data_5GN9
#
_model_server_result.job_id            LTrav5vGnpk7Hv53Io0nwg 
_model_server_result.datetime_utc      '2025-01-19 03:28:13' 
_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          5gn9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":503}' 
#
_entry.id    5GN9 
#
_exptl.entry_id    5GN9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              234.248 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-butyl-7,8-bis(oxidanyl)chromen-2-one 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          114.64 
_cell.angle_gamma         90 
_cell.entry_id            5GN9 
_cell.length_a            150.218 
_cell.length_b            221.812 
_cell.length_c            62.611 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GN9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,I,J 1 1 
C,K,L,M 2 1 
D,N,O,P 2 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_548 -x+1/2,y-1/2,-z+3 -1 0 0 0 1 0 0 0 -1 -3.201481 -110.906 170.729917 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 G N N 
? 3 J N N 
? 3 M N N 
? 3 P N 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
metalc ? metalc1 A OE1 GLU 123 A GLU 123 1_555 E FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc2 A OE2 GLU 123 A GLU 123 1_555 E FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc3 A OE1 GLU 162 A GLU 162 1_555 E FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc4 A OE2 GLU 162 A GLU 162 1_555 F FE FE . A FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc5 A OE1 GLU 213 A GLU 213 1_555 F FE FE . A FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? 
metalc ? metalc6 A OE2 GLU 213 A GLU 213 1_555 F FE FE . A FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc7 A OE1 GLU 266 A GLU 266 1_555 E FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.757 ? 
metalc ? metalc8 A OE2 GLU 266 A GLU 266 1_555 F FE FE . A FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc9 E FE FE . A FE 501 1_555 G OAD 6Y0 . A 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? 
metalc ? metalc10 E FE FE . A FE 501 1_555 G OAC 6Y0 . A 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc11 F FE FE . A FE 502 1_555 G OAC 6Y0 . A 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc12 B OE1 GLU 123 B GLU 123 1_555 H FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? 
metalc ? metalc13 B OE2 GLU 123 B GLU 123 1_555 H FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc14 B OE1 GLU 162 B GLU 162 1_555 H FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc15 B OE2 GLU 162 B GLU 162 1_555 I FE FE . B FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc16 B OE1 GLU 213 B GLU 213 1_555 I FE FE . B FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc17 B OE2 GLU 213 B GLU 213 1_555 I FE FE . B FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc18 B OE1 GLU 266 B GLU 266 1_555 H FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc19 B OE2 GLU 266 B GLU 266 1_555 I FE FE . B FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc20 H FE FE . B FE 501 1_555 J OAC 6Y0 . B 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc21 I FE FE . B FE 502 1_555 J OAC 6Y0 . B 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? 
metalc ? metalc22 C OE1 GLU 123 C GLU 123 1_555 K FE FE . C FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc23 C OE2 GLU 123 C GLU 123 1_555 K FE FE . C FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc24 C OE2 GLU 162 C GLU 162 1_555 L FE FE . C FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc25 C OE1 GLU 213 C GLU 213 1_555 L FE FE . C FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? 
metalc ? metalc26 C OE2 GLU 213 C GLU 213 1_555 L FE FE . C FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
metalc ? metalc27 C OE1 GLU 266 C GLU 266 1_555 K FE FE . C FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? 
metalc ? metalc28 C OE2 GLU 266 C GLU 266 1_555 L FE FE . C FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
metalc ? metalc29 K FE FE . C FE 501 1_555 M OAC 6Y0 . C 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc30 K FE FE . C FE 501 1_555 M OAD 6Y0 . C 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? 
metalc ? metalc31 L FE FE . C FE 502 1_555 M OAC 6Y0 . C 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc32 D OE1 GLU 123 D GLU 123 1_555 N FE FE . D FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? 
metalc ? metalc33 D OE2 GLU 123 D GLU 123 1_555 N FE FE . D FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc34 D OE1 GLU 162 D GLU 162 1_555 N FE FE . D FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? 
metalc ? metalc35 D OE2 GLU 162 D GLU 162 1_555 O FE FE . D FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc36 D OE1 GLU 213 D GLU 213 1_555 O FE FE . D FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc37 D OE2 GLU 213 D GLU 213 1_555 O FE FE . D FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc38 D OE1 GLU 266 D GLU 266 1_555 N FE FE . D FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? 
metalc ? metalc39 D OE2 GLU 266 D GLU 266 1_555 O FE FE . D FE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc40 N FE FE . D FE 501 1_555 P OAC 6Y0 . D 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc41 N FE FE . D FE 501 1_555 P OAD 6Y0 . D 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc42 O FE FE . D FE 502 1_555 P OAC 6Y0 . D 6Y0 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
#
_chem_comp.formula           'C13 H14 O4' 
_chem_comp.formula_weight    234.248 
_chem_comp.id                6Y0 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-butyl-7,8-bis(oxidanyl)chromen-2-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
OAC CAL 6Y0 sing 1 n n 
OAD CAN 6Y0 sing 2 n n 
CAL CAN 6Y0 doub 3 n y 
CAL CAE 6Y0 sing 4 n y 
CAN CAQ 6Y0 sing 5 n y 
CAE CAF 6Y0 doub 6 n y 
CAQ OAK 6Y0 sing 7 n n 
CAQ CAP 6Y0 doub 8 n y 
OAK CAO 6Y0 sing 9 n n 
CAF CAP 6Y0 sing 10 n y 
CAP CAM 6Y0 sing 11 n n 
CAO OAB 6Y0 doub 12 n n 
CAO CAG 6Y0 sing 13 n n 
CAG CAM 6Y0 doub 14 n n 
CAM CAJ 6Y0 sing 15 n n 
CAI CAJ 6Y0 sing 16 n n 
CAI CAH 6Y0 sing 17 n n 
CAA CAH 6Y0 sing 18 n n 
CAA H1 6Y0 sing 19 n n 
CAA H2 6Y0 sing 20 n n 
CAA H3 6Y0 sing 21 n n 
CAH H4 6Y0 sing 22 n n 
CAH H5 6Y0 sing 23 n n 
CAI H6 6Y0 sing 24 n n 
CAI H7 6Y0 sing 25 n n 
CAJ H8 6Y0 sing 26 n n 
CAJ H9 6Y0 sing 27 n n 
CAG H10 6Y0 sing 28 n n 
CAF H11 6Y0 sing 29 n n 
CAE H12 6Y0 sing 30 n n 
OAC H13 6Y0 sing 31 n n 
OAD H14 6Y0 sing 32 n n 
#
_atom_sites.entry_id                     5GN9 
_atom_sites.fract_transf_matrix[1][1]    0.006657 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003053 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004508 
_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]    0.017571 
_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 2 FE A 1 501 501 FE FE . 
F 2 FE A 1 502 502 FE FE . 
G 3 6Y0 A 1 503 604 6Y0 DRG . 
H 2 FE B 1 501 501 FE FE . 
I 2 FE B 1 502 502 FE FE . 
J 3 6Y0 B 1 503 604 6Y0 DRG . 
K 2 FE C 1 501 501 FE FE . 
L 2 FE C 1 502 502 FE FE . 
M 3 6Y0 C 1 503 604 6Y0 DRG . 
N 2 FE D 1 501 501 FE FE . 
O 2 FE D 1 502 502 FE FE . 
P 3 6Y0 D 1 503 604 6Y0 DRG . 
#
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 CAA 6Y0 . . . M 3 -3.768 -37.242 118.159 1 112.1 ? CAA 6Y0 503 C 1 
HETATM 2 C CAH 6Y0 . . . M 3 -2.924 -36.502 117.12 1 114.31 ? CAH 6Y0 503 C 1 
HETATM 3 C CAI 6Y0 . . . M 3 -1.503 -37.086 117.102 1 114.82 ? CAI 6Y0 503 C 1 
HETATM 4 C CAJ 6Y0 . . . M 3 -0.731 -36.613 115.853 1 118.26 ? CAJ 6Y0 503 C 1 
HETATM 5 C CAM 6Y0 . . . M 3 0.018 -37.667 115.271 1 116.76 ? CAM 6Y0 503 C 1 
HETATM 6 C CAG 6Y0 . . . M 3 1.377 -37.75 115.596 1 114.34 ? CAG 6Y0 503 C 1 
HETATM 7 C CAO 6Y0 . . . M 3 2.17 -38.768 115.056 1 116.71 ? CAO 6Y0 503 C 1 
HETATM 8 O OAB 6Y0 . . . M 3 3.351 -38.797 115.401 1 124.75 ? OAB 6Y0 503 C 1 
HETATM 9 O OAK 6Y0 . . . M 3 1.645 -39.688 114.172 1 103.8 ? OAK 6Y0 503 C 1 
HETATM 10 C CAQ 6Y0 . . . M 3 0.311 -39.642 113.846 1 97.5 ? CAQ 6Y0 503 C 1 
HETATM 11 C CAP 6Y0 . . . M 3 -0.526 -38.634 114.382 1 106.1 ? CAP 6Y0 503 C 1 
HETATM 12 C CAF 6Y0 . . . M 3 -1.889 -38.671 114.005 1 100.84 ? CAF 6Y0 503 C 1 
HETATM 13 C CAE 6Y0 . . . M 3 -2.388 -39.663 113.138 1 94.72 ? CAE 6Y0 503 C 1 
HETATM 14 C CAL 6Y0 . . . M 3 -1.529 -40.639 112.612 1 84.99 ? CAL 6Y0 503 C 1 
HETATM 15 O OAC 6Y0 . . . M 3 -1.954 -41.605 111.756 1 65.89 ? OAC 6Y0 503 C 1 
HETATM 16 C CAN 6Y0 . . . M 3 -0.179 -40.62 112.971 1 88.7 ? CAN 6Y0 503 C 1 
HETATM 17 O OAD 6Y0 . . . M 3 0.67 -41.568 112.474 1 85.73 ? OAD 6Y0 503 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           17 
#