data_O05
#

_chem_comp.id                                   O05
_chem_comp.name                                 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H26 N7 O9 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2020-01-13
_chem_comp.pdbx_modified_date                   2020-02-14
_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                       510.356
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    O05
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  Y
_chem_comp.pdbx_model_coordinates_db_code       6TWF
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
O05  C2     C1   C  0  1  Y  N  N  -12.693  24.888  -36.628  ?  ?  ?  C2     O05   1  
O05  C3     C2   C  0  1  N  N  N  -16.799  18.545  -29.799  ?  ?  ?  C3     O05   2  
O05  C4     C3   C  0  1  Y  N  N  -13.822  22.995  -36.195  ?  ?  ?  C4     O05   3  
O05  C5     C4   C  0  1  Y  N  N  -14.494  23.042  -37.405  ?  ?  ?  C5     O05   4  
O05  C6     C5   C  0  1  Y  N  N  -14.227  24.147  -38.235  ?  ?  ?  C6     O05   5  
O05  C8     C6   C  0  1  Y  N  N  -15.118  21.252  -36.452  ?  ?  ?  C8     O05   6  
O05  C9     C7   C  0  1  N  N  N  -11.060  25.927  -35.066  ?  ?  ?  C9     O05   7  
O05  C10    C8   C  0  1  N  N  N  -11.302  27.375  -34.692  ?  ?  ?  C10    O05   8  
O05  C11    C9   C  0  1  N  N  N  -11.327  28.005  -37.028  ?  ?  ?  C11    O05   9  
O05  C12    C10  C  0  1  N  N  N  -11.040  26.575  -37.410  ?  ?  ?  C12    O05  10  
O05  O2A    O1   O  0  1  N  N  N  -19.109  18.960  -31.483  ?  ?  ?  O2A    O05  11  
O05  PA     P1   P  0  1  N  N  N  -17.871  18.141  -31.180  ?  ?  ?  PA     O05  12  
O05  O1A    O2   O  0  1  N  N  N  -18.318  16.671  -30.902  ?  ?  ?  O1A    O05  13  
O05  PB     P2   P  0  1  N  N  N  -17.459  19.842  -28.761  ?  ?  ?  PB     O05  14  
O05  O3B    O3   O  0  1  N  N  N  -18.642  19.308  -28.018  ?  ?  ?  O3B    O05  15  
O05  O1B    O4   O  0  1  N  N  N  -17.800  21.034  -29.679  ?  ?  ?  O1B    O05  16  
O05  O2B    O5   O  0  1  N  N  N  -16.306  20.322  -27.863  ?  ?  ?  O2B    O05  17  
O05  "O5'"  O6   O  0  1  N  N  N  -16.711  18.169  -32.247  ?  ?  ?  "O5'"  O05  18  
O05  "C5'"  C11  C  0  1  N  N  N  -16.339  19.287  -33.106  ?  ?  ?  "C5'"  O05  19  
O05  "C4'"  C12  C  0  1  N  N  R  -14.934  19.778  -32.830  ?  ?  ?  "C4'"  O05  20  
O05  "O4'"  O7   O  0  1  N  N  N  -14.244  20.026  -34.081  ?  ?  ?  "O4'"  O05  21  
O05  "C3'"  C13  C  0  1  N  N  S  -14.844  21.088  -32.047  ?  ?  ?  "C3'"  O05  22  
O05  O7     O8   O  0  1  N  N  N  -13.686  21.118  -31.216  ?  ?  ?  O7     O05  23  
O05  "C2'"  C14  C  0  1  N  N  R  -14.788  22.135  -33.164  ?  ?  ?  "C2'"  O05  24  
O05  O8     O9   O  0  1  N  N  N  -14.114  23.339  -32.812  ?  ?  ?  O8     O05  25  
O05  "C1'"  C15  C  0  1  N  N  R  -13.948  21.408  -34.212  ?  ?  ?  "C1'"  O05  26  
O05  N9     N1   N  0  1  Y  N  N  -14.242  21.840  -35.578  ?  ?  ?  N9     O05  27  
O05  N7     N2   N  0  1  Y  N  N  -15.313  21.935  -37.555  ?  ?  ?  N7     O05  28  
O05  N6     N3   N  0  1  N  N  N  -14.794  24.335  -39.433  ?  ?  ?  N6     O05  29  
O05  N3     N4   N  0  1  Y  N  N  -12.926  23.885  -35.743  ?  ?  ?  N3     O05  30  
O05  N1     N5   N  0  1  Y  N  N  -13.331  25.065  -37.816  ?  ?  ?  N1     O05  31  
O05  N2     N6   N  0  1  N  N  N  -11.594  25.660  -36.405  ?  ?  ?  N2     O05  32  
O05  N4     N7   N  1  1  N  N  N  -10.744  28.284  -35.709  ?  ?  ?  N4     O05  33  
O05  H19    H1   H  0  1  N  N  N  -16.660  17.642  -29.187  ?  ?  ?  H19    O05  34  
O05  H18    H2   H  0  1  N  N  N  -15.826  18.873  -30.194  ?  ?  ?  H18    O05  35  
O05  H15    H3   H  0  1  N  N  N  -15.605  20.309  -36.251  ?  ?  ?  H15    O05  36  
O05  H13    H4   H  0  1  N  N  N  -11.561  25.274  -34.337  ?  ?  ?  H13    O05  37  
O05  H14    H5   H  0  1  N  N  N   -9.979  25.724  -35.058  ?  ?  ?  H14    O05  38  
O05  H11    H6   H  0  1  N  N  N  -10.823  27.581  -33.724  ?  ?  ?  H11    O05  39  
O05  H12    H7   H  0  1  N  N  N  -12.385  27.549  -34.610  ?  ?  ?  H12    O05  40  
O05  H9     H8   H  0  1  N  N  N  -10.885  28.680  -37.775  ?  ?  ?  H9     O05  41  
O05  H8     H9   H  0  1  N  N  N  -12.415  28.163  -36.989  ?  ?  ?  H8     O05  42  
O05  H7     H10  H  0  1  N  N  N  -11.498  26.361  -38.387  ?  ?  ?  H7     O05  43  
O05  H6     H11  H  0  1  N  N  N   -9.952  26.428  -37.475  ?  ?  ?  H6     O05  44  
O05  H20    H12  H  0  1  N  N  N  -19.262  16.606  -30.982  ?  ?  ?  H20    O05  45  
O05  H21    H13  H  0  1  N  N  N  -19.415  19.810  -28.249  ?  ?  ?  H21    O05  46  
O05  H22    H14  H  0  1  N  N  N  -16.084  21.219  -28.084  ?  ?  ?  H22    O05  47  
O05  H16    H15  H  0  1  N  N  N  -17.043  20.115  -32.935  ?  ?  ?  H16    O05  48  
O05  H17    H16  H  0  1  N  N  N  -16.401  18.963  -34.155  ?  ?  ?  H17    O05  49  
O05  H1     H17  H  0  1  N  N  N  -14.397  19.001  -32.266  ?  ?  ?  H1     O05  50  
O05  H2     H18  H  0  1  N  N  N  -15.760  21.229  -31.455  ?  ?  ?  H2     O05  51  
O05  H23    H19  H  0  1  N  N  N  -13.763  20.455  -30.540  ?  ?  ?  H23    O05  52  
O05  H3     H20  H  0  1  N  N  N  -15.798  22.330  -33.553  ?  ?  ?  H3     O05  53  
O05  H24    H21  H  0  1  N  N  N  -14.621  23.807  -32.160  ?  ?  ?  H24    O05  54  
O05  H      H22  H  0  1  N  N  N  -12.885  21.587  -33.993  ?  ?  ?  H      O05  55  
O05  H5     H23  H  0  1  N  N  N  -14.438  25.175  -39.843  ?  ?  ?  H5     O05  56  
O05  H4     H24  H  0  1  N  N  N  -14.583  23.559  -40.027  ?  ?  ?  H4     O05  57  
O05  H10    H25  H  0  1  N  N  N   -9.753  28.158  -35.754  ?  ?  ?  H10    O05  58  
O05  H25    H26  H  0  1  N  N  N  -10.948  29.229  -35.453  ?  ?  ?  H25    O05  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
O05  N6     C6     SING  N  N   1  
O05  C6     N1     DOUB  Y  N   2  
O05  C6     C5     SING  Y  N   3  
O05  N1     C2     SING  Y  N   4  
O05  N7     C5     SING  Y  N   5  
O05  N7     C8     DOUB  Y  N   6  
O05  C12    C11    SING  N  N   7  
O05  C12    N2     SING  N  N   8  
O05  C5     C4     DOUB  Y  N   9  
O05  C11    N4     SING  N  N  10  
O05  C2     N2     SING  N  N  11  
O05  C2     N3     DOUB  Y  N  12  
O05  C8     N9     SING  Y  N  13  
O05  N2     C9     SING  N  N  14  
O05  C4     N3     SING  Y  N  15  
O05  C4     N9     SING  Y  N  16  
O05  N4     C10    SING  N  N  17  
O05  N9     "C1'"  SING  N  N  18  
O05  C9     C10    SING  N  N  19  
O05  "C1'"  "O4'"  SING  N  N  20  
O05  "C1'"  "C2'"  SING  N  N  21  
O05  "O4'"  "C4'"  SING  N  N  22  
O05  "C2'"  O8     SING  N  N  23  
O05  "C2'"  "C3'"  SING  N  N  24  
O05  "C5'"  "C4'"  SING  N  N  25  
O05  "C5'"  "O5'"  SING  N  N  26  
O05  "C4'"  "C3'"  SING  N  N  27  
O05  "O5'"  PA     SING  N  N  28  
O05  "C3'"  O7     SING  N  N  29  
O05  O2A    PA     DOUB  N  N  30  
O05  PA     O1A    SING  N  N  31  
O05  PA     C3     SING  N  N  32  
O05  C3     PB     SING  N  N  33  
O05  O1B    PB     DOUB  N  N  34  
O05  PB     O3B    SING  N  N  35  
O05  PB     O2B    SING  N  N  36  
O05  C3     H19    SING  N  N  37  
O05  C3     H18    SING  N  N  38  
O05  C8     H15    SING  N  N  39  
O05  C9     H13    SING  N  N  40  
O05  C9     H14    SING  N  N  41  
O05  C10    H11    SING  N  N  42  
O05  C10    H12    SING  N  N  43  
O05  C11    H9     SING  N  N  44  
O05  C11    H8     SING  N  N  45  
O05  C12    H7     SING  N  N  46  
O05  C12    H6     SING  N  N  47  
O05  O1A    H20    SING  N  N  48  
O05  O3B    H21    SING  N  N  49  
O05  O2B    H22    SING  N  N  50  
O05  "C5'"  H16    SING  N  N  51  
O05  "C5'"  H17    SING  N  N  52  
O05  "C4'"  H1     SING  N  N  53  
O05  "C3'"  H2     SING  N  N  54  
O05  O7     H23    SING  N  N  55  
O05  "C2'"  H3     SING  N  N  56  
O05  O8     H24    SING  N  N  57  
O05  "C1'"  H      SING  N  N  58  
O05  N6     H5     SING  N  N  59  
O05  N6     H4     SING  N  N  60  
O05  N4     H10    SING  N  N  61  
O05  N4     H25    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
O05  InChI             InChI                 1.03   "InChI=1S/C15H25N7O9P2/c16-12-9-13(20-15(19-12)21-3-1-17-2-4-21)22(6-18-9)14-11(24)10(23)8(31-14)5-30-33(28,29)7-32(25,26)27/h6,8,10-11,14,17,23-24H,1-5,7H2,(H,28,29)(H2,16,19,20)(H2,25,26,27)/p+1/t8-,10-,11-,14-/m1/s1"  
O05  InChIKey          InChI                 1.03   GUHCLCYLXMLIOC-IDTAVKCVSA-O  
O05  SMILES_CANONICAL  CACTVS                3.385  "Nc1nc(nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O)N4CC[NH2+]CC4"  
O05  SMILES            CACTVS                3.385  "Nc1nc(nc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O)N4CC[NH2+]CC4"  
O05  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc2c(nc(nc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(CP(=O)(O)O)O)O)O)N4CC[NH2+]CC4)N"  
O05  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc2c(nc(nc2n1C3C(C(C(O3)COP(=O)(CP(=O)(O)O)O)O)O)N4CC[NH2+]CC4)N"  
#
_pdbx_chem_comp_identifier.comp_id          O05
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic 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
O05  "Create component"  2020-01-13  PDBE  
O05  "Initial release"   2020-02-19  RCSB  
##
