data_6CF
# 
_chem_comp.id                                    6CF 
_chem_comp.name                                  "2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H16 F2 N3 O12 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-04-19 
_chem_comp.pdbx_modified_date                    2012-01-13 
_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                        501.165 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6CF 
_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        3RJH 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
6CF N1     N1     N 0 1 N N N 6.721  7.461  10.613 5.396  0.550  -0.612 N1     6CF 1  
6CF P1     P1     P 0 1 N N N 5.098  5.378  15.144 -1.016 -1.066 0.623  P1     6CF 2  
6CF C2     C2     C 0 1 N N N 7.625  7.861  9.612  5.469  0.882  0.690  C2     6CF 3  
6CF O2     O2     O 0 1 N N N 7.186  8.215  8.504  4.855  0.223  1.513  O2     6CF 4  
6CF P2     P2     P 0 1 N N N 4.017  2.688  14.103 -3.799 -0.033 0.405  P2     6CF 5  
6CF N3     N3     N 0 1 N N N 8.955  7.857  9.881  6.200  1.919  1.095  N3     6CF 6  
6CF P3     P3     P 0 1 N N N 3.894  1.277  16.396 -6.376 1.208  -0.375 P3     6CF 7  
6CF C4     C4     C 0 1 N N N 9.392  7.483  11.086 6.877  2.652  0.222  C4     6CF 8  
6CF N4     N4     N 0 1 N N N 10.709 7.469  11.296 7.630  3.721  0.652  N4     6CF 9  
6CF C5     C5     C 0 1 N N N 8.498  7.101  12.127 6.822  2.331  -1.150 C5     6CF 10 
6CF C6     C6     C 0 1 N N N 7.185  7.108  11.853 6.074  1.274  -1.546 C6     6CF 11 
6CF "C1'"  "C1'"  C 0 1 N N R 5.275  7.402  10.291 4.588  -0.600 -1.027 "C1'"  6CF 12 
6CF F1A    F1A    F 0 1 N N N 6.221  3.774  13.511 -1.691 1.129  -0.683 F1A    6CF 13 
6CF O1A    O1A    O 0 1 N N N 3.876  5.400  15.997 -0.835 -0.285 2.018  O1A    6CF 14 
6CF O1B    O1B    O 0 1 N N N 4.171  2.244  12.695 -3.633 0.686  1.688  O1B    6CF 15 
6CF O1G    O1G    O 0 1 N N N 3.601  2.642  16.906 -6.731 2.326  -1.478 O1G    6CF 16 
6CF "C2'"  "C2'"  C 0 1 N N N 4.872  6.042  9.707  5.129  -1.897 -0.384 "C2'"  6CF 17 
6CF F2A    F2A    F 0 1 N N N 6.049  3.048  15.538 -2.345 -0.835 -1.649 F2A    6CF 18 
6CF O2A    O2A    O 0 1 N N N 6.351  5.956  15.697 -1.541 -2.426 0.883  O2A    6CF 19 
6CF O2B    O2B    O 0 1 N N N 2.738  3.326  14.520 -4.370 -1.512 0.689  O2B    6CF 20 
6CF O2G    O2G    O 0 1 N N N 4.979  0.484  17.038 -7.321 -0.077 -0.589 O2G    6CF 21 
6CF "C3'"  "C3'"  C 0 1 N N S 4.448  5.299  10.967 3.858  -2.713 -0.060 "C3'"  6CF 22 
6CF "O3'"  "O3'"  O 0 1 N N N 3.562  4.218  10.693 3.863  -3.951 -0.774 "O3'"  6CF 23 
6CF C3A    C3A    C 0 1 N N N 5.411  3.703  14.561 -2.187 -0.156 -0.437 C3A    6CF 24 
6CF O3B    O3B    O 0 1 N N N 4.167  1.406  14.906 -4.834 0.771  -0.530 O3B    6CF 25 
6CF O3G    O3G    O 0 1 N N N 2.647  0.492  16.577 -6.597 1.763  0.979  O3G    6CF 26 
6CF "C4'"  "C4'"  C 0 1 N N R 3.708  6.390  11.715 2.700  -1.813 -0.546 "C4'"  6CF 27 
6CF "O4'"  "O4'"  O 0 1 N N N 4.519  7.570  11.487 3.240  -0.474 -0.525 "O4'"  6CF 28 
6CF "C5'"  "C5'"  C 0 1 N N N 3.494  6.124  13.189 1.507  -1.921 0.406  "C5'"  6CF 29 
6CF "O5'"  "O5'"  O 0 1 N N N 4.691  6.338  13.933 0.408  -1.174 -0.121 "O5'"  6CF 30 
6CF HN4    HN4    H 0 1 N N N 11.335 7.733  10.562 7.666  3.939  1.597  HN4    6CF 31 
6CF HN4A   HN4A   H 0 0 N N N 11.070 7.194  12.187 8.124  4.255  0.011  HN4A   6CF 32 
6CF H5     H5     H 0 1 N N N 8.864  6.816  13.102 7.367  2.919  -1.873 H5     6CF 33 
6CF H6     H6     H 0 1 N N N 6.481  6.830  12.623 6.016  1.007  -2.591 H6     6CF 34 
6CF "H1'"  "H1'"  H 0 1 N N N 5.077  8.195  9.555  4.583  -0.687 -2.113 "H1'"  6CF 35 
6CF HO1A   HO1A   H 0 0 N N N 4.079  5.807  16.831 -0.493 0.615  1.923  HO1A   6CF 36 
6CF HO1G   HO1G   H 0 0 N N N 2.704  2.678  17.217 -7.646 2.636  -1.443 HO1G   6CF 37 
6CF "H2'"  "H2'"  H 0 1 N N N 4.055  6.126  8.975  5.761  -2.437 -1.088 "H2'"  6CF 38 
6CF "H2'A" "H2'A" H 0 0 N N N 5.705  5.545  9.188  5.680  -1.670 0.529  "H2'A" 6CF 39 
6CF HO2B   HO2B   H 0 0 N N N 2.147  3.368  13.777 -4.505 -2.041 -0.109 HO2B   6CF 40 
6CF HO2G   HO2G   H 0 0 N N N 4.616  -0.316 17.400 -7.229 -0.493 -1.457 HO2G   6CF 41 
6CF "H3'"  "H3'"  H 0 1 N N N 5.294  4.843  11.502 3.780  -2.890 1.013  "H3'"  6CF 42 
6CF "HO3'" "HO3'" H 0 0 N N N 3.708  3.521  11.322 4.604  -4.530 -0.551 "HO3'" 6CF 43 
6CF "H4'"  "H4'"  H 0 1 N N N 2.676  6.483  11.347 2.403  -2.089 -1.557 "H4'"  6CF 44 
6CF "H5'"  "H5'"  H 0 1 N N N 2.716  6.805  13.564 1.218  -2.967 0.511  "H5'"  6CF 45 
6CF "H5'A" "H5'A" H 0 0 N N N 3.176  5.079  13.319 1.783  -1.521 1.382  "H5'A" 6CF 46 
# 
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 
6CF C2    N1     SING N N 1  
6CF "C1'" N1     SING N N 2  
6CF N1    C6     SING N N 3  
6CF "O5'" P1     SING N N 4  
6CF C3A   P1     SING N N 5  
6CF P1    O2A    DOUB N N 6  
6CF P1    O1A    SING N N 7  
6CF O2    C2     DOUB N N 8  
6CF C2    N3     SING N N 9  
6CF O1B   P2     DOUB N N 10 
6CF P2    O2B    SING N N 11 
6CF P2    C3A    SING N N 12 
6CF P2    O3B    SING N N 13 
6CF N3    C4     DOUB N N 14 
6CF O3B   P3     SING N N 15 
6CF P3    O3G    DOUB N N 16 
6CF P3    O1G    SING N N 17 
6CF P3    O2G    SING N N 18 
6CF C4    N4     SING N N 19 
6CF C4    C5     SING N N 20 
6CF N4    HN4    SING N N 21 
6CF N4    HN4A   SING N N 22 
6CF C6    C5     DOUB N N 23 
6CF C5    H5     SING N N 24 
6CF C6    H6     SING N N 25 
6CF "C2'" "C1'"  SING N N 26 
6CF "C1'" "O4'"  SING N N 27 
6CF "C1'" "H1'"  SING N N 28 
6CF F1A   C3A    SING N N 29 
6CF O1A   HO1A   SING N N 30 
6CF O1G   HO1G   SING N N 31 
6CF "C2'" "C3'"  SING N N 32 
6CF "C2'" "H2'"  SING N N 33 
6CF "C2'" "H2'A" SING N N 34 
6CF C3A   F2A    SING N N 35 
6CF O2B   HO2B   SING N N 36 
6CF O2G   HO2G   SING N N 37 
6CF "O3'" "C3'"  SING N N 38 
6CF "C3'" "C4'"  SING N N 39 
6CF "C3'" "H3'"  SING N N 40 
6CF "O3'" "HO3'" SING N N 41 
6CF "O4'" "C4'"  SING N N 42 
6CF "C4'" "C5'"  SING N N 43 
6CF "C4'" "H4'"  SING N N 44 
6CF "C5'" "O5'"  SING N N 45 
6CF "C5'" "H5'"  SING N N 46 
6CF "C5'" "H5'A" SING N N 47 
# 
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 
6CF SMILES           ACDLabs              12.01 "O=P(O)(O)OP(=O)(O)C(F)(F)P(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O"                                                                                                                                    
6CF SMILES_CANONICAL CACTVS               3.370 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)C(F)(F)[P](O)(=O)O[P](O)(O)=O)O2"                                                                                                               
6CF SMILES           CACTVS               3.370 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)C(F)(F)[P](O)(=O)O[P](O)(O)=O)O2"                                                                                                                   
6CF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@](=O)(C(F)(F)[P@](=O)(O)OP(=O)(O)O)O)O"                                                                                                                 
6CF SMILES           "OpenEye OEToolkits" 1.7.2 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(C(F)(F)P(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                    
6CF InChI            InChI                1.03  "InChI=1S/C10H16F2N3O12P3/c11-10(12,29(20,21)27-30(22,23)24)28(18,19)25-4-6-5(16)3-8(26-6)15-2-1-7(13)14-9(15)17/h1-2,5-6,8,16H,3-4H2,(H,18,19)(H,20,21)(H2,13,14,17)(H2,22,23,24)/t5-,6+,8+/m0/s1" 
6CF InChIKey         InChI                1.03  NCCTXZHZERSHKT-SHYZEUOFSA-N                                                                                                                                                                         
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
6CF "SYSTEMATIC NAME" ACDLabs              12.01 "2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine"                                                            
6CF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3S,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-[bis(fluoranyl)-[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
6CF "Create component"  2011-04-19 RCSB 
6CF "Modify descriptor" 2011-06-04 RCSB 
# 
