data_A1L82 # _chem_comp.id A1L82 _chem_comp.name "[(2~{R},3~{S},5~{R})-5-[(2~{R},4~{R},5~{S})-4-azanyl-5-fluoranyl-5-methyl-2-oxidanyl-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H21 F N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-04-10 _chem_comp.pdbx_modified_date 2025-08-15 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 345.262 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1L82 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 9M5U _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal A1L82 P P1 P 0 1 N N N N N N 111.597 112.987 96.218 4.477 -0.983 0.123 P A1L82 1 A1L82 O1P O1 O 0 1 N N N N N N 111.990 114.007 97.272 5.748 0.002 0.039 O1P A1L82 2 A1L82 O2P O2 O 0 1 N N N N N N 111.477 111.598 96.860 4.260 -1.389 1.529 O2P A1L82 3 A1L82 "O5'" O3 O 0 1 N N N N N N 110.145 113.413 95.533 3.170 -0.219 -0.424 "O5'" A1L82 4 A1L82 "C5'" C1 C 0 1 N N N N N N 109.853 114.791 95.353 2.605 0.921 0.227 "C5'" A1L82 5 A1L82 "C4'" C2 C 0 1 N N R N N N 108.455 114.903 94.653 1.377 1.397 -0.551 "C4'" A1L82 6 A1L82 "O4'" O4 O 0 1 N N N N N N 107.515 114.578 95.464 0.338 0.406 -0.477 "O4'" A1L82 7 A1L82 "C3'" C3 C 0 1 N N S N N N 108.164 116.409 94.253 0.824 2.689 0.081 "C3'" A1L82 8 A1L82 "O3'" O5 O 0 1 N N N N N N 108.196 116.551 92.902 0.846 3.758 -0.867 "O3'" A1L82 9 A1L82 "C2'" C4 C 0 1 N N N N N N 106.804 116.697 94.765 -0.633 2.332 0.461 "C2'" A1L82 10 A1L82 "C1'" C5 C 0 1 N N R N N N 106.280 115.495 95.071 -0.920 1.116 -0.456 "C1'" A1L82 11 A1L82 N1 N1 N 0 1 N N N N N N 105.351 115.610 96.180 -1.979 0.274 0.117 N1 A1L82 12 A1L82 C2 C6 C 0 1 N N R N N N 105.196 114.339 96.880 -3.234 1.025 0.250 C2 A1L82 13 A1L82 O2 O6 O 0 1 N N N N N N 104.790 113.400 95.997 -3.000 2.211 1.012 O2 A1L82 14 A1L82 N3 N2 N 0 1 N N N N N N 104.159 114.447 98.001 -4.235 0.195 0.932 N3 A1L82 15 A1L82 C4 C7 C 0 1 N N R N N N 104.384 115.621 98.889 -4.520 -1.025 0.164 C4 A1L82 16 A1L82 N4 N3 N 0 1 N N N N N N 105.452 115.286 99.853 -5.049 -0.661 -1.157 N4 A1L82 17 A1L82 C5 C8 C 0 1 N N S N N N 104.680 116.902 98.117 -3.227 -1.827 -0.007 C5 A1L82 18 A1L82 C6 C9 C 0 1 N N N N N N 105.739 116.691 97.104 -2.175 -0.943 -0.683 C6 A1L82 19 A1L82 CM5 C10 C 0 1 N N N N N N 103.351 117.377 97.378 -2.717 -2.273 1.365 CM5 A1L82 20 A1L82 F F1 F 0 1 N N N N N N 105.088 117.888 99.012 -3.474 -2.951 -0.801 F A1L82 21 A1L82 O3P O7 O 0 1 N Y N N N N 112.654 112.990 95.008 4.751 -2.290 -0.777 O1 A1L82 22 A1L82 H1 H1 H 0 1 N N N N N N 112.081 113.575 98.113 5.950 0.308 -0.856 H1 A1L82 23 A1L82 H2 H2 H 0 1 N N N N N N 110.625 115.257 94.722 2.311 0.652 1.241 H2 A1L82 24 A1L82 H3 H3 H 0 1 N N N N N N 109.823 115.297 96.329 3.345 1.722 0.263 H3 A1L82 25 A1L82 H4 H4 H 0 1 N N N N N N 108.467 114.293 93.738 1.645 1.576 -1.593 H4 A1L82 26 A1L82 H5 H5 H 0 1 N N N N N N 108.900 117.056 94.753 1.397 2.954 0.970 H5 A1L82 27 A1L82 H6 H6 H 0 1 N N N N N N 108.020 117.456 92.674 0.509 4.596 -0.522 H6 A1L82 28 A1L82 H7 H7 H 0 1 N N N N N N 106.856 117.334 95.660 -0.703 2.052 1.512 H7 A1L82 29 A1L82 H8 H8 H 0 1 N N N N N N 106.199 117.196 93.994 -1.308 3.157 0.235 H8 A1L82 30 A1L82 H9 H9 H 0 1 N N N N N N 105.777 115.040 94.205 -1.191 1.446 -1.458 H9 A1L82 31 A1L82 H11 H11 H 0 1 N N N N N N 106.159 114.057 97.330 -3.601 1.296 -0.740 H11 A1L82 32 A1L82 H12 H12 H 0 1 N N N N N N 104.686 112.568 96.444 -3.787 2.758 1.140 H12 A1L82 33 A1L82 H13 H13 H 0 1 N N N N N N 103.251 114.528 97.589 -3.940 -0.029 1.871 H13 A1L82 34 A1L82 H15 H15 H 0 1 N N N N N N 103.458 115.791 99.458 -5.256 -1.628 0.697 H15 A1L82 35 A1L82 H16 H16 H 0 1 N N N N N N 105.614 116.067 100.457 -5.901 -0.127 -1.071 H16 A1L82 36 A1L82 H17 H17 H 0 1 N N N N N N 105.173 114.496 100.398 -4.361 -0.158 -1.696 H17 A1L82 37 A1L82 H19 H19 H 0 1 N N N N N N 106.677 116.417 97.610 -2.516 -0.671 -1.682 H19 A1L82 38 A1L82 H20 H20 H 0 1 N N N N N N 105.887 117.620 96.534 -1.233 -1.487 -0.755 H20 A1L82 39 A1L82 H21 H21 H 0 1 N N N N N N 102.555 117.537 98.120 -3.469 -2.897 1.848 H21 A1L82 40 A1L82 H22 H22 H 0 1 N N N N N N 103.546 118.317 96.841 -1.796 -2.843 1.243 H22 A1L82 41 A1L82 H23 H23 H 0 1 N N N N N N 103.034 116.605 96.662 -2.521 -1.396 1.983 H23 A1L82 42 A1L82 H24 H24 H 0 1 N N N N N N 113.021 112.120 94.905 5.525 -2.800 -0.504 H24 A1L82 43 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A1L82 "O3'" "C3'" SING N N 1 A1L82 "C3'" "C4'" SING N N 2 A1L82 "C3'" "C2'" SING N N 3 A1L82 "C4'" "C5'" SING N N 4 A1L82 "C4'" "O4'" SING N N 5 A1L82 "C2'" "C1'" SING N N 6 A1L82 "C1'" "O4'" SING N N 7 A1L82 "C1'" N1 SING N N 8 A1L82 "C5'" "O5'" SING N N 9 A1L82 "O5'" P SING N N 10 A1L82 O2 C2 SING N N 11 A1L82 N1 C2 SING N N 12 A1L82 N1 C6 SING N N 13 A1L82 P O2P DOUB N N 14 A1L82 P O1P SING N N 15 A1L82 C2 N3 SING N N 16 A1L82 C6 C5 SING N N 17 A1L82 CM5 C5 SING N N 18 A1L82 N3 C4 SING N N 19 A1L82 C5 C4 SING N N 20 A1L82 C5 F SING N N 21 A1L82 C4 N4 SING N N 22 A1L82 P O3P SING N N 23 A1L82 O1P H1 SING N N 24 A1L82 "C5'" H2 SING N N 25 A1L82 "C5'" H3 SING N N 26 A1L82 "C4'" H4 SING N N 27 A1L82 "C3'" H5 SING N N 28 A1L82 "O3'" H6 SING N N 29 A1L82 "C2'" H7 SING N N 30 A1L82 "C2'" H8 SING N N 31 A1L82 "C1'" H9 SING N N 32 A1L82 C2 H11 SING N N 33 A1L82 O2 H12 SING N N 34 A1L82 N3 H13 SING N N 35 A1L82 C4 H15 SING N N 36 A1L82 N4 H16 SING N N 37 A1L82 N4 H17 SING N N 38 A1L82 C6 H19 SING N N 39 A1L82 C6 H20 SING N N 40 A1L82 CM5 H21 SING N N 41 A1L82 CM5 H22 SING N N 42 A1L82 CM5 H23 SING N N 43 A1L82 O3P H24 SING N N 44 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor A1L82 InChI InChI 1.06 "InChI=1S/C10H21FN3O7P/c1-10(11)4-14(9(16)13-8(10)12)7-2-5(15)6(21-7)3-20-22(17,18)19/h5-9,13,15-16H,2-4,12H2,1H3,(H2,17,18,19)/t5-,6+,7+,8+,9+,10-/m0/s1" A1L82 InChIKey InChI 1.06 BPWPSMUBYMMKQY-LIKBTPFBSA-N A1L82 SMILES_CANONICAL CACTVS 3.385 "C[C@]1(F)CN([C@H](O)N[C@H]1N)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" A1L82 SMILES CACTVS 3.385 "C[C]1(F)CN([CH](O)N[CH]1N)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" A1L82 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@]1(CN([C@@H](N[C@H]1N)O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)F" A1L82 SMILES "OpenEye OEToolkits" 2.0.7 "CC1(CN(C(NC1N)O)C2CC(C(O2)COP(=O)(O)O)O)F" # _pdbx_chem_comp_identifier.comp_id A1L82 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-[(2~{R},4~{R},5~{S})-4-azanyl-5-fluoranyl-5-methyl-2-oxidanyl-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1L82 "Create component" 2025-04-10 PDBJ A1L82 "Initial release" 2025-08-20 RCSB #