data_8JY8
#
_model_server_result.job_id            iteSdY5YKHqKiYgizb076g 
_model_server_result.datetime_utc      '2024-12-26 10:13:43' 
_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          8jy8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    8JY8 
#
_exptl.entry_id    8JY8 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              340.419 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,5-BIS(4-AMIDINOPHENOXY)PENTANE 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            8JY8 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8JY8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C19 H24 N4 O2' 
_chem_comp.formula_weight    340.419 
_chem_comp.id                PNT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,5-BIS(4-AMIDINOPHENOXY)PENTANE 
_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
C1 C2 PNT doub 258 n y 
C1 C6 PNT sing 259 n y 
C1 O1 PNT sing 260 n n 
C2 C3 PNT sing 261 n y 
C2 H2 PNT sing 262 n n 
C3 C4 PNT doub 263 n y 
C3 H3 PNT sing 264 n n 
C4 C5 PNT sing 265 n y 
C4 C9 PNT sing 266 n n 
C5 C6 PNT doub 267 n y 
C5 H5 PNT sing 268 n n 
C6 H6 PNT sing 269 n n 
C7 C8 PNT sing 270 n n 
C7 O1 PNT sing 271 n n 
C7 H71 PNT sing 272 n n 
C7 H72 PNT sing 273 n n 
C8 C10 PNT sing 274 n n 
C8 H81 PNT sing 275 n n 
C8 H82 PNT sing 276 n n 
C9 N1 PNT doub 277 n n 
C9 N2 PNT sing 278 n n 
C10 C8' PNT sing 279 n n 
C10 H101 PNT sing 280 n n 
C10 H102 PNT sing 281 n n 
C1' C2' PNT doub 282 n y 
C1' C6' PNT sing 283 n y 
C1' O1' PNT sing 284 n n 
C2' C3' PNT sing 285 n y 
C2' H2' PNT sing 286 n n 
C3' C4' PNT doub 287 n y 
C3' H3' PNT sing 288 n n 
C4' C5' PNT sing 289 n y 
C4' C9' PNT sing 290 n n 
C5' C6' PNT doub 291 n y 
C5' H5' PNT sing 292 n n 
C6' H6' PNT sing 293 n n 
C7' C8' PNT sing 294 n n 
C7' O1' PNT sing 295 n n 
C7' "H7'1" PNT sing 296 n n 
C7' "H7'2" PNT sing 297 n n 
C8' "H8'1" PNT sing 298 n n 
C8' "H8'2" PNT sing 299 n n 
C9' N1' PNT doub 300 n n 
C9' N2' PNT sing 301 n n 
N1 HN1 PNT sing 302 n n 
N2 HN2 PNT sing 303 n n 
N2 HN3 PNT sing 304 n n 
N1' "HN'1" PNT sing 305 n n 
N2' "HN'2" PNT sing 306 n n 
N2' "HN'3" PNT sing 307 n n 
#
_atom_sites.entry_id                     8JY8 
_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
E 2 PNT A 1 401 1 PNT PNT . 
F 2 PNT B 1 401 1 PNT PNT . 
G 2 PNT C 1 401 1 PNT PNT . 
H 2 PNT D 1 401 1 PNT PNT . 
#
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 PNT . . . F 2 117.404 137.964 121.793 1 30.17 ? C1 PNT 401 B 1 
HETATM 2 C C2 PNT . . . F 2 117.655 136.864 120.963 1 30.17 ? C2 PNT 401 B 1 
HETATM 3 C C3 PNT . . . F 2 117.418 136.945 119.59 1 30.17 ? C3 PNT 401 B 1 
HETATM 4 C C4 PNT . . . F 2 116.933 138.112 119.011 1 30.17 ? C4 PNT 401 B 1 
HETATM 5 C C5 PNT . . . F 2 116.684 139.204 119.834 1 30.17 ? C5 PNT 401 B 1 
HETATM 6 C C6 PNT . . . F 2 116.917 139.134 121.206 1 30.17 ? C6 PNT 401 B 1 
HETATM 7 C C7 PNT . . . F 2 116.944 138.831 124.009 1 30.17 ? C7 PNT 401 B 1 
HETATM 8 C C8 PNT . . . F 2 117.449 138.674 125.475 1 30.17 ? C8 PNT 401 B 1 
HETATM 9 C C9 PNT . . . F 2 116.683 138.192 117.549 1 30.17 ? C9 PNT 401 B 1 
HETATM 10 C C10 PNT . . . F 2 118.177 137.321 125.77 1 30.17 ? C10 PNT 401 B 1 
HETATM 11 C C1' PNT . . . F 2 117.355 137.184 130.502 1 30.17 ? C1' PNT 401 B 1 
HETATM 12 C C2' PNT . . . F 2 117.836 135.894 130.755 1 30.17 ? C2' PNT 401 B 1 
HETATM 13 C C3' PNT . . . F 2 118.101 135.465 132.058 1 30.17 ? C3' PNT 401 B 1 
HETATM 14 C C4' PNT . . . F 2 117.9 136.303 133.15 1 30.17 ? C4' PNT 401 B 1 
HETATM 15 C C5' PNT . . . F 2 117.425 137.583 132.9 1 30.17 ? C5' PNT 401 B 1 
HETATM 16 C C6' PNT . . . F 2 117.155 138.024 131.601 1 30.17 ? C6' PNT 401 B 1 
HETATM 17 C C7' PNT . . . F 2 117.225 136.635 128.14 1 30.17 ? C7' PNT 401 B 1 
HETATM 18 C C8' PNT . . . F 2 118.474 136.967 127.257 1 30.17 ? C8' PNT 401 B 1 
HETATM 19 C C9' PNT . . . F 2 118.184 135.841 134.541 1 30.17 ? C9' PNT 401 B 1 
HETATM 20 O O1 PNT . . . F 2 117.629 137.914 123.155 1 30.17 ? O1 PNT 401 B 1 
HETATM 21 O O1' PNT . . . F 2 117.1 137.583 129.202 1 30.17 ? O1' PNT 401 B 1 
HETATM 22 N N1 PNT . . . F 2 117.23 139.256 116.843 1 30.17 ? N1 PNT 401 B 1 
HETATM 23 N N2 PNT . . . F 2 115.988 137.356 116.817 1 30.17 ? N2 PNT 401 B 1 
HETATM 24 N N1' PNT . . . F 2 118.745 134.687 134.731 1 30.17 ? N1' PNT 401 B 1 
HETATM 25 N N2' PNT . . . F 2 117.813 136.708 135.569 1 30.17 ? N2' PNT 401 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           25 
#