data_3D9E # _model_server_result.job_id SPUn2jNLMcKGu_NuisMFlg _model_server_result.datetime_utc '2025-07-04 15:05:04' _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 3d9e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":600}' # _entry.id 3D9E # _exptl.entry_id 3D9E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 159.226 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-nitrooctane _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 120 _cell.entry_id 3D9E _cell.length_a 107.996 _cell.length_b 107.996 _cell.length_c 338.576 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D9E _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 I N N ? 3 L N N ? 3 O N N # _chem_comp.formula 'C8 H17 N O2' _chem_comp.formula_weight 159.226 _chem_comp.id N8C _chem_comp.mon_nstd_flag . _chem_comp.name 1-nitrooctane _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 O1 N1 N8C doub 341 n n N1 O2 N8C sing 342 n n N1 C1 N8C sing 343 n n C1 C2 N8C sing 344 n n C2 C3 N8C sing 345 n n C3 C4 N8C sing 346 n n C4 C5 N8C sing 347 n n C5 C6 N8C sing 348 n n C6 C7 N8C sing 349 n n C7 C8 N8C sing 350 n n C1 H1 N8C sing 351 n n C1 H1A N8C sing 352 n n C2 H2 N8C sing 353 n n C2 H2A N8C sing 354 n n C3 H3 N8C sing 355 n n C3 H3A N8C sing 356 n n C4 H4 N8C sing 357 n n C4 H4A N8C sing 358 n n C5 H5 N8C sing 359 n n C5 H5A N8C sing 360 n n C6 H6 N8C sing 361 n n C6 H6A N8C sing 362 n n C7 H7 N8C sing 363 n n C7 H7A N8C sing 364 n n C8 H8 N8C sing 365 n n C8 H8A N8C sing 366 n n C8 H8B N8C sing 367 n n # _atom_sites.entry_id 3D9E _atom_sites.fract_transf_matrix[1][1] 0.00926 _atom_sites.fract_transf_matrix[1][2] 0.005346 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010692 _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] 0.002954 _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 FAD A 1 500 500 FAD FAD . F 3 N8C A 1 600 600 N8C N8C . G 4 GOL A 1 700 700 GOL GOL . H 2 FAD B 1 500 500 FAD FAD . I 3 N8C B 1 600 600 N8C N8C . J 4 GOL B 1 700 700 GOL GOL . K 2 FAD C 1 500 500 FAD FAD . L 3 N8C C 1 600 600 N8C N8C . M 4 GOL C 1 700 700 GOL GOL . N 2 FAD D 1 500 500 FAD FAD . O 3 N8C D 1 600 600 N8C N8C . P 4 GOL D 1 700 700 GOL GOL . Q 5 HOH A 1 701 5 HOH HOH . Q 5 HOH A 2 702 10 HOH HOH . Q 5 HOH A 3 703 16 HOH HOH . Q 5 HOH A 4 704 19 HOH HOH . Q 5 HOH A 5 705 21 HOH HOH . Q 5 HOH A 6 706 23 HOH HOH . Q 5 HOH A 7 707 26 HOH HOH . Q 5 HOH A 8 708 27 HOH HOH . Q 5 HOH A 9 709 29 HOH HOH . Q 5 HOH A 10 710 33 HOH HOH . Q 5 HOH A 11 711 43 HOH HOH . Q 5 HOH A 12 712 44 HOH HOH . Q 5 HOH A 13 713 47 HOH HOH . Q 5 HOH A 14 714 56 HOH HOH . Q 5 HOH A 15 715 61 HOH HOH . Q 5 HOH A 16 716 63 HOH HOH . Q 5 HOH A 17 717 70 HOH HOH . Q 5 HOH A 18 718 73 HOH HOH . Q 5 HOH A 19 719 77 HOH HOH . Q 5 HOH A 20 720 87 HOH HOH . Q 5 HOH A 21 721 95 HOH HOH . Q 5 HOH A 22 722 97 HOH HOH . Q 5 HOH A 23 723 99 HOH HOH . Q 5 HOH A 24 724 108 HOH HOH . Q 5 HOH A 25 725 112 HOH HOH . Q 5 HOH A 26 726 115 HOH HOH . Q 5 HOH A 27 727 122 HOH HOH . Q 5 HOH A 28 728 124 HOH HOH . Q 5 HOH A 29 729 125 HOH HOH . Q 5 HOH A 30 730 133 HOH HOH . Q 5 HOH A 31 731 135 HOH HOH . Q 5 HOH A 32 732 137 HOH HOH . Q 5 HOH A 33 733 138 HOH HOH . Q 5 HOH A 34 734 140 HOH HOH . Q 5 HOH A 35 735 142 HOH HOH . Q 5 HOH A 36 736 144 HOH HOH . Q 5 HOH A 37 737 147 HOH HOH . Q 5 HOH A 38 738 160 HOH HOH . Q 5 HOH A 39 739 164 HOH HOH . Q 5 HOH A 40 740 165 HOH HOH . Q 5 HOH A 41 741 166 HOH HOH . Q 5 HOH A 42 742 167 HOH HOH . Q 5 HOH A 43 743 168 HOH HOH . Q 5 HOH A 44 744 183 HOH HOH . Q 5 HOH A 45 745 188 HOH HOH . Q 5 HOH A 46 746 191 HOH HOH . Q 5 HOH A 47 747 193 HOH HOH . Q 5 HOH A 48 748 195 HOH HOH . Q 5 HOH A 49 749 221 HOH HOH . Q 5 HOH A 50 750 237 HOH HOH . Q 5 HOH A 51 751 240 HOH HOH . Q 5 HOH A 52 752 244 HOH HOH . Q 5 HOH A 53 753 249 HOH HOH . Q 5 HOH A 54 754 250 HOH HOH . Q 5 HOH A 55 755 251 HOH HOH . Q 5 HOH A 56 756 262 HOH HOH . Q 5 HOH A 57 757 263 HOH HOH . Q 5 HOH A 58 758 264 HOH HOH . Q 5 HOH A 59 759 265 HOH HOH . Q 5 HOH A 60 760 269 HOH HOH . Q 5 HOH A 61 761 270 HOH HOH . R 5 HOH B 1 701 4 HOH HOH . R 5 HOH B 2 702 30 HOH HOH . R 5 HOH B 3 703 31 HOH HOH . R 5 HOH B 4 704 34 HOH HOH . R 5 HOH B 5 705 40 HOH HOH . R 5 HOH B 6 706 60 HOH HOH . R 5 HOH B 7 707 68 HOH HOH . R 5 HOH B 8 708 69 HOH HOH . R 5 HOH B 9 709 74 HOH HOH . R 5 HOH B 10 710 83 HOH HOH . R 5 HOH B 11 711 84 HOH HOH . R 5 HOH B 12 712 93 HOH HOH . R 5 HOH B 13 713 96 HOH HOH . R 5 HOH B 14 714 100 HOH HOH . R 5 HOH B 15 715 101 HOH HOH . R 5 HOH B 16 716 102 HOH HOH . R 5 HOH B 17 717 104 HOH HOH . R 5 HOH B 18 718 107 HOH HOH . R 5 HOH B 19 719 110 HOH HOH . R 5 HOH B 20 720 114 HOH HOH . R 5 HOH B 21 721 119 HOH HOH . R 5 HOH B 22 722 120 HOH HOH . R 5 HOH B 23 723 126 HOH HOH . R 5 HOH B 24 724 127 HOH HOH . R 5 HOH B 25 725 136 HOH HOH . R 5 HOH B 26 726 139 HOH HOH . R 5 HOH B 27 727 149 HOH HOH . R 5 HOH B 28 728 155 HOH HOH . R 5 HOH B 29 729 161 HOH HOH . R 5 HOH B 30 730 163 HOH HOH . R 5 HOH B 31 731 172 HOH HOH . R 5 HOH B 32 732 174 HOH HOH . R 5 HOH B 33 733 176 HOH HOH . R 5 HOH B 34 734 177 HOH HOH . R 5 HOH B 35 735 186 HOH HOH . R 5 HOH B 36 736 199 HOH HOH . R 5 HOH B 37 737 202 HOH HOH . R 5 HOH B 38 738 209 HOH HOH . R 5 HOH B 39 739 218 HOH HOH . R 5 HOH B 40 740 220 HOH HOH . R 5 HOH B 41 741 232 HOH HOH . R 5 HOH B 42 742 233 HOH HOH . R 5 HOH B 43 743 236 HOH HOH . R 5 HOH B 44 744 245 HOH HOH . R 5 HOH B 45 745 261 HOH HOH . R 5 HOH B 46 746 272 HOH HOH . R 5 HOH B 47 747 273 HOH HOH . S 5 HOH C 1 701 2 HOH HOH . S 5 HOH C 2 702 7 HOH HOH . S 5 HOH C 3 703 8 HOH HOH . S 5 HOH C 4 704 11 HOH HOH . S 5 HOH C 5 705 15 HOH HOH . S 5 HOH C 6 706 18 HOH HOH . S 5 HOH C 7 707 20 HOH HOH . S 5 HOH C 8 708 25 HOH HOH . S 5 HOH C 9 709 32 HOH HOH . S 5 HOH C 10 710 37 HOH HOH . S 5 HOH C 11 711 42 HOH HOH . S 5 HOH C 12 712 46 HOH HOH . S 5 HOH C 13 713 51 HOH HOH . S 5 HOH C 14 714 52 HOH HOH . S 5 HOH C 15 715 53 HOH HOH . S 5 HOH C 16 716 54 HOH HOH . S 5 HOH C 17 717 58 HOH HOH . S 5 HOH C 18 718 59 HOH HOH . S 5 HOH C 19 719 62 HOH HOH . S 5 HOH C 20 720 64 HOH HOH . S 5 HOH C 21 721 71 HOH HOH . S 5 HOH C 22 722 72 HOH HOH . S 5 HOH C 23 723 75 HOH HOH . S 5 HOH C 24 724 76 HOH HOH . S 5 HOH C 25 725 78 HOH HOH . S 5 HOH C 26 726 79 HOH HOH . S 5 HOH C 27 727 80 HOH HOH . S 5 HOH C 28 728 86 HOH HOH . S 5 HOH C 29 729 89 HOH HOH . S 5 HOH C 30 730 98 HOH HOH . S 5 HOH C 31 731 103 HOH HOH . S 5 HOH C 32 732 106 HOH HOH . S 5 HOH C 33 733 111 HOH HOH . S 5 HOH C 34 734 116 HOH HOH . S 5 HOH C 35 735 117 HOH HOH . S 5 HOH C 36 736 121 HOH HOH . S 5 HOH C 37 737 128 HOH HOH . S 5 HOH C 38 738 130 HOH HOH . S 5 HOH C 39 739 131 HOH HOH . S 5 HOH C 40 740 134 HOH HOH . S 5 HOH C 41 741 141 HOH HOH . S 5 HOH C 42 742 143 HOH HOH . S 5 HOH C 43 743 150 HOH HOH . S 5 HOH C 44 744 151 HOH HOH . S 5 HOH C 45 745 153 HOH HOH . S 5 HOH C 46 746 154 HOH HOH . S 5 HOH C 47 747 156 HOH HOH . S 5 HOH C 48 748 158 HOH HOH . S 5 HOH C 49 749 159 HOH HOH . S 5 HOH C 50 750 173 HOH HOH . S 5 HOH C 51 751 179 HOH HOH . S 5 HOH C 52 752 181 HOH HOH . S 5 HOH C 53 753 182 HOH HOH . S 5 HOH C 54 754 189 HOH HOH . S 5 HOH C 55 755 190 HOH HOH . S 5 HOH C 56 756 196 HOH HOH . S 5 HOH C 57 757 197 HOH HOH . S 5 HOH C 58 758 198 HOH HOH . S 5 HOH C 59 759 201 HOH HOH . S 5 HOH C 60 760 204 HOH HOH . S 5 HOH C 61 761 206 HOH HOH . S 5 HOH C 62 762 211 HOH HOH . S 5 HOH C 63 763 214 HOH HOH . S 5 HOH C 64 764 215 HOH HOH . S 5 HOH C 65 765 217 HOH HOH . S 5 HOH C 66 766 222 HOH HOH . S 5 HOH C 67 767 224 HOH HOH . S 5 HOH C 68 768 225 HOH HOH . S 5 HOH C 69 769 228 HOH HOH . S 5 HOH C 70 770 229 HOH HOH . S 5 HOH C 71 771 239 HOH HOH . S 5 HOH C 72 772 241 HOH HOH . S 5 HOH C 73 773 242 HOH HOH . S 5 HOH C 74 774 247 HOH HOH . S 5 HOH C 75 775 248 HOH HOH . S 5 HOH C 76 776 252 HOH HOH . S 5 HOH C 77 777 253 HOH HOH . S 5 HOH C 78 778 254 HOH HOH . S 5 HOH C 79 779 255 HOH HOH . S 5 HOH C 80 780 256 HOH HOH . S 5 HOH C 81 781 258 HOH HOH . S 5 HOH C 82 782 268 HOH HOH . S 5 HOH C 83 783 271 HOH HOH . T 5 HOH D 1 701 1 HOH HOH . T 5 HOH D 2 702 3 HOH HOH . T 5 HOH D 3 703 6 HOH HOH . T 5 HOH D 4 704 9 HOH HOH . T 5 HOH D 5 705 12 HOH HOH . T 5 HOH D 6 706 13 HOH HOH . T 5 HOH D 7 707 14 HOH HOH . T 5 HOH D 8 708 17 HOH HOH . T 5 HOH D 9 709 22 HOH HOH . T 5 HOH D 10 710 24 HOH HOH . T 5 HOH D 11 711 28 HOH HOH . T 5 HOH D 12 712 35 HOH HOH . T 5 HOH D 13 713 36 HOH HOH . T 5 HOH D 14 714 38 HOH HOH . T 5 HOH D 15 715 39 HOH HOH . T 5 HOH D 16 716 41 HOH HOH . T 5 HOH D 17 717 45 HOH HOH . T 5 HOH D 18 718 48 HOH HOH . T 5 HOH D 19 719 49 HOH HOH . T 5 HOH D 20 720 50 HOH HOH . T 5 HOH D 21 721 55 HOH HOH . T 5 HOH D 22 722 57 HOH HOH . T 5 HOH D 23 723 65 HOH HOH . T 5 HOH D 24 724 66 HOH HOH . T 5 HOH D 25 725 67 HOH HOH . T 5 HOH D 26 726 81 HOH HOH . T 5 HOH D 27 727 82 HOH HOH . T 5 HOH D 28 728 85 HOH HOH . T 5 HOH D 29 729 88 HOH HOH . T 5 HOH D 30 730 90 HOH HOH . T 5 HOH D 31 731 91 HOH HOH . T 5 HOH D 32 732 92 HOH HOH . T 5 HOH D 33 733 94 HOH HOH . T 5 HOH D 34 734 105 HOH HOH . T 5 HOH D 35 735 109 HOH HOH . T 5 HOH D 36 736 113 HOH HOH . T 5 HOH D 37 737 118 HOH HOH . T 5 HOH D 38 738 123 HOH HOH . T 5 HOH D 39 739 129 HOH HOH . T 5 HOH D 40 740 132 HOH HOH . T 5 HOH D 41 741 145 HOH HOH . T 5 HOH D 42 742 146 HOH HOH . T 5 HOH D 43 743 148 HOH HOH . T 5 HOH D 44 744 152 HOH HOH . T 5 HOH D 45 745 157 HOH HOH . T 5 HOH D 46 746 162 HOH HOH . T 5 HOH D 47 747 169 HOH HOH . T 5 HOH D 48 748 170 HOH HOH . T 5 HOH D 49 749 171 HOH HOH . T 5 HOH D 50 750 175 HOH HOH . T 5 HOH D 51 751 178 HOH HOH . T 5 HOH D 52 752 180 HOH HOH . T 5 HOH D 53 753 184 HOH HOH . T 5 HOH D 54 754 185 HOH HOH . T 5 HOH D 55 755 187 HOH HOH . T 5 HOH D 56 756 192 HOH HOH . T 5 HOH D 57 757 194 HOH HOH . T 5 HOH D 58 758 200 HOH HOH . T 5 HOH D 59 759 203 HOH HOH . T 5 HOH D 60 760 205 HOH HOH . T 5 HOH D 61 761 207 HOH HOH . T 5 HOH D 62 762 208 HOH HOH . T 5 HOH D 63 763 210 HOH HOH . T 5 HOH D 64 764 212 HOH HOH . T 5 HOH D 65 765 213 HOH HOH . T 5 HOH D 66 766 216 HOH HOH . T 5 HOH D 67 767 219 HOH HOH . T 5 HOH D 68 768 223 HOH HOH . T 5 HOH D 69 769 226 HOH HOH . T 5 HOH D 70 770 227 HOH HOH . T 5 HOH D 71 771 230 HOH HOH . T 5 HOH D 72 772 231 HOH HOH . T 5 HOH D 73 773 234 HOH HOH . T 5 HOH D 74 774 235 HOH HOH . T 5 HOH D 75 775 238 HOH HOH . T 5 HOH D 76 776 243 HOH HOH . T 5 HOH D 77 777 246 HOH HOH . T 5 HOH D 78 778 257 HOH HOH . T 5 HOH D 79 779 259 HOH HOH . T 5 HOH D 80 780 260 HOH HOH . T 5 HOH D 81 781 266 HOH HOH . T 5 HOH D 82 782 267 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 O O1 N8C . . . O 3 65.108 -26.634 -12.072 1 54.41 ? O1 N8C 600 D 1 HETATM 2 N N1 N8C . . . O 3 65.633 -27.177 -13.042 1 55.64 ? N1 N8C 600 D 1 HETATM 3 O O2 N8C . . . O 3 65.01 -28.019 -13.674 1 54.97 ? O2 N8C 600 D 1 HETATM 4 C C1 N8C . . . O 3 67.008 -26.822 -13.398 1 55.55 ? C1 N8C 600 D 1 HETATM 5 C C2 N8C . . . O 3 67.249 -26.956 -14.898 1 55.35 ? C2 N8C 600 D 1 HETATM 6 C C3 N8C . . . O 3 68.556 -26.274 -15.29 1 54.83 ? C3 N8C 600 D 1 HETATM 7 C C4 N8C . . . O 3 68.285 -25.089 -16.216 1 55.88 ? C4 N8C 600 D 1 HETATM 8 C C5 N8C . . . O 3 68.653 -23.75 -15.592 1 56.01 ? C5 N8C 600 D 1 HETATM 9 C C6 N8C . . . O 3 68.904 -22.676 -16.651 1 57.53 ? C6 N8C 600 D 1 HETATM 10 C C7 N8C . . . O 3 69.616 -21.46 -16.048 1 58.36 ? C7 N8C 600 D 1 HETATM 11 C C8 N8C . . . O 3 70.642 -20.861 -16.987 1 58.33 ? C8 N8C 600 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 11 #