data_1FD5 # _model_server_result.job_id cN089Lkkur-kySZmrlCjoQ _model_server_result.datetime_utc '2025-06-21 09:32:39' _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 1fd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":13}' # _entry.id 1FD5 # _exptl.entry_id 1FD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 819.135 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description MACROCYCLIC-BIS-9-AMINO-ACRIDINE _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 1FD5 _cell.length_a 29.584 _cell.length_b 54.038 _cell.length_c 40.215 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1FD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 2' # _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,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 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 3 _struct_asym.id D _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 metalc ? metalc1 A N7 DG 2 A DG 2 1_555 C CO CO . A CO 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc2 C CO CO . A CO 21 1_555 G O HOH . A HOH 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc3 C CO CO . A CO 21 1_555 G O HOH . A HOH 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc4 C CO CO . A CO 21 1_555 G O HOH . A HOH 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc5 C CO CO . A CO 21 1_555 G O HOH . A HOH 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc6 C CO CO . A CO 21 1_555 G O HOH . A HOH 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc7 B OP2 DG 2 B DG 8 1_555 F MG MG . B MG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc8 B OP2 DG 2 B DG 8 4_556 F MG MG . B MG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc9 B N7 DG 6 B DG 12 1_555 E CO CO . B CO 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc10 B N7 DG 6 B DG 12 3_755 E CO CO . B CO 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc11 E CO CO . B CO 22 1_555 H O HOH . B HOH 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc12 E CO CO . B CO 22 1_555 H O HOH . B HOH 170 3_755 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc13 E CO CO . B CO 22 1_555 H O HOH . B HOH 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc14 E CO CO . B CO 22 1_555 H O HOH . B HOH 171 3_755 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc15 F MG MG . B MG 23 1_555 H O HOH . B HOH 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc16 F MG MG . B MG 23 1_555 H O HOH . B HOH 172 4_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc17 F MG MG . B MG 23 1_555 H O HOH . B HOH 172 3_656 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? metalc ? metalc18 F MG MG . B MG 23 1_555 H O HOH . B HOH 172 2_655 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? metalc ? metalc19 F MG MG . B MG 23 1_555 H O HOH . B HOH 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc20 F MG MG . B MG 23 1_555 H O HOH . B HOH 173 4_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? hydrog WATSON-CRICK hydrog1 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DT 3 A DT 3 1_555 B N1 DA 4 B DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 DT 3 A DT 3 1_555 B N6 DA 4 B DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 4 A DA 4 1_555 B N3 DT 3 B DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 4 A DA 4 1_555 B O4 DT 3 B DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C46 H58 N8 O2 S2' _chem_comp.formula_weight 819.135 _chem_comp.id B9A _chem_comp.mon_nstd_flag . _chem_comp.name MACROCYCLIC-BIS-9-AMINO-ACRIDINE _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 C1A C2A B9A doub 1 n y C1A CDA B9A sing 2 n y C1A H1A B9A sing 3 n n C2A C3A B9A sing 4 n y C2A H2A B9A sing 5 n n C3A C4A B9A doub 6 n y C3A H3A B9A sing 7 n n C4A CEA B9A sing 8 n y C4A C28 B9A sing 9 n n C5A C6A B9A doub 10 n y C5A CBA B9A sing 11 n y C5A H5A B9A sing 12 n n C6A C7A B9A sing 13 n y C6A H6A B9A sing 14 n n C7A C8A B9A doub 15 n y C7A H7A B9A sing 16 n n C8A CCA B9A sing 17 n y C8A H8A B9A sing 18 n n C9A N9A B9A sing 19 n n C9A CCA B9A doub 20 n y C9A CDA B9A sing 21 n y N9A C15 B9A sing 22 n n N9A H9A B9A sing 23 n n NAA CBA B9A doub 24 n y NAA CEA B9A sing 25 n y CBA CCA B9A sing 26 n y CDA CEA B9A doub 27 n y C15 C16 B9A sing 28 n n C15 H151 B9A sing 29 n n C15 H152 B9A sing 30 n n C16 C17 B9A sing 31 n n C16 H161 B9A sing 32 n n C16 H162 B9A sing 33 n n C17 N18 B9A sing 34 n n C17 H171 B9A sing 35 n n C17 H172 B9A sing 36 n n N18 C19 B9A sing 37 n n N18 H18 B9A sing 38 n n C19 C20 B9A sing 39 n n C19 H191 B9A sing 40 n n C19 H192 B9A sing 41 n n C20 C21 B9A sing 42 n n C20 H201 B9A sing 43 n n C20 H202 B9A sing 44 n n C21 C22 B9A sing 45 n n C21 H211 B9A sing 46 n n C21 H212 B9A sing 47 n n C22 N23 B9A sing 48 n n C22 H221 B9A sing 49 n n C22 H222 B9A sing 50 n n N23 C24 B9A sing 51 n n N23 H23 B9A sing 52 n n C24 C25 B9A sing 53 n n C24 H241 B9A sing 54 n n C24 H242 B9A sing 55 n n C25 C26 B9A sing 56 n n C25 H251 B9A sing 57 n n C25 H252 B9A sing 58 n n C26 N9B B9A sing 59 n n C26 H261 B9A sing 60 n n C26 H262 B9A sing 61 n n C28 S29 B9A sing 62 n n C28 H281 B9A sing 63 n n C28 H282 B9A sing 64 n n S29 C30 B9A sing 65 n n C30 C31 B9A sing 66 n n C30 H301 B9A sing 67 n n C30 H302 B9A sing 68 n n C31 N32 B9A sing 69 n n C31 H311 B9A sing 70 n n C31 H312 B9A sing 71 n n N32 C33 B9A sing 72 n n N32 H32 B9A sing 73 n n C33 O34 B9A doub 74 n n C33 C35 B9A sing 75 n n C35 C36 B9A sing 76 n n C35 H351 B9A sing 77 n n C35 H352 B9A sing 78 n n C36 C37 B9A sing 79 n n C36 H361 B9A sing 80 n n C36 H362 B9A sing 81 n n C37 O38 B9A sing 82 n n C37 N39 B9A sing 83 n n C37 HC37 B9A sing 84 n n O38 HO38 B9A sing 85 n n N39 C40 B9A sing 86 n n N39 H39 B9A sing 87 n n C40 C41 B9A sing 88 n n C40 H401 B9A sing 89 n n C40 H402 B9A sing 90 n n C41 S42 B9A sing 91 n n C41 H411 B9A sing 92 n n C41 H412 B9A sing 93 n n S42 C43 B9A sing 94 n n C43 C5B B9A sing 95 n n C43 H431 B9A sing 96 n n C43 H432 B9A sing 97 n n C1B C2B B9A doub 98 n y C1B CDB B9A sing 99 n y C1B H1B B9A sing 100 n n C2B C3B B9A sing 101 n y C2B H2B B9A sing 102 n n C3B C4B B9A doub 103 n y C3B H3B B9A sing 104 n n C4B CEB B9A sing 105 n y C4B H4B B9A sing 106 n n C5B C6B B9A doub 107 n y C5B CBB B9A sing 108 n y C6B C7B B9A sing 109 n y C6B H6B B9A sing 110 n n C7B C8B B9A doub 111 n y C7B H7B B9A sing 112 n n C8B CCB B9A sing 113 n y C8B H8B B9A sing 114 n n C9B CCB B9A doub 115 n y C9B CDB B9A sing 116 n y C9B N9B B9A sing 117 n n NAB CBB B9A doub 118 n y NAB CEB B9A sing 119 n y CBB CCB B9A sing 120 n y CDB CEB B9A doub 121 n y N9B H9B B9A sing 122 n n # _atom_sites.entry_id 1FD5 _atom_sites.fract_transf_matrix[1][1] 0.033802 _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] 0.018505 _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] 0.024866 _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 CO A 1 21 21 CO CO5 . D 3 B9A A 1 13 13 B9A TMR . E 2 CO B 1 22 22 CO COS . F 4 MG B 1 23 23 MG MG2 . G 5 HOH A 1 103 103 HOH HOH . G 5 HOH A 2 105 105 HOH HOH . G 5 HOH A 3 106 106 HOH HOH . G 5 HOH A 4 108 108 HOH HOH . G 5 HOH A 5 109 109 HOH HOH . G 5 HOH A 6 110 110 HOH HOH . G 5 HOH A 7 118 118 HOH HOH . G 5 HOH A 8 119 119 HOH HOH . G 5 HOH A 9 122 122 HOH HOH . G 5 HOH A 10 124 124 HOH HOH . G 5 HOH A 11 126 126 HOH HOH . G 5 HOH A 12 127 127 HOH HOH . G 5 HOH A 13 128 128 HOH HOH . G 5 HOH A 14 130 130 HOH HOH . G 5 HOH A 15 132 132 HOH HOH . G 5 HOH A 16 134 134 HOH HOH . G 5 HOH A 17 135 135 HOH HOH . G 5 HOH A 18 136 136 HOH HOH . G 5 HOH A 19 138 138 HOH HOH . G 5 HOH A 20 141 141 HOH HOH . G 5 HOH A 21 143 143 HOH HOH . G 5 HOH A 22 144 144 HOH HOH . G 5 HOH A 23 145 145 HOH HOH . G 5 HOH A 24 146 146 HOH HOH . G 5 HOH A 25 152 152 HOH HOH . G 5 HOH A 26 153 153 HOH HOH . G 5 HOH A 27 155 155 HOH HOH . G 5 HOH A 28 157 157 HOH HOH . G 5 HOH A 29 160 160 HOH HOH . G 5 HOH A 30 161 161 HOH HOH . G 5 HOH A 31 162 162 HOH HOH . G 5 HOH A 32 165 165 HOH HOH . G 5 HOH A 33 169 169 HOH HOH . G 5 HOH A 34 174 21 HOH CO5 . G 5 HOH A 35 175 21 HOH CO5 . G 5 HOH A 36 176 21 HOH CO5 . G 5 HOH A 37 177 21 HOH CO5 . G 5 HOH A 38 178 21 HOH CO5 . H 5 HOH B 1 101 101 HOH HOH . H 5 HOH B 2 102 102 HOH HOH . H 5 HOH B 3 104 104 HOH HOH . H 5 HOH B 4 107 107 HOH HOH . H 5 HOH B 5 111 111 HOH HOH . H 5 HOH B 6 112 112 HOH HOH . H 5 HOH B 7 113 113 HOH HOH . H 5 HOH B 8 114 114 HOH HOH . H 5 HOH B 9 115 115 HOH HOH . H 5 HOH B 10 116 116 HOH HOH . H 5 HOH B 11 117 117 HOH HOH . H 5 HOH B 12 120 120 HOH HOH . H 5 HOH B 13 123 123 HOH HOH . H 5 HOH B 14 125 125 HOH HOH . H 5 HOH B 15 129 129 HOH HOH . H 5 HOH B 16 131 131 HOH HOH . H 5 HOH B 17 133 133 HOH HOH . H 5 HOH B 18 137 137 HOH HOH . H 5 HOH B 19 139 139 HOH HOH . H 5 HOH B 20 140 140 HOH HOH . H 5 HOH B 21 142 142 HOH HOH . H 5 HOH B 22 147 147 HOH HOH . H 5 HOH B 23 148 148 HOH HOH . H 5 HOH B 24 149 149 HOH HOH . H 5 HOH B 25 150 150 HOH HOH . H 5 HOH B 26 151 151 HOH HOH . H 5 HOH B 27 154 154 HOH HOH . H 5 HOH B 28 156 156 HOH HOH . H 5 HOH B 29 158 158 HOH HOH . H 5 HOH B 30 163 163 HOH HOH . H 5 HOH B 31 164 164 HOH HOH . H 5 HOH B 32 166 166 HOH HOH . H 5 HOH B 33 170 22 HOH COS . H 5 HOH B 34 171 22 HOH COS . H 5 HOH B 35 172 23 HOH MG2 . H 5 HOH B 36 173 23 HOH MG2 . # 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 C1A B9A . . . D 3 9.731 5.425 13.04 1 33.88 ? C1A B9A 13 A 1 HETATM 2 C C2A B9A . . . D 3 10.521 5.458 14.186 1 41.38 ? C2A B9A 13 A 1 HETATM 3 C C3A B9A . . . D 3 11.606 4.618 14.398 1 30.78 ? C3A B9A 13 A 1 HETATM 4 C C4A B9A . . . D 3 12.032 3.711 13.42 1 33.77 ? C4A B9A 13 A 1 HETATM 5 C C5A B9A . . . D 3 11.354 1.578 9.349 1 30.8 ? C5A B9A 13 A 1 HETATM 6 C C6A B9A . . . D 3 10.571 1.452 8.213 1 26.26 ? C6A B9A 13 A 1 HETATM 7 C C7A B9A . . . D 3 9.455 2.24 7.981 1 29.5 ? C7A B9A 13 A 1 HETATM 8 C C8A B9A . . . D 3 9.074 3.316 8.75 1 26.5 ? C8A B9A 13 A 1 HETATM 9 C C9A B9A . . . D 3 9.386 4.37 10.914 1 29.07 ? C9A B9A 13 A 1 HETATM 10 N N9A B9A . . . D 3 8.252 5.324 10.622 1 39.97 ? N9A B9A 13 A 1 HETATM 11 N NAA B9A . . . D 3 11.632 2.669 11.36 1 31.29 ? NAA B9A 13 A 1 HETATM 12 C CBA B9A . . . D 3 10.901 2.563 10.237 1 22.93 ? CBA B9A 13 A 1 HETATM 13 C CCA B9A . . . D 3 9.804 3.43 9.951 1 22.25 ? CCA B9A 13 A 1 HETATM 14 C CDA B9A . . . D 3 10.083 4.428 12.123 1 26.83 ? CDA B9A 13 A 1 HETATM 15 C CEA B9A . . . D 3 11.19 3.567 12.308 1 25.03 ? CEA B9A 13 A 1 HETATM 16 C C15 B9A . . . D 3 8.198 5.52 9.082 1 44.56 ? C15 B9A 13 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #