data_VA6
# 
_chem_comp.id                                    VA6 
_chem_comp.name                                  "9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H16 F2 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                    2018-07-13 
_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                        525.190 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VA6 
_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        6CRB 
_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 
VA6 N1    N1  N 0 1 Y N N -14.977 -8.706 66.599 -7.880 2.280  -1.163 N1    VA6 1  
VA6 C2    C1  C 0 1 Y N N -14.968 -8.267 65.340 -7.506 1.198  -1.822 C2    VA6 2  
VA6 N3    N2  N 0 1 Y N N -13.886 -7.721 64.758 -6.472 0.470  -1.456 N3    VA6 3  
VA6 C4    C2  C 0 1 Y N N -12.677 -7.583 65.474 -5.752 0.804  -0.389 C4    VA6 4  
VA6 C5    C3  C 0 1 Y N N -12.643 -8.033 66.821 -6.109 1.947  0.345  C5    VA6 5  
VA6 C6    C4  C 0 1 Y N N -13.827 -8.604 67.391 -7.221 2.692  -0.085 C6    VA6 6  
VA6 N6    N3  N 0 1 N N N -13.797 -9.034 68.702 -7.620 3.827  0.598  N6    VA6 7  
VA6 N7    N4  N 0 1 Y N N -11.390 -7.803 67.291 -5.226 2.058  1.366  N7    VA6 8  
VA6 C8    C5  C 0 1 Y N N -10.684 -7.249 66.317 -4.370 1.080  1.306  C8    VA6 9  
VA6 N9    N5  N 0 1 Y N N -11.434 -7.129 65.207 -4.653 0.278  0.240  N9    VA6 10 
VA6 PA    P1  P 0 1 N N N -7.277  -4.618 65.033 1.604  -2.005 -0.426 PA    VA6 11 
VA6 PB    P2  P 0 1 N N N -7.728  -1.942 64.164 3.959  -0.206 -0.465 PB    VA6 12 
VA6 PG    P3  P 0 1 N N N -5.253  -0.477 65.065 6.076  1.826  0.035  PG    VA6 13 
VA6 "C1'" C6  C 0 1 N N S -10.910 -6.521 64.089 -3.917 -0.924 -0.160 "C1'" VA6 14 
VA6 O1A   O1  O 0 1 N N N -5.950  -4.542 64.261 1.468  -1.920 -1.897 O1A   VA6 15 
VA6 O2B   O2  O 0 1 N N N -9.005  -1.410 63.541 3.708  0.416  -1.929 O2B   VA6 16 
VA6 O1G   O3  O 0 1 N N N -4.559  -1.757 64.678 6.574  2.987  1.034  O1G   VA6 17 
VA6 "C2'" C7  C 0 1 N N N -11.711 -5.302 63.404 -4.570 -2.185 0.460  "C2'" VA6 18 
VA6 O2A   O4  O 0 1 N N N -6.945  -5.020 66.553 2.215  -3.440 -0.026 O2A   VA6 19 
VA6 O1B   O5  O 0 1 N N N -6.720  -2.165 63.050 4.993  -1.262 -0.549 O1B   VA6 20 
VA6 O2G   O6  O 0 1 N N N -4.683  -0.031 66.335 7.201  0.677  -0.055 O2G   VA6 21 
VA6 "C3'" C8  C 0 1 N N S -10.553 -4.661 63.185 -3.362 -3.162 0.481  "C3'" VA6 22 
VA6 "O3'" O7  O 0 1 N N N -10.773 -3.432 62.379 -3.503 -4.122 1.530  "O3'" VA6 23 
VA6 O3A   O8  O 0 1 N N N -8.065  -3.329 64.969 2.588  -0.840 0.091  O3A   VA6 24 
VA6 C3B   C9  C 0 1 N N N -7.045  -0.718 65.305 4.523  1.108  0.665  C3B   VA6 25 
VA6 F1B   F1  F 0 1 N N N -7.576  0.480  65.093 3.546  2.106  0.744  F1B   VA6 26 
VA6 F2B   F2  F 0 1 N N N -7.273  -1.122 66.635 4.742  0.567  1.937  F2B   VA6 27 
VA6 O3G   O9  O 0 1 N N N -5.051  0.676  64.036 5.845  2.398  -1.310 O3G   VA6 28 
VA6 "C4'" C10 C 0 1 N N R -9.695  -5.761 62.549 -2.177 -2.212 0.754  "C4'" VA6 29 
VA6 "O4'" O10 O 0 1 N N N -10.338 -7.118 63.099 -2.582 -0.891 0.370  "O4'" VA6 30 
VA6 "C5'" C11 C 0 1 N N N -8.334  -5.674 62.902 -0.967 -2.645 -0.077 "C5'" VA6 31 
VA6 "O5'" O11 O 0 1 N N N -8.116  -5.727 64.334 0.157  -1.828 0.258  "O5'" VA6 32 
VA6 H1    H1  H 0 1 N N N -15.874 -8.354 64.759 -8.069 0.900  -2.693 H1    VA6 33 
VA6 H2    H2  H 0 1 N N N -14.692 -9.404 68.953 -8.389 4.333  0.291  H2    VA6 34 
VA6 H3    H3  H 0 1 N N N -13.102 -9.746 68.803 -7.131 4.117  1.384  H3    VA6 35 
VA6 H4    H4  H 0 1 N N N -9.653  -6.938 66.402 -3.556 0.925  1.999  H4    VA6 36 
VA6 H5    H5  H 0 1 N N N -10.071 -5.961 64.528 -3.891 -1.006 -1.246 H5    VA6 37 
VA6 H6    H6  H 0 1 N N N -8.892  -1.335 62.601 3.041  1.115  -1.950 H6    VA6 38 
VA6 H7    H7  H 0 1 N N N -4.107  -1.635 63.852 7.398  3.414  0.760  H7    VA6 39 
VA6 H8    H8  H 0 1 N N N -12.394 -4.774 64.086 -4.931 -1.985 1.469  H8    VA6 40 
VA6 H9    H9  H 0 1 N N N -12.251 -5.579 62.487 -5.372 -2.564 -0.174 H9    VA6 41 
VA6 H10   H10 H 0 1 N N N -6.006  -5.126 66.655 2.331  -3.567 0.926  H10   VA6 42 
VA6 H11   H11 H 0 1 N N N -4.329  0.845  66.234 7.403  0.257  0.792  H11   VA6 43 
VA6 H12   H12 H 0 1 N N N -10.084 -4.374 64.138 -3.248 -3.658 -0.484 H12   VA6 44 
VA6 H13   H13 H 0 1 N N N -11.314 -2.824 62.869 -4.284 -4.685 1.446  H13   VA6 45 
VA6 H14   H14 H 0 1 N N N -9.822  -5.734 61.457 -1.923 -2.228 1.813  H14   VA6 46 
VA6 H15   H15 H 0 1 N N N -7.796  -6.512 62.434 -0.734 -3.688 0.136  H15   VA6 47 
VA6 H16   H16 H 0 1 N N N -7.933  -4.723 62.521 -1.195 -2.532 -1.137 H16   VA6 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 
VA6 "O3'" "C3'" SING N N 1  
VA6 "C4'" "C5'" SING N N 2  
VA6 "C4'" "O4'" SING N N 3  
VA6 "C4'" "C3'" SING N N 4  
VA6 "C5'" "O5'" SING N N 5  
VA6 O1B   PB    DOUB N N 6  
VA6 "O4'" "C1'" SING N N 7  
VA6 "C3'" "C2'" SING N N 8  
VA6 "C2'" "C1'" SING N N 9  
VA6 O2B   PB    SING N N 10 
VA6 O3G   PG    DOUB N N 11 
VA6 "C1'" N9    SING N N 12 
VA6 PB    O3A   SING N N 13 
VA6 PB    C3B   SING N N 14 
VA6 O1A   PA    DOUB N N 15 
VA6 "O5'" PA    SING N N 16 
VA6 O1G   PG    SING N N 17 
VA6 N3    C2    DOUB Y N 18 
VA6 N3    C4    SING Y N 19 
VA6 O3A   PA    SING N N 20 
VA6 PA    O2A   SING N N 21 
VA6 PG    C3B   SING N N 22 
VA6 PG    O2G   SING N N 23 
VA6 F1B   C3B   SING N N 24 
VA6 N9    C4    SING Y N 25 
VA6 N9    C8    SING Y N 26 
VA6 C3B   F2B   SING N N 27 
VA6 C2    N1    SING Y N 28 
VA6 C4    C5    DOUB Y N 29 
VA6 C8    N7    DOUB Y N 30 
VA6 N1    C6    DOUB Y N 31 
VA6 C5    N7    SING Y N 32 
VA6 C5    C6    SING Y N 33 
VA6 C6    N6    SING N N 34 
VA6 C2    H1    SING N N 35 
VA6 N6    H2    SING N N 36 
VA6 N6    H3    SING N N 37 
VA6 C8    H4    SING N N 38 
VA6 "C1'" H5    SING N N 39 
VA6 O2B   H6    SING N N 40 
VA6 O1G   H7    SING N N 41 
VA6 "C2'" H8    SING N N 42 
VA6 "C2'" H9    SING N N 43 
VA6 O2A   H10   SING N N 44 
VA6 O2G   H11   SING N N 45 
VA6 "C3'" H12   SING N N 46 
VA6 "O3'" H13   SING N N 47 
VA6 "C4'" H14   SING N N 48 
VA6 "C5'" H15   SING N N 49 
VA6 "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 
VA6 SMILES           ACDLabs              12.01 "n1c(c2c(nc1)n(cn2)C3CC(O)C(COP(O)(=O)OP(C(P(O)(O)=O)(F)F)(O)=O)O3)N"                                                                                                                                 
VA6 InChI            InChI                1.03  "InChI=1S/C11H16F2N5O11P3/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" 
VA6 InChIKey         InChI                1.03  QVHRTXWVFSLQPZ-XVMARJQXSA-N                                                                                                                                                                           
VA6 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)(F)[P](O)(O)=O)O3"                                                                                                                 
VA6 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O3"                                                                                                                      
VA6 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)(F)P(=O)(O)O)O)O)N"                                                                                                                   
VA6 SMILES           "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)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 
VA6 "SYSTEMATIC NAME" ACDLabs              12.01 "9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine"             
VA6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{R},3~{S},5~{S})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-bis(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 
VA6 "Create component" 2018-03-22 RCSB 
VA6 "Initial release"  2018-07-18 RCSB 
# 
