data_9SI
# 
_chem_comp.id                                    9SI 
_chem_comp.name                                  "[(2R,3S,4R,5R)-5-[1-[[4-(aminomethyl)phenyl]methyl]-6-azanyl-purin-1-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C18 H24 N6 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         1-benzylamine-adenosine 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2021-11-19 
_chem_comp.pdbx_modified_date                    2022-08-22 
_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                        467.393 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     9SI 
_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        7Q7Z 
_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 
9SI C4     C1  C 0 1 Y N N 34.147 -50.600 3.423  0.660  0.292  -0.975 C4     9SI 1  
9SI C5     C2  C 0 1 Y N N 33.627 -50.048 2.162  1.261  1.449  -0.451 C5     9SI 2  
9SI C6     C3  C 0 1 Y N N 33.039 -48.688 2.195  2.612  1.689  -0.753 C6     9SI 3  
9SI C1     C4  C 0 1 N N N 32.428 -46.685 3.388  4.665  1.043  -1.846 C1     9SI 4  
9SI C2     C5  C 0 1 Y N N 33.506 -48.598 4.481  2.648  -0.261 -1.987 C2     9SI 5  
9SI C3     C6  C 0 1 Y N N 32.797 -45.934 4.649  5.533  0.504  -0.738 C3     9SI 6  
9SI N1     N1  N 1 1 Y N N 33.014 -48.032 3.360  3.255  0.813  -1.518 N1     9SI 7  
9SI C7     C7  C 0 1 Y N N 34.017 -45.269 4.731  5.976  -0.805 -0.783 C7     9SI 8  
9SI C9     C8  C 0 1 Y N N 34.356 -44.576 5.888  6.772  -1.300 0.233  C9     9SI 9  
9SI C10    C9  C 0 1 Y N N 33.474 -44.543 6.961  7.125  -0.486 1.293  C10    9SI 10 
9SI C11    C10 C 0 1 Y N N 32.253 -45.203 6.879  6.683  0.822  1.337  C11    9SI 11 
9SI C12    C11 C 0 1 Y N N 31.914 -45.895 5.723  5.891  1.319  0.319  C12    9SI 12 
9SI C13    C12 C 0 1 N N N 33.842 -43.791 8.219  7.993  -1.026 2.401  C13    9SI 13 
9SI C8     C13 C 0 1 Y N N 34.425 -52.044 1.822  -0.799 1.428  0.227  C8     9SI 14 
9SI "C1'"  C14 C 0 1 N N R 35.237 -52.772 4.068  -1.662 -0.703 -0.813 "C1'"  9SI 15 
9SI "C2'"  C15 C 0 1 N N R 34.599 -54.155 4.044  -1.603 -1.853 0.226  "C2'"  9SI 16 
9SI "C3'"  C16 C 0 1 N N S 35.740 -55.032 4.557  -3.045 -2.414 0.170  "C3'"  9SI 17 
9SI "C4'"  C17 C 0 1 N N R 36.992 -54.324 4.036  -3.876 -1.262 -0.427 "C4'"  9SI 18 
9SI "C5'"  C18 C 0 1 N N N 37.640 -54.980 2.842  -4.990 -0.866 0.545  "C5'"  9SI 19 
9SI N10    N2  N 0 1 N N N 32.785 -43.975 9.228  9.406  -0.796 2.072  N10    9SI 20 
9SI N3     N3  N 0 1 Y N N 34.056 -49.828 4.533  1.384  -0.527 -1.731 N3     9SI 21 
9SI N6     N4  N 0 1 N N N 32.543 -48.122 1.069  3.257  2.812  -0.266 N6     9SI 22 
9SI N7     N5  N 0 1 Y N N 33.828 -50.985 1.219  0.316  2.097  0.272  N7     9SI 23 
9SI N9     N6  N 0 1 Y N N 34.619 -51.822 3.136  -0.637 0.303  -0.527 N9     9SI 24 
9SI "O2'"  O1  O 0 1 N N N 33.425 -54.202 4.827  -0.654 -2.846 -0.166 "O2'"  9SI 25 
9SI "O3'"  O2  O 0 1 N N N 35.757 -55.030 5.982  -3.102 -3.563 -0.677 "O3'"  9SI 26 
9SI "O4'"  O3  O 0 1 N N N 36.582 -52.972 3.687  -2.984 -0.153 -0.631 "O4'"  9SI 27 
9SI "O5'"  O4  O 0 1 N N N 39.038 -54.710 2.784  -5.825 0.121  -0.064 "O5'"  9SI 28 
9SI OP1    O5  O 0 1 N N N 39.512 -55.492 0.468  -8.011 -0.310 1.121  OP1    9SI 29 
9SI OP2    O6  O 0 1 N N N 41.132 -53.861 1.716  -6.608 1.617  1.951  OP2    9SI 30 
9SI P      P1  P 0 1 N N N 39.729 -54.325 1.403  -7.100 0.768  0.675  P      9SI 31 
9SI H1     H1  H 0 1 N N N 32.794 -46.120 2.518  4.842  2.113  -1.958 H1     9SI 32 
9SI H3     H2  H 0 1 N N N 31.333 -46.773 3.334  4.908  0.535  -2.779 H3     9SI 33 
9SI H2     H3  H 0 1 N N N 33.456 -48.029 5.397  3.208  -0.947 -2.605 H2     9SI 34 
9SI H4     H4  H 0 1 N N N 34.701 -45.291 3.895  5.699  -1.441 -1.611 H4     9SI 35 
9SI H5     H5  H 0 1 N N N 35.305 -44.064 5.952  7.117  -2.323 0.199  H5     9SI 36 
9SI H6     H6  H 0 1 N N N 31.568 -45.178 7.714  6.959  1.458  2.165  H6     9SI 37 
9SI H7     H7  H 0 1 N N N 30.963 -46.403 5.658  5.548  2.343  0.351  H7     9SI 38 
9SI H10    H8  H 0 1 N N N 34.795 -44.177 8.611  7.749  -0.518 3.333  H10    9SI 39 
9SI H9     H9  H 0 1 N N N 33.947 -42.720 7.989  7.815  -2.096 2.513  H9     9SI 40 
9SI H8     H10 H 0 1 N N N 34.709 -52.952 1.311  -1.716 1.717  0.719  H8     9SI 41 
9SI "H1'"  H11 H 0 1 N N N 35.183 -52.373 5.092  -1.544 -1.093 -1.824 "H1'"  9SI 42 
9SI "H2'"  H12 H 0 1 N N N 34.379 -54.429 3.002  -1.374 -1.468 1.219  "H2'"  9SI 43 
9SI "H3'"  H13 H 0 1 N N N 35.667 -56.048 4.142  -3.397 -2.661 1.172  "H3'"  9SI 44 
9SI "H4'"  H14 H 0 1 N N N 37.728 -54.280 4.852  -4.308 -1.571 -1.379 "H4'"  9SI 45 
9SI "H5'"  H15 H 0 1 N N N 37.165 -54.599 1.925  -5.586 -1.744 0.792  "H5'"  9SI 46 
9SI "H5''" H16 H 0 0 N N N 37.490 -56.068 2.908  -4.549 -0.458 1.455  "H5''" 9SI 47 
9SI H17    H17 H 0 1 N N N 33.028 -43.477 10.061 9.583  0.182  1.900  H17    9SI 48 
9SI H18    H18 H 0 1 N N N 31.919 -43.624 8.871  10.009 -1.150 2.800  H18    9SI 49 
9SI H61    H20 H 0 1 N N N 32.152 -47.202 1.102  2.777  3.444  0.291  H61    9SI 50 
9SI H62    H21 H 0 1 N N N 32.568 -48.624 0.204  4.190  2.967  -0.481 H62    9SI 51 
9SI "HO2'" H22 H 0 0 N N N 33.054 -55.076 4.790  -0.581 -3.586 0.452  "HO2'" 9SI 52 
9SI "HO3'" H23 H 0 0 N Y N 34.981 -55.469 6.309  -2.550 -4.299 -0.379 "HO3'" 9SI 53 
9SI HOP2   H25 H 0 0 N N N 41.757 -54.403 1.249  -6.006 2.342  1.733  HOP2   9SI 54 
9SI OP3    O7  O 0 1 N Y N 38.862 -53.068 0.901  -7.878 1.738  -0.347 OP3    9SI 55 
9SI HOP3   H26 H 0 0 N Y N 38.384 -53.306 0.115  -8.660 2.164  0.031  HOP3   9SI 56 
# 
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 
9SI OP1   P      DOUB N N 1  
9SI N6    C6     SING N N 2  
9SI N7    C8     DOUB Y N 3  
9SI N7    C5     SING Y N 4  
9SI P     OP2    SING N N 5  
9SI P     "O5'"  SING N N 6  
9SI C8    N9     SING Y N 7  
9SI C5    C6     DOUB Y N 8  
9SI C5    C4     SING Y N 9  
9SI C6    N1     SING Y N 10 
9SI "O5'" "C5'"  SING N N 11 
9SI "C5'" "C4'"  SING N N 12 
9SI N9    C4     SING Y N 13 
9SI N9    "C1'"  SING N N 14 
9SI N1    C1     SING N N 15 
9SI N1    C2     DOUB Y N 16 
9SI C1    C3     SING N N 17 
9SI C4    N3     DOUB Y N 18 
9SI "O4'" "C4'"  SING N N 19 
9SI "O4'" "C1'"  SING N N 20 
9SI "C4'" "C3'"  SING N N 21 
9SI "C2'" "C1'"  SING N N 22 
9SI "C2'" "C3'"  SING N N 23 
9SI "C2'" "O2'"  SING N N 24 
9SI C2    N3     SING Y N 25 
9SI "C3'" "O3'"  SING N N 26 
9SI C3    C7     DOUB Y N 27 
9SI C3    C12    SING Y N 28 
9SI C7    C9     SING Y N 29 
9SI C12   C11    DOUB Y N 30 
9SI C9    C10    DOUB Y N 31 
9SI C11   C10    SING Y N 32 
9SI C10   C13    SING N N 33 
9SI C13   N10    SING N N 34 
9SI C1    H1     SING N N 35 
9SI C1    H3     SING N N 36 
9SI C2    H2     SING N N 37 
9SI C7    H4     SING N N 38 
9SI C9    H5     SING N N 39 
9SI C11   H6     SING N N 40 
9SI C12   H7     SING N N 41 
9SI C13   H10    SING N N 42 
9SI C13   H9     SING N N 43 
9SI C8    H8     SING N N 44 
9SI "C1'" "H1'"  SING N N 45 
9SI "C2'" "H2'"  SING N N 46 
9SI "C3'" "H3'"  SING N N 47 
9SI "C4'" "H4'"  SING N N 48 
9SI "C5'" "H5'"  SING N N 49 
9SI "C5'" "H5''" SING N N 50 
9SI N10   H17    SING N N 51 
9SI N10   H18    SING N N 52 
9SI N6    H61    SING N N 53 
9SI N6    H62    SING N N 54 
9SI "O2'" "HO2'" SING N N 55 
9SI "O3'" "HO3'" SING N N 56 
9SI OP2   HOP2   SING N N 57 
9SI OP3   P      SING N N 58 
9SI OP3   HOP3   SING N N 59 
# 
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 
9SI InChI            InChI                1.06  "InChI=1S/C18H23N6O7P/c19-5-10-1-3-11(4-2-10)6-23-8-22-17-13(16(23)20)21-9-24(17)18-15(26)14(25)12(31-18)7-30-32(27,28)29/h1-4,8-9,12,14-15,18,20,25-26H,5-7,19H2,(H2,27,28,29)/p+1/t12-,14-,15-,18-/m1/s1" 
9SI InChIKey         InChI                1.06  BZYUSKWOMPCXQZ-SCFUHWHPSA-O                                                                                                                                                                                 
9SI SMILES_CANONICAL CACTVS               3.385 "NCc1ccc(C[n+]2cnc3n(cnc3c2N)[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O)cc1"                                                                                                                              
9SI SMILES           CACTVS               3.385 "NCc1ccc(C[n+]2cnc3n(cnc3c2N)[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O)cc1"                                                                                                                                    
9SI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CN)C[n+]2cnc3c(c2N)ncn3[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O"                                                                                                                              
9SI SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CN)C[n+]2cnc3c(c2N)ncn3C4C(C(C(O4)COP(=O)(O)O)O)O"                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           9SI 
_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-[1-[[4-(aminomethyl)phenyl]methyl]-6-azanyl-purin-1-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      9SI 
_pdbx_chem_comp_synonyms.name         1-benzylamine-adenosine 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
9SI "Create component"         2021-11-19 PDBE 
9SI "Modify aromatic_flag"     2022-03-14 PDBE 
9SI "Modify leaving atom flag" 2022-03-15 PDBE 
9SI "Initial release"          2022-03-23 RCSB 
9SI "Modify descriptor"        2022-08-22 RCSB 
# 
