data_7SN
#

_chem_comp.id                                   7SN
_chem_comp.name                                 "[(2R,3S,4R,5R)-5-(2-azanyl-5-carbamimidoyl-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C12 H17 N6 O8 P"
_chem_comp.mon_nstd_parent_comp_id              G
_chem_comp.pdbx_synonyms                        "archaeosine-5'-monophosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-10-20
_chem_comp.pdbx_modified_date                   2022-04-29
_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                       404.273
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    7SN
_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
7SN  N3     N1   N  0  1  N  N  N  -125.709  22.886  30.054   3.174   1.569   0.796  N3     7SN   1  
7SN  C4     C1   C  0  1  Y  N  N  -124.666  22.319  30.691   2.562   0.465   0.342  C4     7SN   2  
7SN  N2     N2   N  0  1  N  N  N  -127.684  22.415  28.964   5.045   2.738   1.494  N2     7SN   3  
7SN  C7     C2   C  0  1  Y  N  N  -123.264  20.816  31.639   2.379  -1.708  -0.373  C7     7SN   4  
7SN  C6     C3   C  0  1  N  N  N  -125.420  20.033  30.480   4.707  -0.662   0.366  C6     7SN   5  
7SN  C8     C4   C  0  1  Y  N  N  -122.787  22.024  31.796   1.156  -1.115  -0.403  C8     7SN   6  
7SN  C2     C5   C  0  1  N  N  N  -126.594  22.002  29.627   4.467   1.583   1.030  C2     7SN   7  
7SN  C5     C6   C  0  1  Y  N  N  -124.454  20.980  30.944   3.320  -0.688   0.113  C5     7SN   8  
7SN  N1     N3   N  0  1  N  N  N  -126.477  20.648  29.815   5.252   0.488   0.825  N1     7SN   9  
7SN  "C1'"  C7   C  0  1  N  N  R  -123.358  24.449  31.239   0.150   1.120   0.121  "C1'"  7SN  10  
7SN  "C2'"  C8   C  0  1  N  N  R  -124.068  25.170  32.389   0.010   1.927  -1.188  "C2'"  7SN  11  
7SN  "C3'"  C9   C  0  1  N  N  S  -122.933  25.405  33.387  -1.517   2.082  -1.372  "C3'"  7SN  12  
7SN  "C4'"  C10  C  0  1  N  N  R  -121.705  25.539  32.501  -2.118   1.350  -0.152  "C4'"  7SN  13  
7SN  "C5'"  C11  C  0  1  N  N  N  -120.399  25.145  33.148  -3.398   0.613  -0.550  "C5'"  7SN  14  
7SN  CA7    C12  C  0  1  N  N  N  -122.574  19.603  32.125   2.698  -3.098  -0.752  CA7    7SN  15  
7SN  N71    N4   N  0  1  N  N  N  -123.180  18.413  31.998   3.927  -3.531  -0.671  N71    7SN  16  
7SN  N72    N5   N  0  1  N  N  N  -121.346  19.685  32.665   1.699  -3.939  -1.194  N72    7SN  17  
7SN  N9     N6   N  0  1  Y  N  N  -123.590  22.988  31.247   1.266   0.176   0.022  N9     7SN  18  
7SN  "O2'"  O1   O  0  1  N  N  N  -124.567  26.406  31.910   0.631   3.207  -1.056  "O2'"  7SN  19  
7SN  "O3'"  O2   O  0  1  N  N  N  -123.121  26.587  34.151  -1.885   3.463  -1.359  "O3'"  7SN  20  
7SN  "O4'"  O3   O  0  1  N  N  N  -121.975  24.691  31.360  -1.100   0.408   0.252  "O4'"  7SN  21  
7SN  "O5'"  O4   O  0  1  N  N  N  -120.487  23.843  33.702  -4.000   0.041   0.613  "O5'"  7SN  22  
7SN  O6     O5   O  0  1  N  N  N  -125.433  18.800  30.602   5.396  -1.650   0.179  O6     7SN  23  
7SN  OP1    O6   O  0  1  N  N  N  -118.395  23.531  35.053  -6.426  -0.003  -0.082  OP1    7SN  24  
7SN  OP2    O7   O  0  1  N  N  N  -119.698  21.555  34.081  -5.129  -2.159  -0.279  OP2    7SN  25  
7SN  P      P1   P  0  1  N  N  N  -119.193  22.944  33.946  -5.367  -0.809   0.564  P      7SN  26  
7SN  H1     H1   H  0  1  N  N  N  -127.826  23.390  28.794   5.998   2.765   1.672  H1     7SN  27  
7SN  H2     H2   H  0  1  N  N  N  -128.355  21.748  28.640   4.500   3.526   1.645  H2     7SN  28  
7SN  H3     H3   H  0  1  N  N  N  -121.859  22.238  32.305   0.239  -1.592  -0.715  H3     7SN  29  
7SN  H4     H4   H  0  1  N  N  N  -127.201  20.063  29.449   6.203   0.533   1.008  H4     7SN  30  
7SN  H5     H5   H  0  1  N  N  N  -123.729  24.864  30.290   0.295   1.790   0.969  H5     7SN  31  
7SN  H6     H6   H  0  1  N  N  N  -124.853  24.535  32.827   0.441   1.377  -2.024  H6     7SN  32  
7SN  H7     H7   H  0  1  N  N  N  -122.826  24.525  34.038  -1.840   1.611  -2.300  H7     7SN  33  
7SN  H8     H8   H  0  1  N  N  N  -121.629  26.585  32.169  -2.323   2.058   0.652  H8     7SN  34  
7SN  H9     H9   H  0  1  N  N  N  -119.601  25.162  32.391  -4.093   1.315  -1.011  H9     7SN  35  
7SN  H10    H10  H  0  1  N  N  N  -120.161  25.862  33.947  -3.156  -0.177  -1.260  H10    7SN  36  
7SN  H11    H11  H  0  1  N  N  N  -122.613  17.665  32.343   4.136  -4.445  -0.920  H11    7SN  37  
7SN  H12    H12  H  0  1  N  N  N  -120.880  18.856  32.974   0.785  -3.617  -1.254  H12    7SN  38  
7SN  H13    H13  H  0  1  N  N  N  -120.899  20.575  32.757   1.908  -4.853  -1.443  H13    7SN  39  
7SN  H14    H14  H  0  1  N  N  N  -125.010  26.864  32.615   0.573   3.756  -1.850  H14    7SN  40  
7SN  H15    H15  H  0  1  N  N  N  -122.396  26.693  34.755  -1.485   3.983  -2.070  H15    7SN  41  
7SN  H17    H17  H  0  1  N  N  N  -119.425  21.198  34.918  -4.446  -2.737   0.088  H17    7SN  42  
7SN  OP3    OP3  O  0  1  N  Y  N  -118.333  23.084  32.597  -5.818  -1.185   2.063  OP3    7SN  43  
7SN  H16    H16  H  0  1  N  Y  N  -117.505  23.508  32.791  -6.636  -1.698   2.111  H16    7SN  44  
#   #
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
7SN  N2     C2     SING  N  N   1  
7SN  C2     N1     SING  N  N   2  
7SN  C2     N3     DOUB  N  N   3  
7SN  N1     C6     SING  N  N   4  
7SN  N3     C4     SING  N  N   5  
7SN  C6     O6     DOUB  N  N   6  
7SN  C6     C5     SING  N  N   7  
7SN  C4     C5     DOUB  Y  N   8  
7SN  C4     N9     SING  Y  N   9  
7SN  C5     C7     SING  Y  N  10  
7SN  "C1'"  N9     SING  N  N  11  
7SN  "C1'"  "O4'"  SING  N  N  12  
7SN  "C1'"  "C2'"  SING  N  N  13  
7SN  N9     C8     SING  Y  N  14  
7SN  "O4'"  "C4'"  SING  N  N  15  
7SN  C7     C8     DOUB  Y  N  16  
7SN  C7     CA7    SING  N  N  17  
7SN  "O2'"  "C2'"  SING  N  N  18  
7SN  N71    CA7    DOUB  N  N  19  
7SN  CA7    N72    SING  N  N  20  
7SN  "C2'"  "C3'"  SING  N  N  21  
7SN  "C4'"  "C5'"  SING  N  N  22  
7SN  "C4'"  "C3'"  SING  N  N  23  
7SN  "C5'"  "O5'"  SING  N  N  24  
7SN  "C3'"  "O3'"  SING  N  N  25  
7SN  "O5'"  P      SING  N  N  26  
7SN  P      OP2    SING  N  N  27  
7SN  P      OP1    DOUB  N  N  28  
7SN  N2     H1     SING  N  N  29  
7SN  N2     H2     SING  N  N  30  
7SN  C8     H3     SING  N  N  31  
7SN  N1     H4     SING  N  N  32  
7SN  "C1'"  H5     SING  N  N  33  
7SN  "C2'"  H6     SING  N  N  34  
7SN  "C3'"  H7     SING  N  N  35  
7SN  "C4'"  H8     SING  N  N  36  
7SN  "C5'"  H9     SING  N  N  37  
7SN  "C5'"  H10    SING  N  N  38  
7SN  N71    H11    SING  N  N  39  
7SN  N72    H12    SING  N  N  40  
7SN  N72    H13    SING  N  N  41  
7SN  "O2'"  H14    SING  N  N  42  
7SN  "O3'"  H15    SING  N  N  43  
7SN  OP2    H17    SING  N  N  44  
7SN  P      OP3    SING  N  N  45  
7SN  OP3    H16    SING  N  N  46  
#   #
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
7SN  InChI             InChI                 1.03   "InChI=1S/C12H17N6O8P/c13-8(14)3-1-18(9-5(3)10(21)17-12(15)16-9)11-7(20)6(19)4(26-11)2-25-27(22,23)24/h1,4,6-7,11,19-20H,2H2,(H3,13,14)(H2,22,23,24)(H3,15,16,17,21)/t4-,6-,7-,11-/m1/s1"  
7SN  InChIKey          InChI                 1.03   ALFWBBQGYCDFHE-RPKMEZRRSA-N  
7SN  SMILES_CANONICAL  CACTVS                3.385  "NC(=N)c1cn([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13"  
7SN  SMILES            CACTVS                3.385  "NC(=N)c1cn([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13"  
7SN  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "[H]/N=C(\c1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)/N"  
7SN  SMILES            "OpenEye OEToolkits"  2.0.7  "c1c(c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)C(=N)N"  
#
_pdbx_chem_comp_identifier.comp_id          7SN
_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-(2-azanyl-5-carbamimidoyl-4-oxidanylidene-3~{H}-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     7SN
_pdbx_chem_comp_synonyms.name        "archaeosine-5'-monophosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_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
7SN  "Create component"  2021-10-20  PDBJ  
7SN  "Initial release"   2022-05-04  RCSB  
##
