data_DL5
#

_chem_comp.id                                   DL5
_chem_comp.name                                 "Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C17 H19 N8 O18 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        TNP-AMPPCP
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-06-03
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       716.297
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    DL5
_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       5A3R
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
DL5  N1      N1      N   0  1  Y  N  N   1.198  0.881  14.137  -4.009   5.920   0.414  N1      DL5   1  
DL5  C2      C2      C   0  1  Y  N  N   2.497  1.233  13.845  -4.317   4.785   1.015  C2      DL5   2  
DL5  N3      N3      N   0  1  Y  N  N   2.836  2.538  13.563  -3.601   3.691   0.869  N3      DL5   3  
DL5  C4      C4      C   0  1  Y  N  N   1.923  3.602  13.547  -2.520   3.687   0.096  C4      DL5   4  
DL5  C5      C5      C   0  1  Y  N  N   0.597  3.280  13.838  -2.149   4.870  -0.566  C5      DL5   5  
DL5  C6      C6      C   0  1  Y  N  N   0.212  1.921  14.136  -2.946   6.012  -0.378  C6      DL5   6  
DL5  N6      N6      N   0  1  N  N  N  -1.078  1.640  14.418  -2.631   7.206  -1.004  N6      DL5   7  
DL5  N7      N7      N   0  1  Y  N  N  -0.172  4.373  13.791  -1.029   4.596  -1.276  N7      DL5   8  
DL5  C8      C8      C   0  1  Y  N  N   0.650  5.328  13.483  -0.696   3.351  -1.097  C8      DL5   9  
DL5  N9      N9      N   0  1  Y  N  N   1.946  4.952  13.312  -1.585   2.747  -0.259  N9      DL5  10  
DL5  PA      PA      P   0  1  N  N  N  -0.582  7.780  10.265   3.450  -1.465  -0.825  PA      DL5  11  
DL5  PB      PB      P   0  1  N  N  N  -2.967  6.552  11.742   6.241  -0.732  -0.148  PB      DL5  12  
DL5  PG      PG      P   0  1  N  N  N  -4.064  3.716  11.801   8.799   0.135   1.104  PG      DL5  13  
DL5  C01     C01     C   0  1  N  N  N  -3.261  5.029  12.670   7.015  -0.114   1.382  C01     DL5  14  
DL5  "C1'"   "C1'"   C   0  1  N  N  R   3.186  5.732  12.958  -1.549   1.351   0.184  "C1'"   DL5  15  
DL5  O1A     O1A     O   0  1  N  N  N   0.209  7.500   8.922   3.595  -0.905  -2.187  O1A     DL5  16  
DL5  O1B     O1B     O   0  1  N  N  N  -2.660  7.591  12.659   6.920  -2.131  -0.565  O1B     DL5  17  
DL5  C1F     C1F     C   0  1  N  N  N   5.739  6.408  10.760  -3.870  -1.058   0.125  C1F     DL5  18  
DL5  O1G     O1G     O   0  1  N  N  N  -5.010  4.211  10.608   8.996   1.122   0.018  O1G     DL5  19  
DL5  "C2'"   "C2'"   C   0  1  N  N  R   3.644  5.675  11.469  -2.368   0.455  -0.776  "C2'"   DL5  20  
DL5  "O2'"   "O2'"   O   0  1  N  N  N   5.018  5.200  11.391  -3.701   0.317  -0.262  "O2'"   DL5  21  
DL5  O2A     O2A     O   0  1  N  N  N  -1.477  9.003  10.239   3.476  -3.073  -0.900  O2A     DL5  22  
DL5  O2B     O2B     O   0  1  N  N  N  -4.171  6.853  11.116   6.438   0.255  -1.234  O2B     DL5  23  
DL5  C2F     C2F     C   0  1  N  N  N   6.428  5.805   9.489  -4.423  -1.839  -1.027  C2F     DL5  24  
DL5  N2F     N2F     N   1  1  N  N  N   5.711  5.183   8.387  -3.899  -1.561  -2.384  N2F     DL5  25  
DL5  O2F     O2F     O   0  1  N  N  N   6.246  4.718   7.428  -4.346  -0.631  -3.030  O2F     DL5  26  
DL5  O2G     O2G     O   0  1  N  N  N  -5.016  3.032  12.889   9.483   0.681   2.455  O2G     DL5  27  
DL5  "C3'"   "C3'"   C   0  1  N  N  R   3.505  7.148  10.880  -1.695  -0.936  -0.583  "C3'"   DL5  28  
DL5  "O3'"   "O3'"   O   0  1  N  N  N   4.828  7.596  10.453  -2.522  -1.556   0.428  "O3'"   DL5  29  
DL5  O3A     O3A     O   0  1  N  N  N  -1.613  6.593  10.689   4.666  -0.952   0.098  O3A     DL5  30  
DL5  C3F     C3F     C   0  1  N  N  N   7.837  5.818   9.341  -5.355  -2.766  -0.889  C3F     DL5  31  
DL5  O3F     O3F     O  -1  1  N  N  N   4.493  5.092   8.368  -3.022  -2.264  -2.854  O3F     DL5  32  
DL5  O3G     O3G     O   0  1  N  N  N  -3.176  2.713  11.236   9.478  -1.264   0.687  O3G     DL5  33  
DL5  "C4'"   "C4'"   C   0  1  N  N  R   2.990  8.050  11.892  -0.324  -0.607   0.038  "C4'"   DL5  34  
DL5  "O4'"   "O4'"   O   0  1  N  N  N   2.865  7.088  13.010  -0.209   0.824   0.089  "O4'"   DL5  35  
DL5  C4F     C4F     C   0  1  N  N  R   8.784  6.335  10.218  -5.903  -3.050   0.456  C4F     DL5  36  
DL5  N4F     N4F     N   1  1  N  N  N  10.115  6.328  10.039  -6.571  -4.148   0.697  N4F     DL5  37  
DL5  O4F     O4F     O   0  1  N  N  N  10.916  6.797  10.840  -7.084  -4.394   1.993  O4F     DL5  38  
DL5  "C5'"   "C5'"   C   0  1  N  N  N   1.510  8.699  11.783   0.793  -1.188  -0.832  "C5'"   DL5  39  
DL5  "O5'"   "O5'"   O   0  1  N  N  N   0.514  7.671  11.517   2.052  -0.979  -0.190  "O5'"   DL5  40  
DL5  C5F     C5F     C   0  1  N  N  N   8.260  6.917  11.402  -5.667  -2.048   1.519  C5F     DL5  41  
DL5  O5F     O5F     O  -1  1  N  N  N  10.625  5.845   9.046  -6.782  -5.089  -0.339  O5F     DL5  42  
DL5  C6F     C6F     C   0  1  N  N  N   6.796  7.013  11.755  -4.730  -1.132   1.349  C6F     DL5  43  
DL5  N6F     N6F     N   1  1  N  N  N   6.590  7.668  13.056  -4.520  -0.130   2.420  N6F     DL5  44  
DL5  O6F     O6F     O   0  1  N  N  N   7.572  8.073  13.713  -3.664   0.727   2.292  O6F     DL5  45  
DL5  O7F     O7F     O  -1  1  N  N  N   5.555  7.875  13.585  -5.203  -0.164   3.427  O7F     DL5  46  
DL5  H2      H2      H   0  1  N  N  N   3.264  0.472  13.837  -5.190   4.754   1.651  H2      DL5  47  
DL5  HN6     HN6     H   0  1  N  N  N  -1.174  0.662  14.604  -1.853   7.261  -1.581  HN6     DL5  48  
DL5  HN6A    HN6A    H   0  0  N  N  N  -1.365  2.162  15.222  -3.189   7.988  -0.867  HN6A    DL5  49  
DL5  H8      H8      H   0  1  N  N  N   0.327  6.352  13.370   0.158   2.867  -1.547  H8      DL5  50  
DL5  H01     H01     H   0  1  N  N  N  -2.286  4.654  13.014   6.556   0.834   1.665  H01     DL5  51  
DL5  H01A    H01A    H   0  0  N  N  N  -3.884  5.283  13.540   6.870  -0.840   2.182  H01A    DL5  52  
DL5  "H1'"   "H1'"   H   0  1  N  N  N   4.021  5.467  13.623  -1.923   1.264   1.204  "H1'"   DL5  53  
DL5  HO1B    HO1B    H   0  0  N  N  N  -3.345  8.249  12.633   6.829  -2.826   0.101  HO1B    DL5  54  
DL5  "H2'"   "H2'"   H   0  1  N  N  N   2.972  5.007  10.910  -2.344   0.804  -1.809  "H2'"   DL5  55  
DL5  HO2A    HO2A    H   0  0  N  N  N  -1.417  9.421   9.388   3.385  -3.509  -0.041  HO2A    DL5  56  
DL5  HO2G    HO2G    H   0  0  N  N  N  -5.917  3.071  12.591  10.434   0.837   2.380  HO2G    DL5  57  
DL5  "H3'"   "H3'"   H   0  1  N  N  N   2.822  7.113  10.018  -1.620  -1.512  -1.505  "H3'"   DL5  58  
DL5  H3F     H3F     H   0  1  N  N  N   8.223  5.372   8.436  -5.715  -3.310  -1.750  H3F     DL5  59  
DL5  HO3G    HO3G    H   0  0  N  N  N  -3.372  2.600  10.313   9.387  -1.959   1.353  HO3G    DL5  60  
DL5  "H4'"   "H4'"   H   0  1  N  N  N   3.714  8.842  12.132  -0.265  -1.020   1.045  "H4'"   DL5  61  
DL5  "H5'"   "H5'"   H   0  1  N  N  N   1.266  9.201  12.731   0.627  -2.256  -0.970  "H5'"   DL5  62  
DL5  "H5'A"  "H5'A"  H   0  0  N  N  N   1.498  9.434  10.964   0.793  -0.692  -1.802  "H5'A"  DL5  63  
DL5  H5F     H5F     H   0  1  N  N  N   8.968  7.325  12.109  -6.254  -2.066   2.425  H5F     DL5  64  
DL5  H4F     H4F     H   0  1  N  N  N  11.799  6.683  10.509  -7.564  -5.230   2.074  H4F     DL5  65  
#   #
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
DL5  C2     N1      DOUB  Y  N   1  
DL5  C6     N1      SING  Y  N   2  
DL5  N3     C2      SING  Y  N   3  
DL5  C2     H2      SING  N  N   4  
DL5  C4     N3      DOUB  Y  N   5  
DL5  N9     C4      SING  Y  N   6  
DL5  C4     C5      SING  Y  N   7  
DL5  N7     C5      SING  Y  N   8  
DL5  C5     C6      DOUB  Y  N   9  
DL5  C6     N6      SING  N  N  10  
DL5  N6     HN6     SING  N  N  11  
DL5  N6     HN6A    SING  N  N  12  
DL5  C8     N7      DOUB  Y  N  13  
DL5  N9     C8      SING  Y  N  14  
DL5  C8     H8      SING  N  N  15  
DL5  "C1'"  N9      SING  N  N  16  
DL5  O1A    PA      DOUB  N  N  17  
DL5  O2A    PA      SING  N  N  18  
DL5  PA     O3A     SING  N  N  19  
DL5  PA     "O5'"   SING  N  N  20  
DL5  O3A    PB      SING  N  N  21  
DL5  O2B    PB      DOUB  N  N  22  
DL5  PB     O1B     SING  N  N  23  
DL5  PB     C01     SING  N  N  24  
DL5  O1G    PG      DOUB  N  N  25  
DL5  O3G    PG      SING  N  N  26  
DL5  PG     C01     SING  N  N  27  
DL5  PG     O2G     SING  N  N  28  
DL5  C01    H01     SING  N  N  29  
DL5  C01    H01A    SING  N  N  30  
DL5  "C2'"  "C1'"   SING  N  N  31  
DL5  "C1'"  "O4'"   SING  N  N  32  
DL5  "C1'"  "H1'"   SING  N  N  33  
DL5  O1B    HO1B    SING  N  N  34  
DL5  C2F    C1F     SING  N  N  35  
DL5  "O3'"  C1F     SING  N  N  36  
DL5  C1F    "O2'"   SING  N  N  37  
DL5  C1F    C6F     SING  N  N  38  
DL5  "C3'"  "C2'"   SING  N  N  39  
DL5  "O2'"  "C2'"   SING  N  N  40  
DL5  "C2'"  "H2'"   SING  N  N  41  
DL5  O2A    HO2A    SING  N  N  42  
DL5  N2F    C2F     SING  N  N  43  
DL5  C3F    C2F     DOUB  N  N  44  
DL5  O2F    N2F     DOUB  N  N  45  
DL5  O3F    N2F     SING  N  N  46  
DL5  O2G    HO2G    SING  N  N  47  
DL5  "O3'"  "C3'"   SING  N  N  48  
DL5  "C3'"  "C4'"   SING  N  N  49  
DL5  "C3'"  "H3'"   SING  N  N  50  
DL5  C3F    C4F     SING  N  N  51  
DL5  C3F    H3F     SING  N  N  52  
DL5  O3G    HO3G    SING  N  N  53  
DL5  "C5'"  "C4'"   SING  N  N  54  
DL5  "C4'"  "O4'"   SING  N  N  55  
DL5  "C4'"  "H4'"   SING  N  N  56  
DL5  N4F    C4F     DOUB  N  N  57  
DL5  C4F    C5F     SING  N  N  58  
DL5  O5F    N4F     SING  N  N  59  
DL5  N4F    O4F     SING  N  N  60  
DL5  "O5'"  "C5'"   SING  N  N  61  
DL5  "C5'"  "H5'"   SING  N  N  62  
DL5  "C5'"  "H5'A"  SING  N  N  63  
DL5  C5F    C6F     DOUB  N  N  64  
DL5  C5F    H5F     SING  N  N  65  
DL5  C6F    N6F     SING  N  N  66  
DL5  N6F    O7F     SING  N  N  67  
DL5  N6F    O6F     DOUB  N  N  68  
DL5  H4F    O4F     SING  N  N  69  
#   #
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
DL5  InChI             InChI                 1.03   "InChI=1S/C17H19N8O18P3/c18-14-11-15(20-4-19-14)22(5-21-11)16-13-12(8(40-16)3-39-46(37,38)43-45(35,36)6-44(32,33)34)41-17(42-13)9(24(28)29)1-7(23(26)27)2-10(17)25(30)31/h1-2,4-5,8,12-13,16H,3,6H2,(H,26,27)(H,35,36)(H,37,38)(H2,18,19,20)(H2,32,33,34)/t8-,12-,13-,16-/m1/s1"  
DL5  InChIKey          InChI                 1.03   WOUJMFLAWZHYLK-KWDXPJCYSA-N  
DL5  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[C@H]4O[C]5(O[C@@H]34)C(=C[C@@](C=C5[N+]([O-])=O)=[N+](O)[O-])[N+]([O-])=O"  
DL5  SMILES            CACTVS                3.385  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH]4O[C]5(O[CH]34)C(=C[C](C=C5[N+]([O-])=O)=[N+](O)[O-])[N+]([O-])=O"  
DL5  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N"  
DL5  SMILES            "OpenEye OEToolkits"  1.7.6  "c1nc(c2c(n1)n(cn2)C3C4C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N"  
#
_pdbx_chem_comp_identifier.comp_id          DL5
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.7.6
_pdbx_chem_comp_identifier.identifier       "(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-3',5'-dinitro-N-oxidanyl-6-[[oxidanyl-[oxidanyl(phosphonomethyl)phosphoryl]oxy-phosphoryl]oxymethyl]spiro[3a,4,6,6a-tetrahydrofuro[3,4-d][1,3]dioxole-2,4'-cyclohexa-2,5-diene]-1'-imine oxide"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DL5  "Create component"    2015-06-03  EBI   
DL5  "Other modification"  2015-09-12  EBI   
DL5  "Initial release"     2016-04-13  RCSB  
DL5  "Modify synonyms"     2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     DL5
_pdbx_chem_comp_synonyms.name        TNP-AMPPCP
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
