data_7S3
# 
_chem_comp.id                                    7S3 
_chem_comp.name                                  "[(2R,3S,4R,5R)-5-(1-methyl-6-oxidanylidene-purin-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                               "C11 H15 N4 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               G 
_chem_comp.pdbx_synonyms                         "1-methyl inosinic acid" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-10-15 
_chem_comp.pdbx_modified_date                    2022-06-08 
_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                        362.233 
_chem_comp.one_letter_code                       G 
_chem_comp.three_letter_code                     7S3 
_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        7VNV 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
7S3 C2     C1  C 0 1 N N N -138.486 30.583 34.381 4.882  0.749  0.786  C2     7S3 1  
7S3 C4     C2  C 0 1 Y N N -140.442 29.581 34.210 2.791  -0.038 0.221  C4     7S3 2  
7S3 "C1'"  C3  C 0 1 N N R -141.707 28.462 32.299 0.431  0.853  0.377  "C1'"  7S3 3  
7S3 "C2'"  C4  C 0 1 N N R -141.083 27.114 31.952 0.238  1.852  -0.792 "C2'"  7S3 4  
7S3 "C3'"  C5  C 0 1 N N S -142.280 26.186 32.084 -1.199 2.369  -0.543 "C3'"  7S3 5  
7S3 "C4'"  C6  C 0 1 N N R -143.429 27.044 31.584 -1.844 1.283  0.339  "C4'"  7S3 6  
7S3 C5     C7  C 0 1 Y N N -140.735 29.810 35.541 3.349  -1.231 -0.249 C5     7S3 7  
7S3 "C5'"  C8  C 0 1 N N N -144.796 26.652 32.088 -3.088 0.718  -0.350 "C5'"  7S3 8  
7S3 C6     C9  C 0 1 N N N -139.783 30.517 36.306 4.756  -1.391 -0.179 C6     7S3 9  
7S3 C8     C10 C 0 1 Y N N -142.411 28.761 34.735 1.206  -1.369 -0.533 C8     7S3 10 
7S3 CM1    C11 C 0 1 N N N -137.573 31.623 36.374 6.943  -0.516 0.447  CM1    7S3 11 
7S3 N1     N1  N 0 1 N N N -138.640 30.898 35.679 5.487  -0.384 0.348  N1     7S3 12 
7S3 N3     N2  N 0 1 N N N -139.319 29.931 33.558 3.590  0.913  0.724  N3     7S3 13 
7S3 N7     N3  N 0 1 Y N N -141.988 29.289 35.859 2.332  -2.003 -0.696 N7     7S3 14 
7S3 N9     N4  N 0 1 Y N N -141.522 28.880 33.702 1.441  -0.152 0.035  N9     7S3 15 
7S3 "O2'"  O1  O 0 1 N N N -140.677 27.179 30.593 1.186  2.919  -0.712 "O2'"  7S3 16 
7S3 "O3'"  O2  O 0 1 N N N -142.147 25.007 31.322 -1.168 3.622  0.144  "O3'"  7S3 17 
7S3 "O4'"  O3  O 0 1 N N N -143.094 28.380 32.032 -0.868 0.241  0.519  "O4'"  7S3 18 
7S3 "O5'"  O4  O 0 1 N N N -144.787 26.490 33.501 -3.734 -0.211 0.522  "O5'"  7S3 19 
7S3 O6     O5  O 0 1 N N N -139.960 30.776 37.513 5.290  -2.412 -0.575 O6     7S3 20 
7S3 OP1    O6  O 0 1 N N N -146.813 25.095 33.714 -6.122 -0.027 -0.274 OP1    7S3 21 
7S3 OP2    O7  O 0 1 N N N -145.918 26.345 35.777 -4.774 -1.990 -1.111 OP2    7S3 22 
7S3 P      P1  P 0 1 N N N -146.144 26.297 34.304 -5.080 -1.000 0.121  P      7S3 23 
7S3 OP3    O8  O 0 1 N Y N -147.050 27.554 33.864 -5.596 -1.857 1.383  OP3    7S3 24 
7S3 "H1'"  H1  H 0 1 N N N -137.555 30.902 33.937 5.489  1.538  1.203  "H1'"  7S3 25 
7S3 H1     H2  H 0 1 N N N -141.254 29.222 31.645 0.709  1.380  1.290  H1     7S3 26 
7S3 "H2'"  H3  H 0 1 N N N -140.272 26.844 32.644 0.308  1.344  -1.754 "H2'"  7S3 27 
7S3 "H3'"  H4  H 0 1 N N N -142.440 25.949 33.146 -1.739 2.466  -1.485 "H3'"  7S3 28 
7S3 "H4'"  H5  H 0 1 N N N -143.436 27.015 30.484 -2.114 1.709  1.306  "H4'"  7S3 29 
7S3 "H5'"  H6  H 0 1 N N N -145.518 27.437 31.820 -3.774 1.532  -0.585 "H5'"  7S3 30 
7S3 "H5''" H7  H 0 0 N N N -145.095 25.703 31.618 -2.796 0.211  -1.269 "H5''" 7S3 31 
7S3 H8     H8  H 0 1 N N N -143.371 28.277 34.635 0.233  -1.751 -0.803 H8     7S3 32 
7S3 H9     H9  H 0 1 N N N -137.867 31.795 37.420 7.360  0.387  0.893  H9     7S3 33 
7S3 H10    H10 H 0 1 N N N -136.648 31.029 36.346 7.189  -1.375 1.070  H10    7S3 34 
7S3 H11    H11 H 0 1 N N N -137.403 32.590 35.878 7.364  -0.656 -0.549 H11    7S3 35 
7S3 "HO2'" H12 H 0 0 N N N -139.929 27.759 30.513 1.049  3.616  -1.369 "HO2'" 7S3 36 
7S3 "HO3'" H13 H 0 0 N N N -141.422 24.493 31.658 -0.721 4.327  -0.344 "HO3'" 7S3 37 
7S3 HOP2   H14 H 0 0 N N N -146.252 25.550 36.175 -4.099 -2.655 -0.923 HOP2   7S3 38 
7S3 HOP3   H15 H 0 0 N Y N -147.784 27.249 33.343 -6.405 -2.359 1.213  HOP3   7S3 39 
# 
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 
7S3 "O2'" "C2'"  SING N N 1  
7S3 "O3'" "C3'"  SING N N 2  
7S3 "C4'" "O4'"  SING N N 3  
7S3 "C4'" "C3'"  SING N N 4  
7S3 "C4'" "C5'"  SING N N 5  
7S3 "C2'" "C3'"  SING N N 6  
7S3 "C2'" "C1'"  SING N N 7  
7S3 "O4'" "C1'"  SING N N 8  
7S3 "C5'" "O5'"  SING N N 9  
7S3 "C1'" N9     SING N N 10 
7S3 "O5'" P      SING N N 11 
7S3 N3    C4     SING N N 12 
7S3 N3    C2     DOUB N N 13 
7S3 N9    C4     SING Y N 14 
7S3 N9    C8     SING Y N 15 
7S3 OP1   P      DOUB N N 16 
7S3 C4    C5     DOUB Y N 17 
7S3 P     OP2    SING N N 18 
7S3 C2    N1     SING N N 19 
7S3 C8    N7     DOUB Y N 20 
7S3 C5    N7     SING Y N 21 
7S3 C5    C6     SING N N 22 
7S3 N1    C6     SING N N 23 
7S3 N1    CM1    SING N N 24 
7S3 C6    O6     DOUB N N 25 
7S3 P     OP3    SING N N 26 
7S3 C2    "H1'"  SING N N 27 
7S3 "C1'" H1     SING N N 28 
7S3 "C2'" "H2'"  SING N N 29 
7S3 "C3'" "H3'"  SING N N 30 
7S3 "C4'" "H4'"  SING N N 31 
7S3 "C5'" "H5'"  SING N N 32 
7S3 "C5'" "H5''" SING N N 33 
7S3 C8    H8     SING N N 34 
7S3 CM1   H9     SING N N 35 
7S3 CM1   H10    SING N N 36 
7S3 CM1   H11    SING N N 37 
7S3 "O2'" "HO2'" SING N N 38 
7S3 "O3'" "HO3'" SING N N 39 
7S3 OP2   HOP2   SING N N 40 
7S3 OP3   HOP3   SING N N 41 
# 
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 
7S3 InChI            InChI                1.03  "InChI=1S/C11H15N4O8P/c1-14-3-13-9-6(10(14)18)12-4-15(9)11-8(17)7(16)5(23-11)2-22-24(19,20)21/h3-5,7-8,11,16-17H,2H2,1H3,(H2,19,20,21)/t5-,7-,8-,11-/m1/s1" 
7S3 InChIKey         InChI                1.03  CPKNFRPSNBOHIM-IOSLPCCCSA-N                                                                                                                                 
7S3 SMILES_CANONICAL CACTVS               3.385 "CN1C=Nc2n(cnc2C1=O)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O"                                                                                           
7S3 SMILES           CACTVS               3.385 "CN1C=Nc2n(cnc2C1=O)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O"                                                                                                 
7S3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1C=Nc2c(ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)C1=O"                                                                                           
7S3 SMILES           "OpenEye OEToolkits" 2.0.7 "CN1C=Nc2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)C1=O"                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           7S3 
_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-methyl-6-oxidanylidene-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      7S3 
_pdbx_chem_comp_synonyms.name         "1-methyl inosinic acid" 
_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 
7S3 "Create component"      2021-10-15 PDBJ 
7S3 "Initial release"       2022-05-04 RCSB 
7S3 "Modify parent residue" 2022-06-08 PDBJ 
# 
