data_1D64 # _model_server_result.job_id kPE4WZ-MNNyP6l-W27PYkw _model_server_result.datetime_utc '2024-12-02 13:21:10' _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 1d64 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":25}' # _entry.id 1D64 # _exptl.entry_id 1D64 _exptl.method 'X-RAY DIFFRACTION' # _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 1 _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 1D64 _cell.length_a 24.37 _cell.length_b 40 _cell.length_c 66.07 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D64 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 x,y,z _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 5 A DA 5 1_555 B N3 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 5 A DA 5 1_555 B O4 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 DA 6 A DA 6 1_555 B N3 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 DA 6 A DA 6 1_555 B O4 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DT 7 A DT 7 1_555 B N1 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O4 DT 7 A DT 7 1_555 B N6 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DT 8 A DT 8 1_555 B N1 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O4 DT 8 A DT 8 1_555 B N6 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N1 DG 12 A DG 12 1_555 B N3 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N2 DG 12 A DG 12 1_555 B O2 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A O6 DG 12 A DG 12 1_555 B N4 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 152 n y C1 C6 PNT sing 153 n y C1 O1 PNT sing 154 n n C2 C3 PNT sing 155 n y C2 H2 PNT sing 156 n n C3 C4 PNT doub 157 n y C3 H3 PNT sing 158 n n C4 C5 PNT sing 159 n y C4 C9 PNT sing 160 n n C5 C6 PNT doub 161 n y C5 H5 PNT sing 162 n n C6 H6 PNT sing 163 n n C7 C8 PNT sing 164 n n C7 O1 PNT sing 165 n n C7 H71 PNT sing 166 n n C7 H72 PNT sing 167 n n C8 C10 PNT sing 168 n n C8 H81 PNT sing 169 n n C8 H82 PNT sing 170 n n C9 N1 PNT doub 171 n n C9 N2 PNT sing 172 n n C10 C8' PNT sing 173 n n C10 H101 PNT sing 174 n n C10 H102 PNT sing 175 n n C1' C2' PNT doub 176 n y C1' C6' PNT sing 177 n y C1' O1' PNT sing 178 n n C2' C3' PNT sing 179 n y C2' H2' PNT sing 180 n n C3' C4' PNT doub 181 n y C3' H3' PNT sing 182 n n C4' C5' PNT sing 183 n y C4' C9' PNT sing 184 n n C5' C6' PNT doub 185 n y C5' H5' PNT sing 186 n n C6' H6' PNT sing 187 n n C7' C8' PNT sing 188 n n C7' O1' PNT sing 189 n n C7' "H7'1" PNT sing 190 n n C7' "H7'2" PNT sing 191 n n C8' "H8'1" PNT sing 192 n n C8' "H8'2" PNT sing 193 n n C9' N1' PNT doub 194 n n C9' N2' PNT sing 195 n n N1 HN1 PNT sing 196 n n N2 HN2 PNT sing 197 n n N2 HN3 PNT sing 198 n n N1' "HN'1" PNT sing 199 n n N2' "HN'2" PNT sing 200 n n N2' "HN'3" PNT sing 201 n n # _atom_sites.entry_id 1D64 _atom_sites.fract_transf_matrix[1][1] 0.041034 _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] 0.025 _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] 0.015135 _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 PNT B 1 25 25 PNT PNT . D 3 HOH A 1 27 27 HOH HOH . D 3 HOH A 2 29 29 HOH HOH . D 3 HOH A 3 30 30 HOH HOH . D 3 HOH A 4 31 31 HOH HOH . D 3 HOH A 5 34 34 HOH HOH . D 3 HOH A 6 35 35 HOH HOH . D 3 HOH A 7 36 36 HOH HOH . D 3 HOH A 8 39 39 HOH HOH . D 3 HOH A 9 40 40 HOH HOH . D 3 HOH A 10 44 44 HOH HOH . D 3 HOH A 11 47 47 HOH HOH . D 3 HOH A 12 48 48 HOH HOH . D 3 HOH A 13 49 49 HOH HOH . D 3 HOH A 14 52 52 HOH HOH . D 3 HOH A 15 53 53 HOH HOH . D 3 HOH A 16 55 55 HOH HOH . D 3 HOH A 17 57 57 HOH HOH . D 3 HOH A 18 59 59 HOH HOH . D 3 HOH A 19 61 61 HOH HOH . D 3 HOH A 20 63 63 HOH HOH . D 3 HOH A 21 64 64 HOH HOH . D 3 HOH A 22 66 66 HOH HOH . D 3 HOH A 23 73 73 HOH HOH . D 3 HOH A 24 76 76 HOH HOH . D 3 HOH A 25 79 79 HOH HOH . D 3 HOH A 26 83 83 HOH HOH . D 3 HOH A 27 85 85 HOH HOH . D 3 HOH A 28 86 86 HOH HOH . D 3 HOH A 29 88 88 HOH HOH . D 3 HOH A 30 92 92 HOH HOH . D 3 HOH A 31 93 93 HOH HOH . D 3 HOH A 32 94 94 HOH HOH . D 3 HOH A 33 96 96 HOH HOH . D 3 HOH A 34 97 97 HOH HOH . D 3 HOH A 35 98 98 HOH HOH . D 3 HOH A 36 100 100 HOH HOH . D 3 HOH A 37 102 102 HOH HOH . E 3 HOH B 1 26 26 HOH HOH . E 3 HOH B 2 28 28 HOH HOH . E 3 HOH B 3 32 32 HOH HOH . E 3 HOH B 4 33 33 HOH HOH . E 3 HOH B 5 37 37 HOH HOH . E 3 HOH B 6 38 38 HOH HOH . E 3 HOH B 7 41 41 HOH HOH . E 3 HOH B 8 42 42 HOH HOH . E 3 HOH B 9 43 43 HOH HOH . E 3 HOH B 10 45 45 HOH HOH . E 3 HOH B 11 46 46 HOH HOH . E 3 HOH B 12 50 50 HOH HOH . E 3 HOH B 13 51 51 HOH HOH . E 3 HOH B 14 54 54 HOH HOH . E 3 HOH B 15 56 56 HOH HOH . E 3 HOH B 16 58 58 HOH HOH . E 3 HOH B 17 60 60 HOH HOH . E 3 HOH B 18 62 62 HOH HOH . E 3 HOH B 19 65 65 HOH HOH . E 3 HOH B 20 67 67 HOH HOH . E 3 HOH B 21 68 68 HOH HOH . E 3 HOH B 22 69 69 HOH HOH . E 3 HOH B 23 70 70 HOH HOH . E 3 HOH B 24 71 71 HOH HOH . E 3 HOH B 25 72 72 HOH HOH . E 3 HOH B 26 74 74 HOH HOH . E 3 HOH B 27 75 75 HOH HOH . E 3 HOH B 28 77 77 HOH HOH . E 3 HOH B 29 78 78 HOH HOH . E 3 HOH B 30 80 80 HOH HOH . E 3 HOH B 31 81 81 HOH HOH . E 3 HOH B 32 82 82 HOH HOH . E 3 HOH B 33 84 84 HOH HOH . E 3 HOH B 34 87 87 HOH HOH . E 3 HOH B 35 89 89 HOH HOH . E 3 HOH B 36 90 90 HOH HOH . E 3 HOH B 37 91 91 HOH HOH . E 3 HOH B 38 95 95 HOH HOH . E 3 HOH B 39 99 99 HOH HOH . E 3 HOH B 40 101 101 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 C1 PNT . . . C 2 8.015 20.256 12.89 1 55.35 ? C1 PNT 25 B 1 HETATM 2 C C2 PNT . . . C 2 9.314 19.968 12.659 1 55.72 ? C2 PNT 25 B 1 HETATM 3 C C3 PNT . . . C 2 10.045 19.34 13.643 1 59.36 ? C3 PNT 25 B 1 HETATM 4 C C4 PNT . . . C 2 9.47 18.916 14.839 1 60.03 ? C4 PNT 25 B 1 HETATM 5 C C5 PNT . . . C 2 8.144 19.196 15.024 1 60.24 ? C5 PNT 25 B 1 HETATM 6 C C6 PNT . . . C 2 7.416 19.828 14.086 1 58.21 ? C6 PNT 25 B 1 HETATM 7 C C7 PNT . . . C 2 8.364 21.636 11.159 1 55.63 ? C7 PNT 25 B 1 HETATM 8 C C8 PNT . . . C 2 7.387 22.136 10.109 1 56.24 ? C8 PNT 25 B 1 HETATM 9 C C9 PNT . . . C 2 10.177 18.28 15.804 1 60.61 ? C9 PNT 25 B 1 HETATM 10 C C10 PNT . . . C 2 8.461 22.38 9.091 1 53.76 ? C10 PNT 25 B 1 HETATM 11 C C1' PNT . . . C 2 9.529 24.644 5.028 1 61.94 ? C1' PNT 25 B 1 HETATM 12 C C2' PNT . . . C 2 10.557 23.8 4.883 1 63.41 ? C2' PNT 25 B 1 HETATM 13 C C3' PNT . . . C 2 11.412 23.992 3.832 1 67.16 ? C3' PNT 25 B 1 HETATM 14 C C4' PNT . . . C 2 11.252 25.036 2.927 1 63.17 ? C4' PNT 25 B 1 HETATM 15 C C5' PNT . . . C 2 10.223 25.88 3.092 1 65.16 ? C5' PNT 25 B 1 HETATM 16 C C6' PNT . . . C 2 9.346 25.688 4.136 1 64.7 ? C6' PNT 25 B 1 HETATM 17 C C7' PNT . . . C 2 9.192 23.54 6.997 1 58.43 ? C7' PNT 25 B 1 HETATM 18 C C8' PNT . . . C 2 8.093 23.404 8.061 1 56.7 ? C8' PNT 25 B 1 HETATM 19 C C9' PNT . . . C 2 12.117 25.232 1.909 1 63.65 ? C9' PNT 25 B 1 HETATM 20 O O1 PNT . . . C 2 7.362 20.928 11.992 1 56.54 ? O1 PNT 25 B 1 HETATM 21 O O1' PNT . . . C 2 8.683 24.468 5.993 1 63.11 ? O1' PNT 25 B 1 HETATM 22 N N1 PNT . . . C 2 11.515 18.168 15.665 1 54.11 ? N1 PNT 25 B 1 HETATM 23 N N2 PNT . . . C 2 9.577 17.848 16.967 1 61 ? N2 PNT 25 B 1 HETATM 24 N N1' PNT . . . C 2 13.228 24.464 1.83 1 67.47 ? N1' PNT 25 B 1 HETATM 25 N N2' PNT . . . C 2 11.893 26.224 0.971 1 65.48 ? N2' PNT 25 B 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 25 #