data_VA4
# 
_chem_comp.id                                    VA4 
_chem_comp.name                                  "5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H17 Cl 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                    2018-06-29 
_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                        523.654 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VA4 
_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        6CR8 
_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 
VA4 N1    N1  N  0 1 Y N N 9.737  8.481  8.240  -8.240 -2.235 -0.773 N1    VA4 1  
VA4 C2    C1  C  0 1 Y N N 8.574  8.562  7.641  -7.774 -1.451 -1.727 C2    VA4 2  
VA4 N3    N2  N  0 1 Y N N 7.434  8.260  8.240  -6.682 -0.730 -1.579 N3    VA4 3  
VA4 C4    C2  C  0 1 Y N N 7.455  7.887  9.521  -5.996 -0.766 -0.442 C4    VA4 4  
VA4 C5    C3  C  0 1 Y N N 8.666  7.795  10.234 -6.452 -1.586 0.605  C5    VA4 5  
VA4 C6    C4  C  0 1 Y N N 9.835  8.108  9.512  -7.622 -2.336 0.399  C6    VA4 6  
VA4 N6    N3  N  0 1 N N N 11.163 8.007  10.166 -8.118 -3.161 1.393  N6    VA4 7  
VA4 N7    N4  N  0 1 Y N N 8.373  7.362  11.525 -5.583 -1.439 1.634  N7    VA4 8  
VA4 C8    C5  C  0 1 Y N N 7.066  7.230  11.602 -4.646 -0.603 1.294  C8    VA4 9  
VA4 N9    N5  N  0 1 Y N N 6.484  7.541  10.395 -4.856 -0.160 0.022  N9    VA4 10 
VA4 PA    P1  P  0 1 N N N 4.909  5.345  14.703 1.584  1.626  0.788  PA    VA4 11 
VA4 PB    P2  P  0 1 N N N 3.850  2.708  13.872 4.200  0.345  0.238  PB    VA4 12 
VA4 PG    P3  P  0 1 N N N 3.963  1.321  16.588 6.479  -1.348 -0.658 PG    VA4 13 
VA4 "C1'" C6  C  0 1 N N R 5.056  7.476  10.061 -4.019 0.790  -0.714 "C1'" VA4 14 
VA4 O1A   O1  O  0 1 N N N 3.918  5.448  15.862 1.375  1.314  2.354  O1A   VA4 15 
VA4 O2B   O2  O  0 1 N N N 3.765  2.203  12.398 4.601  0.140  1.648  O2B   VA4 16 
VA4 O1G   O3  O  0 1 N N N 3.576  2.738  17.003 6.915  -1.571 0.876  O1G   VA4 17 
VA4 "C2'" C7  C  0 1 N N N 4.767  6.262  9.698  -4.533 2.233  -0.508 "C2'" VA4 18 
VA4 O2A   O4  O  0 1 N N N 6.286  5.505  15.212 2.139  2.988  0.626  O2A   VA4 19 
VA4 O1B   O5  O  0 1 N N N 2.414  3.047  14.380 4.940  1.650  -0.346 O1B   VA4 20 
VA4 O2G   O6  O  0 1 N N N 5.069  0.803  17.602 6.897  -2.637 -1.528 O2G   VA4 21 
VA4 "C3'" C8  C  0 1 N N S 4.250  5.582  10.914 -3.245 3.083  -0.434 "C3'" VA4 22 
VA4 "O3'" O7  O  0 1 N N N 3.448  4.483  10.659 -3.216 4.041  -1.493 "O3'" VA4 23 
VA4 O3A   O8  O  0 1 N N N 4.858  3.938  13.888 2.605  0.552  0.159  O3A   VA4 24 
VA4 C3B   C9  C  0 1 N N R 4.681  1.401  14.936 4.673  -1.114 -0.747 C3B   VA4 25 
VA4 CL1   CL1 CL 0 0 N N N 4.632  -0.196 14.210 3.844  -2.576 -0.093 CL3B  VA4 26 
VA4 O3G   O9  O  0 1 N N N 2.819  0.413  16.632 7.159  -0.148 -1.195 O3G   VA4 27 
VA4 "C4'" C10 C  0 1 N N R 3.439  6.773  11.576 -2.105 2.054  -0.604 "C4'" VA4 28 
VA4 "O4'" O10 O  0 1 N N N 4.160  7.750  11.383 -2.677 0.797  -0.181 "O4'" VA4 29 
VA4 "C5'" C11 C  0 1 N N N 3.297  6.523  13.073 -0.916 2.424  0.285  "C5'" VA4 30 
VA4 "O5'" O11 O  0 1 N N N 4.589  6.461  13.598 0.168  1.529  0.028  "O5'" VA4 31 
VA4 H1    H1  H  0 1 N N N 8.545  8.890  6.612  -8.308 -1.398 -2.665 H1    VA4 32 
VA4 H2    H2  H  0 1 N N N 11.877 8.253  9.511  -8.927 -3.674 1.238  H2    VA4 33 
VA4 H3    H3  H  0 1 N N N 11.198 8.630  10.947 -7.658 -3.227 2.244  H3    VA4 34 
VA4 H4    H4  H  0 1 N N N 6.528  6.922  12.486 -3.823 -0.303 1.926  H4    VA4 35 
VA4 H5    H5  H  0 1 N N N 4.801  8.231  9.303  -4.004 0.539  -1.775 H5    VA4 36 
VA4 H6    H6  H  0 1 N N N 4.392  5.594  16.672 1.013  0.436  2.535  H6    VA4 37 
VA4 H7    H7  H  0 1 N N N 2.650  2.765  17.215 6.507  -2.342 1.293  H7    VA4 38 
VA4 H8    H8  H  0 1 N N N 4.000  6.271  8.910  -5.147 2.543  -1.353 H8    VA4 39 
VA4 H9    H9  H  0 1 N N N 5.667  5.750  9.327  -5.095 2.308  0.422  H9    VA4 40 
VA4 H10   H10 H  0 1 N N N 1.785  2.877  13.689 4.723  1.846  -1.268 H10   VA4 41 
VA4 H11   H11 H  0 1 N N N 4.762  0.012  18.029 7.846  -2.822 -1.526 H11   VA4 42 
VA4 H12   H12 H  0 1 N N N 5.087  5.320  11.577 -3.170 3.579  0.534  H12   VA4 43 
VA4 H13   H13 H  0 1 N N N 3.638  3.799  11.290 -3.945 4.676  -1.469 H13   VA4 44 
VA4 H14   H14 H  0 1 N N N 5.735  1.697  15.043 4.377  -0.963 -1.785 H14   VA4 45 
VA4 H15   H15 H  0 1 N N N 2.444  6.832  11.111 -1.795 1.999  -1.647 H15   VA4 46 
VA4 H16   H16 H  0 1 N N N 2.737  7.345  13.542 -0.604 3.445  0.068  H16   VA4 47 
VA4 H17   H17 H  0 1 N N N 2.771  5.573  13.250 -1.208 2.349  1.333  H17   VA4 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 
VA4 C2    N1    DOUB Y N 1  
VA4 C2    N3    SING Y N 2  
VA4 N1    C6    SING Y N 3  
VA4 N3    C4    DOUB Y N 4  
VA4 C6    N6    SING N N 5  
VA4 C6    C5    DOUB Y N 6  
VA4 C4    C5    SING Y N 7  
VA4 C4    N9    SING Y N 8  
VA4 "C2'" "C1'" SING N N 9  
VA4 "C2'" "C3'" SING N N 10 
VA4 "C1'" N9    SING N N 11 
VA4 "C1'" "O4'" SING N N 12 
VA4 C5    N7    SING Y N 13 
VA4 N9    C8    SING Y N 14 
VA4 "O3'" "C3'" SING N N 15 
VA4 "C3'" "C4'" SING N N 16 
VA4 "O4'" "C4'" SING N N 17 
VA4 N7    C8    DOUB Y N 18 
VA4 "C4'" "C5'" SING N N 19 
VA4 O2B   PB    DOUB N N 20 
VA4 "C5'" "O5'" SING N N 21 
VA4 "O5'" PA    SING N N 22 
VA4 PB    O3A   SING N N 23 
VA4 PB    O1B   SING N N 24 
VA4 PB    C3B   SING N N 25 
VA4 O3A   PA    SING N N 26 
VA4 CL1   C3B   SING N N 27 
VA4 PA    O2A   DOUB N N 28 
VA4 PA    O1A   SING N N 29 
VA4 C3B   PG    SING N N 30 
VA4 PG    O3G   DOUB N N 31 
VA4 PG    O1G   SING N N 32 
VA4 PG    O2G   SING N N 33 
VA4 C2    H1    SING N N 34 
VA4 N6    H2    SING N N 35 
VA4 N6    H3    SING N N 36 
VA4 C8    H4    SING N N 37 
VA4 "C1'" H5    SING N N 38 
VA4 O1A   H6    SING N N 39 
VA4 O1G   H7    SING N N 40 
VA4 "C2'" H8    SING N N 41 
VA4 "C2'" H9    SING N N 42 
VA4 O1B   H10   SING N N 43 
VA4 O2G   H11   SING N N 44 
VA4 "C3'" H12   SING N N 45 
VA4 "O3'" H13   SING N N 46 
VA4 C3B   H14   SING N N 47 
VA4 "C4'" H15   SING N N 48 
VA4 "C5'" H16   SING N N 49 
VA4 "C5'" H17   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 
VA4 SMILES           ACDLabs              12.01 "n1c(c2c(nc1)n(cn2)C3OC(C(C3)O)COP(=O)(O)OP(O)(C(P(=O)(O)O)Cl)=O)N"                                                                                                                                       
VA4 InChI            InChI                1.03  "InChI=1S/C11H17ClN5O11P3/c12-11(29(19,20)21)30(22,23)28-31(24,25)26-2-6-5(18)1-7(27-6)17-4-16-8-9(13)14-3-15-10(8)17/h3-7,11,18H,1-2H2,(H,22,23)(H,24,25)(H2,13,14,15)(H2,19,20,21)/t5-,6+,7+,11+/m0/s1" 
VA4 InChIKey         InChI                1.03  VNWJWEHIFBMHOO-ZSJKCOSDSA-N                                                                                                                                                                               
VA4 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@H](Cl)[P](O)(O)=O)O3"                                                                                                                    
VA4 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](Cl)[P](O)(O)=O)O3"                                                                                                                         
VA4 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@@H](P(=O)(O)O)Cl)O)O)N"                                                                                                                     
VA4 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)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 
VA4 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine"                                                       
VA4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-[[[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-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 
VA4 "Create component" 2018-03-22 RCSB 
VA4 "Initial release"  2018-07-04 RCSB 
# 
