data_VT7
# 
_chem_comp.id                                    VT7 
_chem_comp.name                                  "5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H17 F2 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                        516.176 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VT7 
_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        6CTO 
_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 
VT7 O4    O1  O 0 1 N N N 10.876 7.731  10.924 -7.478 -3.049 1.385  O4    VT7 1  
VT7 C4    C1  C 0 1 N N N 9.480  7.683  10.641 -6.765 -2.247 0.810  C4    VT7 2  
VT7 C5    C2  C 0 1 N N N 8.620  7.214  11.641 -6.584 -2.326 -0.592 C5    VT7 3  
VT7 C5M   C3  C 0 1 N N N 9.112  6.772  13.000 -7.272 -3.403 -1.390 C5M   VT7 4  
VT7 C6    C4  C 0 1 N N N 7.252  7.171  11.330 -5.789 -1.423 -1.204 C6    VT7 5  
VT7 N3    N1  N 0 1 N N N 8.990  8.052  9.450  -6.144 -1.270 1.503  N3    VT7 6  
VT7 C2    C5  C 0 1 N N N 7.681  7.980  9.229  -5.356 -0.383 0.868  C2    VT7 7  
VT7 O2    O2  O 0 1 N N N 7.259  8.295  8.146  -4.803 0.492  1.505  O2    VT7 8  
VT7 N1    N2  N 0 1 N N N 6.817  7.558  10.146 -5.172 -0.451 -0.463 N1    VT7 9  
VT7 "C1'" C6  C 0 1 N N R 5.397  7.438  9.854  -4.309 0.529  -1.128 "C1'" VT7 10 
VT7 "C2'" C7  C 0 1 N N N 5.136  6.214  9.530  -4.876 1.955  -0.947 "C2'" VT7 11 
VT7 "C3'" C8  C 0 1 N N S 4.522  5.557  10.777 -3.621 2.838  -0.770 "C3'" VT7 12 
VT7 "O3'" O3  O 0 1 N N N 3.724  4.459  10.547 -3.540 3.809  -1.816 "O3'" VT7 13 
VT7 "O4'" O4  O 0 1 N N N 4.535  7.748  11.179 -3.011 0.566  -0.495 "O4'" VT7 14 
VT7 "C4'" C9  C 0 1 N N R 3.757  6.744  11.398 -2.444 1.842  -0.864 "C4'" VT7 15 
VT7 "C5'" C10 C 0 1 N N N 3.543  6.496  12.940 -1.335 2.234  0.114  "C5'" VT7 16 
VT7 "O5'" O5  O 0 1 N N N 4.850  6.410  13.589 -0.211 1.372  -0.070 "O5'" VT7 17 
VT7 PA    P1  P 0 1 N N N 5.092  5.241  14.671 1.142  1.498  0.794  PA    VT7 18 
VT7 O1A   O6  O 0 1 N N N 3.993  5.270  15.712 0.826  1.164  2.337  O1A   VT7 19 
VT7 O2A   O7  O 0 1 N N N 6.453  5.424  15.313 1.670  2.876  0.686  O2A   VT7 20 
VT7 O3A   O8  O 0 1 N N N 5.165  3.865  13.928 2.236  0.458  0.233  O3A   VT7 21 
VT7 PB    P2  P 0 1 N N N 4.089  2.682  13.830 3.826  0.293  0.429  PB    VT7 22 
VT7 O2B   O9  O 0 1 N N N 4.044  2.275  12.369 4.127  0.084  1.862  O2B   VT7 23 
VT7 O1B   O10 O 0 1 N N N 2.685  3.142  14.221 4.570  1.624  -0.087 O1B   VT7 24 
VT7 C3B   C11 C 0 1 N N N 4.735  1.242  14.796 4.410  -1.142 -0.532 C3B   VT7 25 
VT7 PG    P3  P 0 1 N N N 3.848  1.225  16.415 6.210  -1.328 -0.310 PG    VT7 26 
VT7 O3G   O11 O 0 1 N N N 2.445  0.773  16.194 6.512  -1.538 1.123  O3G   VT7 27 
VT7 O2G   O12 O 0 1 N N N 4.498  0.299  17.342 6.727  -2.595 -1.158 O2G   VT7 28 
VT7 O1G   O13 O 0 1 N N N 3.848  2.656  16.890 6.955  0.002  -0.826 O1G   VT7 29 
VT7 F2B   F1  F 0 1 N N N 6.091  1.323  14.908 3.763  -2.298 -0.083 F2B   VT7 30 
VT7 F3B   F2  F 0 1 N N N 4.393  0.090  14.185 4.125  -0.943 -1.887 F3B   VT7 31 
VT7 H1    H1  H 0 1 N N N 8.258  6.446  13.612 -7.865 -4.028 -0.722 H1    VT7 32 
VT7 H2    H2  H 0 1 N N N 9.817  5.936  12.881 -7.924 -2.944 -2.133 H2    VT7 33 
VT7 H3    H3  H 0 1 N N N 9.620  7.612  13.497 -6.524 -4.016 -1.893 H3    VT7 34 
VT7 H4    H4  H 0 1 N N N 6.548  6.817  12.068 -5.639 -1.468 -2.272 H4    VT7 35 
VT7 H5    H5  H 0 1 N N N 9.605  8.379  8.732  -6.265 -1.207 2.464  H5    VT7 36 
VT7 H6    H6  H 0 1 N N N 5.105  8.159  9.077  -4.209 0.290  -2.186 H6    VT7 37 
VT7 H7    H7  H 0 1 N N N 4.421  6.186  8.694  -5.435 2.258  -1.833 H7    VT7 38 
VT7 H8    H8  H 0 1 N N N 6.060  5.692  9.241  -5.508 2.005  -0.060 H8    VT7 39 
VT7 H9    H9  H 0 1 N N N 5.343  5.291  11.459 -3.632 3.326  0.205  H9    VT7 40 
VT7 H10   H10 H 0 1 N N N 3.904  3.794  11.201 -4.286 4.423  -1.840 H10   VT7 41 
VT7 H11   H11 H 0 1 N N N 2.775  6.839  10.912 -2.058 1.806  -1.882 H11   VT7 42 
VT7 H12   H12 H 0 1 N N N 2.970  7.329  13.372 -1.036 3.266  -0.071 H12   VT7 43 
VT7 H13   H13 H 0 1 N N N 2.993  5.555  13.090 -1.702 2.140  1.136  H13   VT7 44 
VT7 H14   H14 H 0 1 N N N 4.375  5.398  16.572 0.476  0.275  2.484  H14   VT7 45 
VT7 H15   H15 H 0 1 N N N 2.107  3.070  13.470 4.417  1.824  -1.021 H15   VT7 46 
VT7 H16   H16 H 0 1 N N N 3.884  -0.380 17.595 7.678  -2.755 -1.087 H16   VT7 47 
VT7 H17   H17 H 0 1 N N N 2.954  2.970  16.949 6.802  0.202  -1.760 H17   VT7 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 
VT7 O2    C2    DOUB N N 1  
VT7 C2    N3    SING N N 2  
VT7 C2    N1    SING N N 3  
VT7 N3    C4    SING N N 4  
VT7 "C2'" "C1'" SING N N 5  
VT7 "C2'" "C3'" SING N N 6  
VT7 "C1'" N1    SING N N 7  
VT7 "C1'" "O4'" SING N N 8  
VT7 N1    C6    SING N N 9  
VT7 "O3'" "C3'" SING N N 10 
VT7 C4    O4    DOUB N N 11 
VT7 C4    C5    SING N N 12 
VT7 "C3'" "C4'" SING N N 13 
VT7 "O4'" "C4'" SING N N 14 
VT7 C6    C5    DOUB N N 15 
VT7 "C4'" "C5'" SING N N 16 
VT7 C5    C5M   SING N N 17 
VT7 O2B   PB    DOUB N N 18 
VT7 "C5'" "O5'" SING N N 19 
VT7 "O5'" PA    SING N N 20 
VT7 PB    O3A   SING N N 21 
VT7 PB    O1B   SING N N 22 
VT7 PB    C3B   SING N N 23 
VT7 O3A   PA    SING N N 24 
VT7 F3B   C3B   SING N N 25 
VT7 PA    O2A   DOUB N N 26 
VT7 PA    O1A   SING N N 27 
VT7 C3B   F2B   SING N N 28 
VT7 C3B   PG    SING N N 29 
VT7 O3G   PG    DOUB N N 30 
VT7 PG    O1G   SING N N 31 
VT7 PG    O2G   SING N N 32 
VT7 C5M   H1    SING N N 33 
VT7 C5M   H2    SING N N 34 
VT7 C5M   H3    SING N N 35 
VT7 C6    H4    SING N N 36 
VT7 N3    H5    SING N N 37 
VT7 "C1'" H6    SING N N 38 
VT7 "C2'" H7    SING N N 39 
VT7 "C2'" H8    SING N N 40 
VT7 "C3'" H9    SING N N 41 
VT7 "O3'" H10   SING N N 42 
VT7 "C4'" H11   SING N N 43 
VT7 "C5'" H12   SING N N 44 
VT7 "C5'" H13   SING N N 45 
VT7 O1A   H14   SING N N 46 
VT7 O1B   H15   SING N N 47 
VT7 O2G   H16   SING N N 48 
VT7 O1G   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 
VT7 SMILES           ACDLabs              12.01 "O=C1C(C)=CN(C(N1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(F)(P(O)(O)=O)F)=O"                                                                                                                                
VT7 InChI            InChI                1.03  "InChI=1S/C11H17F2N2O13P3/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" 
VT7 InChIKey         InChI                1.03  PZJVGXNXDJKXPK-XLPZGREQSA-N                                                                                                                                                                          
VT7 SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                               
VT7 SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                   
VT7 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(F)(F)P(=O)(O)O)O)O"                                                                                                                     
VT7 SMILES           "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)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 
VT7 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"                                                                                           
VT7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[bis(fluoranyl)-[[[(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 
VT7 "Create component" 2018-03-26 RCSB 
VT7 "Initial release"  2018-06-20 RCSB 
# 
