data_R5I
# 
_chem_comp.id                                    R5I 
_chem_comp.name                                  "inosine diphosphate ribose" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H22 N4 O15 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-09-18 
_chem_comp.pdbx_modified_date                    2018-11-23 
_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                        560.301 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     R5I 
_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        6HOZ 
_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 
R5I O1    O1  O 0 1 N N N 19.520 6.945  -3.299  8.227  2.884  2.477  O1    R5I 1  
R5I C6    C1  C 0 1 N N N 18.284 7.027  -3.421  7.724  2.643  1.393  C6    R5I 2  
R5I N1    N1  N 0 1 N N N 17.536 8.043  -2.808  8.161  3.261  0.272  N1    R5I 3  
R5I C2    C2  C 0 1 N N N 16.203 8.221  -2.906  7.593  2.986  -0.929 C2    R5I 4  
R5I N3    N2  N 0 1 N N N 15.400 7.444  -3.590  6.619  2.128  -1.056 N3    R5I 5  
R5I C4    C3  C 0 1 Y N N 16.074 6.433  -4.209  6.127  1.472  0.004  C4    R5I 6  
R5I C5    C4  C 0 1 Y N N 17.429 6.181  -4.179  6.670  1.704  1.271  C5    R5I 7  
R5I N7    N3  N 0 1 Y N N 17.738 5.071  -4.951  5.996  0.922  2.147  N7    R5I 8  
R5I C8    C5  C 0 1 Y N N 16.580 4.673  -5.440  5.092  0.239  1.505  C8    R5I 9  
R5I N9    N4  N 0 1 Y N N 15.531 5.471  -5.015  5.144  0.537  0.177  N9    R5I 10 
R5I "C1'" C6  C 0 1 N N R 14.118 5.326  -5.306  4.289  -0.025 -0.872 "C1'" R5I 11 
R5I "O4'" O2  O 0 1 N N N 13.926 4.084  -5.946  3.064  -0.535 -0.302 "O4'" R5I 12 
R5I "C4'" C7  C 0 1 N N R 13.268 4.290  -7.213  2.552  -1.471 -1.276 "C4'" R5I 13 
R5I "C5'" C8  C 0 1 N N N 13.697 3.210  -8.172  1.571  -2.442 -0.616 "C5'" R5I 14 
R5I "O5'" O3  O 0 1 N N N 15.114 3.330  -8.438  0.409  -1.728 -0.189 "O5'" R5I 15 
R5I PA    P1  P 0 1 N N N 15.633 3.529  -9.939  -0.835 -2.438 0.547  PA    R5I 16 
R5I O2A   O4  O 0 1 N N N 14.925 4.680  -10.575 -1.332 -3.553 -0.289 O2A   R5I 17 
R5I O1A   O5  O 0 1 N N N 17.156 3.513  -9.928  -0.358 -3.009 1.975  O1A   R5I 18 
R5I O3A   O6  O 0 1 N N N 15.043 2.249  -10.703 -2.014 -1.363 0.765  O3A   R5I 19 
R5I PB    P2  P 0 1 N N N 15.320 0.670  -10.613 -3.576 -1.476 1.139  PB    R5I 20 
R5I O2B   O7  O 0 1 N N N 16.118 0.371  -9.400  -3.733 -1.696 2.727  O2B   R5I 21 
R5I O1B   O8  O 0 1 N N N 15.734 0.211  -11.966 -4.173 -2.624 0.421  O1B   R5I 22 
R5I O5D   O9  O 0 1 N N N 13.831 0.188  -10.375 -4.331 -0.122 0.708  O5D   R5I 23 
R5I C5D   C9  C 0 1 N N N 13.591 -1.204 -10.406 -5.746 0.048  0.813  C5D   R5I 24 
R5I C4D   C10 C 0 1 N N R 12.139 -1.343 -10.041 -6.130 1.445  0.320  C4D   R5I 25 
R5I O4D   O10 O 0 1 N N N 11.387 -0.566 -11.015 -5.877 1.553  -1.090 O4D   R5I 26 
R5I C1D   C11 C 0 1 N N R 10.403 -1.436 -11.556 -6.898 2.415  -1.637 C1D   R5I 27 
R5I O1D   O11 O 0 1 N N N 10.282 -1.270 -12.845 -7.040 2.195  -3.042 O1D   R5I 28 
R5I C2D   C12 C 0 1 N N R 10.984 -2.838 -11.477 -8.180 1.979  -0.884 C2D   R5I 29 
R5I O2D   O12 O 0 1 N N N 10.031 -3.882 -11.650 -9.137 3.039  -0.850 O2D   R5I 30 
R5I C3D   C13 C 0 1 N N S 11.584 -2.764 -10.075 -7.637 1.681  0.538  C3D   R5I 31 
R5I O3D   O13 O 0 1 N N N 10.614 -2.917 -9.036  -7.852 2.801  1.400  O3D   R5I 32 
R5I "C3'" C14 C 0 1 N N S 13.606 5.732  -7.584  3.797  -2.227 -1.789 "C3'" R5I 33 
R5I "O3'" O14 O 0 1 N N N 12.698 6.304  -8.526  3.681  -2.491 -3.188 "O3'" R5I 34 
R5I "C2'" C15 C 0 1 N N R 13.522 6.398  -6.208  4.968  -1.252 -1.519 "C2'" R5I 35 
R5I "O2'" O15 O 0 1 N N N 12.194 6.627  -5.795  5.607  -0.887 -2.744 "O2'" R5I 36 
R5I H1    H1  H 0 1 N N N 18.039 8.698  -2.244  8.884  3.905  0.328  H1    R5I 37 
R5I H2    H2  H 0 1 N N N 15.768 9.061  -2.385  7.960  3.493  -1.809 H2    R5I 38 
R5I H3    H3  H 0 1 N N N 16.463 3.823  -6.096  4.413  -0.470 1.957  H3    R5I 39 
R5I H4    H4  H 0 1 N N N 13.560 5.336  -4.358  4.070  0.730  -1.627 H4    R5I 40 
R5I H5    H5  H 0 1 N N N 12.179 4.218  -7.073  2.067  -0.939 -2.094 H5    R5I 41 
R5I H6    H6  H 0 1 N N N 13.138 3.314  -9.114  1.282  -3.210 -1.334 H6    R5I 42 
R5I H7    H7  H 0 1 N N N 13.490 2.224  -7.729  2.046  -2.911 0.245  H7    R5I 43 
R5I H8    H8  H 0 1 N N N 17.484 4.294  -10.358 -0.019 -2.331 2.576  H8    R5I 44 
R5I H9    H9  H 0 1 N N N 16.886 -0.133 -9.642  -3.362 -0.981 3.261  H9    R5I 45 
R5I H10   H10 H 0 1 N N N 13.780 -1.609 -11.411 -6.248 -0.703 0.203  H10   R5I 46 
R5I H11   H11 H 0 1 N N N 14.227 -1.725 -9.675  -6.049 -0.067 1.853  H11   R5I 47 
R5I H12   H12 H 0 1 N N N 11.981 -0.927 -9.035  -5.555 2.198  0.859  H12   R5I 48 
R5I H13   H13 H 0 1 N N N 9.453  -1.380 -11.004 -6.669 3.461  -1.432 H13   R5I 49 
R5I H14   H14 H 0 1 N N N 9.920  -0.409 -13.021 -6.265 2.451  -3.560 H14   R5I 50 
R5I H15   H15 H 0 1 N N N 11.797 -2.933 -12.211 -8.610 1.083  -1.333 H15   R5I 51 
R5I H16   H16 H 0 1 N N N 10.468 -4.723 -11.588 -9.440 3.324  -1.724 H16   R5I 52 
R5I H17   H17 H 0 1 N N N 12.402 -3.492 -9.975  -8.107 0.787  0.947  H17   R5I 53 
R5I H18   H18 H 0 1 N N N 11.044 -2.862 -8.190  -8.784 3.029  1.523  H18   R5I 54 
R5I H19   H19 H 0 1 N N N 14.641 5.784  -7.954  3.936  -3.155 -1.234 H19   R5I 55 
R5I H20   H20 H 0 1 N N N 12.959 7.197  -8.716  4.436  -2.965 -3.563 H20   R5I 56 
R5I H21   H21 H 0 1 N N N 14.134 7.312  -6.183  5.686  -1.699 -0.832 H21   R5I 57 
R5I H22   H22 H 0 1 N N N 12.195 7.040  -4.939  5.998  -1.632 -3.221 H22   R5I 58 
# 
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 
R5I O1D   C1D   SING N N 1  
R5I O1B   PB    DOUB N N 2  
R5I O2D   C2D   SING N N 3  
R5I C1D   C2D   SING N N 4  
R5I C1D   O4D   SING N N 5  
R5I C2D   C3D   SING N N 6  
R5I O4D   C4D   SING N N 7  
R5I O3A   PB    SING N N 8  
R5I O3A   PA    SING N N 9  
R5I PB    O5D   SING N N 10 
R5I PB    O2B   SING N N 11 
R5I O2A   PA    DOUB N N 12 
R5I C5D   O5D   SING N N 13 
R5I C5D   C4D   SING N N 14 
R5I C3D   C4D   SING N N 15 
R5I C3D   O3D   SING N N 16 
R5I PA    O1A   SING N N 17 
R5I PA    "O5'" SING N N 18 
R5I "O3'" "C3'" SING N N 19 
R5I "O5'" "C5'" SING N N 20 
R5I "C5'" "C4'" SING N N 21 
R5I "C3'" "C4'" SING N N 22 
R5I "C3'" "C2'" SING N N 23 
R5I "C4'" "O4'" SING N N 24 
R5I "C2'" "O2'" SING N N 25 
R5I "C2'" "C1'" SING N N 26 
R5I "O4'" "C1'" SING N N 27 
R5I C8    N9    SING Y N 28 
R5I C8    N7    DOUB Y N 29 
R5I "C1'" N9    SING N N 30 
R5I N9    C4    SING Y N 31 
R5I N7    C5    SING Y N 32 
R5I C4    C5    DOUB Y N 33 
R5I C4    N3    SING N N 34 
R5I C5    C6    SING N N 35 
R5I N3    C2    DOUB N N 36 
R5I C6    O1    DOUB N N 37 
R5I C6    N1    SING N N 38 
R5I C2    N1    SING N N 39 
R5I N1    H1    SING N N 40 
R5I C2    H2    SING N N 41 
R5I C8    H3    SING N N 42 
R5I "C1'" H4    SING N N 43 
R5I "C4'" H5    SING N N 44 
R5I "C5'" H6    SING N N 45 
R5I "C5'" H7    SING N N 46 
R5I O1A   H8    SING N N 47 
R5I O2B   H9    SING N N 48 
R5I C5D   H10   SING N N 49 
R5I C5D   H11   SING N N 50 
R5I C4D   H12   SING N N 51 
R5I C1D   H13   SING N N 52 
R5I O1D   H14   SING N N 53 
R5I C2D   H15   SING N N 54 
R5I O2D   H16   SING N N 55 
R5I C3D   H17   SING N N 56 
R5I O3D   H18   SING N N 57 
R5I "C3'" H19   SING N N 58 
R5I "O3'" H20   SING N N 59 
R5I "C2'" H21   SING N N 60 
R5I "O2'" H22   SING N N 61 
# 
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 
R5I InChI            InChI                1.03  
"InChI=1S/C15H22N4O15P2/c20-8-5(32-14(10(8)22)19-4-18-7-12(19)16-3-17-13(7)24)1-30-35(26,27)34-36(28,29)31-2-6-9(21)11(23)15(25)33-6/h3-6,8-11,14-15,20-23,25H,1-2H2,(H,26,27)(H,28,29)(H,16,17,24)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1" 
R5I InChIKey         InChI                1.03  GKBLKKRZILWFNP-KEOHHSTQSA-N 
R5I SMILES_CANONICAL CACTVS               3.385 "O[C@@H]1O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC=Nc34)[C@@H](O)[C@H]1O" 
R5I SMILES           CACTVS               3.385 "O[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC=Nc34)[CH](O)[CH]1O" 
R5I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N=CNC2=O" 
R5I SMILES           "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N=CNC2=O" 
# 
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 
R5I "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 
"[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen 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 
R5I "Create component" 2018-09-18 EBI  
R5I "Initial release"  2018-11-28 RCSB 
# 
