data_7VCH
#
_model_server_result.job_id            xirjvr2DUqHQ_QunkiukQA 
_model_server_result.datetime_utc      '2024-10-10 11:24:52' 
_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          7vch 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":401}' 
#
_entry.id    7VCH 
#
_exptl.entry_id    7VCH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              548.33 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" 
_entity.pdbx_number_of_molecules    2 
_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            7VCH 
_cell.length_a            47.407 
_cell.length_b            124.402 
_cell.length_c            127.647 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7VCH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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,F 1 1 
B,G,H,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 G N N 
#
_chem_comp.formula           'C16 H26 N2 O15 P2' 
_chem_comp.formula_weight    548.33 
_chem_comp.id                TRH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" 
_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
O4P P2 TRH sing 308 n n 
O4P H4PO TRH sing 309 n n 
P2 O3P TRH doub 310 n n 
P2 O1 TRH sing 311 n n 
P2 OPP TRH sing 312 n n 
O1 C1 TRH sing 313 n n 
C1 C2 TRH sing 314 n n 
C1 O5 TRH sing 315 n n 
C1 HC1 TRH sing 316 n n 
C2 O2 TRH sing 317 n n 
C2 C3 TRH sing 318 n n 
C2 HC2 TRH sing 319 n n 
O2 HO2 TRH sing 320 n n 
C3 O3 TRH sing 321 n n 
C3 C4 TRH sing 322 n n 
C3 HC3 TRH sing 323 n n 
O3 HO3 TRH sing 324 n n 
C4 O4 TRH sing 325 n n 
C4 C5 TRH sing 326 n n 
C4 HC4 TRH sing 327 n n 
O4 HO4 TRH sing 328 n n 
C5 O5 TRH sing 329 n n 
C5 C6 TRH sing 330 n n 
C5 HC5 TRH sing 331 n n 
C6 HC61 TRH sing 332 n n 
C6 HC62 TRH sing 333 n n 
C6 HC63 TRH sing 334 n n 
OPP P TRH sing 335 n n 
P O1P TRH sing 336 n n 
P O2P TRH doub 337 n n 
P O5' TRH sing 338 n n 
O1P H1PO TRH sing 339 n n 
O5' C5' TRH sing 340 n n 
C5' C4' TRH sing 341 n n 
C5' "H5'1" TRH sing 342 n n 
C5' "H5'2" TRH sing 343 n n 
C4' O4' TRH sing 344 n n 
C4' C3' TRH sing 345 n n 
C4' "H4'C" TRH sing 346 n n 
O4' C1' TRH sing 347 n n 
C3' O3' TRH sing 348 n n 
C3' C2' TRH sing 349 n n 
C3' "H3'C" TRH sing 350 n n 
O3' "H3'O" TRH sing 351 n n 
C2' C1' TRH sing 352 n n 
C2' "H2'1" TRH sing 353 n n 
C2' "H2'2" TRH sing 354 n n 
C1' N11 TRH sing 355 n n 
C1' "H1'C" TRH sing 356 n n 
N11 C21 TRH sing 357 n n 
N11 C61 TRH sing 358 n n 
C21 O21 TRH doub 359 n n 
C21 N31 TRH sing 360 n n 
N31 C41 TRH sing 361 n n 
N31 H31N TRH sing 362 n n 
C41 O41 TRH doub 363 n n 
C41 C51 TRH sing 364 n n 
C51 C5A TRH sing 365 n n 
C51 C61 TRH doub 366 n n 
C5A HCA1 TRH sing 367 n n 
C5A HCA2 TRH sing 368 n n 
C5A HCA3 TRH sing 369 n n 
C61 H61C TRH sing 370 n n 
#
_atom_sites.entry_id                     7VCH 
_atom_sites.fract_transf_matrix[1][1]    0.021094 
_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]    0.008038 
_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]    0.007834 
_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 TRH A 1 401 401 TRH TRH . 
D 3 SO4 A 1 402 1 SO4 SO4 . 
E 3 SO4 A 1 403 2 SO4 SO4 . 
F 3 SO4 A 1 404 3 SO4 SO4 . 
G 2 TRH F 1 401 401 TRH TRH . 
H 3 SO4 F 1 402 4 SO4 SO4 . 
I 3 SO4 F 1 403 5 SO4 SO4 . 
#
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 O4P TRH . . . G 2 25.423 18.808 13.085 1 72.28 ? O4P TRH 401 F 1 
HETATM 2 P P2 TRH . . . G 2 24.322 18.761 12.086 1 74.2 ? P2 TRH 401 F 1 
HETATM 3 O O3P TRH . . . G 2 24.301 19.82 11.047 1 78.2 ? O3P TRH 401 F 1 
HETATM 4 O O1 TRH . . . G 2 24.322 17.338 11.36 1 78.72 ? O1 TRH 401 F 1 
HETATM 5 C C1 TRH . . . G 2 23.608 17.11 10.18 1 80.22 ? C1 TRH 401 F 1 
HETATM 6 C C2 TRH . . . G 2 23.223 15.656 10.11 1 80.8 ? C2 TRH 401 F 1 
HETATM 7 O O2 TRH . . . G 2 24.399 14.863 9.99 1 81.35 ? O2 TRH 401 F 1 
HETATM 8 C C3 TRH . . . G 2 22.342 15.466 8.906 1 82.59 ? C3 TRH 401 F 1 
HETATM 9 O O3 TRH . . . G 2 21.956 14.102 8.803 1 85.34 ? O3 TRH 401 F 1 
HETATM 10 C C4 TRH . . . G 2 23.075 15.898 7.652 1 92.05 ? C4 TRH 401 F 1 
HETATM 11 O O4 TRH . . . G 2 22.193 15.821 6.536 1 99.92 ? O4 TRH 401 F 1 
HETATM 12 C C5 TRH . . . G 2 23.576 17.327 7.819 1 86.17 ? C5 TRH 401 F 1 
HETATM 13 O O5 TRH . . . G 2 24.359 17.437 9.028 1 81.41 ? O5 TRH 401 F 1 
HETATM 14 C C6 TRH . . . G 2 24.449 17.801 6.684 1 96.59 ? C6 TRH 401 F 1 
HETATM 15 O OPP TRH . . . G 2 22.92 18.789 12.845 1 71.31 ? OPP TRH 401 F 1 
HETATM 16 P P TRH . . . G 2 22.17 17.797 13.842 1 72.12 ? P TRH 401 F 1 
HETATM 17 O O1P TRH . . . G 2 21.058 18.535 14.486 1 58.05 ? O1P TRH 401 F 1 
HETATM 18 O O2P TRH . . . G 2 21.81 16.549 13.119 1 73.81 ? O2P TRH 401 F 1 
HETATM 19 O O5' TRH . . . G 2 23.306 17.493 14.92 1 69.59 ? O5' TRH 401 F 1 
HETATM 20 C C5' TRH . . . G 2 23.824 18.57 15.735 1 73.09 ? C5' TRH 401 F 1 
HETATM 21 C C4' TRH . . . G 2 24.354 17.991 17.02 1 68.28 ? C4' TRH 401 F 1 
HETATM 22 O O4' TRH . . . G 2 24.954 19.032 17.823 1 66.76 ? O4' TRH 401 F 1 
HETATM 23 C C3' TRH . . . G 2 23.279 17.361 17.898 1 64.35 ? C3' TRH 401 F 1 
HETATM 24 O O3' TRH . . . G 2 23.814 16.199 18.516 1 62.75 ? O3' TRH 401 F 1 
HETATM 25 C C2' TRH . . . G 2 23.043 18.429 18.953 1 65.29 ? C2' TRH 401 F 1 
HETATM 26 C C1' TRH . . . G 2 24.463 18.907 19.148 1 70.3 ? C1' TRH 401 F 1 
HETATM 27 N N11 TRH . . . G 2 24.606 20.213 19.811 1 78.75 ? N11 TRH 401 F 1 
HETATM 28 C C21 TRH . . . G 2 25.316 20.253 20.989 1 75.36 ? C21 TRH 401 F 1 
HETATM 29 O O21 TRH . . . G 2 25.826 19.262 21.483 1 68.28 ? O21 TRH 401 F 1 
HETATM 30 N N31 TRH . . . G 2 25.44 21.498 21.55 1 80.89 ? N31 TRH 401 F 1 
HETATM 31 C C41 TRH . . . G 2 24.922 22.682 21.065 1 82.46 ? C41 TRH 401 F 1 
HETATM 32 O O41 TRH . . . G 2 25.116 23.729 21.68 1 80.53 ? O41 TRH 401 F 1 
HETATM 33 C C51 TRH . . . G 2 24.179 22.569 19.83 1 79.1 ? C51 TRH 401 F 1 
HETATM 34 C C5A TRH . . . G 2 23.599 23.816 19.232 1 79.32 ? C5A TRH 401 F 1 
HETATM 35 C C61 TRH . . . G 2 24.048 21.354 19.269 1 77.92 ? C61 TRH 401 F 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           35 
#