data_7D9Q # _model_server_result.job_id A6LVgIkoLd8HTI9_DFVEkg _model_server_result.datetime_utc '2024-11-24 23:43:53' _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 7d9q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 7D9Q # _exptl.entry_id 7D9Q _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-[(3-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 7D9Q _cell.length_a 104.649 _cell.length_b 104.649 _cell.length_c 324.403 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7D9Q _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,G 1 1 B,D,F,H 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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -108.134333 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf2 A SG CYS 267 A CYS 257 1_555 A SG CYS 282 A CYS 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf3 A SG CYS 419 A CYS 409 1_555 A SG CYS 539 A CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf4 B SG CYS 79 B CYS 69 1_555 B SG CYS 106 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf5 B SG CYS 267 B CYS 257 1_555 B SG CYS 282 B CYS 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf6 B SG CYS 419 B CYS 409 1_555 B SG CYS 539 B CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? covale ? covale1 A ND2 ASN 360 A ASN 350 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale2 B ND2 ASN 360 B ASN 350 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? # _chem_comp.formula 'C24 H27 F2 N O3' _chem_comp.formula_weight 415.473 _chem_comp.id H1R _chem_comp.mon_nstd_flag . _chem_comp.name (2S)-2-[[4-fluoranyl-1-[(3-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 H1R sing 152 n n O9 C8 H1R sing 153 n n C7 C8 H1R doub 154 n y C7 C6 H1R sing 155 n y C8 C3 H1R sing 156 n y O12 C11 H1R doub 157 n n C6 C11 H1R sing 158 n n C6 C5 H1R doub 159 n y C11 C13 H1R sing 160 n n C3 O2 H1R sing 161 n n C3 C4 H1R doub 162 n y O2 C1 H1R sing 163 n n C5 C4 H1R sing 164 n y C5 C30 H1R sing 165 n n C13 C14 H1R sing 166 n n C13 C30 H1R sing 167 n n C14 C15 H1R sing 168 n n F16 C15 H1R sing 169 n n C29 C15 H1R sing 170 n n C29 C28 H1R sing 171 n n C15 C17 H1R sing 172 n n C28 N19 H1R sing 173 n n C17 C18 H1R sing 174 n n N19 C18 H1R sing 175 n n N19 C20 H1R sing 176 n n C22 C23 H1R doub 177 n y C22 C21 H1R sing 178 n y C20 C21 H1R sing 179 n n C23 C24 H1R sing 180 n y C21 C27 H1R doub 181 n y C24 C25 H1R doub 182 n y C27 C25 H1R sing 183 n y C25 F26 H1R sing 184 n n C1 H1 H1R sing 185 n n C1 H2 H1R sing 186 n n C1 H3 H1R sing 187 n n C4 H4 H1R sing 188 n n C7 H5 H1R sing 189 n n C10 H6 H1R sing 190 n n C10 H7 H1R sing 191 n n C10 H8 H1R sing 192 n n C13 H9 H1R sing 193 n n C14 H10 H1R sing 194 n n C14 H11 H1R sing 195 n n C17 H12 H1R sing 196 n n C17 H13 H1R sing 197 n n C18 H14 H1R sing 198 n n C18 H15 H1R sing 199 n n C20 H16 H1R sing 200 n n C20 H17 H1R sing 201 n n C22 H18 H1R sing 202 n n C23 H19 H1R sing 203 n n C24 H20 H1R sing 204 n n C27 H21 H1R sing 205 n n C28 H22 H1R sing 206 n n C28 H23 H1R sing 207 n n C29 H24 H1R sing 208 n n C29 H25 H1R sing 209 n n C30 H26 H1R sing 210 n n C30 H27 H1R sing 211 n n # _atom_sites.entry_id 7D9Q _atom_sites.fract_transf_matrix[1][1] 0.009556 _atom_sites.fract_transf_matrix[1][2] 0.005517 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011034 _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] 0.003083 _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 H1R A 1 601 601 H1R 21 . F 3 H1R B 1 601 601 H1R 21 . G 4 HOH A 1 701 1 HOH HOH . G 4 HOH A 2 702 19 HOH HOH . G 4 HOH A 3 703 18 HOH HOH . G 4 HOH A 4 704 38 HOH HOH . G 4 HOH A 5 705 24 HOH HOH . G 4 HOH A 6 706 3 HOH HOH . G 4 HOH A 7 707 12 HOH HOH . G 4 HOH A 8 708 40 HOH HOH . G 4 HOH A 9 709 46 HOH HOH . G 4 HOH A 10 710 41 HOH HOH . G 4 HOH A 11 711 49 HOH HOH . G 4 HOH A 12 712 9 HOH HOH . G 4 HOH A 13 713 5 HOH HOH . G 4 HOH A 14 714 16 HOH HOH . G 4 HOH A 15 715 29 HOH HOH . G 4 HOH A 16 716 6 HOH HOH . G 4 HOH A 17 717 42 HOH HOH . G 4 HOH A 18 718 27 HOH HOH . G 4 HOH A 19 719 35 HOH HOH . G 4 HOH A 20 720 21 HOH HOH . G 4 HOH A 21 721 44 HOH HOH . H 4 HOH B 1 701 20 HOH HOH . H 4 HOH B 2 702 7 HOH HOH . H 4 HOH B 3 703 45 HOH HOH . H 4 HOH B 4 704 47 HOH HOH . H 4 HOH B 5 705 28 HOH HOH . H 4 HOH B 6 706 32 HOH HOH . H 4 HOH B 7 707 4 HOH HOH . H 4 HOH B 8 708 10 HOH HOH . H 4 HOH B 9 709 25 HOH HOH . H 4 HOH B 10 710 37 HOH HOH . H 4 HOH B 11 711 2 HOH HOH . H 4 HOH B 12 712 11 HOH HOH . H 4 HOH B 13 713 26 HOH HOH . H 4 HOH B 14 714 15 HOH HOH . H 4 HOH B 15 715 34 HOH HOH . H 4 HOH B 16 716 17 HOH HOH . H 4 HOH B 17 717 31 HOH HOH . H 4 HOH B 18 718 48 HOH HOH . H 4 HOH B 19 719 36 HOH HOH . H 4 HOH B 20 720 22 HOH HOH . H 4 HOH B 21 721 23 HOH HOH . H 4 HOH B 22 722 43 HOH HOH . H 4 HOH B 23 723 14 HOH HOH . H 4 HOH B 24 724 13 HOH HOH . H 4 HOH B 25 725 8 HOH HOH . H 4 HOH B 26 726 30 HOH HOH . H 4 HOH B 27 727 39 HOH HOH . H 4 HOH B 28 728 33 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 H1R . . . F 3 -36.346 37.597 -27.224 1 42.35 ? C1 H1R 601 B 1 HETATM 2 C C3 H1R . . . F 3 -37.123 36.651 -29.246 1 41.67 ? C3 H1R 601 B 1 HETATM 3 C C4 H1R . . . F 3 -38.368 37.23 -28.982 1 34.44 ? C4 H1R 601 B 1 HETATM 4 C C5 H1R . . . F 3 -39.426 36.972 -29.855 1 36.52 ? C5 H1R 601 B 1 HETATM 5 C C6 H1R . . . F 3 -39.272 36.131 -30.98 1 38.17 ? C6 H1R 601 B 1 HETATM 6 C C7 H1R . . . F 3 -38.023 35.547 -31.243 1 42.26 ? C7 H1R 601 B 1 HETATM 7 C C8 H1R . . . F 3 -36.963 35.802 -30.385 1 43.57 ? C8 H1R 601 B 1 HETATM 8 C C10 H1R . . . F 3 -35.779 34.528 -31.904 1 38.46 ? C10 H1R 601 B 1 HETATM 9 C C11 H1R . . . F 3 -40.594 36.055 -31.732 1 42.96 ? C11 H1R 601 B 1 HETATM 10 C C13 H1R . . . F 3 -41.657 36.707 -30.897 1 34.91 ? C13 H1R 601 B 1 HETATM 11 C C14 H1R . . . F 3 -42.36 37.769 -31.815 1 43.37 ? C14 H1R 601 B 1 HETATM 12 C C15 H1R . . . F 3 -43.85 38.007 -31.405 1 46.25 ? C15 H1R 601 B 1 HETATM 13 C C17 H1R . . . F 3 -43.896 38.657 -30.106 1 47.9 ? C17 H1R 601 B 1 HETATM 14 C C18 H1R . . . F 3 -45.073 39.577 -29.779 1 48.99 ? C18 H1R 601 B 1 HETATM 15 C C20 H1R . . . F 3 -47.073 40.171 -30.432 1 63.4 ? C20 H1R 601 B 1 HETATM 16 C C21 H1R . . . F 3 -48.443 39.438 -30.318 1 61.66 ? C21 H1R 601 B 1 HETATM 17 C C22 H1R . . . F 3 -49.29 39.317 -31.426 1 49.36 ? C22 H1R 601 B 1 HETATM 18 C C23 H1R . . . F 3 -50.512 38.641 -31.323 1 43.96 ? C23 H1R 601 B 1 HETATM 19 C C24 H1R . . . F 3 -50.887 38.085 -30.107 1 50.7 ? C24 H1R 601 B 1 HETATM 20 C C25 H1R . . . F 3 -50.03 38.205 -29.001 1 48.89 ? C25 H1R 601 B 1 HETATM 21 C C27 H1R . . . F 3 -48.823 38.873 -29.088 1 41.15 ? C27 H1R 601 B 1 HETATM 22 C C28 H1R . . . F 3 -45.718 39.542 -32.082 1 49.86 ? C28 H1R 601 B 1 HETATM 23 C C29 H1R . . . F 3 -44.539 38.675 -32.511 1 50.62 ? C29 H1R 601 B 1 HETATM 24 C C30 H1R . . . F 3 -40.905 37.465 -29.815 1 35.43 ? C30 H1R 601 B 1 HETATM 25 F F16 H1R . . . F 3 -44.492 36.729 -31.318 1 42.41 ? F16 H1R 601 B 1 HETATM 26 F F26 H1R . . . F 3 -50.382 37.656 -27.8 1 60.24 ? F26 H1R 601 B 1 HETATM 27 N N19 H1R . . . F 3 -46.164 39.396 -30.712 1 62.89 ? N19 H1R 601 B 1 HETATM 28 O O2 H1R . . . F 3 -36.031 36.88 -28.392 1 44.6 ? O2 H1R 601 B 1 HETATM 29 O O9 H1R . . . F 3 -35.709 35.201 -30.657 1 40.08 ? O9 H1R 601 B 1 HETATM 30 O O12 H1R . . . F 3 -40.723 35.596 -32.82 1 39.78 ? O12 H1R 601 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 30 #