data_4DER
#
_model_server_result.job_id            gg2xj5qLbJDdCvazORQPpQ 
_model_server_result.datetime_utc      '2024-11-22 09:00:33' 
_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          4der 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    4DER 
#
_exptl.entry_id    4DER 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              270.237 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-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         90 
_cell.entry_id            4DER 
_cell.length_a            43.152 
_cell.length_b            85.132 
_cell.length_c            64.458 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DER 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 43.152 85.132 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N N 
#
_chem_comp.formula           'C15 H10 O5' 
_chem_comp.formula_weight    270.237 
_chem_comp.id                AGI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Apigenin 
#
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
CAG CAE AGI doub 1 n y 
CAG CAP AGI sing 2 n y 
CAE CAM AGI sing 3 n y 
CAM OAB AGI sing 4 n n 
CAM CAF AGI doub 5 n y 
CAF CAH AGI sing 6 n y 
CAH CAP AGI doub 7 n y 
CAP CAQ AGI sing 8 n n 
CAQ OAL AGI sing 9 n n 
CAQ CAJ AGI doub 10 n n 
OAL CAS AGI sing 11 n n 
CAJ CAR AGI sing 12 n n 
CAR OAA AGI doub 13 n n 
CAR CAT AGI sing 14 n n 
CAT CAS AGI doub 15 n y 
CAT CAO AGI sing 16 n y 
CAS CAK AGI sing 17 n y 
CAK CAN AGI doub 18 n y 
CAN OAC AGI sing 19 n n 
CAN CAI AGI sing 20 n y 
CAI CAO AGI doub 21 n y 
CAO OAD AGI sing 22 n n 
CAG HAG AGI sing 23 n n 
CAE HAE AGI sing 24 n n 
OAB HOAB AGI sing 25 n n 
CAF HAF AGI sing 26 n n 
CAH HAH AGI sing 27 n n 
CAJ HAJ AGI sing 28 n n 
CAK HAK AGI sing 29 n n 
OAC HOAC AGI sing 30 n n 
CAI HAI AGI sing 31 n n 
OAD HOAD AGI sing 32 n n 
#
_atom_sites.entry_id                     4DER 
_atom_sites.fract_transf_matrix[1][1]    0.023174 
_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]    0.011746 
_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]    0.015514 
_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
C 2 AGI A 1 201 1 AGI AGI . 
D 3 GOL A 1 202 1 GOL GOL . 
E 2 AGI B 1 201 1 AGI AGI . 
F 4 HOH A 1 301 2 HOH HOH . 
F 4 HOH A 2 302 3 HOH HOH . 
F 4 HOH A 3 303 5 HOH HOH . 
F 4 HOH A 4 304 6 HOH HOH . 
F 4 HOH A 5 305 11 HOH HOH . 
F 4 HOH A 6 306 12 HOH HOH . 
F 4 HOH A 7 307 13 HOH HOH . 
F 4 HOH A 8 308 14 HOH HOH . 
F 4 HOH A 9 309 16 HOH HOH . 
F 4 HOH A 10 310 17 HOH HOH . 
F 4 HOH A 11 311 21 HOH HOH . 
F 4 HOH A 12 312 23 HOH HOH . 
F 4 HOH A 13 313 24 HOH HOH . 
F 4 HOH A 14 314 26 HOH HOH . 
F 4 HOH A 15 315 27 HOH HOH . 
F 4 HOH A 16 316 28 HOH HOH . 
F 4 HOH A 17 317 29 HOH HOH . 
F 4 HOH A 18 318 30 HOH HOH . 
F 4 HOH A 19 319 31 HOH HOH . 
F 4 HOH A 20 320 32 HOH HOH . 
F 4 HOH A 21 321 36 HOH HOH . 
F 4 HOH A 22 322 38 HOH HOH . 
F 4 HOH A 23 323 41 HOH HOH . 
F 4 HOH A 24 324 42 HOH HOH . 
F 4 HOH A 25 325 43 HOH HOH . 
F 4 HOH A 26 326 44 HOH HOH . 
F 4 HOH A 27 327 45 HOH HOH . 
F 4 HOH A 28 328 46 HOH HOH . 
F 4 HOH A 29 329 47 HOH HOH . 
F 4 HOH A 30 330 48 HOH HOH . 
F 4 HOH A 31 331 49 HOH HOH . 
F 4 HOH A 32 332 52 HOH HOH . 
F 4 HOH A 33 333 53 HOH HOH . 
F 4 HOH A 34 334 55 HOH HOH . 
F 4 HOH A 35 335 56 HOH HOH . 
F 4 HOH A 36 336 59 HOH HOH . 
F 4 HOH A 37 337 61 HOH HOH . 
F 4 HOH A 38 338 63 HOH HOH . 
F 4 HOH A 39 339 64 HOH HOH . 
F 4 HOH A 40 340 66 HOH HOH . 
F 4 HOH A 41 341 67 HOH HOH . 
F 4 HOH A 42 342 69 HOH HOH . 
F 4 HOH A 43 343 70 HOH HOH . 
F 4 HOH A 44 344 71 HOH HOH . 
F 4 HOH A 45 345 73 HOH HOH . 
F 4 HOH A 46 346 74 HOH HOH . 
F 4 HOH A 47 347 75 HOH HOH . 
F 4 HOH A 48 348 76 HOH HOH . 
F 4 HOH A 49 349 77 HOH HOH . 
F 4 HOH A 50 350 80 HOH HOH . 
F 4 HOH A 51 351 82 HOH HOH . 
F 4 HOH A 52 352 83 HOH HOH . 
F 4 HOH A 53 353 85 HOH HOH . 
F 4 HOH A 54 354 89 HOH HOH . 
F 4 HOH A 55 355 90 HOH HOH . 
F 4 HOH A 56 356 91 HOH HOH . 
F 4 HOH A 57 357 94 HOH HOH . 
F 4 HOH A 58 358 95 HOH HOH . 
F 4 HOH A 59 359 96 HOH HOH . 
F 4 HOH A 60 360 97 HOH HOH . 
F 4 HOH A 61 361 100 HOH HOH . 
F 4 HOH A 62 362 101 HOH HOH . 
F 4 HOH A 63 363 102 HOH HOH . 
F 4 HOH A 64 364 103 HOH HOH . 
F 4 HOH A 65 365 108 HOH HOH . 
F 4 HOH A 66 366 109 HOH HOH . 
F 4 HOH A 67 367 110 HOH HOH . 
F 4 HOH A 68 368 112 HOH HOH . 
F 4 HOH A 69 369 113 HOH HOH . 
F 4 HOH A 70 370 117 HOH HOH . 
F 4 HOH A 71 371 118 HOH HOH . 
F 4 HOH A 72 372 123 HOH HOH . 
F 4 HOH A 73 373 124 HOH HOH . 
F 4 HOH A 74 374 128 HOH HOH . 
F 4 HOH A 75 375 139 HOH HOH . 
F 4 HOH A 76 376 142 HOH HOH . 
F 4 HOH A 77 377 144 HOH HOH . 
F 4 HOH A 78 378 145 HOH HOH . 
F 4 HOH A 79 379 147 HOH HOH . 
F 4 HOH A 80 380 152 HOH HOH . 
F 4 HOH A 81 381 154 HOH HOH . 
G 4 HOH B 1 301 1 HOH HOH . 
G 4 HOH B 2 302 4 HOH HOH . 
G 4 HOH B 3 303 7 HOH HOH . 
G 4 HOH B 4 304 8 HOH HOH . 
G 4 HOH B 5 305 9 HOH HOH . 
G 4 HOH B 6 306 15 HOH HOH . 
G 4 HOH B 7 307 18 HOH HOH . 
G 4 HOH B 8 308 20 HOH HOH . 
G 4 HOH B 9 309 22 HOH HOH . 
G 4 HOH B 10 310 25 HOH HOH . 
G 4 HOH B 11 311 33 HOH HOH . 
G 4 HOH B 12 312 34 HOH HOH . 
G 4 HOH B 13 313 37 HOH HOH . 
G 4 HOH B 14 314 39 HOH HOH . 
G 4 HOH B 15 315 40 HOH HOH . 
G 4 HOH B 16 316 50 HOH HOH . 
G 4 HOH B 17 317 51 HOH HOH . 
G 4 HOH B 18 318 54 HOH HOH . 
G 4 HOH B 19 319 57 HOH HOH . 
G 4 HOH B 20 320 58 HOH HOH . 
G 4 HOH B 21 321 60 HOH HOH . 
G 4 HOH B 22 322 65 HOH HOH . 
G 4 HOH B 23 323 68 HOH HOH . 
G 4 HOH B 24 324 72 HOH HOH . 
G 4 HOH B 25 325 79 HOH HOH . 
G 4 HOH B 26 326 81 HOH HOH . 
G 4 HOH B 27 327 88 HOH HOH . 
G 4 HOH B 28 328 93 HOH HOH . 
G 4 HOH B 29 329 98 HOH HOH . 
G 4 HOH B 30 330 99 HOH HOH . 
G 4 HOH B 31 331 104 HOH HOH . 
G 4 HOH B 32 332 106 HOH HOH . 
G 4 HOH B 33 333 107 HOH HOH . 
G 4 HOH B 34 334 111 HOH HOH . 
G 4 HOH B 35 335 114 HOH HOH . 
G 4 HOH B 36 336 115 HOH HOH . 
G 4 HOH B 37 337 116 HOH HOH . 
G 4 HOH B 38 338 133 HOH HOH . 
G 4 HOH B 39 339 143 HOH HOH . 
G 4 HOH B 40 340 146 HOH HOH . 
G 4 HOH B 41 341 150 HOH HOH . 
G 4 HOH B 42 342 151 HOH HOH . 
G 4 HOH B 43 343 153 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 CAG AGI . . . C 2 21.333 43.748 40.284 0.35 45.72 ? CAG AGI 201 A 1 
HETATM 2 C CAE AGI . . . C 2 21.353 43.755 41.636 0.35 45.7 ? CAE AGI 201 A 1 
HETATM 3 C CAM AGI . . . C 2 21.566 42.564 42.296 0.35 45.8 ? CAM AGI 201 A 1 
HETATM 4 O OAB AGI . . . C 2 21.583 42.564 43.622 0.35 46.15 ? OAB AGI 201 A 1 
HETATM 5 C CAF AGI . . . C 2 21.763 41.371 41.638 0.35 45.7 ? CAF AGI 201 A 1 
HETATM 6 C CAH AGI . . . C 2 21.748 41.374 40.287 0.35 45.71 ? CAH AGI 201 A 1 
HETATM 7 C CAP AGI . . . C 2 21.535 42.559 39.612 0.35 45.63 ? CAP AGI 201 A 1 
HETATM 8 C CAQ AGI . . . C 2 21.514 42.533 38.255 0.35 45.52 ? CAQ AGI 201 A 1 
HETATM 9 O OAL AGI . . . C 2 22.504 43.128 37.566 0.35 45.83 ? OAL AGI 201 A 1 
HETATM 10 C CAJ AGI . . . C 2 20.475 41.878 37.631 0.35 45.92 ? CAJ AGI 201 A 1 
HETATM 11 C CAR AGI . . . C 2 20.437 41.781 36.274 0.35 45.73 ? CAR AGI 201 A 1 
HETATM 12 O OAA AGI . . . C 2 19.517 41.178 35.726 0.35 46.81 ? OAA AGI 201 A 1 
HETATM 13 C CAT AGI . . . C 2 21.416 42.424 35.57 0.35 45.62 ? CAT AGI 201 A 1 
HETATM 14 C CAS AGI . . . C 2 22.416 43.094 36.233 0.35 45.35 ? CAS AGI 201 A 1 
HETATM 15 C CAK AGI . . . C 2 23.389 43.761 35.538 0.35 45.56 ? CAK AGI 201 A 1 
HETATM 16 C CAN AGI . . . C 2 23.335 43.741 34.165 0.35 44.77 ? CAN AGI 201 A 1 
HETATM 17 O OAC AGI . . . C 2 24.298 44.376 33.514 0.35 44.7 ? OAC AGI 201 A 1 
HETATM 18 C CAI AGI . . . C 2 22.328 43.068 33.492 0.35 45.38 ? CAI AGI 201 A 1 
HETATM 19 C CAO AGI . . . C 2 21.364 42.41 34.205 0.35 45.42 ? CAO AGI 201 A 1 
HETATM 20 O OAD AGI . . . C 2 20.359 41.739 33.618 0.35 45.89 ? OAD AGI 201 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           20 
#