data_9SY
# 
_chem_comp.id                                    9SY 
_chem_comp.name                                  "[(2R,3S,4R,5R)-5-[6-azanyl-1-(phenylmethyl)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                               "C17 H21 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         "1-benzyl-adenosine derivative" 
_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                        438.352 
_chem_comp.one_letter_code                       A 
_chem_comp.three_letter_code                     9SY 
_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        7Q7Y 
_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 
9SY C11    C1  C 0 1 Y N N 45.493 19.902 45.915 7.391  1.663  -0.426 C11    9SY 1  
9SY C12    C2  C 0 1 Y N N 45.899 19.801 44.589 6.608  1.050  0.535  C12    9SY 2  
9SY C1     C3  C 0 1 N N N 46.869 20.802 42.489 5.366  -0.935 1.420  C1     9SY 3  
9SY "C1'"  C4  C 0 1 N N R 53.168 18.838 43.062 -1.024 0.635  0.499  "C1'"  9SY 4  
9SY C10    C5  C 0 1 Y N N 45.613 21.113 46.588 7.782  0.960  -1.550 C10    9SY 5  
9SY C2     C6  C 0 1 Y N N 49.061 20.372 43.461 3.298  0.272  1.656  C2     9SY 6  
9SY "C2'"  C7  C 0 1 N N R 54.383 18.028 42.625 -1.010 1.865  -0.435 "C2'"  9SY 7  
9SY C3     C8  C 0 1 Y N N 46.427 20.909 43.935 6.218  -0.266 0.372  C3     9SY 8  
9SY "C3'"  C9  C 0 1 N N S 55.468 18.629 43.510 -2.505 2.199  -0.639 "C3'"  9SY 9  
9SY C4     C10 C 0 1 Y N N 50.875 19.389 42.326 1.338  -0.270 0.585  C4     9SY 10 
9SY "C4'"  C11 C 0 1 N N R 55.072 20.105 43.564 -3.245 1.131  0.197  "C4'"  9SY 11 
9SY C5     C12 C 0 1 Y N N 50.132 19.267 41.171 1.990  -1.349 -0.037 C5     9SY 12 
9SY "C5'"  C13 C 0 1 N N N 55.791 20.998 42.586 -4.527 0.692  -0.514 "C5'"  9SY 13 
9SY C6     C14 C 0 1 Y N N 48.731 19.749 41.195 3.347  -1.562 0.256  C6     9SY 14 
9SY C7     C15 C 0 1 Y N N 46.542 22.122 44.611 6.610  -0.969 -0.752 C7     9SY 15 
9SY C8     C16 C 0 1 Y N N 52.123 18.473 40.807 -0.065 -1.350 -0.729 C8     9SY 16 
9SY C9     C17 C 0 1 Y N N 46.139 22.222 45.937 7.396  -0.358 -1.711 C9     9SY 17 
9SY N1     N1  N 1 1 Y N N 48.247 20.300 42.398 3.951  -0.732 1.100  N1     9SY 18 
9SY N3     N2  N 0 1 Y N N 50.327 19.933 43.438 2.025  0.507  1.416  N3     9SY 19 
9SY N6     N3  N 0 1 N N N 47.950 19.660 40.095 4.041  -2.609 -0.326 N6     9SY 20 
9SY N7     N4  N 0 1 Y N N 50.917 18.698 40.236 1.076  -1.968 -0.823 N7     9SY 21 
9SY N9     N5  N 0 1 Y N N 52.086 18.896 42.078 0.043  -0.299 0.132  N9     9SY 22 
9SY OP1    O1  O 0 1 N N N 58.354 20.141 41.107 -6.497 -1.568 -1.398 OP1    9SY 23 
9SY "O2'"  O2  O 0 1 N N N 54.183 16.640 42.802 -0.333 2.959  0.186  "O2'"  9SY 24 
9SY OP2    O3  O 0 1 N N N 56.824 20.115 38.991 -7.122 -1.921 1.022  OP2    9SY 25 
9SY "O3'"  O4  O 0 1 N N N 55.366 18.070 44.817 -2.797 3.509  -0.149 "O3'"  9SY 26 
9SY "O4'"  O5  O 0 1 N N N 53.645 20.150 43.286 -2.317 0.028  0.291  "O4'"  9SY 27 
9SY "O5'"  O6  O 0 1 N N N 55.869 20.404 41.296 -5.254 -0.206 0.326  "O5'"  9SY 28 
9SY P      P1  P 0 1 N N N 57.137 20.648 40.370 -6.657 -0.868 -0.104 P      9SY 29 
9SY H1     H1  H 0 1 N N N 45.085 19.040 46.422 7.692  2.692  -0.301 H1     9SY 30 
9SY H5     H2  H 0 1 N N N 45.804 18.861 44.066 6.302  1.599  1.413  H5     9SY 31 
9SY H3     H3  H 0 1 N N N 46.816 21.796 42.022 5.585  -2.003 1.439  H3     9SY 32 
9SY H4     H4  H 0 1 N N N 46.198 20.111 41.957 5.584  -0.502 2.396  H4     9SY 33 
9SY "H1'"  H5  H 0 1 N N N 52.784 18.412 44.000 -0.914 0.947  1.538  "H1'"  9SY 34 
9SY H6     H6  H 0 1 N N N 45.297 21.192 47.618 8.389  1.440  -2.303 H6     9SY 35 
9SY H2     H7  H 0 1 N N N 48.680 20.802 44.375 3.827  0.922  2.337  H2     9SY 36 
9SY "H2'"  H8  H 0 1 N N N 54.609 18.257 41.573 -0.539 1.617  -1.387 "H2'"  9SY 37 
9SY "H3'"  H9  H 0 1 N N N 56.466 18.499 43.065 -2.776 2.115  -1.692 "H3'"  9SY 38 
9SY "H4'"  H10 H 0 1 N N N 55.257 20.477 44.582 -3.476 1.518  1.189  "H4'"  9SY 39 
9SY "H5'"  H11 H 0 1 N N N 56.810 21.185 42.955 -5.141 1.567  -0.727 "H5'"  9SY 40 
9SY "H5''" H12 H 0 0 N N N 55.249 21.952 42.508 -4.272 0.191  -1.447 "H5''" 9SY 41 
9SY H13    H13 H 0 1 N N N 46.945 22.986 44.103 6.305  -1.997 -0.879 H13    9SY 42 
9SY H8     H14 H 0 1 N N N 52.976 18.026 40.318 -0.968 -1.632 -1.251 H8     9SY 43 
9SY H15    H15 H 0 1 N N N 46.235 23.161 46.461 7.702  -0.907 -2.589 H15    9SY 44 
9SY H61    H16 H 0 1 N N N 47.006 19.989 40.124 3.591  -3.206 -0.944 H61    9SY 45 
9SY H62    H17 H 0 1 N N N 48.316 19.265 39.252 4.978  -2.746 -0.116 H62    9SY 46 
9SY "HO2'" H19 H 0 0 N N N 54.958 16.169 42.520 -0.295 3.758  -0.357 "HO2'" 9SY 47 
9SY HOP2   H20 H 0 0 N N N 57.483 19.478 38.740 -7.962 -2.359 0.828  HOP2   9SY 48 
9SY "HO3'" H21 H 0 0 N Y N 56.040 18.441 45.374 -2.312 4.214  -0.599 "HO3'" 9SY 49 
9SY OP3    OP3 O 0 1 N Y N 57.240 22.249 40.295 -7.771 0.285  -0.252 OP3    9SY 50 
9SY HOP3   H23 H 0 0 N Y N 58.037 22.536 40.726 -7.929 0.786  0.560  HOP3   9SY 51 
# 
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 
9SY OP2   P      SING N N 1  
9SY N6    C6     SING N N 2  
9SY N7    C8     DOUB Y N 3  
9SY N7    C5     SING Y N 4  
9SY P     OP1    DOUB N N 5  
9SY P     "O5'"  SING N N 6  
9SY C8    N9     SING Y N 7  
9SY C5    C6     DOUB Y N 8  
9SY C5    C4     SING Y N 9  
9SY C6    N1     SING Y N 10 
9SY "O5'" "C5'"  SING N N 11 
9SY N9    C4     SING Y N 12 
9SY N9    "C1'"  SING N N 13 
9SY C4    N3     DOUB Y N 14 
9SY N1    C1     SING N N 15 
9SY N1    C2     DOUB Y N 16 
9SY C1    C3     SING N N 17 
9SY "C5'" "C4'"  SING N N 18 
9SY "C2'" "O2'"  SING N N 19 
9SY "C2'" "C1'"  SING N N 20 
9SY "C2'" "C3'"  SING N N 21 
9SY "C1'" "O4'"  SING N N 22 
9SY "O4'" "C4'"  SING N N 23 
9SY N3    C2     SING Y N 24 
9SY "C3'" "C4'"  SING N N 25 
9SY "C3'" "O3'"  SING N N 26 
9SY C3    C12    DOUB Y N 27 
9SY C3    C7     SING Y N 28 
9SY C12   C11    SING Y N 29 
9SY C7    C9     DOUB Y N 30 
9SY C11   C10    DOUB Y N 31 
9SY C9    C10    SING Y N 32 
9SY C11   H1     SING N N 33 
9SY C12   H5     SING N N 34 
9SY C1    H3     SING N N 35 
9SY C1    H4     SING N N 36 
9SY "C1'" "H1'"  SING N N 37 
9SY C10   H6     SING N N 38 
9SY C2    H2     SING N N 39 
9SY "C2'" "H2'"  SING N N 40 
9SY "C3'" "H3'"  SING N N 41 
9SY "C4'" "H4'"  SING N N 42 
9SY "C5'" "H5'"  SING N N 43 
9SY "C5'" "H5''" SING N N 44 
9SY C7    H13    SING N N 45 
9SY C8    H8     SING N N 46 
9SY C9    H15    SING N N 47 
9SY N6    H61    SING N N 48 
9SY N6    H62    SING N N 49 
9SY "O2'" "HO2'" SING N N 50 
9SY OP2   HOP2   SING N N 51 
9SY "O3'" "HO3'" SING N N 52 
9SY P     OP3    SING N N 53 
9SY OP3   HOP3   SING N N 54 
# 
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 
9SY InChI            InChI                1.06  "InChI=1S/C17H20N5O7P/c18-15-12-16(20-8-21(15)6-10-4-2-1-3-5-10)22(9-19-12)17-14(24)13(23)11(29-17)7-28-30(25,26)27/h1-5,8-9,11,13-14,17-18,23-24H,6-7H2,(H2,25,26,27)/p+1/t11-,13-,14-,17-/m1/s1" 
9SY InChIKey         InChI                1.06  KJQXIIOGOTYLOM-LSCFUAHRSA-O                                                                                                                                                                        
9SY SMILES_CANONICAL CACTVS               3.385 "Nc1c2ncn([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)c2nc[n+]1Cc4ccccc4"                                                                                                                         
9SY SMILES           CACTVS               3.385 "Nc1c2ncn([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)c2nc[n+]1Cc4ccccc4"                                                                                                                               
9SY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C[n+]2cnc3c(c2N)ncn3[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O"                                                                                                                       
9SY SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C[n+]2cnc3c(c2N)ncn3C4C(C(C(O4)COP(=O)(O)O)O)O"                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           9SY 
_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-1-(phenylmethyl)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      9SY 
_pdbx_chem_comp_synonyms.name         "1-benzyl-adenosine derivative" 
_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 
9SY "Create component"         2021-11-19 PDBE 
9SY "Modify aromatic_flag"     2022-03-14 PDBE 
9SY "Modify leaving atom flag" 2022-03-15 PDBE 
9SY "Initial release"          2022-03-23 RCSB 
9SY "Modify descriptor"        2022-08-22 RCSB 
# 
