data_3X04
#
_model_server_result.job_id            8NkUFxwls31Qww1BY_PDFQ 
_model_server_result.datetime_utc      '2024-11-04 23:09:06' 
_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          3x04 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    3X04 
#
_exptl.entry_id    3X04 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 
_entity.pdbx_number_of_molecules    4 
_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            3X04 
_cell.length_a            109.804 
_cell.length_b            185.222 
_cell.length_c            106.449 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3X04 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_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 
#
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 E N N 
? 2 F N N 
#
_chem_comp.formula           'C10 H17 N6 O13 P3' 
_chem_comp.formula_weight    522.196 
_chem_comp.id                GNP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 
_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
PG O1G GNP doub 129 n n 
PG O2G GNP sing 130 n n 
PG O3G GNP sing 131 n n 
PG N3B GNP sing 132 n n 
O2G HOG2 GNP sing 133 n n 
O3G HOG3 GNP sing 134 n n 
N3B PB GNP sing 135 n n 
N3B HNB3 GNP sing 136 n n 
PB O1B GNP doub 137 n n 
PB O2B GNP sing 138 n n 
PB O3A GNP sing 139 n n 
O2B HOB2 GNP sing 140 n n 
O3A PA GNP sing 141 n n 
PA O1A GNP doub 142 n n 
PA O2A GNP sing 143 n n 
PA O5' GNP sing 144 n n 
O2A HOA2 GNP sing 145 n n 
O5' C5' GNP sing 146 n n 
C5' C4' GNP sing 147 n n 
C5' "H5'2" GNP sing 148 n n 
C5' "H5'1" GNP sing 149 n n 
C4' O4' GNP sing 150 n n 
C4' C3' GNP sing 151 n n 
C4' H4' GNP sing 152 n n 
O4' C1' GNP sing 153 n n 
C3' O3' GNP sing 154 n n 
C3' C2' GNP sing 155 n n 
C3' H3' GNP sing 156 n n 
O3' HO3' GNP sing 157 n n 
C2' O2' GNP sing 158 n n 
C2' C1' GNP sing 159 n n 
C2' H2' GNP sing 160 n n 
O2' HO2' GNP sing 161 n n 
C1' N9 GNP sing 162 n n 
C1' H1' GNP sing 163 n n 
N9 C8 GNP sing 164 n y 
N9 C4 GNP sing 165 n y 
C8 N7 GNP doub 166 n y 
C8 H8 GNP sing 167 n n 
N7 C5 GNP sing 168 n y 
C5 C6 GNP sing 169 n y 
C5 C4 GNP doub 170 n y 
C6 O6 GNP doub 171 n n 
C6 N1 GNP sing 172 n y 
N1 C2 GNP sing 173 n y 
N1 HN1 GNP sing 174 n n 
C2 N2 GNP sing 175 n n 
C2 N3 GNP doub 176 n y 
N2 HN21 GNP sing 177 n n 
N2 HN22 GNP sing 178 n n 
N3 C4 GNP sing 179 n y 
#
_atom_sites.entry_id                     3X04 
_atom_sites.fract_transf_matrix[1][1]    0.009107 
_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]    0.005399 
_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]    0.009394 
_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 GNP A 1 501 501 GNP GNP . 
D 2 GNP A 1 502 502 GNP GNP . 
E 2 GNP A 1 503 503 GNP GNP . 
F 2 GNP B 1 501 501 GNP GNP . 
G 3 HOH A 1 601 601 HOH HOH . 
G 3 HOH A 2 602 602 HOH HOH . 
G 3 HOH A 3 603 603 HOH HOH . 
G 3 HOH A 4 604 604 HOH HOH . 
G 3 HOH A 5 605 605 HOH HOH . 
G 3 HOH A 6 606 606 HOH HOH . 
G 3 HOH A 7 607 607 HOH HOH . 
G 3 HOH A 8 608 608 HOH HOH . 
G 3 HOH A 9 609 609 HOH HOH . 
H 3 HOH B 1 601 601 HOH HOH . 
H 3 HOH B 2 602 602 HOH HOH . 
H 3 HOH B 3 603 603 HOH HOH . 
H 3 HOH B 4 604 604 HOH HOH . 
H 3 HOH B 5 605 605 HOH HOH . 
H 3 HOH B 6 606 606 HOH HOH . 
H 3 HOH B 7 607 607 HOH HOH . 
H 3 HOH B 8 608 608 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 P PG GNP . . . D 2 46.858 45.889 -27.099 1 122.51 ? PG GNP 502 A 1 
HETATM 2 O O1G GNP . . . D 2 46.235 47.228 -26.759 1 116.03 ? O1G GNP 502 A 1 
HETATM 3 O O2G GNP . . . D 2 46.522 45.345 -28.47 1 124.75 ? O2G GNP 502 A 1 
HETATM 4 O O3G GNP . . . D 2 46.563 44.946 -25.957 1 121.33 ? O3G GNP 502 A 1 
HETATM 5 N N3B GNP . . . D 2 48.433 46.044 -27.069 1 286.6 ? N3B GNP 502 A 1 
HETATM 6 P PB GNP . . . D 2 49.175 46.835 -25.909 1 93.66 ? PB GNP 502 A 1 
HETATM 7 O O1B GNP . . . D 2 50.276 45.985 -25.379 1 85.47 ? O1B GNP 502 A 1 
HETATM 8 O O2B GNP . . . D 2 49.446 48.178 -26.47 1 80.08 ? O2B GNP 502 A 1 
HETATM 9 O O3A GNP . . . D 2 48.187 47.128 -24.782 1 103.8 ? O3A GNP 502 A 1 
HETATM 10 P PA GNP . . . D 2 48.457 47.538 -23.318 1 85.18 ? PA GNP 502 A 1 
HETATM 11 O O1A GNP . . . D 2 47.305 48.452 -23.085 1 72.29 ? O1A GNP 502 A 1 
HETATM 12 O O2A GNP . . . D 2 48.69 46.304 -22.515 1 63.5 ? O2A GNP 502 A 1 
HETATM 13 O O5' GNP . . . D 2 49.78 48.373 -23.068 1 56.53 ? O5' GNP 502 A 1 
HETATM 14 C C5' GNP . . . D 2 49.805 49.627 -22.381 1 66.26 ? C5' GNP 502 A 1 
HETATM 15 C C4' GNP . . . D 2 51.173 50.295 -22.54 1 79.24 ? C4' GNP 502 A 1 
HETATM 16 O O4' GNP . . . D 2 52.191 49.649 -21.721 1 75.73 ? O4' GNP 502 A 1 
HETATM 17 C C3' GNP . . . D 2 51.698 50.302 -23.978 1 81.27 ? C3' GNP 502 A 1 
HETATM 18 O O3' GNP . . . D 2 52.003 51.625 -24.413 1 83.76 ? O3' GNP 502 A 1 
HETATM 19 C C2' GNP . . . D 2 52.949 49.433 -23.932 1 77.68 ? C2' GNP 502 A 1 
HETATM 20 O O2' GNP . . . D 2 53.938 49.926 -24.824 1 72.06 ? O2' GNP 502 A 1 
HETATM 21 C C1' GNP . . . D 2 53.376 49.479 -22.453 1 70.48 ? C1' GNP 502 A 1 
HETATM 22 N N9 GNP . . . D 2 54 48.22 -22.056 1 58.61 ? N9 GNP 502 A 1 
HETATM 23 C C8 GNP . . . D 2 53.395 46.98 -22.014 1 59.07 ? C8 GNP 502 A 1 
HETATM 24 N N7 GNP . . . D 2 54.214 46.016 -21.65 1 60.15 ? N7 GNP 502 A 1 
HETATM 25 C C5 GNP . . . D 2 55.441 46.656 -21.458 1 53.88 ? C5 GNP 502 A 1 
HETATM 26 C C6 GNP . . . D 2 56.695 46.129 -21.061 1 66.92 ? C6 GNP 502 A 1 
HETATM 27 O O6 GNP . . . D 2 56.98 44.95 -20.797 1 75.4 ? O6 GNP 502 A 1 
HETATM 28 N N1 GNP . . . D 2 57.683 47.116 -20.974 1 71.73 ? N1 GNP 502 A 1 
HETATM 29 C C2 GNP . . . D 2 57.476 48.451 -21.253 1 68.35 ? C2 GNP 502 A 1 
HETATM 30 N N2 GNP . . . D 2 58.542 49.254 -21.109 1 65.08 ? N2 GNP 502 A 1 
HETATM 31 N N3 GNP . . . D 2 56.298 48.96 -21.622 1 61.15 ? N3 GNP 502 A 1 
HETATM 32 C C4 GNP . . . D 2 55.326 48.012 -21.704 1 55.22 ? C4 GNP 502 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          19 
_model_server_stats.element_count           32 
#