data_VC6
# 
_chem_comp.id                                    VC6 
_chem_comp.name                                  "4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H16 Cl F 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                        517.620 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VC6 
_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        6CTU 
_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 
VC6 C4    C1  C  0 1 N N N 9.305  7.554  10.929 -6.450 -3.047 -0.219 C4    VC6 1  
VC6 N4    N1  N  0 1 N N N 10.736 7.526  11.131 -7.069 -4.271 -0.108 N4    VC6 2  
VC6 C5    C2  C  0 1 N N N 8.482  7.194  11.977 -6.344 -2.417 -1.476 C5    VC6 3  
VC6 C6    C3  C  0 1 N N N 7.116  7.223  11.744 -5.729 -1.213 -1.556 C6    VC6 4  
VC6 N3    N2  N  0 1 N N N 8.787  7.893  9.757  -5.955 -2.451 0.858  N3    VC6 5  
VC6 C2    C4  C  0 1 N N N 7.475  7.907  9.586  -5.353 -1.266 0.762  C2    VC6 6  
VC6 O2    O1  O  0 1 N N N 7.027  8.217  8.522  -4.905 -0.739 1.767  O2    VC6 7  
VC6 N1    N3  N  0 1 N N N 6.639  7.589  10.561 -5.231 -0.643 -0.424 N1    VC6 8  
VC6 "C1'" C5  C  0 1 N N R 5.193  7.583  10.278 -4.564 0.660  -0.497 "C1'" VC6 9  
VC6 "C2'" C6  C  0 1 N N N 4.823  6.176  9.675  -5.339 1.709  0.340  "C2'" VC6 10 
VC6 "C3'" C7  C  0 1 N N S 4.481  5.283  10.896 -4.209 2.725  0.658  "C3'" VC6 11 
VC6 "O3'" O2  O  0 1 N N N 3.348  4.357  10.682 -4.039 3.650  -0.417 "O3'" VC6 12 
VC6 "O4'" O3  O  0 1 N N N 4.442  7.668  11.348 -3.262 0.587  0.106  "O4'" VC6 13 
VC6 "C4'" C8  C  0 1 N N S 4.398  6.163  11.884 -2.974 1.809  0.796  "C4'" VC6 14 
VC6 "C5'" C9  C  0 1 N N N 3.504  6.059  13.075 -1.754 2.485  0.167  "C5'" VC6 15 
VC6 "O5'" O4  O  0 1 N N N 4.614  6.172  13.923 -0.593 1.685  0.401  "O5'" VC6 16 
VC6 PA    P1  P  0 1 N N N 4.997  4.899  14.869 0.874  2.094  -0.123 PA    VC6 17 
VC6 O1A   O5  O  0 1 N N N 3.967  4.876  15.957 1.351  3.442  0.618  O1A   VC6 18 
VC6 O2A   O6  O  0 1 N N N 6.398  4.997  15.361 0.830  2.323  -1.584 O2A   VC6 19 
VC6 O3A   O7  O  0 1 N N N 4.904  3.592  13.888 1.911  0.907  0.204  O3A   VC6 20 
VC6 PB    P2  P  0 1 N N N 3.762  2.427  13.857 3.397  0.550  -0.301 PB    VC6 21 
VC6 O1B   O8  O  0 1 N N N 2.435  2.938  14.387 3.385  0.336  -1.897 O1B   VC6 22 
VC6 O2B   O9  O  0 1 N N N 3.669  2.053  12.411 4.314  1.660  0.041  O2B   VC6 23 
VC6 C3B   C10 C  0 1 N N S 4.366  0.941  14.820 3.964  -0.980 0.513  C3B   VC6 24 
VC6 CL1   CL1 CL 0 0 N N N 6.093  1.144  15.068 2.847  -2.332 0.096  CL1   VC6 25 
VC6 F4B   F1  F  0 1 N N N 4.196  -0.250 14.126 3.975  -0.794 1.899  F4B   VC6 26 
VC6 PG    P3  P  0 1 N N N 3.556  0.898  16.507 5.648  -1.384 -0.059 PG    VC6 27 
VC6 O2G   O10 O  0 1 N N N 3.495  2.324  17.026 6.645  -0.176 0.313  O2G   VC6 28 
VC6 O1G   O11 O  0 1 N N N 4.384  0.057  17.439 6.149  -2.734 0.660  O1G   VC6 29 
VC6 O3G   O12 O  0 1 N N N 2.183  0.339  16.365 5.637  -1.581 -1.526 O3G   VC6 30 
VC6 H1    H1  H  0 1 N N N 11.352 7.765  10.380 -7.434 -4.703 -0.897 H1    VC6 31 
VC6 H2    H2  H  0 1 N N N 11.110 7.268  12.022 -7.141 -4.702 0.758  H2    VC6 32 
VC6 H3    H3  H  0 1 N N N 8.885  6.903  12.936 -6.746 -2.888 -2.361 H3    VC6 33 
VC6 H4    H4  H  0 1 N N N 6.433  6.945  12.533 -5.635 -0.711 -2.508 H4    VC6 34 
VC6 H5    H5  H  0 1 N N N 4.954  8.357  9.534  -4.483 0.985  -1.534 H5    VC6 35 
VC6 H6    H6  H  0 1 N N N 3.955  6.261  9.005  -6.131 2.173  -0.249 H6    VC6 36 
VC6 H7    H7  H  0 1 N N N 5.676  5.759  9.120  -5.739 1.266  1.252  H7    VC6 37 
VC6 H8    H8  H  0 1 N N N 5.369  4.656  11.063 -4.410 3.248  1.593  H8    VC6 38 
VC6 H9    H9  H  0 1 N N N 3.447  3.599  11.246 -4.821 4.189  -0.600 H9    VC6 39 
VC6 H10   H10 H  0 1 N N N 5.390  6.090  12.355 -2.782 1.603  1.849  H10   VC6 40 
VC6 H11   H11 H  0 1 N N N 2.783  6.884  13.168 -1.911 2.593  -0.906 H11   VC6 41 
VC6 H12   H12 H  0 1 N N N 2.974  5.098  13.155 -1.613 3.469  0.614  H12   VC6 42 
VC6 H13   H13 H  0 1 N N N 4.397  4.930  16.802 1.403  3.365  1.580  H13   VC6 43 
VC6 H14   H14 H  0 1 N N N 1.789  2.923  13.691 2.804  -0.378 -2.194 H14   VC6 44 
VC6 H15   H15 H  0 1 N N N 2.588  2.575  17.157 6.702  0.009  1.260  H15   VC6 45 
VC6 H16   H16 H  0 1 N N N 3.863  -0.671 17.756 7.039  -3.010 0.403  H16   VC6 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 
VC6 O2    C2    DOUB N N 1  
VC6 C2    N3    SING N N 2  
VC6 C2    N1    SING N N 3  
VC6 "C2'" "C1'" SING N N 4  
VC6 "C2'" "C3'" SING N N 5  
VC6 N3    C4    DOUB N N 6  
VC6 "C1'" N1    SING N N 7  
VC6 "C1'" "O4'" SING N N 8  
VC6 N1    C6    SING N N 9  
VC6 "O3'" "C3'" SING N N 10 
VC6 "C3'" "C4'" SING N N 11 
VC6 C4    N4    SING N N 12 
VC6 C4    C5    SING N N 13 
VC6 "O4'" "C4'" SING N N 14 
VC6 C6    C5    DOUB N N 15 
VC6 "C4'" "C5'" SING N N 16 
VC6 O2B   PB    DOUB N N 17 
VC6 "C5'" "O5'" SING N N 18 
VC6 PB    O3A   SING N N 19 
VC6 PB    O1B   SING N N 20 
VC6 PB    C3B   SING N N 21 
VC6 O3A   PA    SING N N 22 
VC6 "O5'" PA    SING N N 23 
VC6 F4B   C3B   SING N N 24 
VC6 C3B   CL1   SING N N 25 
VC6 C3B   PG    SING N N 26 
VC6 PA    O2A   DOUB N N 27 
VC6 PA    O1A   SING N N 28 
VC6 O3G   PG    DOUB N N 29 
VC6 PG    O2G   SING N N 30 
VC6 PG    O1G   SING N N 31 
VC6 N4    H1    SING N N 32 
VC6 N4    H2    SING N N 33 
VC6 C5    H3    SING N N 34 
VC6 C6    H4    SING N N 35 
VC6 "C1'" H5    SING N N 36 
VC6 "C2'" H6    SING N N 37 
VC6 "C2'" H7    SING N N 38 
VC6 "C3'" H8    SING N N 39 
VC6 "O3'" H9    SING N N 40 
VC6 "C4'" H10   SING N N 41 
VC6 "C5'" H11   SING N N 42 
VC6 "C5'" H12   SING N N 43 
VC6 O1A   H13   SING N N 44 
VC6 O1B   H14   SING N N 45 
VC6 O2G   H15   SING N N 46 
VC6 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 
VC6 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)F)=O"                                                                                                                                   
VC6 InChI            InChI                1.03  "InChI=1S/C10H16ClFN3O12P3/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+,10+/m0/s1" 
VC6 InChIKey         InChI                1.03  KEKPFSDJAHISFV-VBOXYBSHSA-N                                                                                                                                                                              
VC6 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@@](F)(Cl)[P](O)(O)=O)O2"                                                                                                                
VC6 SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[C](F)(Cl)[P](O)(O)=O)O2"                                                                                                                     
VC6 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@](F)(P(=O)(O)O)Cl)O)O"                                                                                                                       
VC6 SMILES           "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(F)(P(=O)(O)O)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 
VC6 "SYSTEMATIC NAME" ACDLabs              12.01 "4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one"                                
VC6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{S})-[[[(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]-chloranyl-fluoranyl-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 
VC6 "Create component" 2018-03-26 RCSB 
VC6 "Initial release"  2018-06-20 RCSB 
# 
