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 
# 
