data_2M5D # _model_server_result.job_id Vm2kfPYpPMqcTFKh3o0khg _model_server_result.datetime_utc '2025-07-02 06:29:08' _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 2m5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 2M5D # _exptl.entry_id 2M5D _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 168.213 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-phenyl(sulfanyl)ethanoic acid' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 86 A HIS 86 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc2 A ND1 HIS 88 A HIS 88 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc3 A OD2 ASP 90 A ASP 90 1_555 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc4 A NE2 HIS 149 A HIS 149 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc5 A SG CYS 168 A CYS 168 1_555 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc6 A NE2 HIS 210 A HIS 210 1_555 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc7 B ZN ZN . A ZN 301 1_555 D S1 RTD . A RTD 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc8 C ZN ZN . A ZN 302 1_555 D S1 RTD . A RTD 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? # _chem_comp.formula 'C8 H8 O2 S' _chem_comp.formula_weight 168.213 _chem_comp.id RTD _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-phenyl(sulfanyl)ethanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'alpha-mercaptophenylacetic acid, R-thiomandelic acid' # 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 CD2 CG2 RTD doub 275 n y CD2 CE RTD sing 276 n y CG2 CB RTD sing 277 n y O1 C RTD doub 278 n n CE CD1 RTD doub 279 n y O2 C RTD sing 280 n n C CA RTD sing 281 n n CB CA RTD sing 282 n n CB CG1 RTD doub 283 n y S1 CA RTD sing 284 n n CD1 CG1 RTD sing 285 n y O2 H1 RTD sing 286 n n CA HA RTD sing 287 n n S1 H2 RTD sing 288 n n CG1 HG1 RTD sing 289 n n CD1 HD1 RTD sing 290 n n CE HE RTD sing 291 n n CD2 HD2 RTD sing 292 n n CG2 HG2 RTD sing 293 n n # _atom_sites.entry_id 2M5D _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 B 2 ZN A 1 301 241 ZN ZN . C 2 ZN A 1 302 254 ZN ZN . D 3 RTD A 1 303 268 RTD RTD . # 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 O1 RTD . . . D 3 6.35 11.875 0.454 1 3.21 ? O1 RTD 303 A 1 HETATM 2 C C RTD . . . D 3 5.733 10.844 0.813 1 55.02 ? C RTD 303 A 1 HETATM 3 O O2 RTD . . . D 3 6.144 9.677 0.645 1 44.44 ? O2 RTD 303 A 1 HETATM 4 C CA RTD . . . D 3 4.324 11.073 1.524 1 21.23 ? CA RTD 303 A 1 HETATM 5 S S1 RTD . . . D 3 3.153 9.675 1.252 1 13.45 ? S1 RTD 303 A 1 HETATM 6 C CB RTD . . . D 3 3.779 12.425 1.189 1 32 ? CB RTD 303 A 1 HETATM 7 C CG1 RTD . . . D 3 3.387 13.337 2.171 1 60.3 ? CG1 RTD 303 A 1 HETATM 8 C CD1 RTD . . . D 3 2.933 14.604 1.817 1 73.51 ? CD1 RTD 303 A 1 HETATM 9 C CE RTD . . . D 3 2.859 14.98 0.482 1 60.12 ? CE RTD 303 A 1 HETATM 10 C CD2 RTD . . . D 3 3.242 14.074 -0.504 1 23.1 ? CD2 RTD 303 A 1 HETATM 11 C CG2 RTD . . . D 3 3.701 12.81 -0.157 1 34.5 ? CG2 RTD 303 A 1 HETATM 12 H HA RTD . . . D 3 4.491 11.057 2.627 1 54.34 ? HA RTD 303 A 1 HETATM 13 H HG1 RTD . . . D 3 3.439 13.037 3.227 1 22.04 ? HG1 RTD 303 A 1 HETATM 14 H HD1 RTD . . . D 3 2.631 15.308 2.601 1 33.2 ? HD1 RTD 303 A 1 HETATM 15 H HE RTD . . . D 3 2.502 15.971 0.208 1 0.11 ? HE RTD 303 A 1 HETATM 16 H HD2 RTD . . . D 3 3.175 14.354 -1.558 1 63.32 ? HD2 RTD 303 A 1 HETATM 17 H HG2 RTD . . . D 3 3.995 12.089 -0.934 1 43.42 ? HG2 RTD 303 A 1 # _model_server_stats.io_time_ms 138 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 69 _model_server_stats.query_time_ms 6135 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #