data_UY1
#

_chem_comp.id                                   UY1
_chem_comp.name                                 "2'-O-methylpseudouridine-5'-monophosphate"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H15 N2 O9 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-06-04
_chem_comp.pdbx_modified_date                   2021-05-27
_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                       338.208
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    UY1
_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       6XA1
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
UY1  "C1'"   C1      C  0  1  N  N  S  262.981  252.145  234.489   1.279  -0.682  -0.879  "C1'"   UY1   1  
UY1  C2      C2      C  0  1  N  N  N  260.199  255.111  233.582   4.336   2.067   0.114  C2      UY1   2  
UY1  "C2'"   C3      C  0  1  N  N  R  262.335  250.771  234.671   1.340  -1.894   0.070  "C2'"   UY1   3  
UY1  "C3'"   C4      C  0  1  N  N  R  262.713  250.055  233.381  -0.052  -1.917   0.746  "C3'"   UY1   4  
UY1  C4      C5      C  0  1  N  N  N  261.455  254.067  235.191   2.365   0.966   0.715  C4      UY1   5  
UY1  "C4'"   C6      C  0  1  N  N  R  264.039  250.690  233.027  -0.911  -1.097  -0.250  "C4'"   UY1   6  
UY1  C5      C7      C  0  1  N  N  N  262.002  253.184  234.164   2.372   0.297  -0.532  C5      UY1   7  
UY1  "C5'"   C8      C  0  1  N  N  N  264.418  250.657  231.580  -2.119  -0.482   0.459  "C5'"   UY1   8  
UY1  C6      C9      C  0  1  N  N  N  261.575  253.379  232.879   3.370   0.546  -1.406  C6      UY1   9  
UY1  CM2     C10     C  0  1  N  N  N  261.974  249.782  236.732   2.275  -4.101   0.052  CM2     UY1  10  
UY1  N1      N1      N  0  1  N  N  N  260.690  254.326  232.629   4.354   1.437  -1.075  N1      UY1  11  
UY1  N3      N2      N  0  1  N  N  N  260.577  254.988  234.844   3.353   1.837   1.004  N3      UY1  12  
UY1  O2      O1      O  0  1  N  N  N  259.370  255.993  233.296   5.223   2.852   0.390  O2      UY1  13  
UY1  "O2'"   O2      O  0  1  N  N  N  262.954  250.147  235.776   1.558  -3.098  -0.669  "O2'"   UY1  14  
UY1  "O3'"   O3      O  0  1  N  N  N  262.802  248.647  233.523  -0.542  -3.255   0.860  "O3'"   UY1  15  
UY1  O4      O4      O  0  1  N  N  N  261.814  253.947  236.369   1.474   0.758   1.520  O4      UY1  16  
UY1  "O4'"   O5      O  0  1  N  N  N  263.886  252.059  233.427  -0.007  -0.065  -0.703  "O4'"   UY1  17  
UY1  "O5'"   O6      O  0  1  N  N  N  265.150  249.492  231.289  -2.953   0.170  -0.501  "O5'"   UY1  18  
UY1  OP1     O7      O  0  1  N  N  N  267.017  251.015  230.810  -5.202  -0.002   0.633  OP1     UY1  19  
UY1  OP2     O8      O  0  1  N  N  N  267.378  248.778  231.987  -3.977   2.196   0.826  OP2     UY1  20  
UY1  P       P1      P  0  1  N  N  N  266.686  249.571  230.941  -4.318   0.928  -0.105  P       UY1  21  
UY1  "H1'"   "H1'"   H  0  1  N  N  N  263.504  252.413  235.419   1.393  -1.013  -1.911  "H1'"   UY1  22  
UY1  "H2'"   "H2'"   H  0  1  N  N  N  261.243  250.854  234.778   2.125  -1.757   0.814  "H2'"   UY1  23  
UY1  "H3'"   "H3'"   H  0  1  N  N  N  261.977  250.312  232.605  -0.019  -1.433   1.722  "H3'"   UY1  24  
UY1  "H4'"   "H4'"   H  0  1  N  N  N  264.833  250.212  233.619  -1.230  -1.720  -1.085  "H4'"   UY1  25  
UY1  "H5'"   "H5'"   H  0  1  N  N  N  265.033  251.539  231.347  -2.685  -1.267   0.959  "H5'"   UY1  26  
UY1  "H5''"  "H5''"  H  0  0  N  N  N  263.505  250.674  230.966  -1.777   0.245   1.196  "H5''"  UY1  27  
UY1  H6      H6      H  0  1  N  N  N  261.958  252.765  232.078   3.392   0.044  -2.362  H6      UY1  28  
UY1  H21     H21     H  0  1  N  N  N  262.461  249.297  237.590   1.718  -4.371   0.950  H21     UY1  29  
UY1  H23     H23     H  0  1  N  N  N  261.442  250.682  237.073   2.398  -4.983  -0.577  H23     UY1  30  
UY1  H22     H22     H  0  1  N  N  N  261.258  249.084  236.274   3.254  -3.716   0.335  H22     UY1  31  
UY1  HN3     HN3     H  0  1  N  N  N  260.195  255.597  235.539   3.355   2.300   1.856  HN3     UY1  32  
UY1  HO3     HO3     H  0  1  N  N  N  261.947  248.296  233.744  -1.412  -3.321   1.277  HO3     UY1  33  
UY1  HOP2    HOP2    H  0  0  N  N  N  267.979  249.338  232.464  -3.399   2.849   0.405  HOP2    UY1  34  
UY1  OP3     OP3     O  0  1  N  Y  N  266.763  248.813  229.534  -5.061   1.428  -1.443  OP3     UY1  35  
UY1  HOP3    HOP3    H  0  0  N  N  N  267.010  249.429  228.855  -5.892   1.894  -1.280  HOP3    UY1  36  
UY1  HN1     HN1     H  0  1  N  N  N  260.378  254.457  231.688   5.072   1.616  -1.703  HN1     UY1  37  
#   #
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
UY1  OP1    P       DOUB  N  N   1  
UY1  P      "O5'"   SING  N  N   2  
UY1  P      OP2     SING  N  N   3  
UY1  "O5'"  "C5'"   SING  N  N   4  
UY1  "C5'"  "C4'"   SING  N  N   5  
UY1  N1     C6      SING  N  N   6  
UY1  N1     C2      SING  N  N   7  
UY1  C6     C5      DOUB  N  N   8  
UY1  "C4'"  "C3'"   SING  N  N   9  
UY1  "C4'"  "O4'"   SING  N  N  10  
UY1  O2     C2      DOUB  N  N  11  
UY1  "C3'"  "O3'"   SING  N  N  12  
UY1  "C3'"  "C2'"   SING  N  N  13  
UY1  "O4'"  "C1'"   SING  N  N  14  
UY1  C2     N3      SING  N  N  15  
UY1  C5     "C1'"   SING  N  N  16  
UY1  C5     C4      SING  N  N  17  
UY1  "C1'"  "C2'"   SING  N  N  18  
UY1  "C2'"  "O2'"   SING  N  N  19  
UY1  N3     C4      SING  N  N  20  
UY1  C4     O4      DOUB  N  N  21  
UY1  "O2'"  CM2     SING  N  N  22  
UY1  "C1'"  "H1'"   SING  N  N  23  
UY1  "C2'"  "H2'"   SING  N  N  24  
UY1  "C3'"  "H3'"   SING  N  N  25  
UY1  "C4'"  "H4'"   SING  N  N  26  
UY1  "C5'"  "H5'"   SING  N  N  27  
UY1  "C5'"  "H5''"  SING  N  N  28  
UY1  C6     H6      SING  N  N  29  
UY1  CM2    H21     SING  N  N  30  
UY1  CM2    H23     SING  N  N  31  
UY1  CM2    H22     SING  N  N  32  
UY1  N3     HN3     SING  N  N  33  
UY1  "O3'"  HO3     SING  N  N  34  
UY1  OP2    HOP2    SING  N  N  35  
UY1  P      OP3     SING  N  N  36  
UY1  OP3    HOP3    SING  N  N  37  
UY1  N1     HN1     SING  N  N  38  
#   #
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
UY1  SMILES            ACDLabs               12.01  "C1(C(OC)C(O)C(O1)COP(=O)(O)O)C2C(=O)NC(N=C2)=O"  
UY1  InChI             InChI                 1.03   "InChI=1S/C10H15N2O9P/c1-19-8-6(13)5(3-20-22(16,17)18)21-7(8)4-2-11-10(15)12-9(4)14/h2,5-8,13H,3H2,1H3,(H2,16,17,18)(H2,11,12,14,15)/t5-,6-,7+,8-/m1/s1"  
UY1  InChIKey          InChI                 1.03   VLDJGRCZRDFORR-OOJXKGFFSA-N  
UY1  SMILES_CANONICAL  CACTVS                3.385  "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1C2=CNC(=O)NC2=O"  
UY1  SMILES            CACTVS                3.385  "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1C2=CNC(=O)NC2=O"  
UY1  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CO[C@@H]1[C@@H]([C@H](O[C@H]1C2=CNC(=O)NC2=O)COP(=O)(O)O)O"  
UY1  SMILES            "OpenEye OEToolkits"  2.0.7  "COC1C(C(OC1C2=CNC(=O)NC2=O)COP(=O)(O)O)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
UY1  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1S)-1,4-anhydro-1-[(5S)-2,6-dioxo-1,2,5,6-tetrahydropyrimidin-5-yl]-2-O-methyl-5-O-phosphono-D-ribitol"  
UY1  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{R},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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
UY1  "Create component"               2020-06-04  RCSB  
UY1  "Initial release"                2020-10-07  RCSB  
UY1  "Modify model coordinates code"  2021-05-12  PDBE  
UY1  "Modify name"                    2021-05-27  PDBE  
##
