data_4PD4
#
_model_server_result.job_id            9EZvEyFd20v1hZDoT18qaQ 
_model_server_result.datetime_utc      '2025-02-28 13:30:27' 
_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          4pd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":4003}' 
#
_entry.id    4PD4 
#
_exptl.entry_id    4PD4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              366.837 
_entity.id                          15 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          115.18 
_cell.angle_gamma         90 
_cell.entry_id            4PD4 
_cell.length_a            212.26 
_cell.length_b            150.88 
_cell.length_c            143.09 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PD4 
_symmetry.cell_setting             . 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    22-meric 
_pdbx_struct_assembly.oligomeric_count      22 
_pdbx_struct_assembly.details               author_and_software_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 2_756 -x+2,y,-z+1 -1 0 0 0 1 0 0 0 -1 363.640439 0 129.492962 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      15 
_struct_asym.id                             P 
_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
disulf ? disulf1 E SG CYS 134 E CYS 164 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
disulf ? disulf2 F SG CYS 28 F CYS 101 1_555 F SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf3 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf4 K SG CYS 23 K CYS 23 1_555 K SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc1 C NE2 HIS 82 C HIS 82 1_555 N FE HEM . C HEM 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? 
metalc ? metalc2 C NE2 HIS 96 C HIS 96 1_555 O FE HEM . C HEM 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 N FE HEM . C HEM 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 O FE HEM . C HEM 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 T FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc6 D SD MET 164 D MET 225 1_555 T FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc7 E SG CYS 129 E CYS 159 1_555 U FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc8 E ND1 HIS 131 E HIS 161 1_555 U FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc9 E SG CYS 148 E CYS 178 1_555 U FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc10 E ND1 HIS 151 E HIS 181 1_555 U FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? 
#
_chem_comp.formula           'C22 H19 Cl O3' 
_chem_comp.formula_weight    366.837 
_chem_comp.id                AOQ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Atovaquone 
#
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
C7 C8 AOQ doub 269 n y 
C7 C6 AOQ sing 270 n y 
C8 C9 AOQ sing 271 n y 
O1 C1 AOQ doub 272 n n 
C6 C5 AOQ doub 273 n y 
C9 C1 AOQ sing 274 n n 
C9 C10 AOQ doub 275 n y 
C1 C2 AOQ sing 276 n n 
C11 C12 AOQ sing 277 n n 
C11 C16 AOQ sing 278 n n 
C12 C13 AOQ sing 279 n n 
C5 C10 AOQ sing 280 n y 
C18 C19 AOQ doub 281 n y 
C18 C17 AOQ sing 282 n y 
C13 C17 AOQ sing 283 n n 
C13 C14 AOQ sing 284 n n 
C10 C4 AOQ sing 285 n n 
C19 C20 AOQ sing 286 n y 
C17 C22 AOQ doub 287 n y 
C20 C21 AOQ doub 288 n y 
C20 CL AOQ sing 289 n n 
C2 C16 AOQ sing 290 n n 
C2 C3 AOQ doub 291 n n 
C22 C21 AOQ sing 292 n y 
C16 C15 AOQ sing 293 n n 
C15 C14 AOQ sing 294 n n 
C4 C3 AOQ sing 295 n n 
C4 O2 AOQ doub 296 n n 
C3 O6 AOQ sing 297 n n 
C5 H1 AOQ sing 298 n n 
C6 H2 AOQ sing 299 n n 
C7 H3 AOQ sing 300 n n 
C8 H4 AOQ sing 301 n n 
O6 H5 AOQ sing 302 n n 
C11 H6 AOQ sing 303 n n 
C11 H7 AOQ sing 304 n n 
C12 H8 AOQ sing 305 n n 
C12 H9 AOQ sing 306 n n 
C13 H10 AOQ sing 307 n n 
C14 H11 AOQ sing 308 n n 
C14 H12 AOQ sing 309 n n 
C15 H13 AOQ sing 310 n n 
C15 H14 AOQ sing 311 n n 
C16 H15 AOQ sing 312 n n 
C18 H16 AOQ sing 313 n n 
C19 H17 AOQ sing 314 n n 
C21 H18 AOQ sing 315 n n 
C22 H19 AOQ sing 316 n n 
#
_atom_sites.entry_id                     4PD4 
_atom_sites.fract_transf_matrix[1][1]    0.004711 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002215 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006628 
_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]    0.007722 
_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
L 12 UMQ A 1 501 721 UMQ UMQ . 
M 13 3PH A 1 502 713 3PH 3PH . 
N 14 HEM C 1 4001 4001 HEM HEM . 
O 14 HEM C 1 4002 4002 HEM HEM . 
P 15 AOQ C 1 4003 1 AOQ AOQ . 
Q 16 3PE C 1 4004 711 3PE 3PE . 
R 17 UQ6 C 1 4005 506 UQ6 UQ6 . 
S 13 3PH C 1 4006 710 3PH 3PH . 
T 14 HEM D 1 401 4003 HEM HEM . 
U 18 FES E 1 301 4004 FES FES . 
V 13 3PH E 1 302 714 3PH 3PH . 
#
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 AOQ . . . P 15 199.993 -27.813 79.126 1 15.22 ? O1 AOQ 4003 C 1 
HETATM 2 O O2 AOQ . . . P 15 200.516 -30.794 83.463 1 13.45 ? O2 AOQ 4003 C 1 
HETATM 3 C C1 AOQ . . . P 15 200.121 -28.488 80.194 1 13.96 ? C1 AOQ 4003 C 1 
HETATM 4 C C2 AOQ . . . P 15 200.135 -27.926 81.484 1 12.19 ? C2 AOQ 4003 C 1 
HETATM 5 C C3 AOQ . . . P 15 200.256 -28.739 82.603 1 11.84 ? C3 AOQ 4003 C 1 
HETATM 6 C C4 AOQ . . . P 15 200.389 -30.093 82.442 1 13.21 ? C4 AOQ 4003 C 1 
HETATM 7 C C5 AOQ . . . P 15 200.502 -32.054 81.008 1 17.67 ? C5 AOQ 4003 C 1 
HETATM 8 C C6 AOQ . . . P 15 200.504 -32.629 79.745 1 13.17 ? C6 AOQ 4003 C 1 
HETATM 9 C C7 AOQ . . . P 15 200.374 -31.796 78.65 1 12.17 ? C7 AOQ 4003 C 1 
HETATM 10 C C8 AOQ . . . P 15 200.251 -30.427 78.802 1 10.55 ? C8 AOQ 4003 C 1 
HETATM 11 C C9 AOQ . . . P 15 200.254 -29.864 80.059 1 11.38 ? C9 AOQ 4003 C 1 
HETATM 12 C C10 AOQ . . . P 15 200.379 -30.668 81.172 1 15.21 ? C10 AOQ 4003 C 1 
HETATM 13 O O6 AOQ . . . P 15 200.263 -28.217 83.875 1 10.47 ? O6 AOQ 4003 C 1 
HETATM 14 C C11 AOQ . . . P 15 200.575 -25.531 80.742 1 8.72 ? C11 AOQ 4003 C 1 
HETATM 15 C C12 AOQ . . . P 15 200.109 -24.114 81.004 1 10.13 ? C12 AOQ 4003 C 1 
HETATM 16 C C13 AOQ . . . P 15 198.588 -24.088 81.125 1 12.2 ? C13 AOQ 4003 C 1 
HETATM 17 C C14 AOQ . . . P 15 198.203 -24.843 82.381 1 7.94 ? C14 AOQ 4003 C 1 
HETATM 18 C C15 AOQ . . . P 15 198.505 -26.289 82.078 1 7.98 ? C15 AOQ 4003 C 1 
HETATM 19 C C16 AOQ . . . P 15 199.986 -26.483 81.789 1 9.49 ? C16 AOQ 4003 C 1 
HETATM 20 CL CL AOQ . . . P 15 196.289 -18.577 81.615 1 22.04 ? CL AOQ 4003 C 1 
HETATM 21 C C17 AOQ . . . P 15 198.078 -22.715 81.24 1 10.41 ? C17 AOQ 4003 C 1 
HETATM 22 C C18 AOQ . . . P 15 198.923 -21.624 81.09 1 10.06 ? C18 AOQ 4003 C 1 
HETATM 23 C C19 AOQ . . . P 15 198.377 -20.353 81.21 1 13.67 ? C19 AOQ 4003 C 1 
HETATM 24 C C20 AOQ . . . P 15 197.008 -20.203 81.46 1 16.11 ? C20 AOQ 4003 C 1 
HETATM 25 C C21 AOQ . . . P 15 196.169 -21.302 81.599 1 13.08 ? C21 AOQ 4003 C 1 
HETATM 26 C C22 AOQ . . . P 15 196.72 -22.57 81.488 1 12.68 ? C22 AOQ 4003 C 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           26 
#