data_IB2
#

_chem_comp.id                                   IB2
_chem_comp.name                                 "P1-P2-METHYLENE-P3-THIO-DIADENOSINE TRIPHOSPHATE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C21 H29 N10 O14 P3 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ADO-P-CH2-P-PS-ADO
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-08
_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                       770.500
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    IB2
_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  N
_chem_comp.pdbx_model_coordinates_db_code       2FHI
_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
IB2  PA      PA      P  0  1  N  N  S   9.263  12.986  23.227  -0.622   1.325    2.707  PA      IB2   1  
IB2  O1A     O1A     O  0  1  N  N  N  10.376  13.188  22.200  -1.719   2.235    2.309  O1A     IB2   2  
IB2  O2A     O2A     O  0  1  N  N  N   8.027  12.209  22.726   0.688   2.189    3.062  O2A     IB2   3  
IB2  C3A     C3A     C  0  1  N  N  N   8.651  14.692  23.665  -0.247   0.187    1.334  C3A     IB2   4  
IB2  PB      PB      P  0  1  N  N  S   8.321  15.940  22.351   0.261   1.148   -0.129  PB      IB2   5  
IB2  O1B     O1B     O  0  1  N  N  N   7.177  16.769  22.887   1.466   1.942    0.196  O1B     IB2   6  
IB2  O2B     O2B     O  0  1  N  N  N   8.039  15.200  21.076  -0.932   2.137   -0.563  O2B     IB2   7  
IB2  O3B     O3B     O  0  1  N  N  N   9.570  16.814  22.137   0.592   0.143   -1.342  O3B     IB2   8  
IB2  PG      PG      P  0  1  N  N  R  10.059  17.936  21.167   1.032   1.054   -2.594  PG      IB2   9  
IB2  O1G     O1G     O  0  1  N  N  N   9.076  18.418  20.266   2.226   1.850   -2.230  O1G     IB2  10  
IB2  S2G     S2G     S  0  1  N  N  N  11.198  17.465  20.425  -0.556   2.359   -3.111  S2G     IB2  11  
IB2  O5D     O5*     O  0  1  N  N  N   9.882  12.256  24.549  -1.071   0.477    4.000  O5D     IB2  12  
IB2  C5D     C5*     C  0  1  N  N  N  10.249  10.898  24.461  -1.350   1.420    5.037  C5D     IB2  13  
IB2  C4D     C4*     C  0  1  N  N  R  11.446  10.779  25.359  -1.785   0.675    6.300  C4D     IB2  14  
IB2  O4D     O4*     O  0  1  N  N  N  11.085   9.893  26.436  -0.726  -0.190    6.763  O4D     IB2  15  
IB2  C3D     C3*     C  0  1  N  N  S  12.663  10.160  24.643  -2.018   1.668    7.460  C3D     IB2  16  
IB2  O3D     O3*     O  0  1  N  N  N  13.870  10.845  25.008  -3.409   1.968    7.591  O3D     IB2  17  
IB2  C2D     C2*     C  0  1  N  N  R  12.717   8.678  25.063  -1.506   0.915    8.710  C2D     IB2  18  
IB2  O2D     O2*     O  0  1  N  N  N  14.103   8.105  25.051  -2.564   0.729    9.651  O2D     IB2  19  
IB2  C1D     C1*     C  0  1  N  N  R  12.010   8.736  26.446  -1.021  -0.442    8.154  C1D     IB2  20  
IB2  "O5'"   "O5'"   O  0  1  N  N  N  10.513  19.059  22.212   1.380   0.109   -3.850  "O5'"   IB2  21  
IB2  "C5'"   "C5'"   C  0  1  N  N  N   9.522  19.922  22.826   1.761   0.971   -4.924  "C5'"   IB2  22  
IB2  "C4'"   "C4'"   C  0  1  N  N  R   9.641  19.743  24.350   2.106   0.132   -6.155  "C4'"   IB2  23  
IB2  "O4'"   "O4'"   O  0  1  N  N  N   9.851  21.047  24.963   0.953  -0.614   -6.577  "O4'"   IB2  24  
IB2  "C3'"   "C3'"   C  0  1  N  N  S   8.338  19.146  24.944   2.511   1.054   -7.322  "C3'"   IB2  25  
IB2  "O3'"   "O3'"   O  0  1  N  N  N   8.569  18.100  25.912   3.846   0.774   -7.748  "O3'"   IB2  26  
IB2  "C2'"   "C2'"   C  0  1  N  N  R   7.610  20.318  25.544   1.499   0.707   -8.444  "C2'"   IB2  27  
IB2  "O2'"   "O2'"   O  0  1  N  N  N   6.768  19.973  26.678   2.147   0.657   -9.717  "O2'"   IB2  28  
IB2  "C1'"   "C1'"   C  0  1  N  N  R   8.742  21.285  25.880   1.010  -0.700   -8.017  "C1'"   IB2  29  
IB2  N9      N9      N  0  1  Y  N  N   8.273  22.716  25.789  -0.317  -0.978   -8.571  N9      IB2  30  
IB2  C8      C8      C  0  1  Y  N  N   7.901  23.367  24.656  -1.512  -0.623   -8.019  C8      IB2  31  
IB2  N7      N7      N  0  1  Y  N  N   7.546  24.636  24.927  -2.489  -1.029   -8.775  N7      IB2  32  
IB2  C5      C5      C  0  1  Y  N  N   7.681  24.806  26.235  -1.986  -1.669   -9.858  C5      IB2  33  
IB2  C6      C6      C  0  1  Y  N  N   7.474  25.883  27.091  -2.546  -2.299  -10.982  C6      IB2  34  
IB2  N6      N6      N  0  1  N  N  N   7.052  27.076  26.632  -3.918  -2.354  -11.153  N6      IB2  35  
IB2  N1      N1      N  0  1  Y  N  N   7.733  25.680  28.496  -1.726  -2.841  -11.878  N1      IB2  36  
IB2  C2      C2      C  0  1  Y  N  N   8.183  24.462  29.023  -0.416  -2.792  -11.723  C2      IB2  37  
IB2  N3      N3      N  0  1  Y  N  N   8.380  23.440  28.166   0.152  -2.213  -10.687  N3      IB2  38  
IB2  C4      C4      C  0  1  Y  N  N   8.143  23.563  26.756  -0.586  -1.639   -9.743  C4      IB2  39  
IB2  N9A     AN9     N  0  1  Y  N  N  11.294   7.452  26.725   0.184  -0.881    8.860  N9A     IB2  40  
IB2  C8A     AC8     C  0  1  Y  N  N  11.871   6.231  26.842   1.470  -0.574    8.527  C8A     IB2  41  
IB2  N7A     AN7     N  0  1  Y  N  N  10.934   5.304  27.083   2.292  -1.130    9.369  N7A     IB2  42  
IB2  C5A     AC5     C  0  1  Y  N  N   9.753   5.933  27.120   1.588  -1.823   10.296  C5A     IB2  43  
IB2  C6A     AC6     C  0  1  Y  N  N   8.426   5.510  27.326   1.927  -2.608   11.411  C6A     IB2  44  
IB2  N6A     AN6     N  0  1  N  N  N   8.119   4.235  27.540   3.251  -2.794   11.770  N6A     IB2  45  
IB2  N1A     AN1     N  0  1  Y  N  N   7.402   6.493  27.297   0.947  -3.164   12.115  N1A     IB2  46  
IB2  C2A     AC2     C  0  1  Y  N  N   7.682   7.862  27.070  -0.318  -2.993   11.780  C2A     IB2  47  
IB2  N3A     AN3     N  0  1  Y  N  N   8.986   8.246  26.867  -0.682  -2.271   10.741  N3A     IB2  48  
IB2  C4A     AC4     C  0  1  Y  N  N  10.044   7.302  26.889   0.227  -1.676    9.977  C4A     IB2  49  
IB2  HOA2    2HOA    H  0  0  N  N  N   7.334  12.083  23.364   1.377   1.560    3.316  HOA2    IB2  50  
IB2  H3A1    1H3A    H  0  0  N  N  N   7.728  14.583  24.280   0.560  -0.482    1.627  H3A1    IB2  51  
IB2  H3A2    2H3A    H  0  0  N  N  N   9.361  15.138  24.398  -1.135  -0.397    1.094  H3A2    IB2  52  
IB2  HOB2    2HOB    H  0  0  N  N  N   7.868  15.843  20.398  -1.696   1.581   -0.766  HOB2    IB2  53  
IB2  HSG2    2HSG    H  0  0  N  N  N  11.495  18.147  19.834  -1.513   1.459   -3.399  HSG2    IB2  54  
IB2  "H5'1"  1H5*    H  0  0  N  N  N   9.425  10.186  24.701  -2.150   2.087    4.715  "H5'1"  IB2  55  
IB2  "H5'2"  2H5*    H  0  0  N  N  N  10.421  10.538  23.419  -0.454   2.002    5.249  "H5'2"  IB2  56  
IB2  H4D     H4*     H  0  1  N  N  N  11.728  11.801  25.702  -2.690   0.098    6.107  H4D     IB2  57  
IB2  H3D     H3*     H  0  1  N  N  N  12.566  10.252  23.536  -1.445   2.582    7.301  H3D     IB2  58  
IB2  "HO3'"  *HO3    H  0  0  N  N  N  14.619  10.463  24.566  -3.493   2.590    8.326  "HO3'"  IB2  59  
IB2  H2D     H2*     H  0  1  N  N  N  12.217   7.968  24.362  -0.678   1.455    9.169  H2D     IB2  60  
IB2  "HO2'"  *HO2    H  0  0  N  N  N  14.136   7.191  25.309  -2.863   1.610    9.914  "HO2'"  IB2  61  
IB2  H1D     H1*     H  0  1  N  N  N  12.756   8.867  27.263  -1.807  -1.192    8.246  H1D     IB2  62  
IB2  H51X    "1H5'"  H  0  0  N  N  N   9.610  20.985  22.503   0.935   1.642   -5.161  H51X    IB2  63  
IB2  H52X    "2H5'"  H  0  0  N  N  N   8.489  19.741  22.444   2.631   1.557   -4.628  H52X    IB2  64  
IB2  "H4'"   "H4'"   H  0  1  N  N  N  10.492  19.052  24.555   2.924  -0.550   -5.921  "H4'"   IB2  65  
IB2  "H3'"   "H3'"   H  0  1  N  N  N   7.741  18.638  24.150   2.416   2.100   -7.031  "H3'"   IB2  66  
IB2  HO3X    "'HO3"  H  0  0  N  N  N   7.771  17.734  26.275   4.019   1.338   -8.515  HO3X    IB2  67  
IB2  "H2'"   "H2'"   H  0  1  N  N  N   6.860  20.761  24.847   0.673   1.418   -8.458  "H2'"   IB2  68  
IB2  HO2X    "'HO2"  H  0  0  N  N  N   6.308  20.713  27.056   2.426   1.559   -9.924  HO2X    IB2  69  
IB2  "H1'"   "H1'"   H  0  1  N  N  N   9.079  21.110  26.928   1.722  -1.464   -8.328  "H1'"   IB2  70  
IB2  H8      H8      H  0  1  N  N  N   7.888  22.922  23.646  -1.629  -0.084   -7.090  H8      IB2  71  
IB2  HN61    1HN6    H  0  0  N  N  N   6.900  27.865  27.259  -4.292  -2.793  -11.933  HN61    IB2  72  
IB2  HN62    2HN6    H  0  0  N  N  N   6.191  26.923  26.106  -4.505  -1.955  -10.492  HN62    IB2  73  
IB2  H2      H2      H  0  1  N  N  N   8.379  24.309  30.097   0.212  -3.245  -12.475  H2      IB2  74  
IB2  H8A     AH8     H  0  1  N  N  N  12.950   6.021  26.753   1.763   0.039    7.689  H8A     IB2  75  
IB2  HNA1    1HNA    H  0  0  N  N  N   7.157   3.928  27.689   3.472  -3.335   12.544  HNA1    IB2  76  
IB2  HNA2    2HNA    H  0  0  N  N  N   8.675   3.909  28.330   3.957  -2.386   11.245  HNA2    IB2  77  
IB2  H2A     AH2     H  0  1  N  N  N   6.887   8.626  27.051  -1.083  -3.463   12.380  H2A     IB2  78  
#   #
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
IB2  PA     O1A     DOUB  N  N   1  
IB2  PA     O2A     SING  N  N   2  
IB2  PA     C3A     SING  N  N   3  
IB2  PA     O5D     SING  N  N   4  
IB2  O2A    HOA2    SING  N  N   5  
IB2  C3A    PB      SING  N  N   6  
IB2  C3A    H3A1    SING  N  N   7  
IB2  C3A    H3A2    SING  N  N   8  
IB2  PB     O1B     DOUB  N  N   9  
IB2  PB     O2B     SING  N  N  10  
IB2  PB     O3B     SING  N  N  11  
IB2  O2B    HOB2    SING  N  N  12  
IB2  O3B    PG      SING  N  N  13  
IB2  PG     O1G     DOUB  N  N  14  
IB2  PG     S2G     SING  N  N  15  
IB2  PG     "O5'"   SING  N  N  16  
IB2  S2G    HSG2    SING  N  N  17  
IB2  O5D    C5D     SING  N  N  18  
IB2  C5D    C4D     SING  N  N  19  
IB2  C5D    "H5'1"  SING  N  N  20  
IB2  C5D    "H5'2"  SING  N  N  21  
IB2  C4D    O4D     SING  N  N  22  
IB2  C4D    C3D     SING  N  N  23  
IB2  C4D    H4D     SING  N  N  24  
IB2  O4D    C1D     SING  N  N  25  
IB2  C3D    O3D     SING  N  N  26  
IB2  C3D    C2D     SING  N  N  27  
IB2  C3D    H3D     SING  N  N  28  
IB2  O3D    "HO3'"  SING  N  N  29  
IB2  C2D    O2D     SING  N  N  30  
IB2  C2D    C1D     SING  N  N  31  
IB2  C2D    H2D     SING  N  N  32  
IB2  O2D    "HO2'"  SING  N  N  33  
IB2  C1D    N9A     SING  N  N  34  
IB2  C1D    H1D     SING  N  N  35  
IB2  "O5'"  "C5'"   SING  N  N  36  
IB2  "C5'"  "C4'"   SING  N  N  37  
IB2  "C5'"  H51X    SING  N  N  38  
IB2  "C5'"  H52X    SING  N  N  39  
IB2  "C4'"  "O4'"   SING  N  N  40  
IB2  "C4'"  "C3'"   SING  N  N  41  
IB2  "C4'"  "H4'"   SING  N  N  42  
IB2  "O4'"  "C1'"   SING  N  N  43  
IB2  "C3'"  "O3'"   SING  N  N  44  
IB2  "C3'"  "C2'"   SING  N  N  45  
IB2  "C3'"  "H3'"   SING  N  N  46  
IB2  "O3'"  HO3X    SING  N  N  47  
IB2  "C2'"  "O2'"   SING  N  N  48  
IB2  "C2'"  "C1'"   SING  N  N  49  
IB2  "C2'"  "H2'"   SING  N  N  50  
IB2  "O2'"  HO2X    SING  N  N  51  
IB2  "C1'"  N9      SING  N  N  52  
IB2  "C1'"  "H1'"   SING  N  N  53  
IB2  N9     C8      SING  Y  N  54  
IB2  N9     C4      SING  Y  N  55  
IB2  C8     N7      DOUB  Y  N  56  
IB2  C8     H8      SING  N  N  57  
IB2  N7     C5      SING  Y  N  58  
IB2  C5     C6      SING  Y  N  59  
IB2  C5     C4      DOUB  Y  N  60  
IB2  C6     N6      SING  N  N  61  
IB2  C6     N1      DOUB  Y  N  62  
IB2  N6     HN61    SING  N  N  63  
IB2  N6     HN62    SING  N  N  64  
IB2  N1     C2      SING  Y  N  65  
IB2  C2     N3      DOUB  Y  N  66  
IB2  C2     H2      SING  N  N  67  
IB2  N3     C4      SING  Y  N  68  
IB2  N9A    C8A     SING  Y  N  69  
IB2  N9A    C4A     SING  Y  N  70  
IB2  C8A    N7A     DOUB  Y  N  71  
IB2  C8A    H8A     SING  N  N  72  
IB2  N7A    C5A     SING  Y  N  73  
IB2  C5A    C6A     SING  Y  N  74  
IB2  C5A    C4A     DOUB  Y  N  75  
IB2  C6A    N6A     SING  N  N  76  
IB2  C6A    N1A     DOUB  Y  N  77  
IB2  N6A    HNA1    SING  N  N  78  
IB2  N6A    HNA2    SING  N  N  79  
IB2  N1A    C2A     SING  Y  N  80  
IB2  C2A    N3A     DOUB  Y  N  81  
IB2  C2A    H2A     SING  N  N  82  
IB2  N3A    C4A     SING  Y  N  83  
#   #
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
IB2  SMILES_CANONICAL  CACTVS                3.341  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)C[P@@](O)(=O)O[P@@](S)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O"  
IB2  SMILES            CACTVS                3.341  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](S)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O"  
IB2  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(C[P@](=O)(O)O[P@@](=O)(OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)S)O)O)O)N"  
IB2  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)S)O)O)O)N"  
IB2  InChI             InChI                 1.03   "InChI=1S/C21H29N10O14P3S/c22-16-10-18(26-3-24-16)30(5-28-10)20-14(34)12(32)8(43-20)1-41-46(36,37)7-47(38,39)45-48(40,49)42-2-9-13(33)15(35)21(44-9)31-6-29-11-17(23)25-4-27-19(11)31/h3-6,8-9,12-15,20-21,32-35H,1-2,7H2,(H,36,37)(H,38,39)(H,40,49)(H2,22,24,26)(H2,23,25,27)/t8-,9-,12-,13-,14-,15-,20-,21-,48-/m1/s1"  
IB2  InChIKey          InChI                 1.03   UJCWOSLCGXVJOD-LCHUORCTSA-N  
#
_pdbx_chem_comp_identifier.comp_id          IB2
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.5.0
_pdbx_chem_comp_identifier.identifier       "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-hydroxy-phosphoryl]methyl]phosphinic 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
IB2  "Create component"   1999-07-08  RCSB  
IB2  "Modify descriptor"  2011-06-04  RCSB  
IB2  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     IB2
_pdbx_chem_comp_synonyms.name        ADO-P-CH2-P-PS-ADO
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
