data_V3A
# 
_chem_comp.id                                    V3A 
_chem_comp.name                                  "9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(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 H17 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                        507.199 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     V3A 
_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        6CR7 
_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 
V3A PA    P1  P 0 1 N N N 4.864  5.335 14.790 1.685  -1.585 -0.661 PA    V3A 1  
V3A O1A   O1  O 0 1 N N N 3.789  5.474 15.820 1.441  -1.411 -2.243 O1A   V3A 2  
V3A O2A   O2  O 0 1 N N N 6.172  5.580 15.440 2.269  -2.918 -0.395 O2A   V3A 3  
V3A O3A   O3  O 0 1 N N N 4.935  3.884 14.203 2.696  -0.443 -0.146 O3A   V3A 4  
V3A "O5'" O4  O 0 1 N N N 4.606  6.363 13.545 0.281  -1.448 0.116  "O5'" V3A 5  
V3A PB    P2  P 0 1 N N N 3.771  2.796 13.912 4.285  -0.216 -0.274 PB    V3A 6  
V3A O2B   O5  O 0 1 N N N 3.771  2.466 12.453 4.657  -0.125 -1.704 O2B   V3A 7  
V3A O1B   O6  O 0 1 N N N 2.385  3.275 14.345 5.061  -1.454 0.404  O1B   V3A 8  
V3A C3B   C1  C 0 1 N N R 4.264  1.303 14.826 4.748  1.329  0.574  C3B   V3A 9  
V3A F3B   F1  F 0 1 N N N 3.871  0.208 14.147 4.075  2.405  -0.015 F3B   V3A 10 
V3A PG    P3  P 0 1 N N N 3.615  1.246 16.530 6.548  1.587  0.429  PG    V3A 11 
V3A O1G   O7  O 0 1 N N N 3.150  2.681 16.919 6.952  1.686  -1.126 O1G   V3A 12 
V3A O2G   O8  O 0 1 N N N 4.729  0.805 17.469 6.957  2.952  1.178  O2G   V3A 13 
V3A O3G   O9  O 0 1 N N N 2.483  0.320 16.599 7.260  0.449  1.052  O3G   V3A 14 
V3A "C5'" C2  C 0 1 N N N 3.308  6.646 13.076 -0.790 -2.381 -0.043 "C5'" V3A 15 
V3A "C4'" C3  C 0 1 N N R 3.357  6.746 11.610 -1.969 -1.957 0.835  "C4'" V3A 16 
V3A "O4'" O10 O 0 1 N N N 4.260  8.079 11.102 -2.514 -0.723 0.353  "O4'" V3A 17 
V3A "C1'" C4  C 0 1 N N S 5.265  7.333 10.708 -3.876 -0.916 -0.060 "C1'" V3A 18 
V3A N9    N1  N 0 1 Y N N 6.660  7.601 10.606 -4.681 0.263  0.270  N9    V3A 19 
V3A C4    C5  C 0 1 Y N N 7.473  7.918 9.600  -5.853 0.641  -0.334 C4    V3A 20 
V3A N3    N2  N 0 1 Y N N 7.354  8.256 8.274  -6.605 0.151  -1.314 N3    V3A 21 
V3A C2    C6  C 0 1 Y N N 8.415  8.549 7.579  -7.713 0.761  -1.679 C2    V3A 22 
V3A N1    N3  N 0 1 Y N N 9.683  8.554 8.081  -8.132 1.873  -1.105 N1    V3A 23 
V3A C6    C7  C 0 1 Y N N 9.885  8.238 9.369  -7.447 2.437  -0.116 C6    V3A 24 
V3A N6    N4  N 0 1 N N N 11.203 8.196 10.011 -7.895 3.603  0.481  N6    V3A 25 
V3A C5    C8  C 0 1 Y N N 8.770  7.917 10.169 -6.257 1.823  0.310  C5    V3A 26 
V3A N7    N5  N 0 1 Y N N 8.668  7.566 11.471 -5.327 2.100  1.256  N7    V3A 27 
V3A C8    C9  C 0 1 Y N N 7.405  7.356 11.708 -4.404 1.183  1.237  C8    V3A 28 
V3A "C2'" C10 C 0 1 N N N 4.673  6.241 9.765  -4.371 -2.148 0.739  "C2'" V3A 29 
V3A "C3'" C11 C 0 1 N N S 3.972  5.656 11.066 -3.085 -3.021 0.763  "C3'" V3A 30 
V3A "O3'" O11 O 0 1 N N N 3.128  4.471 10.789 -3.064 -3.863 1.917  "O3'" V3A 31 
V3A H1    H1  H 0 1 N N N 4.180  5.688 16.659 1.059  -0.558 -2.491 H1    V3A 32 
V3A H2    H2  H 0 1 N N N 1.799  3.267 13.597 4.864  -1.574 1.343  H2    V3A 33 
V3A H3    H3  H 0 1 N N N 5.359  1.354 14.921 4.475  1.262  1.627  H3    V3A 34 
V3A H4    H4  H 0 1 N N N 2.222  2.669 17.124 6.521  2.411  -1.599 H4    V3A 35 
V3A H5    H5  H 0 1 N N N 4.469  0.010 17.918 7.902  3.152  1.141  H5    V3A 36 
V3A H6    H6  H 0 1 N N N 2.958  7.598 13.502 -1.103 -2.400 -1.087 H6    V3A 37 
V3A H7    H7  H 0 1 N N N 2.622  5.838 13.371 -0.454 -3.374 0.254  H7    V3A 38 
V3A H8    H8  H 0 1 N N N 2.340  6.873 11.211 -1.638 -1.837 1.866  H8    V3A 39 
V3A H9    H9  H 0 1 N N N 5.323  6.695 11.602 -3.922 -1.116 -1.131 H9    V3A 40 
V3A H10   H10 H 0 1 N N N 8.283  8.805 6.538  -8.300 0.336  -2.480 H10   V3A 41 
V3A H11   H11 H 0 1 N N N 11.907 8.437 9.343  -8.717 4.018  0.178  H11   V3A 42 
V3A H12   H12 H 0 1 N N N 11.225 8.848 10.769 -7.386 4.005  1.202  H12   V3A 43 
V3A H13   H13 H 0 1 N N N 7.006  7.030 12.657 -3.544 1.156  1.891  H13   V3A 44 
V3A H14   H14 H 0 1 N N N 3.983  6.617 8.995  -4.672 -1.867 1.748  H14   V3A 45 
V3A H15   H15 H 0 1 N N N 5.416  5.577 9.299  -5.181 -2.656 0.216  H15   V3A 46 
V3A H16   H16 H 0 1 N N N 4.784  5.333 11.734 -2.999 -3.611 -0.150 H16   V3A 47 
V3A H17   H17 H 0 1 N N N 3.364  3.768 11.383 -3.798 -4.490 1.960  H17   V3A 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 
V3A C2    N1    DOUB Y N 1  
V3A C2    N3    SING Y N 2  
V3A N1    C6    SING Y N 3  
V3A N3    C4    DOUB Y N 4  
V3A C6    N6    SING N N 5  
V3A C6    C5    DOUB Y N 6  
V3A C4    C5    SING Y N 7  
V3A C4    N9    SING Y N 8  
V3A "C2'" "C1'" SING N N 9  
V3A "C2'" "C3'" SING N N 10 
V3A C5    N7    SING Y N 11 
V3A N9    "C1'" SING N N 12 
V3A N9    C8    SING Y N 13 
V3A "C1'" "O4'" SING N N 14 
V3A "O3'" "C3'" SING N N 15 
V3A "C3'" "C4'" SING N N 16 
V3A "O4'" "C4'" SING N N 17 
V3A N7    C8    DOUB Y N 18 
V3A "C4'" "C5'" SING N N 19 
V3A O2B   PB    DOUB N N 20 
V3A "C5'" "O5'" SING N N 21 
V3A "O5'" PA    SING N N 22 
V3A PB    O3A   SING N N 23 
V3A PB    O1B   SING N N 24 
V3A PB    C3B   SING N N 25 
V3A F3B   C3B   SING N N 26 
V3A O3A   PA    SING N N 27 
V3A PA    O2A   DOUB N N 28 
V3A PA    O1A   SING N N 29 
V3A C3B   PG    SING N N 30 
V3A PG    O3G   DOUB N N 31 
V3A PG    O1G   SING N N 32 
V3A PG    O2G   SING N N 33 
V3A O1A   H1    SING N N 34 
V3A O1B   H2    SING N N 35 
V3A C3B   H3    SING N N 36 
V3A O1G   H4    SING N N 37 
V3A O2G   H5    SING N N 38 
V3A "C5'" H6    SING N N 39 
V3A "C5'" H7    SING N N 40 
V3A "C4'" H8    SING N N 41 
V3A "C1'" H9    SING N N 42 
V3A C2    H10   SING N N 43 
V3A N6    H11   SING N N 44 
V3A N6    H12   SING N N 45 
V3A C8    H13   SING N N 46 
V3A "C2'" H14   SING N N 47 
V3A "C2'" H15   SING N N 48 
V3A "C3'" H16   SING N N 49 
V3A "O3'" 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 
V3A SMILES           ACDLabs              12.01 "P(=O)(O)(OP(O)(C(P(=O)(O)O)F)=O)OCC3OC(n1cnc2c1ncnc2N)CC3O"                                                                                                                                             
V3A InChI            InChI                1.03  "InChI=1S/C11H17FN5O11P3/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" 
V3A InChIKey         InChI                1.03  AHVBRAYGASDMPK-QMWPFBOUSA-N                                                                                                                                                                              
V3A 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](F)[P](O)(O)=O)O3"                                                                                                                   
V3A SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](F)[P](O)(O)=O)O3"                                                                                                                         
V3A 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](F)P(=O)(O)O)O)O)N"                                                                                                                     
V3A 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)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 
V3A "SYSTEMATIC NAME" ACDLabs              12.01 "9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine"              
V3A "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-[[[(2~{R},3~{S},5~{S})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-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 
V3A "Create component" 2018-03-22 RCSB 
V3A "Initial release"  2018-07-04 RCSB 
# 
