
C1 H1B MY6 sing 323 n n 
C3 N2 MY6 doub 324 n y 
N2 C12 MY6 sing 325 n y 
C3 N4 MY6 sing 326 n y 
C3 H3 MY6 sing 327 n n 
N4 C5 MY6 sing 328 n y 
C12 C5 MY6 doub 329 n y 
C5 C6 MY6 sing 330 n n 
C6 N8 MY6 sing 331 n n 
C6 O7 MY6 doub 332 n n 
C9 N8 MY6 sing 333 n n 
N8 HN8 MY6 sing 334 n n 
N11 C9 MY6 doub 335 n n 
C9 N10 MY6 sing 336 n n 
N10 HN10 MY6 sing 337 n n 
N10 HN1A MY6 sing 338 n n 
C12 N11 MY6 sing 339 n n 
#
_atom_sites.entry_id                     8DIO 
_atom_sites.fract_transf_matrix[1][1]    0.020855 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003793 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01675 
_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]    0.016833 
_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 91P A 1 1001 1001 91P 91P . 
D 3 MY6 B 1 1001 1001 MY6 MY6 . 
E 4 HOH A 1 1101 55 HOH HOH . 
E 4 HOH A 2 1102 90 HOH HOH . 
E 4 HOH A 3 1103 54 HOH HOH . 
E 4 HOH A 4 1104 83 HOH HOH . 
E 4 HOH A 5 1105 45 HOH HOH . 
E 4 HOH A 6 1106 3 HOH HOH . 
E 4 HOH A 7 1107 88 HOH HOH . 
E 4 HOH A 8 1108 14 HOH HOH . 
E 4 HOH A 9 1109 38 HOH HOH . 
E 4 HOH A 10 1110 37 HOH HOH . 
E 4 HOH A 11 1111 1 HOH HOH . 
E 4 HOH A 12 1112 27 HOH HOH . 
E 4 HOH A 13 1113 63 HOH HOH . 
E 4 HOH A 14 1114 66 HOH HOH . 
E 4 HOH A 15 1115 5 HOH HOH . 
E 4 HOH A 16 1116 44 HOH HOH . 
E 4 HOH A 17 1117 93 HOH HOH . 
E 4 HOH A 18 1118 6 HOH HOH . 
E 4 HOH A 19 1119 29 HOH HOH . 
E 4 HOH A 20 1120 84 HOH HOH . 
E 4 HOH A 21 1121 67 HOH HOH . 
E 4 HOH A 22 1122 41 HOH HOH . 
E 4 HOH A 23 1123 47 HOH HOH . 
E 4 HOH A 24 1124 4 HOH HOH . 
E 4 HOH A 25 1125 36 HOH HOH . 
E 4 HOH A 26 1126 30 HOH HOH . 
E 4 HOH A 27 1127 70 HOH HOH . 
E 4 HOH A 28 1128 22 HOH HOH . 
E 4 HOH A 29 1129 2 HOH HOH . 
E 4 HOH A 30 1130 76 HOH HOH . 
E 4 HOH A 31 1131 50 HOH HOH . 
E 4 HOH A 32 1132 51 HOH HOH . 
E 4 HOH A 33 1133 89 HOH HOH . 
E 4 HOH A 34 1134 18 HOH HOH . 
E 4 HOH A 35 1135 68 HOH HOH . 
E 4 HOH A 36 1136 39 HOH HOH . 
E 4 HOH A 37 1137 49 HOH HOH . 
E 4 HOH A 38 1138 58 HOH HOH . 
E 4 HOH A 39 1139 25 HOH HOH . 
E 4 HOH A 40 1140 32 HOH HOH . 
E 4 HOH A 41 1141 20 HOH HOH . 
E 4 HOH A 42 1142 48 HOH HOH . 
E 4 HOH A 43 1143 91 HOH HOH . 
E 4 HOH A 44 1144 92 HOH HOH . 
E 4 HOH A 45 1145 71 HOH HOH . 
E 4 HOH A 46 1146 82 HOH HOH . 
E 4 HOH A 47 1147 75 HOH HOH . 
E 4 HOH A 48 1148 81 HOH HOH . 
E 4 HOH A 49 1149 86 HOH HOH . 
F 4 HOH B 1 1101 80 HOH HOH . 
F 4 HOH B 2 1102 72 HOH HOH . 
F 4 HOH B 3 1103 73 HOH HOH . 
F 4 HOH B 4 1104 31 HOH HOH . 
F 4 HOH B 5 1105 77 HOH HOH . 
F 4 HOH B 6 1106 42 HOH HOH . 
F 4 HOH B 7 1107 87 HOH HOH . 
F 4 HOH B 8 1108 64 HOH HOH . 
F 4 HOH B 9 1109 26 HOH HOH . 
F 4 HOH B 10 1110 33 HOH HOH . 
F 4 HOH B 11 1111 46 HOH HOH . 
F 4 HOH B 12 1112 52 HOH HOH . 
F 4 HOH B 13 1113 56 HOH HOH . 
F 4 HOH B 14 1114 43 HOH HOH . 
F 4 HOH B 15 1115 7 HOH HOH . 
F 4 HOH B 16 1116 61 HOH HOH . 
F 4 HOH B 17 1117 8 HOH HOH . 
F 4 HOH B 18 1118 78 HOH HOH . 
F 4 HOH B 19 1119 53 HOH HOH . 
F 4 HOH B 20 1120 62 HOH HOH . 
F 4 HOH B 21 1121 85 HOH HOH . 
F 4 HOH B 22 1122 28 HOH HOH . 
F 4 HOH B 23 1123 74 HOH HOH . 
F 4 HOH B 24 1124 57 HOH HOH . 
F 4 HOH B 25 1125 79 HOH HOH . 
F 4 HOH B 26 1126 40 HOH HOH . 
F 4 HOH B 27 1127 60 HOH HOH . 
F 4 HOH B 28 1128 59 HOH HOH . 
F 4 HOH B 29 1129 35 HOH HOH . 
F 4 HOH B 30 1130 65 HOH HOH . 
F 4 HOH B 31 1131 69 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 C1 MY6 . . . D 3 0.803 8.707 -27.165 1 40.04 ? C1 MY6 1001 B 1 
HETATM 2 N N2 MY6 . . . D 3 1.519 10.88 -24.749 1 35.66 ? N2 MY6 1001 B 1 
HETATM 3 C C3 MY6 . . . D 3 1.202 9.793 -25.231 1 36.57 ? C3 MY6 1001 B 1 
HETATM 4 N N4 MY6 . . . D 3 1.192 9.897 -26.414 1 38.2 ? N4 MY6 1001 B 1 
HETATM 5 C C5 MY6 . . . D 3 1.487 10.948 -27.138 1 39.19 ? C5 MY6 1001 B 1 
HETATM 6 C C6 MY6 . . . D 3 1.554 11.367 -28.509 1 41.35 ? C6 MY6 1001 B 1 
HETATM 7 O O7 MY6 . . . D 3 1.276 10.491 -29.547 1 43.67 ? O7 MY6 1001 B 1 
HETATM 8 N N8 MY6 . . . D 3 1.925 12.667 -28.82 1 41.52 ? N8 MY6 1001 B 1 
HETATM 9 C C9 MY6 . . . D 3 2.244 13.574 -27.671 1 39.7 ? C9 MY6 1001 B 1 
HETATM 10 N N10 MY6 . . . D 3 2.637 14.944 -27.948 1 40.17 ? N10 MY6 1001 B 1 
HETATM 11 N N11 MY6 . . . D 3 2.161 13.138 -26.3 1 37.54 ? N11 MY6 1001 B 1 
HETATM 12 C C12 MY6 . . . D 3 1.781 11.847 -25.913 1 36.99 ? C12 MY6 1001 B 1 
HETATM 13 H H1 MY6 . . . D 3 0.178 8.995 -28.001 1 20.16 ? H1 MY6 1001 B 1 
HETATM 14 H H1A MY6 . . . D 3 0.253 8.035 -26.517 1 20.16 ? H1A MY6 1001 B 1 
HETATM 15 H H1B MY6 . . . D 3 1.69 8.206 -27.533 1 20.16 ? H1B MY6 1001 B 1 
HETATM 16 H H3 MY6 . . . D 3 0.677 9.018 -24.687 1 17.51 ? H3 MY6 1001 B 1 
HETATM 17 H HN8 MY6 . . . D 3 1.978 12.984 -29.768 1 17.37 ? HN8 MY6 1001 B 1 
HETATM 18 H HN10 MY6 . . . D 3 3.358 15.13 -28.61 1 22.87 ? HN10 MY6 1001 B 1 
HETATM 19 H HN1A MY6 . . . D 3 2.169 15.706 -27.481 1 22.87 ? HN1A MY6 1001 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           19 
#