data_VT8
# 
_chem_comp.id                                    VT8 
_chem_comp.name                                  "5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H17 Cl2 N2 O13 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                        549.086 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VT8 
_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        6CTI 
_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 
VT8 N1    N1  N  0 1 N N N 6.800  7.539  10.183 5.375  -0.462 0.447  N1    VT8 1  
VT8 C2    C1  C  0 1 N N N 7.664  7.948  9.246  5.579  -0.373 -0.879 C2    VT8 2  
VT8 O2    O1  O  0 1 N N N 7.255  8.251  8.167  5.053  0.525  -1.508 O2    VT8 3  
VT8 N3    N2  N  0 1 N N N 8.988  8.000  9.463  6.357  -1.265 -1.521 N3    VT8 4  
VT8 C4    C2  C  0 1 N N N 9.509  7.659  10.665 6.947  -2.267 -0.839 C4    VT8 5  
VT8 O4    O2  O  0 1 N N N 10.706 7.723  10.856 7.652  -3.073 -1.419 O4    VT8 6  
VT8 C5    C3  C  0 1 N N N 8.647  7.220  11.702 6.740  -2.372 0.558  C5    VT8 7  
VT8 C7    C4  C  0 1 N N N 9.139  6.805  13.086 7.388  -3.483 1.344  C7    VT8 8  
VT8 C6    C5  C  0 1 N N N 7.269  7.188  11.402 5.955  -1.464 1.176  C6    VT8 9  
VT8 PA    P1  P  0 1 N N N 5.122  5.208  14.603 -0.879 1.656  -0.841 PA    VT8 10 
VT8 PB    P2  P  0 1 N N N 4.060  2.618  13.795 -3.593 0.510  -0.523 PB    VT8 11 
VT8 PG    P3  P  0 1 N N N 4.080  1.311  16.425 -6.023 -1.067 0.164  PG    VT8 12 
VT8 "C1'" C6  C  0 1 N N R 5.480  7.450  9.914  4.528  0.526  1.119  "C1'" VT8 13 
VT8 O1A   O3  O  0 1 N N N 4.077  5.287  15.721 -0.555 1.341  -2.386 O1A   VT8 14 
VT8 O2B   O4  O  0 1 N N N 3.964  2.158  12.327 -3.885 0.331  -1.963 O2B   VT8 15 
VT8 O1G   O5  O  0 1 N N N 3.916  2.736  16.793 -6.340 -1.261 -1.402 O1G   VT8 16 
VT8 "C2'" C7  C  0 1 N N N 5.081  6.025  9.540  5.130  1.941  0.969  "C2'" VT8 17 
VT8 O2A   O6  O  0 1 N N N 6.546  5.321  15.137 -1.375 3.045  -0.714 O2A   VT8 18 
VT8 O1B   O7  O  0 1 N N N 2.681  2.982  14.268 -4.312 1.849  0.008  O1B   VT8 19 
VT8 CL1   CL1 CL 0 0 N N N 4.724  -0.307 14.094 -3.417 -2.427 -0.188 CL1   VT8 20 
VT8 O2G   O8  O  0 1 N N N 4.971  0.663  17.459 -6.578 -2.336 0.985  O2G   VT8 21 
VT8 "C3'" C8  C  0 1 N N S 4.635  5.503  10.665 3.898  2.857  0.794  "C3'" VT8 22 
VT8 "O3'" O9  O  0 1 N N N 3.793  4.301  10.551 3.829  3.811  1.855  "O3'" VT8 23 
VT8 O3A   O10 O  0 1 N N N 5.040  3.844  13.783 -2.003 0.634  -0.309 O3A   VT8 24 
VT8 C3B   C9  C  0 1 N N N 4.856  1.292  14.805 -4.222 -0.927 0.407  C3B   VT8 25 
VT8 O3G   O11 O  0 1 N N N 2.752  0.590  16.282 -6.684 0.164  0.652  O3G   VT8 26 
VT8 "C4'" C10 C  0 1 N N R 3.837  6.737  11.338 2.697  1.887  0.859  "C4'" VT8 27 
VT8 "O4'" O12 O  0 1 N N N 4.588  7.732  11.157 3.238  0.604  0.475  "O4'" VT8 28 
VT8 "C5'" C11 C  0 1 N N N 3.595  6.473  12.871 1.608  2.322  -0.123 "C5'" VT8 29 
VT8 "O5'" O13 O  0 1 N N N 4.878  6.383  13.512 0.462  1.484  0.035  "O5'" VT8 30 
VT8 CL2   CL2 CL 0 0 N N N 6.536  1.575  15.017 -3.867 -0.710 2.161  CL2   VT8 31 
VT8 H1    H1  H  0 1 N N N 9.597  8.295  8.727  6.493  -1.186 -2.478 H1    VT8 32 
VT8 H2    H2  H  0 1 N N N 8.281  6.507  13.706 7.978  -4.107 0.672  H2    VT8 33 
VT8 H3    H3  H  0 1 N N N 9.834  5.958  12.989 8.038  -3.056 2.108  H3    VT8 34 
VT8 H4    H4  H  0 1 N N N 9.657  7.652  13.560 6.617  -4.089 1.819  H4    VT8 35 
VT8 H5    H5  H  0 1 N N N 6.571  6.875  12.165 5.787  -1.528 2.241  H5    VT8 36 
VT8 H6    H6  H  0 1 N N N 5.183  8.132  9.104  4.411  0.272  2.173  H6    VT8 37 
VT8 H7    H7  H  0 1 N N N 4.515  5.394  16.557 -0.224 0.446  -2.544 H7    VT8 38 
VT8 H8    H8  H  0 1 N N N 2.991  2.938  16.873 -5.938 -2.050 -1.790 H8    VT8 39 
VT8 H9    H9  H  0 1 N N N 4.292  6.030  8.774  5.686  2.216  1.865  H9    VT8 40 
VT8 H10   H10 H  0 1 N N N 5.950  5.463  9.168  5.772  1.992  0.090  H10   VT8 41 
VT8 H11   H11 H  0 1 N N N 2.059  2.849  13.563 -4.164 2.029  0.947  H11   VT8 42 
VT8 H12   H12 H  0 1 N N N 4.527  -0.088 17.834 -7.532 -2.472 0.902  H12   VT8 43 
VT8 H13   H13 H  0 1 N N N 5.474  5.271  11.337 3.931  3.360  -0.172 H13   VT8 44 
VT8 H14   H14 H  0 1 N N N 4.008  3.695  11.251 4.589  4.408  1.898  H14   VT8 45 
VT8 H15   H15 H  0 1 N N N 2.861  6.827  10.838 2.298  1.845  1.872  H15   VT8 46 
VT8 H16   H16 H  0 1 N N N 3.017  7.302  13.306 1.331  3.357  0.076  H16   VT8 47 
VT8 H17   H17 H  0 1 N N N 3.043  5.531  13.005 1.983  2.237  -1.143 H17   VT8 48 
# 
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 
VT8 O2    C2    DOUB N N 1  
VT8 C2    N3    SING N N 2  
VT8 C2    N1    SING N N 3  
VT8 N3    C4    SING N N 4  
VT8 "C2'" "C1'" SING N N 5  
VT8 "C2'" "C3'" SING N N 6  
VT8 "C1'" N1    SING N N 7  
VT8 "C1'" "O4'" SING N N 8  
VT8 N1    C6    SING N N 9  
VT8 "O3'" "C3'" SING N N 10 
VT8 "C3'" "C4'" SING N N 11 
VT8 C4    O4    DOUB N N 12 
VT8 C4    C5    SING N N 13 
VT8 "O4'" "C4'" SING N N 14 
VT8 "C4'" "C5'" SING N N 15 
VT8 C6    C5    DOUB N N 16 
VT8 C5    C7    SING N N 17 
VT8 O2B   PB    DOUB N N 18 
VT8 "C5'" "O5'" SING N N 19 
VT8 "O5'" PA    SING N N 20 
VT8 O3A   PB    SING N N 21 
VT8 O3A   PA    SING N N 22 
VT8 PB    O1B   SING N N 23 
VT8 PB    C3B   SING N N 24 
VT8 CL1   C3B   SING N N 25 
VT8 PA    O2A   DOUB N N 26 
VT8 PA    O1A   SING N N 27 
VT8 C3B   CL2   SING N N 28 
VT8 C3B   PG    SING N N 29 
VT8 O3G   PG    DOUB N N 30 
VT8 PG    O1G   SING N N 31 
VT8 PG    O2G   SING N N 32 
VT8 N3    H1    SING N N 33 
VT8 C7    H2    SING N N 34 
VT8 C7    H3    SING N N 35 
VT8 C7    H4    SING N N 36 
VT8 C6    H5    SING N N 37 
VT8 "C1'" H6    SING N N 38 
VT8 O1A   H7    SING N N 39 
VT8 O1G   H8    SING N N 40 
VT8 "C2'" H9    SING N N 41 
VT8 "C2'" H10   SING N N 42 
VT8 O1B   H11   SING N N 43 
VT8 O2G   H12   SING N N 44 
VT8 "C3'" H13   SING N N 45 
VT8 "O3'" H14   SING N N 46 
VT8 "C4'" H15   SING N N 47 
VT8 "C5'" H16   SING N N 48 
VT8 "C5'" H17   SING N N 49 
# 
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 
VT8 SMILES           ACDLabs              12.01 "N1(C=C(C(NC1=O)=O)C)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)(Cl)Cl)=O"                                                                                                                               
VT8 InChI            InChI                1.03  "InChI=1S/C11H17Cl2N2O13P3/c1-5-3-15(10(18)14-9(5)17)8-2-6(16)7(27-8)4-26-31(24,25)28-30(22,23)11(12,13)29(19,20)21/h3,6-8,16H,2,4H2,1H3,(H,22,23)(H,24,25)(H,14,17,18)(H2,19,20,21)/t6-,7+,8+/m0/s1" 
VT8 InChIKey         InChI                1.03  SHEBHODIZXGBLE-XLPZGREQSA-N                                                                                                                                                                           
VT8 SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                              
VT8 SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                  
VT8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O"                                                                                                                    
VT8 SMILES           "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)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 
VT8 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"                                                                                           
VT8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[bis(chloranyl)-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]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 
VT8 "Create component" 2018-03-26 RCSB 
VT8 "Initial release"  2018-06-20 RCSB 
# 
