data_R7I
# 
_chem_comp.id                                    R7I 
_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                     2018-09-20 
_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                     R7I 
_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 
R7I O1B   O1  O 0 1 N N N 16.176 0.420  -9.412  3.644  1.127  2.962  O1B   R7I 1  
R7I PB    P1  P 0 1 N N N 15.330 0.696  -10.605 3.558  1.170  1.355  PB    R7I 2  
R7I O2B   O2  O 0 1 N N N 15.692 0.189  -11.960 4.159  2.430  0.863  O2B   R7I 3  
R7I O5D   O3  O 0 1 N N N 13.842 0.251  -10.280 4.360  -0.083 0.740  O5D   R7I 4  
R7I C5D   C1  C 0 1 N N N 13.526 -1.117 -10.497 5.773  -0.247 0.879  C5D   R7I 5  
R7I C4D   C2  C 0 1 N N R 12.060 -1.255 -10.195 6.208  -1.537 0.182  C4D   R7I 6  
R7I C3D   C3  C 0 1 N N S 11.492 -2.668 -10.340 7.710  -1.784 0.425  C3D   R7I 7  
R7I O3D   O4  O 0 1 N N N 10.632 -2.882 -9.225  7.916  -3.068 1.016  O3D   R7I 8  
R7I C2D   C4  C 0 1 N N R 10.784 -2.581 -11.692 8.337  -1.730 -0.989 C2D   R7I 9  
R7I O2D   O5  O 0 1 N N N 9.853  -3.627 -11.910 8.506  -3.045 -1.523 O2D   R7I 10 
R7I C1D   C5  C 0 1 N N S 10.198 -1.178 -11.541 7.269  -0.942 -1.789 C1D   R7I 11 
R7I O1D   O6  O 0 1 N N N 9.213  -1.202 -10.535 7.353  -1.250 -3.181 O1D   R7I 12 
R7I O4D   O7  O 0 1 N N N 11.318 -0.418 -11.124 6.017  -1.413 -1.238 O4D   R7I 13 
R7I O3A   O8  O 0 1 N N N 15.083 2.278  -10.735 2.016  1.097  0.897  O3A   R7I 14 
R7I PA    P2  P 0 1 N N N 15.634 3.552  -9.927  0.824  2.175  0.806  PA    R7I 15 
R7I O2A   O9  O 0 1 N N N 14.909 4.722  -10.523 1.332  3.421  0.189  O2A   R7I 16 
R7I O1A   O10 O 0 1 N N N 17.149 3.549  -9.919  0.276  2.495  2.286  O1A   R7I 17 
R7I "O5'" O11 O 0 1 N N N 15.104 3.288  -8.435  -0.372 1.579  -0.092 "O5'" R7I 18 
R7I "C5'" C6  C 0 1 N N N 13.678 3.200  -8.194  -1.530 2.336  -0.448 "C5'" R7I 19 
R7I "C4'" C7  C 0 1 N N R 13.259 4.275  -7.224  -2.461 1.473  -1.301 "C4'" R7I 20 
R7I "O4'" O12 O 0 1 N N N 13.927 4.066  -5.958  -2.984 0.391  -0.512 "O4'" R7I 21 
R7I "C3'" C8  C 0 1 N N S 13.612 5.717  -7.592  -3.662 2.313  -1.780 "C3'" R7I 22 
R7I "O3'" O13 O 0 1 N N N 12.700 6.292  -8.523  -3.704 2.357  -3.207 "O3'" R7I 23 
R7I "C2'" C9  C 0 1 N N R 13.533 6.384  -6.218  -4.896 1.561  -1.224 "C2'" R7I 24 
R7I "O2'" O14 O 0 1 N N N 12.205 6.656  -5.828  -5.950 1.529  -2.188 "O2'" R7I 25 
R7I "C1'" C10 C 0 1 N N R 14.112 5.306  -5.309  -4.327 0.140  -0.978 "C1'" R7I 26 
R7I N9    N1  N 0 1 Y N N 15.530 5.457  -5.008  -5.107 -0.557 0.047  N9    R7I 27 
R7I C4    C11 C 0 1 Y N N 16.075 6.431  -4.216  -6.211 -1.336 -0.167 C4    R7I 28 
R7I N3    N2  N 0 1 N N N 15.405 7.440  -3.600  -6.901 -1.704 -1.256 N3    R7I 29 
R7I C2    C12 C 0 1 N N N 16.208 8.220  -2.921  -7.946 -2.478 -1.165 C2    R7I 30 
R7I N1    N3  N 0 1 N N N 17.539 8.054  -2.826  -8.392 -2.953 0.025  N1    R7I 31 
R7I C8    C13 C 0 1 Y N N 16.573 4.656  -5.423  -4.862 -0.553 1.388  C8    R7I 32 
R7I N7    N4  N 0 1 Y N N 17.732 5.060  -4.948  -5.753 -1.278 2.001  N7    R7I 33 
R7I C5    C14 C 0 1 Y N N 17.429 6.181  -4.185  -6.616 -1.790 1.092  C5    R7I 34 
R7I C6    C15 C 0 1 N N N 18.285 7.037  -3.436  -7.754 -2.630 1.173  C6    R7I 35 
R7I O1    O15 O 0 1 N N N 19.512 6.962  -3.307  -8.147 -3.052 2.247  O1    R7I 36 
R7I H1    H1  H 0 1 N N N 16.928 -0.100 -9.670  3.267  0.327  3.354  H1    R7I 37 
R7I H2    H2  H 0 1 N N N 13.729 -1.395 -11.542 6.284  0.602  0.424  H2    R7I 38 
R7I H3    H3  H 0 1 N N N 14.117 -1.757 -9.825  6.030  -0.301 1.937  H3    R7I 39 
R7I H4    H4  H 0 1 N N N 11.877 -0.911 -9.166  5.628  -2.378 0.562  H4    R7I 40 
R7I H5    H5  H 0 1 N N N 12.306 -3.406 -10.380 8.127  -1.002 1.059  H5    R7I 41 
R7I H6    H6  H 0 1 N N N 11.149 -2.923 -8.429  8.844  -3.276 1.191  H6    R7I 42 
R7I H7    H7  H 0 1 N N N 11.541 -2.567 -12.490 9.286  -1.194 -0.973 H7    R7I 43 
R7I H8    H8  H 0 1 N N N 10.316 -4.452 -11.990 8.812  -3.061 -2.440 H8    R7I 44 
R7I H9    H9  H 0 1 N N N 9.798  -0.826 -12.503 7.381  0.130  -1.625 H9    R7I 45 
R7I H10   H10 H 0 1 N N N 8.842  -0.333 -10.433 6.707  -0.783 -3.728 H10   R7I 46 
R7I H11   H11 H 0 1 N N N 17.470 4.347  -10.322 -0.073 1.723  2.751  H11   R7I 47 
R7I H12   H12 H 0 1 N N N 13.138 3.333  -9.143  -2.052 2.649  0.457  H12   R7I 48 
R7I H13   H13 H 0 1 N N N 13.439 2.213  -7.771  -1.228 3.217  -1.015 H13   R7I 49 
R7I H14   H14 H 0 1 N N N 12.171 4.212  -7.078  -1.917 1.078  -2.159 H14   R7I 50 
R7I H15   H15 H 0 1 N N N 14.645 5.762  -7.967  -3.611 3.320  -1.367 H15   R7I 51 
R7I H16   H16 H 0 1 N N N 12.964 7.184  -8.716  -4.440 2.873  -3.563 H16   R7I 52 
R7I H17   H17 H 0 1 N N N 14.164 7.285  -6.194  -5.238 2.010  -0.292 H17   R7I 53 
R7I H18   H18 H 0 1 N N N 12.204 7.068  -4.972  -6.278 2.403  -2.442 H18   R7I 54 
R7I H19   H19 H 0 1 N N N 13.545 5.315  -4.366  -4.311 -0.432 -1.906 H19   R7I 55 
R7I H20   H20 H 0 1 N N N 15.769 9.058  -2.399  -8.474 -2.750 -2.067 H20   R7I 56 
R7I H21   H21 H 0 1 N N N 18.042 8.716  -2.270  -9.174 -3.526 0.053  H21   R7I 57 
R7I H22   H22 H 0 1 N N N 16.453 3.796  -6.064  -4.051 -0.028 1.869  H22   R7I 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 
R7I O2B   PB    DOUB N N 1  
R7I O2D   C2D   SING N N 2  
R7I C2D   C1D   SING N N 3  
R7I C2D   C3D   SING N N 4  
R7I C1D   O4D   SING N N 5  
R7I C1D   O1D   SING N N 6  
R7I O4D   C4D   SING N N 7  
R7I O3A   PB    SING N N 8  
R7I O3A   PA    SING N N 9  
R7I PB    O5D   SING N N 10 
R7I PB    O1B   SING N N 11 
R7I O2A   PA    DOUB N N 12 
R7I C5D   O5D   SING N N 13 
R7I C5D   C4D   SING N N 14 
R7I C3D   C4D   SING N N 15 
R7I C3D   O3D   SING N N 16 
R7I PA    O1A   SING N N 17 
R7I PA    "O5'" SING N N 18 
R7I "O3'" "C3'" SING N N 19 
R7I "O5'" "C5'" SING N N 20 
R7I "C5'" "C4'" SING N N 21 
R7I "C3'" "C4'" SING N N 22 
R7I "C3'" "C2'" SING N N 23 
R7I "C4'" "O4'" SING N N 24 
R7I "C2'" "O2'" SING N N 25 
R7I "C2'" "C1'" SING N N 26 
R7I "O4'" "C1'" SING N N 27 
R7I C8    N9    SING Y N 28 
R7I C8    N7    DOUB Y N 29 
R7I "C1'" N9    SING N N 30 
R7I N9    C4    SING Y N 31 
R7I N7    C5    SING Y N 32 
R7I C4    C5    DOUB Y N 33 
R7I C4    N3    SING N N 34 
R7I C5    C6    SING N N 35 
R7I N3    C2    DOUB N N 36 
R7I C6    O1    DOUB N N 37 
R7I C6    N1    SING N N 38 
R7I C2    N1    SING N N 39 
R7I O1B   H1    SING N N 40 
R7I C5D   H2    SING N N 41 
R7I C5D   H3    SING N N 42 
R7I C4D   H4    SING N N 43 
R7I C3D   H5    SING N N 44 
R7I O3D   H6    SING N N 45 
R7I C2D   H7    SING N N 46 
R7I O2D   H8    SING N N 47 
R7I C1D   H9    SING N N 48 
R7I O1D   H10   SING N N 49 
R7I O1A   H11   SING N N 50 
R7I "C5'" H12   SING N N 51 
R7I "C5'" H13   SING N N 52 
R7I "C4'" H14   SING N N 53 
R7I "C3'" H15   SING N N 54 
R7I "O3'" H16   SING N N 55 
R7I "C2'" H17   SING N N 56 
R7I "O2'" H18   SING N N 57 
R7I "C1'" H19   SING N N 58 
R7I C2    H20   SING N N 59 
R7I N1    H21   SING N N 60 
R7I C8    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 
R7I 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" 
R7I InChIKey         InChI                1.03  GKBLKKRZILWFNP-ZQSHOCFMSA-N 
R7I 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" 
R7I 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" 
R7I 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" 
R7I 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 
R7I "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~{S})-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 
R7I "Create component" 2018-09-20 EBI  
R7I "Initial release"  2018-11-28 RCSB 
# 
