data_VA7
# 
_chem_comp.id                                    VA7 
_chem_comp.name                                  "2'-deoxy-5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H16 Cl2 N5 O11 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-03-22 
_chem_comp.pdbx_modified_date                    2018-07-20 
_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                        558.099 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VA7 
_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        6CRC 
_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 
VA7 N1    N1  N  0 1 Y N N 68.034 8.099  7.531  -8.458 -2.309 -0.709 N1    VA7 1  
VA7 C2    C1  C  0 1 Y N N 66.870 7.813  6.961  -7.975 -1.574 -1.694 C2    VA7 2  
VA7 N3    N2  N  0 1 Y N N 65.870 7.317  7.653  -6.894 -0.834 -1.559 N3    VA7 3  
VA7 C4    C2  C  0 1 Y N N 66.006 7.082  8.994  -6.237 -0.799 -0.404 C4    VA7 4  
VA7 C5    C3  C  0 1 Y N N 67.212 7.363  9.666  -6.711 -1.564 0.675  C5    VA7 5  
VA7 C6    C4  C  0 1 Y N N 68.261 7.893  8.861  -7.868 -2.338 0.482  C6    VA7 6  
VA7 N6    N3  N  0 1 N N N 69.552 8.224  9.435  -8.382 -3.111 1.508  N6    VA7 7  
VA7 N7    N4  N  0 1 Y N N 67.022 7.024  10.981 -5.871 -1.350 1.716  N7    VA7 8  
VA7 C8    C5  C  0 1 Y N N 65.765 6.559  11.131 -4.933 -0.523 1.353  C8    VA7 9  
VA7 N9    N5  N  0 1 Y N N 65.153 6.590  9.943  -5.116 -0.154 0.053  N9    VA7 10 
VA7 PA    P1  P  0 1 N N N 63.971 4.016  14.306 1.285  1.744  0.878  PA    VA7 11 
VA7 PB    P2  P  0 1 N N N 63.496 1.308  13.514 3.926  0.464  0.467  PB    VA7 12 
VA7 PG    P3  P  0 1 N N N 63.455 -0.145 16.143 6.244  -1.251 -0.275 PG    VA7 13 
VA7 "C1'" C6  C  0 1 N N R 63.805 6.168  9.647  -4.269 0.762  -0.715 "C1'" VA7 14 
VA7 O1A   O1  O  0 1 N N N 62.926 3.842  15.396 1.039  1.518  2.454  O1A   VA7 15 
VA7 O2B   O2  O  0 1 N N N 63.484 0.684  12.154 4.294  0.342  1.896  O2B   VA7 16 
VA7 O1G   O3  O  0 1 N N N 63.503 1.072  17.049 6.644  -1.383 1.279  O1G   VA7 17 
VA7 "C2'" C7  C  0 1 N N N 63.820 4.942  9.317  -4.802 2.208  -0.603 "C2'" VA7 18 
VA7 O2A   O4  O  0 1 N N N 65.294 4.414  14.938 1.831  3.101  0.654  O2A   VA7 19 
VA7 O1B   O5  O  0 1 N N N 62.085 1.435  14.024 4.668  1.742  -0.171 O1B   VA7 20 
VA7 O2G   O6  O  0 1 N N N 64.163 -1.350 16.706 6.697  -2.581 -1.061 O2G   VA7 21 
VA7 "C3'" C8  C  0 1 N N S 63.480 4.209  10.576 -3.525 3.076  -0.544 "C3'" VA7 22 
VA7 "O3'" O7  O  0 1 N N N 63.021 2.937  10.314 -3.478 3.974  -1.654 "O3'" VA7 23 
VA7 O3A   O8  O  0 1 N N N 64.190 2.716  13.391 2.332  0.648  0.336  O3A   VA7 24 
VA7 C3B   C9  C  0 1 N N N 64.441 0.271  14.672 4.439  -1.043 -0.423 C3B   VA7 25 
VA7 CL1   CL1 CL 0 0 N N N 64.897 -1.279 13.965 3.609  -2.474 0.292  CL1B  VA7 26 
VA7 CL2   CL2 CL 0 0 N N N 65.799 1.167  15.300 3.992  -0.894 -2.163 CL2B  VA7 27 
VA7 O3G   O9  O  0 1 N N N 62.016 -0.540 15.802 6.926  -0.075 -0.861 O3G   VA7 28 
VA7 "C4'" C10 C  0 1 N N R 62.413 5.160  11.172 -2.371 2.052  -0.627 "C4'" VA7 29 
VA7 "O4'" O10 O  0 1 N N N 62.896 6.295  10.968 -2.941 0.814  -0.148 "O4'" VA7 30 
VA7 "C5'" C11 C  0 1 N N N 62.202 4.962  12.708 -1.209 2.484  0.269  "C5'" VA7 31 
VA7 "O5'" O11 O  0 1 N N N 63.479 5.136  13.307 -0.110 1.589  0.090  "O5'" VA7 32 
VA7 H1    H1  H  0 1 N N N 66.742 7.992  5.904  -8.485 -1.580 -2.645 H1    VA7 33 
VA7 H2    H2  H  0 1 N N N 70.151 8.588  8.722  -9.181 -3.641 1.362  H2    VA7 34 
VA7 H3    H3  H  0 1 N N N 69.432 8.911  10.152 -7.943 -3.124 2.373  H3    VA7 35 
VA7 H4    H4  H  0 1 N N N 65.326 6.218  12.057 -4.130 -0.180 1.988  H4    VA7 36 
VA7 H5    H5  H  0 1 N N N 63.368 6.815  8.872  -4.225 0.452  -1.758 H5    VA7 37 
VA7 H6    H6  H  0 1 N N N 63.319 4.018  16.243 0.681  0.647  2.675  H6    VA7 38 
VA7 H7    H7  H  0 1 N N N 62.618 1.363  17.236 6.232  -2.134 1.729  H7    VA7 39 
VA7 H8    H8  H  0 1 N N N 63.072 4.741  8.536  -5.398 2.464  -1.479 H8    VA7 40 
VA7 H9    H9  H  0 1 N N N 64.816 4.650  8.954  -5.389 2.329  0.308  H9    VA7 41 
VA7 H10   H10 H  0 1 N N N 61.481 1.092  13.375 4.473  1.884  -1.107 H10   VA7 42 
VA7 H11   H11 H  0 1 N N N 63.565 -2.088 16.726 7.648  -2.755 -1.024 H11   VA7 43 
VA7 H12   H12 H  0 1 N N N 64.355 4.191  11.242 -3.480 3.626  0.396  H12   VA7 44 
VA7 H13   H13 H  0 1 N N N 63.271 2.357  11.024 -4.214 4.600  -1.684 H13   VA7 45 
VA7 H14   H14 H  0 1 N N N 61.455 4.988  10.659 -2.034 1.942  -1.658 H14   VA7 46 
VA7 H15   H15 H  0 1 N N N 61.494 5.709  13.095 -0.902 3.495  0.002  H15   VA7 47 
VA7 H16   H16 H  0 1 N N N 61.818 3.952  12.914 -1.528 2.465  1.312  H16   VA7 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 
VA7 C2    N1    DOUB Y N 1  
VA7 C2    N3    SING Y N 2  
VA7 N1    C6    SING Y N 3  
VA7 N3    C4    DOUB Y N 4  
VA7 C6    N6    SING N N 5  
VA7 C6    C5    DOUB Y N 6  
VA7 C4    C5    SING Y N 7  
VA7 C4    N9    SING Y N 8  
VA7 "C2'" "C1'" SING N N 9  
VA7 "C2'" "C3'" SING N N 10 
VA7 "C1'" N9    SING N N 11 
VA7 "C1'" "O4'" SING N N 12 
VA7 C5    N7    SING Y N 13 
VA7 N9    C8    SING Y N 14 
VA7 "O3'" "C3'" SING N N 15 
VA7 "C3'" "C4'" SING N N 16 
VA7 "O4'" "C4'" SING N N 17 
VA7 N7    C8    DOUB Y N 18 
VA7 "C4'" "C5'" SING N N 19 
VA7 O2B   PB    DOUB N N 20 
VA7 "C5'" "O5'" SING N N 21 
VA7 "O5'" PA    SING N N 22 
VA7 O3A   PB    SING N N 23 
VA7 O3A   PA    SING N N 24 
VA7 PB    O1B   SING N N 25 
VA7 PB    C3B   SING N N 26 
VA7 CL1   C3B   SING N N 27 
VA7 PA    O2A   DOUB N N 28 
VA7 PA    O1A   SING N N 29 
VA7 C3B   CL2   SING N N 30 
VA7 C3B   PG    SING N N 31 
VA7 O3G   PG    DOUB N N 32 
VA7 PG    O2G   SING N N 33 
VA7 PG    O1G   SING N N 34 
VA7 C2    H1    SING N N 35 
VA7 N6    H2    SING N N 36 
VA7 N6    H3    SING N N 37 
VA7 C8    H4    SING N N 38 
VA7 "C1'" H5    SING N N 39 
VA7 O1A   H6    SING N N 40 
VA7 O1G   H7    SING N N 41 
VA7 "C2'" H8    SING N N 42 
VA7 "C2'" H9    SING N N 43 
VA7 O1B   H10   SING N N 44 
VA7 O2G   H11   SING N N 45 
VA7 "C3'" H12   SING N N 46 
VA7 "O3'" H13   SING N N 47 
VA7 "C4'" H14   SING N N 48 
VA7 "C5'" H15   SING N N 49 
VA7 "C5'" H16   SING N N 50 
# 
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 
VA7 SMILES           ACDLabs              12.01 "n1c(c2c(nc1)n(cn2)C3OC(C(C3)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)(Cl)Cl)=O)N"                                                                                                                                
VA7 InChI            InChI                1.03  "InChI=1S/C11H16Cl2N5O11P3/c12-11(13,30(20,21)22)31(23,24)29-32(25,26)27-2-6-5(19)1-7(28-6)18-4-17-8-9(14)15-3-16-10(8)18/h3-7,19H,1-2H2,(H,23,24)(H,25,26)(H2,14,15,16)(H2,20,21,22)/t5-,6+,7+/m0/s1" 
VA7 InChIKey         InChI                1.03  AQFODBPFKZIBHW-RRKCRQDMSA-N                                                                                                                                                                            
VA7 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O3"                                                                                                                 
VA7 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O3"                                                                                                                     
VA7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O)N"                                                                                                                   
VA7 SMILES           "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O)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 
VA7 "SYSTEMATIC NAME" ACDLabs              12.01 "2'-deoxy-5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine"                                                      
VA7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-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 
VA7 "Create component" 2018-03-22 RCSB 
VA7 "Initial release"  2018-07-25 RCSB 
# 
