data_VA5
# 
_chem_comp.id                                    VA5 
_chem_comp.name                                  "9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H16 Cl F 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                        541.644 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VA5 
_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        6CR9 
_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 
VA5 PA    P1  P  0 1 N N N 5.011  5.096  14.702 1.356  -1.793 -0.485 PA    VA5 1  
VA5 O1A   O1  O  0 1 N N N 4.000  5.112  15.827 1.054  -1.907 -2.062 O1A   VA5 2  
VA5 O2A   O2  O  0 1 N N N 6.364  5.225  15.259 1.934  -3.066 -0.000 O2A   VA5 3  
VA5 O3A   O3  O  0 1 N N N 4.948  3.724  13.873 2.401  -0.596 -0.225 O3A   VA5 4  
VA5 "O5'" O4  O  0 1 N N N 4.754  6.290  13.646 -0.014 -1.490 0.304  "O5'" VA5 5  
VA5 PB    P2  P  0 1 N N N 3.756  2.653  13.833 3.987  -0.427 -0.449 PB    VA5 6  
VA5 O2B   O5  O  0 1 N N N 3.659  2.195  12.370 4.303  -0.605 -1.884 O2B   VA5 7  
VA5 O1B   O6  O  0 1 N N N 2.420  3.256  14.299 4.773  -1.534 0.416  O1B   VA5 8  
VA5 C3B   C1  C  0 1 N N S 4.229  1.187  14.816 4.501  1.239  0.084  C3B   VA5 9  
VA5 F3B   F1  F  0 1 N N N 4.048  0.029  14.102 3.819  2.201  -0.667 F3B   VA5 10 
VA5 CL1   CL1 CL 0 0 N N N 5.923  1.289  15.118 4.115  1.456  1.832  F3CL  VA5 11 
VA5 PG    P3  P  0 1 N N N 3.377  1.141  16.420 6.296  1.431  -0.170 PG    VA5 12 
VA5 O1G   O7  O  0 1 N N N 3.429  2.529  17.027 6.751  2.901  0.301  O1G   VA5 13 
VA5 O2G   O8  O  0 1 N N N 4.070  0.158  17.275 7.082  0.323  0.695  O2G   VA5 14 
VA5 O3G   O9  O  0 1 N N N 1.929  0.712  16.215 6.613  1.252  -1.605 O3G   VA5 15 
VA5 "C5'" C2  C  0 1 N N N 3.490  6.360  12.971 -1.102 -2.415 0.357  "C5'" VA5 16 
VA5 "C4'" C3  C  0 1 N N R 3.456  6.988  11.524 -2.241 -1.815 1.184  "C4'" VA5 17 
VA5 "O4'" O10 O  0 1 N N N 4.247  7.958  11.302 -2.789 -0.680 0.505  "O4'" VA5 18 
VA5 "C1'" C4  C  0 1 N N S 5.322  7.130  10.655 -4.168 -0.919 0.183  "C1'" VA5 19 
VA5 N9    N1  N  0 1 Y N N 6.608  7.480  10.566 -4.945 0.315  0.320  N9    VA5 20 
VA5 C4    C5  C  0 1 Y N N 7.436  7.853  9.556  -6.135 0.599  -0.299 C4    VA5 21 
VA5 N3    N2  N  0 1 Y N N 7.327  8.190  8.226  -6.930 -0.047 -1.146 N3    VA5 22 
VA5 C2    C6  C  0 1 Y N N 8.434  8.546  7.557  -8.044 0.506  -1.577 C2    VA5 23 
VA5 N1    N3  N  0 1 Y N N 9.645  8.583  8.114  -8.427 1.713  -1.201 N1    VA5 24 
VA5 C6    C7  C  0 1 Y N N 9.836  8.260  9.411  -7.697 2.435  -0.357 C6    VA5 25 
VA5 N6    N4  N  0 1 N N N 11.084 8.273  10.067 -8.107 3.699  0.032  N6    VA5 26 
VA5 C5    C8  C  0 1 Y N N 8.708  7.878  10.163 -6.499 1.886  0.131  C5    VA5 27 
VA5 N7    N5  N  0 1 Y N N 8.592  7.510  11.468 -5.530 2.313  0.976  N7    VA5 28 
VA5 C8    C9  C  0 1 Y N N 7.320  7.248  11.667 -4.620 1.391  1.092  C8    VA5 29 
VA5 "C2'" C10 C  0 1 N N N 4.694  6.246  9.619  -4.647 -1.975 1.212  "C2'" VA5 30 
VA5 "C3'" C11 C  0 1 N N R 3.656  5.887  10.327 -3.372 -2.854 1.349  "C3'" VA5 31 
VA5 "O3'" O11 O  0 1 N N N 3.682  4.492  10.875 -3.315 -3.834 0.311  "O3'" VA5 32 
VA5 H1    H1  H  0 1 N N N 4.452  5.202  16.658 0.673  -1.106 -2.448 H1    VA5 33 
VA5 H2    H2  H  0 1 N N N 1.793  3.227  13.586 4.611  -1.477 1.367  H2    VA5 34 
VA5 H3    H3  H  0 1 N N N 2.545  2.852  17.157 7.696  3.074  0.194  H3    VA5 35 
VA5 H4    H4  H  0 1 N N N 3.466  -0.534 17.516 6.921  0.380  1.647  H4    VA5 36 
VA5 H5    H5  H  0 1 N N N 2.815  6.956  13.602 -1.455 -2.619 -0.654 H5    VA5 37 
VA5 H6    H6  H  0 1 N N N 3.105  5.333  12.891 -0.767 -3.344 0.819  H6    VA5 38 
VA5 H7    H7  H  0 1 N N N 2.423  7.343  11.396 -1.868 -1.516 2.164  H7    VA5 39 
VA5 H8    H8  H  0 1 N N N 5.416  6.374  11.449 -4.258 -1.311 -0.830 H8    VA5 40 
VA5 H9    H9  H  0 1 N N N 8.340  8.816  6.516  -8.667 -0.046 -2.264 H9    VA5 41 
VA5 H10   H10 H  0 1 N N N 11.796 8.557  9.425  -8.936 4.067  -0.312 H10   VA5 42 
VA5 H11   H11 H  0 1 N N N 11.051 8.915  10.833 -7.565 4.216  0.648  H11   VA5 43 
VA5 H12   H12 H  0 1 N N N 6.907  6.892  12.599 -3.736 1.467  1.708  H12   VA5 44 
VA5 H13   H13 H  0 1 N N N 5.334  5.394  9.348  -4.905 -1.507 2.161  H13   VA5 45 
VA5 H14   H14 H  0 1 N N N 4.413  6.797  8.709  -5.483 -2.555 0.821  H14   VA5 46 
VA5 H15   H15 H  0 1 N N N 2.750  5.966  9.708  -3.330 -3.327 2.330  H15   VA5 47 
VA5 H16   H16 H  0 1 N N N 3.575  4.520  11.819 -4.055 -4.456 0.317  H16   VA5 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 
VA5 C2    N1    DOUB Y N 1  
VA5 C2    N3    SING Y N 2  
VA5 N1    C6    SING Y N 3  
VA5 N3    C4    DOUB Y N 4  
VA5 C6    N6    SING N N 5  
VA5 C6    C5    DOUB Y N 6  
VA5 C4    C5    SING Y N 7  
VA5 C4    N9    SING Y N 8  
VA5 "C2'" "C3'" SING N N 9  
VA5 "C2'" "C1'" SING N N 10 
VA5 C5    N7    SING Y N 11 
VA5 "C3'" "O3'" SING N N 12 
VA5 "C3'" "C4'" SING N N 13 
VA5 N9    "C1'" SING N N 14 
VA5 N9    C8    SING Y N 15 
VA5 "C1'" "O4'" SING N N 16 
VA5 "O4'" "C4'" SING N N 17 
VA5 N7    C8    DOUB Y N 18 
VA5 "C4'" "C5'" SING N N 19 
VA5 O2B   PB    DOUB N N 20 
VA5 "C5'" "O5'" SING N N 21 
VA5 "O5'" PA    SING N N 22 
VA5 PB    O3A   SING N N 23 
VA5 PB    O1B   SING N N 24 
VA5 PB    C3B   SING N N 25 
VA5 O3A   PA    SING N N 26 
VA5 F3B   C3B   SING N N 27 
VA5 PA    O2A   DOUB N N 28 
VA5 PA    O1A   SING N N 29 
VA5 C3B   CL1   SING N N 30 
VA5 C3B   PG    SING N N 31 
VA5 O3G   PG    DOUB N N 32 
VA5 PG    O1G   SING N N 33 
VA5 PG    O2G   SING N N 34 
VA5 O1A   H1    SING N N 35 
VA5 O1B   H2    SING N N 36 
VA5 O1G   H3    SING N N 37 
VA5 O2G   H4    SING N N 38 
VA5 "C5'" H5    SING N N 39 
VA5 "C5'" H6    SING N N 40 
VA5 "C4'" H7    SING N N 41 
VA5 "C1'" H8    SING N N 42 
VA5 C2    H9    SING N N 43 
VA5 N6    H10   SING N N 44 
VA5 N6    H11   SING N N 45 
VA5 C8    H12   SING N N 46 
VA5 "C2'" H13   SING N N 47 
VA5 "C2'" H14   SING N N 48 
VA5 "C3'" H15   SING N N 49 
VA5 "O3'" 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 
VA5 SMILES           ACDLabs              12.01 "P(=O)(O)(OP(O)(C(Cl)(P(O)(O)=O)F)=O)OCC3OC(n1cnc2c1ncnc2N)CC3O"                                                                                                                                           
VA5 InChI            InChI                1.03  "InChI=1S/C11H16ClFN5O11P3/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+,11-/m1/s1" 
VA5 InChIKey         InChI                1.03  MGXOAMBWOAGILL-FHZUQPTBSA-N                                                                                                                                                                                
VA5 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3C[C@@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@@](F)(Cl)[P](O)(O)=O)O3"                                                                                                                
VA5 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[C](F)(Cl)[P](O)(O)=O)O3"                                                                                                                        
VA5 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@](F)(P(=O)(O)O)Cl)O)O)N"                                                                                                                     
VA5 SMILES           "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(F)(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 
VA5 "SYSTEMATIC NAME" ACDLabs              12.01 "9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine"                    
VA5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{S})-[[[(2~{R},3~{R},5~{S})-5-(6-aminopurin-9-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 
VA5 "Create component" 2018-03-22 RCSB 
VA5 "Initial release"  2018-07-04 RCSB 
# 
