data_84E
# 
_chem_comp.id                                    84E 
_chem_comp.name                                  "[(2S,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-2-(trifluoromethylsulfanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H14 F3 N2 O8 P S" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-11-24 
_chem_comp.pdbx_modified_date                    2022-11-11 
_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                        422.271 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     84E 
_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        7W0V 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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.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 
84E "O5'"  O1  O 0 1 N N N 6.571 -5.033 6.355  1.731  1.499  -0.194 "O5'"  84E 1  
84E P      P1  P 0 1 N N N 8.024 -4.320 6.266  2.619  2.732  0.339  P      84E 2  
84E OP3    O2  O 0 1 N Y N 8.992 -5.139 7.038  3.930  2.888  -0.584 OP1    84E 3  
84E OP2    O3  O 0 1 N N N 8.316 -4.020 4.842  1.752  4.087  0.273  OP2    84E 4  
84E "O3'"  O4  O 0 1 N N N 4.203 -8.547 7.129  1.057  -1.447 -3.086 "O3'"  84E 5  
84E "C5'"  C1  C 0 1 N N N 6.018 -5.392 7.622  2.182  0.144  -0.163 "C5'"  84E 6  
84E "C4'"  C2  C 0 1 N N S 4.677 -6.143 7.568  1.099  -0.768 -0.742 "C4'"  84E 7  
84E "S4'"  S1  S 0 1 N N N 4.225 -6.529 9.302  1.652  -2.495 -0.688 "S4'"  84E 8  
84E "C6'"  C3  C 0 1 N N N 2.403 -6.496 9.394  1.799  -2.821 1.090  "C6'"  84E 9  
84E F1     F1  F 0 1 N N N 1.989 -6.964 10.625 0.555  -2.636 1.703  F1     84E 10 
84E F2     F2  F 0 1 N N N 1.812 -7.293 8.436  2.225  -4.139 1.289  F2     84E 11 
84E F3     F3  F 0 1 N N N 1.908 -5.214 9.261  2.730  -1.940 1.651  F3     84E 12 
84E "O4'"  O5  O 0 1 N N N 3.703 -5.249 7.054  -0.117 -0.621 0.011  "O4'"  84E 13 
84E "C1'"  C4  C 0 1 N N R 3.093 -5.806 5.902  -1.210 -0.777 -0.919 "C1'"  84E 14 
84E N1     N1  N 0 1 N N N 2.793 -4.738 4.918  -2.431 -0.164 -0.388 N1     84E 15 
84E C6     C5  C 0 1 N N N 3.817 -4.077 4.275  -3.580 -0.901 -0.310 C6     84E 16 
84E C5     C6  C 0 1 N N N 3.555 -3.062 3.410  -4.705 -0.336 0.180  C5     84E 17 
84E C7     C7  C 0 1 N N N 4.715 -2.390 2.698  -5.981 -1.133 0.274  C7     84E 18 
84E C4     C8  C 0 1 N N N 2.174 -2.631 3.166  -4.669 1.014  0.604  C4     84E 19 
84E O4     O6  O 0 1 N N N 1.804 -1.705 2.446  -5.671 1.545  1.049  O4     84E 20 
84E N3     N2  N 0 1 N N N 1.216 -3.365 3.822  -3.516 1.707  0.510  N3     84E 21 
84E C2     C9  C 0 1 N N N 1.452 -4.425 4.663  -2.409 1.117  0.023  C2     84E 22 
84E O2     O7  O 0 1 N N N 0.496 -5.037 5.138  -1.376 1.754  -0.056 O2     84E 23 
84E "C3'"  C10 C 0 1 N N S 4.769 -7.350 6.599  0.793  -0.361 -2.196 "C3'"  84E 24 
84E "C2'"  C11 C 0 1 N N N 4.044 -6.865 5.353  -0.721 -0.023 -2.181 "C2'"  84E 25 
84E HP3    H1  H 0 1 N Y N 9.255 -4.667 7.819  3.736  3.057  -1.516 H1     84E 26 
84E HP2    H2  H 0 1 N N N 8.308 -3.080 4.708  2.226  4.872  0.580  H2     84E 27 
84E "HO3'" H3  H 0 1 N N N 4.687 -8.811 7.903  0.882  -1.246 -4.015 H4     84E 28 
84E "H5'"  H4  H 0 1 N N N 6.746 -6.034 8.140  3.092  0.050  -0.757 "H5'"  84E 29 
84E "H5''" H5  H 0 0 N N N 5.867 -4.468 8.200  2.389  -0.147 0.867  "H5''" 84E 30 
84E "H1'"  H6  H 0 1 N N N 2.152 -6.302 6.184  -1.377 -1.831 -1.142 "H1'"  84E 31 
84E H6     H7  H 0 1 N N N 4.840 -4.369 4.461  -3.589 -1.930 -0.638 H6     84E 32 
84E H72    H8  H 0 1 N N N 5.660 -2.855 3.016  -6.029 -1.629 1.244  H72    84E 33 
84E H73    H9  H 0 1 N N N 4.596 -2.508 1.611  -6.835 -0.465 0.165  H73    84E 34 
84E H71    H10 H 0 1 N N N 4.730 -1.320 2.951  -6.001 -1.882 -0.518 H71    84E 35 
84E H3     H11 H 0 1 N N N 0.262 -3.104 3.674  -3.484 2.632  0.798  H3     84E 36 
84E "H3'"  H12 H 0 1 N N N 5.828 -7.513 6.350  1.379  0.514  -2.478 "H3'"  84E 37 
84E "H2'"  H13 H 0 1 N N N 3.489 -7.685 4.874  -1.212 -0.404 -3.077 "H2'"  84E 38 
84E "H2''" H14 H 0 0 N N N 4.749 -6.428 4.630  -0.880 1.051  -2.079 "H2''" 84E 39 
84E OP1    O8  O 0 1 N N N 7.799 -2.935 7.071  3.029  2.476  1.738  O1     84E 40 
# 
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 
84E O4    C4     DOUB N N 1  
84E C7    C5     SING N N 2  
84E C4    C5     SING N N 3  
84E C4    N3     SING N N 4  
84E C5    C6     DOUB N N 5  
84E N3    C2     SING N N 6  
84E C6    N1     SING N N 7  
84E C2    N1     SING N N 8  
84E C2    O2     DOUB N N 9  
84E OP2   P      SING N N 10 
84E N1    "C1'"  SING N N 11 
84E "C2'" "C1'"  SING N N 12 
84E "C2'" "C3'"  SING N N 13 
84E "C1'" "O4'"  SING N N 14 
84E P     "O5'"  SING N N 15 
84E P     OP3    SING N N 16 
84E "O5'" "C5'"  SING N N 17 
84E "C3'" "O3'"  SING N N 18 
84E "C3'" "C4'"  SING N N 19 
84E "O4'" "C4'"  SING N N 20 
84E "C4'" "C5'"  SING N N 21 
84E "C4'" "S4'"  SING N N 22 
84E F2    "C6'"  SING N N 23 
84E F3    "C6'"  SING N N 24 
84E "S4'" "C6'"  SING N N 25 
84E "C6'" F1     SING N N 26 
84E OP3   HP3    SING N N 27 
84E OP2   HP2    SING N N 28 
84E "O3'" "HO3'" SING N N 29 
84E "C5'" "H5'"  SING N N 30 
84E "C5'" "H5''" SING N N 31 
84E "C1'" "H1'"  SING N N 32 
84E C6    H6     SING N N 33 
84E C7    H72    SING N N 34 
84E C7    H73    SING N N 35 
84E C7    H71    SING N N 36 
84E N3    H3     SING N N 37 
84E "C3'" "H3'"  SING N N 38 
84E "C2'" "H2'"  SING N N 39 
84E "C2'" "H2''" SING N N 40 
84E P     OP1    DOUB N N 41 
# 
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 
84E InChI            InChI                1.03  "InChI=1S/C11H14F3N2O8PS/c1-5-3-16(9(19)15-8(5)18)7-2-6(17)10(24-7,26-11(12,13)14)4-23-25(20,21)22/h3,6-7,17H,2,4H2,1H3,(H,15,18,19)(H2,20,21,22)/t6-,7+,10-/m0/s1" 
84E InChIKey         InChI                1.03  JESWWYATFFIOBE-PJKMHFRUSA-N                                                                                                                                         
84E SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@](CO[P](O)(O)=O)(O2)SC(F)(F)F)C(=O)NC1=O"                                                                                                
84E SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[C](CO[P](O)(O)=O)(O2)SC(F)(F)F)C(=O)NC1=O"                                                                                                    
84E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@](O2)(COP(=O)(O)O)SC(F)(F)F)O"                                                                                                  
84E SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)(COP(=O)(O)O)SC(F)(F)F)O"                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           84E 
_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~{S},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-2-(trifluoromethylsulfanyl)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 
84E "Create component" 2021-11-24 PDBJ 
84E "Initial release"  2022-11-16 RCSB 
# 
