data_VC8
# 
_chem_comp.id                                    VC8 
_chem_comp.name                                  "4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H16 Cl2 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                     2018-03-26 
_chem_comp.pdbx_modified_date                    2018-06-15 
_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                        534.074 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VC8 
_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        6CTW 
_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 
VC8 C4    C1  C  0 1 N N N 9.363  7.537  10.928 -6.561 -3.057 -0.243 C4    VC8 1  
VC8 N4    N1  N  0 1 N N N 10.794 7.560  11.151 -7.172 -4.285 -0.144 N4    VC8 2  
VC8 C5    C2  C  0 1 N N N 8.556  7.153  11.969 -6.481 -2.403 -1.489 C5    VC8 3  
VC8 C6    C3  C  0 1 N N N 7.195  7.138  11.718 -5.874 -1.194 -1.559 C6    VC8 4  
VC8 N3    N2  N  0 1 N N N 8.823  7.874  9.764  -6.050 -2.477 0.836  N3    VC8 5  
VC8 C2    C4  C  0 1 N N N 7.507  7.838  9.587  -5.456 -1.288 0.752  C2    VC8 6  
VC8 O2    O1  O  0 1 N N N 7.028  8.138  8.534  -4.993 -0.776 1.758  O2    VC8 7  
VC8 N1    N3  N  0 1 N N N 6.680  7.473  10.542 -5.359 -0.642 -0.425 N1    VC8 8  
VC8 "C1'" C5  C  0 1 N N R 5.237  7.423  10.188 -4.700 0.665  -0.486 "C1'" VC8 9  
VC8 "C2'" C6  C  0 1 N N N 4.906  6.225  9.724  -5.465 1.694  0.384  "C2'" VC8 10 
VC8 "C3'" C7  C  0 1 N N S 4.491  5.347  10.924 -4.335 2.711  0.701  "C3'" VC8 11 
VC8 "O3'" O2  O  0 1 N N N 3.498  4.398  10.735 -4.189 3.657  -0.360 "O3'" VC8 12 
VC8 "O4'" O3  O  0 1 N N N 4.198  7.640  11.383 -3.387 0.589  0.092  "O4'" VC8 13 
VC8 "C4'" C8  C  0 1 N N S 4.246  6.490  11.946 -3.093 1.799  0.800  "C4'" VC8 14 
VC8 "C5'" C9  C  0 1 N N N 3.422  6.280  13.225 -1.888 2.494  0.162  "C5'" VC8 15 
VC8 "O5'" O4  O  0 1 N N N 4.635  6.221  13.933 -0.719 1.696  0.360  "O5'" VC8 16 
VC8 PA    P1  P  0 1 N N N 4.899  4.921  14.888 0.736  2.123  -0.182 PA    VC8 17 
VC8 O1A   O5  O  0 1 N N N 3.830  4.946  15.934 1.220  3.459  0.575  O1A   VC8 18 
VC8 O2A   O6  O  0 1 N N N 6.286  5.014  15.444 0.665  2.378  -1.638 O2A   VC8 19 
VC8 O3A   O7  O  0 1 N N N 4.865  3.632  13.887 1.785  0.935  0.104  O3A   VC8 20 
VC8 PB    P2  P  0 1 N N N 3.828  2.388  13.872 3.264  0.596  -0.434 PB    VC8 21 
VC8 O1B   O8  O  0 1 N N N 2.483  2.804  14.392 3.224  0.411  -2.033 O1B   VC8 22 
VC8 O2B   O9  O  0 1 N N N 3.719  1.922  12.436 4.181  1.704  -0.088 O2B   VC8 23 
VC8 C3B   C10 C  0 1 N N N 4.553  1.055  14.951 3.854  -0.945 0.341  C3B   VC8 24 
VC8 CL1   CL1 CL 0 0 N N N 6.259  1.421  15.278 3.898  -0.738 2.132  CL1   VC8 25 
VC8 CL2   CL2 CL 0 0 N N N 4.509  -0.532 14.160 2.736  -2.296 -0.080 CL2   VC8 26 
VC8 PG    P3  P  0 1 N N N 3.713  0.965  16.600 5.529  -1.329 -0.267 PG    VC8 27 
VC8 O2G   O10 O  0 1 N N N 3.539  2.372  17.109 6.526  -0.123 0.109  O2G   VC8 28 
VC8 O1G   O11 O  0 1 N N N 4.602  0.204  17.535 6.049  -2.690 0.417  O1G   VC8 29 
VC8 O3G   O12 O  0 1 N N N 2.402  0.249  16.453 5.492  -1.499 -1.737 O3G   VC8 30 
VC8 H1    H1  H  0 1 N N N 11.411 7.837  10.414 -7.549 -4.705 -0.933 H1    VC8 31 
VC8 H2    H2  H  0 1 N N N 11.165 7.299  12.042 -7.226 -4.733 0.715  H2    VC8 32 
VC8 H3    H3  H  0 1 N N N 8.961  6.877  12.932 -6.896 -2.860 -2.376 H3    VC8 33 
VC8 H4    H4  H  0 1 N N N 6.525  6.842  12.512 -5.800 -0.674 -2.502 H4    VC8 34 
VC8 H5    H5  H  0 1 N N N 5.035  8.202  9.438  -4.639 1.010  -1.518 H5    VC8 35 
VC8 H6    H6  H  0 1 N N N 4.066  6.316  9.020  -6.269 2.165  -0.182 H6    VC8 36 
VC8 H7    H7  H  0 1 N N N 5.767  5.773  9.210  -5.846 1.233  1.295  H7    VC8 37 
VC8 H8    H8  H  0 1 N N N 5.402  4.829  11.257 -4.522 3.216  1.649  H8    VC8 38 
VC8 H9    H9  H  0 1 N N N 3.344  3.933  11.549 -4.977 4.194  -0.519 H9    VC8 39 
VC8 H10   H10 H  0 1 N N N 5.249  6.528  12.396 -2.881 1.575  1.845  H10   VC8 40 
VC8 H11   H11 H  0 1 N N N 2.775  7.127  13.496 -2.065 2.620  -0.906 H11   VC8 41 
VC8 H12   H12 H  0 1 N N N 2.836  5.350  13.244 -1.744 3.470  0.625  H12   VC8 42 
VC8 H13   H13 H  0 1 N N N 4.229  5.019  16.793 1.289  3.365  1.535  H13   VC8 43 
VC8 H14   H14 H  0 1 N N N 1.831  2.690  13.711 2.642  -0.300 -2.332 H14   VC8 44 
VC8 H15   H15 H  0 1 N N N 2.615  2.548  17.245 6.600  0.045  1.058  H15   VC8 45 
VC8 H16   H16 H  0 1 N N N 4.150  -0.574 17.840 6.936  -2.956 0.139  H16   VC8 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 
VC8 O2    C2    DOUB N N 1  
VC8 C2    N3    SING N N 2  
VC8 C2    N1    SING N N 3  
VC8 "C2'" "C1'" SING N N 4  
VC8 "C2'" "C3'" SING N N 5  
VC8 N3    C4    DOUB N N 6  
VC8 "C1'" N1    SING N N 7  
VC8 "C1'" "O4'" SING N N 8  
VC8 N1    C6    SING N N 9  
VC8 "O3'" "C3'" SING N N 10 
VC8 "C3'" "C4'" SING N N 11 
VC8 C4    N4    SING N N 12 
VC8 C4    C5    SING N N 13 
VC8 "O4'" "C4'" SING N N 14 
VC8 C6    C5    DOUB N N 15 
VC8 "C4'" "C5'" SING N N 16 
VC8 O2B   PB    DOUB N N 17 
VC8 "C5'" "O5'" SING N N 18 
VC8 PB    O3A   SING N N 19 
VC8 PB    O1B   SING N N 20 
VC8 PB    C3B   SING N N 21 
VC8 O3A   PA    SING N N 22 
VC8 "O5'" PA    SING N N 23 
VC8 CL2   C3B   SING N N 24 
VC8 PA    O2A   DOUB N N 25 
VC8 PA    O1A   SING N N 26 
VC8 C3B   CL1   SING N N 27 
VC8 C3B   PG    SING N N 28 
VC8 O3G   PG    DOUB N N 29 
VC8 PG    O2G   SING N N 30 
VC8 PG    O1G   SING N N 31 
VC8 N4    H1    SING N N 32 
VC8 N4    H2    SING N N 33 
VC8 C5    H3    SING N N 34 
VC8 C6    H4    SING N N 35 
VC8 "C1'" H5    SING N N 36 
VC8 "C2'" H6    SING N N 37 
VC8 "C2'" H7    SING N N 38 
VC8 "C3'" H8    SING N N 39 
VC8 "O3'" H9    SING N N 40 
VC8 "C4'" H10   SING N N 41 
VC8 "C5'" H11   SING N N 42 
VC8 "C5'" H12   SING N N 43 
VC8 O1A   H13   SING N N 44 
VC8 O1B   H14   SING N N 45 
VC8 O2G   H15   SING N N 46 
VC8 O1G   H16   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 
VC8 SMILES           ACDLabs              12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(Cl)(P(O)(O)=O)Cl)=O"                                                                                                                              
VC8 InChI            InChI                1.03  "InChI=1S/C10H16Cl2N3O12P3/c11-10(12,28(18,19)20)29(21,22)27-30(23,24)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,21,22)(H,23,24)(H2,13,14,17)(H2,18,19,20)/t5-,6-,8+/m0/s1" 
VC8 InChIKey         InChI                1.03  UVMWAJJREHNIPG-VMHSAVOQSA-N                                                                                                                                                                          
VC8 SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O2"                                                                                                               
VC8 SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O2"                                                                                                                  
VC8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O"                                                                                                                     
VC8 SMILES           "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O"                                                                                                                                   
# 
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 
VC8 "SYSTEMATIC NAME" ACDLabs              12.01 "4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one"                           
VC8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{S},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-bis(chloranyl)methyl]phosphonic 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 
VC8 "Create component" 2018-03-26 RCSB 
VC8 "Initial release"  2018-06-20 RCSB 
# 
