data_V3L
# 
_chem_comp.id                                    V3L 
_chem_comp.name                                  
;2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C15 H23 N5 O14 P2" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-12-21 
_chem_comp.pdbx_modified_date                    2014-05-29 
_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                        559.316 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     V3L 
_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        3V3L 
_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 
V3L N1     N1     N 0 1 Y N N 28.211 58.899 82.245 -4.929 4.245  -0.019 N1     V3L 1  
V3L C2     C2     C 0 1 Y N N 28.319 57.552 82.335 -3.902 4.069  -0.831 C2     V3L 2  
V3L N3     N3     N 0 1 Y N N 27.257 56.733 82.413 -3.257 2.926  -0.917 N3     V3L 3  
V3L C4     C4     C 0 1 Y N N 25.997 57.224 82.403 -3.622 1.885  -0.175 C4     V3L 4  
V3L C5     C5     C 0 1 Y N N 25.787 58.667 82.310 -4.708 2.020  0.705  C5     V3L 5  
V3L C6     C6     C 0 1 Y N N 26.994 59.507 82.257 -5.366 3.261  0.761  C6     V3L 6  
V3L N6     N6     N 0 1 N N N 26.832 60.832 82.183 -6.443 3.454  1.608  N6     V3L 7  
V3L N7     N7     N 0 1 Y N N 24.461 58.886 82.321 -4.867 0.829  1.330  N7     V3L 8  
V3L C8     C8     C 0 1 Y N N 23.867 57.699 82.423 -3.968 -0.009 0.900  C8     V3L 9  
V3L N9     N9     N 0 1 Y N N 24.775 56.712 82.436 -3.176 0.595  -0.030 N9     V3L 10 
V3L P      P      P 0 1 N N N 19.716 56.794 82.543 -1.478 -5.770 0.006  P      V3L 11 
V3L PB     PB     P 0 1 N N N 24.488 54.108 91.278 5.999  -0.090 0.481  PB     V3L 12 
V3L C10    "C1''" C 0 1 N N R 25.041 55.306 86.244 0.597  2.217  0.528  C10    V3L 13 
V3L "C1'"  "C1'"  C 0 1 N N R 24.458 55.279 82.613 -2.054 -0.020 -0.743 "C1'"  V3L 14 
V3L OP3    OP3    O 0 1 N Y N 18.517 56.028 83.082 -2.640 -6.627 -0.706 OP3    V3L 15 
V3L O1B    O1B    O 0 1 N N N 25.321 55.169 91.928 6.189  -0.047 2.079  O1B    V3L 16 
V3L C12    "C2''" C 0 1 N N R 26.416 55.222 86.903 0.915  3.648  0.055  C12    V3L 17 
V3L O12    "O2''" O 0 1 N N N 27.449 55.609 86.008 0.321  3.897  -1.221 O12    V3L 18 
V3L "C2'"  "C2'"  C 0 1 N N R 23.976 55.101 84.057 -0.715 0.289  -0.026 "C2'"  V3L 19 
V3L "O2'"  "O2'"  O 0 1 N N N 25.115 54.848 84.894 -0.179 1.539  -0.463 "O2'"  V3L 20 
V3L OP1    OP1    O 0 1 N N N 19.750 56.971 81.034 -1.743 -5.692 1.460  OP1    V3L 21 
V3L O2B    O2B    O 0 1 N N N 23.039 54.513 91.163 7.074  0.695  -0.165 O2B    V3L 22 
V3L C13    "C3''" C 0 1 N N S 26.520 53.755 87.309 2.460  3.678  -0.052 C13    V3L 23 
V3L O13    "O3''" O 0 1 N N N 27.172 52.954 86.316 2.877  4.386  -1.221 O13    V3L 24 
V3L "C3'"  "C3'"  C 0 1 N N R 22.966 53.952 83.949 0.179  -0.888 -0.488 "C3'"  V3L 25 
V3L "O3'"  "O3'"  O 0 1 N N N 23.518 52.668 84.245 1.002  -0.489 -1.586 "O3'"  V3L 26 
V3L OP2    OP2    O 0 1 N N N 20.039 58.031 83.341 -0.056 -6.482 -0.243 OP2    V3L 27 
V3L O3B    O3B    O 0 1 N N N 24.673 52.708 91.802 6.070  -1.617 -0.027 O3B    V3L 28 
V3L C14    "C4''" C 0 1 N N R 25.070 53.316 87.455 2.806  2.171  -0.164 C14    V3L 29 
V3L O14    "O4''" O 0 1 N N N 24.240 54.389 86.987 1.850  1.539  0.714  O14    V3L 30 
V3L "C4'"  "C4'"  C 0 1 N N R 22.498 53.993 82.498 -0.822 -1.972 -0.930 "C4'"  V3L 31 
V3L "O4'"  "O4'"  O 0 1 N N N 23.393 54.860 81.791 -2.143 -1.460 -0.686 "O4'"  V3L 32 
V3L C15    "C5''" C 0 1 N N N 24.700 52.968 88.894 4.235  1.910  0.316  C15    V3L 33 
V3L O15    "O5''" O 0 1 N N N 25.068 54.012 89.794 4.569  0.538  0.094  O15    V3L 34 
V3L "C5'"  "C5'"  C 0 1 N N N 21.097 54.542 82.301 -0.598 -3.250 -0.119 "C5'"  V3L 35 
V3L "O5'"  "O5'"  O 0 1 N N N 20.963 55.849 82.897 -1.450 -4.284 -0.615 "O5'"  V3L 36 
V3L H2     H2     H 0 1 N N N 29.307 57.115 82.345 -3.580 4.896  -1.447 H2     V3L 37 
V3L HN6    HN6    H 0 1 N N N 27.726 61.275 82.120 -6.888 4.316  1.638  HN6    V3L 38 
V3L HN6A   HN6A   H 0 0 N N N 26.291 61.057 81.372 -6.752 2.729  2.172  HN6A   V3L 39 
V3L H8     H8     H 0 1 N N N 22.799 57.551 82.487 -3.866 -1.031 1.232  H8     V3L 40 
V3L "H1''" "H1''" H 0 0 N N N 24.650 56.332 86.306 0.050  2.251  1.470  "H1''" V3L 41 
V3L "H1'"  "H1'"  H 0 1 N N N 25.356 54.666 82.447 -2.024 0.324  -1.777 "H1'"  V3L 42 
V3L HOP3   HOP3   H 0 0 N N N 17.955 55.770 82.361 -2.715 -7.535 -0.381 HOP3   V3L 43 
V3L HO1B   HO1B   H 0 0 N N N 24.772 55.912 92.150 5.518  -0.542 2.569  HO1B   V3L 44 
V3L "H2''" "H2''" H 0 0 N N N 26.425 55.851 87.806 0.570  4.378  0.787  "H2''" V3L 45 
V3L "HO2'" "HO2'" H 0 0 N N N 28.289 55.546 86.447 -0.643 3.834  -1.225 "HO2'" V3L 46 
V3L "H2'"  "H2'"  H 0 1 N N N 23.454 56.014 84.380 -0.843 0.279  1.056  "H2'"  V3L 47 
V3L "H3''" "H3''" H 0 0 N N N 27.032 53.675 88.279 2.903  4.113  0.844  "H3''" V3L 48 
V3L HO13   HO3A   H 0 0 N N N 27.213 52.052 86.613 2.603  5.313  -1.237 HO13   V3L 49 
V3L "H3'"  "H3'"  H 0 1 N N N 22.112 54.164 84.609 0.793  -1.247 0.338  "H3'"  V3L 50 
V3L "HO3'" "HO3'" H 0 0 N Y N 22.843 52.005 84.160 1.583  -1.188 -1.915 "HO3'" V3L 51 
V3L HOP2   HOP2   H 0 0 N N N 20.219 58.752 82.749 0.183  -6.568 -1.176 HOP2   V3L 52 
V3L HO3B   HO3B   H 0 0 N N N 23.823 52.318 91.972 6.907  -2.059 0.173  HO3B   V3L 53 
V3L "H4''" "H4''" H 0 0 N N N 24.911 52.425 86.830 2.677  1.823  -1.189 "H4''" V3L 54 
V3L "H4'"  "H4'"  H 0 1 N N N 22.546 52.977 82.080 -0.697 -2.181 -1.993 "H4'"  V3L 55 
V3L "H5''" "H5''" H 0 0 N N N 23.613 52.809 88.956 4.926  2.546  -0.237 "H5''" V3L 56 
V3L H5AA   H5AA   H 0 0 N N N 25.223 52.045 89.184 4.307  2.133  1.380  H5AA   V3L 57 
V3L "H5'"  "H5'"  H 0 1 N N N 20.888 54.615 81.224 0.443  -3.561 -0.212 "H5'"  V3L 58 
V3L "H5'A" "H5'A" H 0 0 N N N 20.374 53.858 82.769 -0.829 -3.060 0.929  "H5'A" V3L 59 
# 
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 
V3L N1    C6     DOUB Y N 1  
V3L N1    C2     SING Y N 2  
V3L C2    N3     DOUB Y N 3  
V3L C2    H2     SING N N 4  
V3L C4    N3     SING Y N 5  
V3L C5    C4     DOUB Y N 6  
V3L C4    N9     SING Y N 7  
V3L C6    C5     SING Y N 8  
V3L C5    N7     SING Y N 9  
V3L N6    C6     SING N N 10 
V3L N6    HN6    SING N N 11 
V3L N6    HN6A   SING N N 12 
V3L N7    C8     DOUB Y N 13 
V3L C8    N9     SING Y N 14 
V3L C8    H8     SING N N 15 
V3L N9    "C1'"  SING N N 16 
V3L OP1   P      DOUB N N 17 
V3L P     "O5'"  SING N N 18 
V3L P     OP3    SING N N 19 
V3L P     OP2    SING N N 20 
V3L O15   PB     SING N N 21 
V3L O2B   PB     DOUB N N 22 
V3L PB    O3B    SING N N 23 
V3L PB    O1B    SING N N 24 
V3L "O2'" C10    SING N N 25 
V3L C10   C12    SING N N 26 
V3L C10   O14    SING N N 27 
V3L C10   "H1''" SING N N 28 
V3L "O4'" "C1'"  SING N N 29 
V3L "C1'" "C2'"  SING N N 30 
V3L "C1'" "H1'"  SING N N 31 
V3L OP3   HOP3   SING N N 32 
V3L O1B   HO1B   SING N N 33 
V3L O12   C12    SING N N 34 
V3L C12   C13    SING N N 35 
V3L C12   "H2''" SING N N 36 
V3L O12   "HO2'" SING N N 37 
V3L "C3'" "C2'"  SING N N 38 
V3L "C2'" "O2'"  SING N N 39 
V3L "C2'" "H2'"  SING N N 40 
V3L O13   C13    SING N N 41 
V3L C13   C14    SING N N 42 
V3L C13   "H3''" SING N N 43 
V3L O13   HO13   SING N N 44 
V3L "C4'" "C3'"  SING N N 45 
V3L "C3'" "O3'"  SING N N 46 
V3L "C3'" "H3'"  SING N N 47 
V3L "O3'" "HO3'" SING N N 48 
V3L OP2   HOP2   SING N N 49 
V3L O3B   HO3B   SING N N 50 
V3L O14   C14    SING N N 51 
V3L C14   C15    SING N N 52 
V3L C14   "H4''" SING N N 53 
V3L "O4'" "C4'"  SING N N 54 
V3L "C5'" "C4'"  SING N N 55 
V3L "C4'" "H4'"  SING N N 56 
V3L C15   O15    SING N N 57 
V3L C15   "H5''" SING N N 58 
V3L C15   H5AA   SING N N 59 
V3L "C5'" "O5'"  SING N N 60 
V3L "C5'" "H5'"  SING N N 61 
V3L "C5'" "H5'A" SING N N 62 
# 
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 
V3L SMILES           ACDLabs              12.01 "O=P(O)(O)OCC4OC(n1c2ncnc(N)c2nc1)C(OC3OC(C(O)C3O)COP(=O)(O)O)C4O" 
V3L InChI            InChI                1.03  
"InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(9(22)6(32-14)2-31-36(27,28)29)34-15-10(23)8(21)5(33-15)1-30-35(24,25)26/h3-6,8-11,14-15,21-23H,1-2H2,(H2,16,17,18)(H2,24,25,26)(H2,27,28,29)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1" 
V3L InChIKey         InChI                1.03  BHIWBSNWEZIHHL-KEOHHSTQSA-N 
V3L SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O[C@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O" 
V3L SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O" 
V3L SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O[C@@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)N" 
V3L SMILES           "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)OC4C(C(C(O4)COP(=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 
V3L "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)
;
V3L "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
V3L "Create component" 2011-12-21 RCSB 
V3L "Modify atom id"   2014-05-29 RCSB 
# 
