data_7D9P # _model_server_result.job_id lQHVaSKT7uuVGmoP4CzhlA _model_server_result.datetime_utc '2025-08-31 20:53:04' _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 7d9p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 7D9P # _exptl.entry_id 7D9P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 415.473 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S)-2-[[4-fluoranyl-1-[(2-fluorophenyl)methyl]piperidin-4-yl]methyl]-5,6-dimethoxy-2,3-dihydroinden-1-one _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 120 _cell.entry_id 7D9P _cell.length_a 104.944 _cell.length_b 104.944 _cell.length_c 323.616 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7D9P _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 # 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 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 1 FUC NAG C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG C 1 NAG 2 n C NAG 2 C 2 NAG C 2 NAG 2 n C FUC 3 C 3 FUC C 3 FUC 2 n D NAG 1 D 1 NAG D 1 NAG 2 n D NAG 2 D 2 NAG D 2 NAG 2 n D FUC 3 D 3 FUC D 3 FUC # 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 disulf ? disulf1 A SG CYS 79 A CYS 69 1_555 A SG CYS 106 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf2 A SG CYS 267 A CYS 257 1_555 A SG CYS 282 A CYS 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf3 A SG CYS 419 A CYS 409 1_555 A SG CYS 539 A CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf4 B SG CYS 79 B CYS 69 1_555 B SG CYS 106 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf5 B SG CYS 267 B CYS 257 1_555 B SG CYS 282 B CYS 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf6 B SG CYS 419 B CYS 409 1_555 B SG CYS 539 B CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? covale ? covale1 A ND2 ASN 360 A ASN 350 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale2 B ND2 ASN 360 B ASN 350 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _chem_comp.formula 'C24 H27 F2 N O3' _chem_comp.formula_weight 415.473 _chem_comp.id H0R _chem_comp.mon_nstd_flag . _chem_comp.name (2S)-2-[[4-fluoranyl-1-[(2-fluorophenyl)methyl]piperidin-4-yl]methyl]-5,6-dimethoxy-2,3-dihydroinden-1-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 C10 O9 H0R sing 152 n n O9 C8 H0R sing 153 n n C7 C8 H0R doub 154 n y C7 C6 H0R sing 155 n y C8 C3 H0R sing 156 n y O12 C11 H0R doub 157 n n C6 C11 H0R sing 158 n n C6 C5 H0R doub 159 n y C11 C13 H0R sing 160 n n C3 O2 H0R sing 161 n n C3 C4 H0R doub 162 n y O2 C1 H0R sing 163 n n C5 C4 H0R sing 164 n y C5 C30 H0R sing 165 n n C13 C14 H0R sing 166 n n C13 C30 H0R sing 167 n n F16 C15 H0R sing 168 n n C14 C15 H0R sing 169 n n C17 C15 H0R sing 170 n n C17 C18 H0R sing 171 n n C15 C29 H0R sing 172 n n C18 N19 H0R sing 173 n n C29 C28 H0R sing 174 n n N19 C28 H0R sing 175 n n N19 C20 H0R sing 176 n n F27 C26 H0R sing 177 n n C20 C21 H0R sing 178 n n C26 C21 H0R doub 179 n y C26 C25 H0R sing 180 n y C21 C22 H0R sing 181 n y C25 C24 H0R doub 182 n y C22 C23 H0R doub 183 n y C24 C23 H0R sing 184 n y C1 H1 H0R sing 185 n n C1 H2 H0R sing 186 n n C1 H3 H0R sing 187 n n C4 H4 H0R sing 188 n n C7 H5 H0R sing 189 n n C10 H6 H0R sing 190 n n C10 H7 H0R sing 191 n n C10 H8 H0R sing 192 n n C13 H9 H0R sing 193 n n C14 H10 H0R sing 194 n n C14 H11 H0R sing 195 n n C17 H12 H0R sing 196 n n C17 H13 H0R sing 197 n n C18 H14 H0R sing 198 n n C18 H15 H0R sing 199 n n C20 H16 H0R sing 200 n n C20 H17 H0R sing 201 n n C22 H18 H0R sing 202 n n C23 H19 H0R sing 203 n n C24 H20 H0R sing 204 n n C25 H21 H0R sing 205 n n C28 H22 H0R sing 206 n n C28 H23 H0R sing 207 n n C29 H24 H0R sing 208 n n C29 H25 H0R sing 209 n n C30 H26 H0R sing 210 n n C30 H27 H0R sing 211 n n # _atom_sites.entry_id 7D9P _atom_sites.fract_transf_matrix[1][1] 0.009529 _atom_sites.fract_transf_matrix[1][2] 0.005502 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011003 _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] 0.00309 _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 E 3 H0R A 1 601 601 H0R DC2 . F 3 H0R B 1 601 601 H0R DC2 . # 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 C11 H0R . . . E 3 15.011 42.535 25.182 1 35.11 ? C11 H0R 601 A 1 HETATM 2 C C1 H0R . . . E 3 20.504 40.079 26.933 1 34.61 ? C1 H0R 601 A 1 HETATM 3 C C3 H0R . . . E 3 19.082 40.97 25.387 1 36.23 ? C3 H0R 601 A 1 HETATM 4 C C4 H0R . . . E 3 18.309 41.342 26.505 1 33.23 ? C4 H0R 601 A 1 HETATM 5 C C5 H0R . . . E 3 16.992 41.833 26.321 1 34.24 ? C5 H0R 601 A 1 HETATM 6 C C6 H0R . . . E 3 16.469 41.964 25.058 1 31.89 ? C6 H0R 601 A 1 HETATM 7 C C7 H0R . . . E 3 17.278 41.583 23.901 1 32.07 ? C7 H0R 601 A 1 HETATM 8 C C8 H0R . . . E 3 18.558 41.092 24.084 1 43.35 ? C8 H0R 601 A 1 HETATM 9 C C10 H0R . . . E 3 18.639 40.711 21.743 1 44.71 ? C10 H0R 601 A 1 HETATM 10 C C13 H0R . . . E 3 14.657 42.656 26.651 1 34.4 ? C13 H0R 601 A 1 HETATM 11 C C14 H0R . . . E 3 14.063 44.083 27.062 1 35.57 ? C14 H0R 601 A 1 HETATM 12 C C15 H0R . . . E 3 12.659 43.972 27.767 1 40.12 ? C15 H0R 601 A 1 HETATM 13 C C17 H0R . . . E 3 12.277 45.309 27.415 1 40.1 ? C17 H0R 601 A 1 HETATM 14 C C18 H0R . . . E 3 11.52 45.924 28.596 1 46.37 ? C18 H0R 601 A 1 HETATM 15 C C20 H0R . . . E 3 11.094 45.652 30.848 1 55.3 ? C20 H0R 601 A 1 HETATM 16 C C21 H0R . . . E 3 9.832 44.885 31.433 1 56.85 ? C21 H0R 601 A 1 HETATM 17 C C22 H0R . . . E 3 10.047 43.729 32.204 1 48.75 ? C22 H0R 601 A 1 HETATM 18 C C23 H0R . . . E 3 8.927 43.016 32.735 1 50.45 ? C23 H0R 601 A 1 HETATM 19 C C24 H0R . . . E 3 7.62 43.439 32.507 1 46.65 ? C24 H0R 601 A 1 HETATM 20 C C25 H0R . . . E 3 7.386 44.585 31.747 1 48.57 ? C25 H0R 601 A 1 HETATM 21 C C26 H0R . . . E 3 8.503 45.314 31.209 1 62.32 ? C26 H0R 601 A 1 HETATM 22 C C28 H0R . . . E 3 12.93 44.665 30.135 1 39.68 ? C28 H0R 601 A 1 HETATM 23 C C29 H0R . . . E 3 13.324 43.671 29.05 1 40.1 ? C29 H0R 601 A 1 HETATM 24 C C30 H0R . . . E 3 15.926 42.317 27.38 1 36.45 ? C30 H0R 601 A 1 HETATM 25 F F16 H0R . . . E 3 12.331 42.965 26.848 1 56.27 ? F16 H0R 601 A 1 HETATM 26 F F27 H0R . . . E 3 8.229 46.414 30.478 1 62.49 ? F27 H0R 601 A 1 HETATM 27 N N19 H0R . . . E 3 11.596 45.13 29.846 1 59.62 ? N19 H0R 601 A 1 HETATM 28 O O2 H0R . . . E 3 20.365 40.479 25.605 1 33.03 ? O2 H0R 601 A 1 HETATM 29 O O9 H0R . . . E 3 19.341 40.716 23.009 1 45.09 ? O9 H0R 601 A 1 HETATM 30 O O12 H0R . . . E 3 14.311 42.797 24.263 1 37.52 ? O12 H0R 601 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 393 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 30 #