data_7LDE # _model_server_result.job_id cxatVz4e-1OeS6LobQFZOg _model_server_result.datetime_utc '2025-07-31 09:32:58' _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 7lde # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LB","auth_seq_id":504}' # _entry.id 7LDE # _exptl.entry_id 7LDE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 328.674 _entity.id 18 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetradecameric _pdbx_struct_assembly.oligomeric_count 14 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB _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 ? _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 ? 18 FB N N ? 18 LB N N # _pdbx_entity_branch.entity_id 8 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 8 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 8 n O NAG 1 O 1 NAG A 1003 NAG 8 n O NAG 2 O 2 NAG A 1004 NAG 8 n P NAG 1 P 1 NAG A 1005 NAG 8 n P NAG 2 P 2 NAG A 1006 NAG 8 n Q NAG 1 Q 1 NAG B 1003 NAG 8 n Q NAG 2 Q 2 NAG B 1004 NAG 8 n R NAG 1 R 1 NAG C 1003 NAG 8 n R NAG 2 R 2 NAG C 1004 NAG 8 n S NAG 1 S 1 NAG D 1003 NAG 8 n S NAG 2 S 2 NAG D 1004 NAG # 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 75 A CYS 57 1_555 A SG CYS 323 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 732 A CYS 714 1_555 A SG CYS 787 A CYS 769 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 78 B CYS 57 1_555 B SG CYS 330 B CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 739 B CYS 718 1_555 B SG CYS 794 B CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 75 C CYS 57 1_555 C SG CYS 323 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 C SG CYS 732 C CYS 714 1_555 C SG CYS 787 C CYS 769 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 D SG CYS 78 D CYS 57 1_555 D SG CYS 330 D CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 D SG CYS 739 D CYS 718 1_555 D SG CYS 794 D CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 G SG CYS 90 G CYS 90 1_555 G SG CYS 100 G CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf10 H SG CYS 90 H CYS 90 1_555 H SG CYS 100 H CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A ND2 ASN 63 A ASN 45 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 249 A ASN 231 1_555 Y C1 NAG . A NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 257 A ASN 239 1_555 Z C1 NAG . A NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 363 A ASN 345 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 B ND2 ASN 256 B ASN 235 1_555 Q C1 NAG . Q NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 B ND2 ASN 370 B ASN 349 1_555 CA C1 NAG . B NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 C ND2 ASN 63 C ASN 45 1_555 R C1 NAG . R NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 C ND2 ASN 249 C ASN 231 1_555 NA C1 NAG . C NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 C ND2 ASN 257 C ASN 239 1_555 OA C1 NAG . C NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale10 C ND2 ASN 363 C ASN 345 1_555 PA C1 NAG . C NAG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 D ND2 ASN 256 D ASN 235 1_555 S C1 NAG . S NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 D ND2 ASN 370 D ASN 349 1_555 XA C1 NAG . D NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale13 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale14 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale15 Q O4 NAG . Q NAG 1 1_555 Q C1 NAG . Q NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale16 R O4 NAG . R NAG 1 1_555 R C1 NAG . R NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale17 S O4 NAG . S NAG 1 1_555 S C1 NAG . S NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? # _chem_comp.formula 'C14 H8 Cl F3 N2 O2' _chem_comp.formula_weight 328.674 _chem_comp.id XVD _chem_comp.mon_nstd_flag . _chem_comp.name 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol _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 N1 C10 XVD sing 639 n y N1 C13 XVD doub 640 n y C11 C10 XVD doub 641 n y C11 C12 XVD sing 642 n y CL1 C1 XVD sing 643 n n O1 C13 XVD sing 644 n n C10 C9 XVD sing 645 n y C13 N2 XVD sing 646 n y C12 C7 XVD doub 647 n y C9 N2 XVD sing 648 n y C9 C8 XVD doub 649 n y C7 C8 XVD sing 650 n y C7 C6 XVD sing 651 n n C1 C6 XVD doub 652 n y C1 C2 XVD sing 653 n y C6 C5 XVD sing 654 n y C2 C3 XVD doub 655 n y F3 C14 XVD sing 656 n n C5 O2 XVD sing 657 n n C5 C4 XVD doub 658 n y C3 C4 XVD sing 659 n y C14 F2 XVD sing 660 n n C14 O2 XVD sing 661 n n C14 F1 XVD sing 662 n n C4 H2 XVD sing 663 n n C8 H3 XVD sing 664 n n C11 H4 XVD sing 665 n n C12 H5 XVD sing 666 n n C2 H6 XVD sing 667 n n C3 H7 XVD sing 668 n n N2 H8 XVD sing 669 n n O1 H1 XVD sing 670 n n # _atom_sites.entry_id 7LDE _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 T 9 ZK1 A 1 901 901 ZK1 ZK1 . U 10 R16 A 1 902 902 R16 R16 . V 11 OCT A 1 903 903 OCT OCT . W 12 HP6 A 1 904 905 HP6 HP6 . X 13 D10 A 1 905 907 D10 D10 . Y 14 NAG A 1 906 1002 NAG NAG . Z 14 NAG A 1 907 1007 NAG NAG . AA 12 HP6 A 1 908 503 HP6 HP6 . BA 9 ZK1 B 1 901 901 ZK1 ZK1 . CA 14 NAG B 1 902 1002 NAG NAG . DA 15 D12 B 1 903 904 D12 C14 . EA 16 C14 B 1 904 904 C14 C14 . FA 17 DD9 B 1 905 905 DD9 DD9 . GA 11 OCT B 1 906 906 OCT OCT . HA 17 DD9 B 1 907 907 DD9 DD9 . IA 9 ZK1 C 1 901 901 ZK1 ZK1 . JA 10 R16 C 1 902 902 R16 R16 . KA 11 OCT C 1 903 903 OCT OCT . LA 12 HP6 C 1 904 905 HP6 HP6 . MA 13 D10 C 1 905 907 D10 D10 . NA 14 NAG C 1 906 1002 NAG NAG . OA 14 NAG C 1 907 1005 NAG NAG . PA 14 NAG C 1 908 1006 NAG NAG . QA 12 HP6 C 1 909 503 HP6 HP6 . RA 15 D12 D 1 901 904 D12 C14 . SA 16 C14 D 1 902 904 C14 C14 . TA 17 DD9 D 1 903 905 DD9 DD9 . UA 11 OCT D 1 904 906 OCT OCT . VA 17 DD9 D 1 905 907 DD9 DD9 . WA 9 ZK1 D 1 906 901 ZK1 ZK1 . XA 14 NAG D 1 907 1002 NAG NAG . YA 13 D10 E 1 201 908 D10 D10 . ZA 16 C14 E 1 202 502 C14 C14 . AB 13 D10 F 1 201 908 D10 D10 . BB 16 C14 F 1 202 502 C14 C14 . CB 13 D10 G 1 501 906 D10 D10 . DB 15 D12 G 1 502 902 D12 D12 . EB 15 D12 G 1 503 903 D12 D12 . FB 18 XVD G 1 504 501 XVD LIG . GB 11 OCT G 1 505 504 OCT OCT . HB 16 C14 G 1 506 505 C14 C14 . IB 15 D12 H 1 501 902 D12 D12 . JB 15 D12 H 1 502 903 D12 D12 . KB 13 D10 H 1 503 906 D10 D10 . LB 18 XVD H 1 504 501 XVD LIG . MB 11 OCT H 1 505 504 OCT OCT . NB 16 C14 H 1 506 505 C14 C14 . # 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 N N1 XVD . . . LB 18 226.892 245.479 196.145 1 85.2 ? N1 XVD 504 H 1 HETATM 2 C C4 XVD . . . LB 18 233.55 242.964 199.584 1 85.2 ? C4 XVD 504 H 1 HETATM 3 C C5 XVD . . . LB 18 232.446 243.596 199.051 1 85.2 ? C5 XVD 504 H 1 HETATM 4 C C6 XVD . . . LB 18 231.644 242.921 198.107 1 85.2 ? C6 XVD 504 H 1 HETATM 5 C C7 XVD . . . LB 18 230.392 243.637 197.506 1 85.2 ? C7 XVD 504 H 1 HETATM 6 C C8 XVD . . . LB 18 229.202 243.647 198.198 1 85.2 ? C8 XVD 504 H 1 HETATM 7 C C10 XVD . . . LB 18 228.122 244.955 196.395 1 85.2 ? C10 XVD 504 H 1 HETATM 8 C C13 XVD . . . LB 18 226.085 245.192 197.164 1 85.2 ? C13 XVD 504 H 1 HETATM 9 C C1 XVD . . . LB 18 231.978 241.601 197.707 1 85.2 ? C1 XVD 504 H 1 HETATM 10 C C11 XVD . . . LB 18 229.339 244.948 195.684 1 85.2 ? C11 XVD 504 H 1 HETATM 11 C C12 XVD . . . LB 18 230.484 244.287 196.239 1 85.2 ? C12 XVD 504 H 1 HETATM 12 C C14 XVD . . . LB 18 233.171 245.857 199.655 1 85.2 ? C14 XVD 504 H 1 HETATM 13 C C2 XVD . . . LB 18 233.082 240.977 198.241 1 85.2 ? C2 XVD 504 H 1 HETATM 14 C C3 XVD . . . LB 18 233.882 241.65 199.185 1 85.2 ? C3 XVD 504 H 1 HETATM 15 C C9 XVD . . . LB 18 228.039 244.316 197.64 1 85.2 ? C9 XVD 504 H 1 HETATM 16 F F1 XVD . . . LB 18 233.81 245.594 200.864 1 85.2 ? F1 XVD 504 H 1 HETATM 17 F F2 XVD . . . LB 18 232.675 247.11 199.694 1 85.2 ? F2 XVD 504 H 1 HETATM 18 F F3 XVD . . . LB 18 234.071 245.772 198.616 1 85.2 ? F3 XVD 504 H 1 HETATM 19 N N2 XVD . . . LB 18 226.78 244.484 198.073 1 85.2 ? N2 XVD 504 H 1 HETATM 20 O O1 XVD . . . LB 18 224.681 245.579 197.275 1 85.2 ? O1 XVD 504 H 1 HETATM 21 O O2 XVD . . . LB 18 232.089 244.926 199.44 1 85.2 ? O2 XVD 504 H 1 HETATM 22 CL CL1 XVD . . . LB 18 230.961 240.729 196.498 1 85.2 ? CL1 XVD 504 H 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 399 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #