data_UZL
# 
_chem_comp.id                                    UZL 
_chem_comp.name                                  "O2'-methylycytidine" 
_chem_comp.type                                  "RNA OH 3 prime terminus" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N3 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "4-azanyl-1-[(2R,3R,4R,5R)-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-17 
_chem_comp.pdbx_modified_date                    2023-02-24 
_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                        257.243 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     UZL 
_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        8CLM 
_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 
UZL N1     N1  N 0 1 N N N -0.961 -7.921  9.226  1.128  -0.037 0.501  N1     UZL 1  
UZL C2     C1  C 0 1 N N N -2.129 -7.207  8.985  1.529  -0.517 -0.690 C2     UZL 2  
UZL N3     N2  N 0 1 N N N -2.071 -5.864  8.941  2.822  -0.673 -0.968 N3     UZL 3  
UZL C4     C2  C 0 1 N N N -0.908 -5.217  9.086  3.750  -0.357 -0.073 C4     UZL 4  
UZL C5     C3  C 0 1 N N N 0.293  -5.934  9.343  3.362  0.148  1.184  C5     UZL 5  
UZL C6     C4  C 0 1 N N N 0.225  -7.270  9.378  2.044  0.305  1.450  C6     UZL 6  
UZL O2     O1  O 0 1 N N N -3.161 -7.867  8.832  0.695  -0.814 -1.530 O2     UZL 7  
UZL N4     N3  N 0 1 N N N -0.905 -3.891  9.067  5.083  -0.523 -0.371 N4     UZL 8  
UZL "C1'"  C5  C 0 1 N N R -1.115 -9.398  9.310  -0.302 0.123  0.778  "C1'"  UZL 9  
UZL "C2'"  C6  C 0 1 N N R -1.341 -10.112 7.968  -0.932 1.128  -0.213 "C2'"  UZL 10 
UZL "O2'"  O2  O 0 1 N N N -2.098 -11.292 8.200  -1.041 2.420  0.387  "O2'"  UZL 11 
UZL CM2    C7  C 0 1 N N N -3.504 -11.122 8.354  -0.951 3.501  -0.543 CM2    UZL 12 
UZL "C3'"  C8  C 0 1 N N R 0.111  -10.378 7.545  -2.334 0.544  -0.499 "C3'"  UZL 13 
UZL "C4'"  C9  C 0 1 N N R 0.691  -10.818 8.893  -2.385 -0.744 0.352  "C4'"  UZL 14 
UZL "O4'"  O3  O 0 1 N N N 0.064  -9.945  9.875  -1.003 -1.118 0.540  "O4'"  UZL 15 
UZL "O3'"  O4  O 0 1 N N N 0.267  -11.398 6.547  -3.351 1.458  -0.085 "O3'"  UZL 16 
UZL "C5'"  C10 C 0 1 N N N 2.190  -10.741 9.042  -3.137 -1.847 -0.396 "C5'"  UZL 17 
UZL "O5'"  O5  O 0 1 N N N 2.657  -9.431  8.671  -3.275 -2.989 0.452  "O5'"  UZL 18 
UZL "H1'"  H1  H 0 1 N N N 1.228  -5.418  9.504  4.105  0.409  1.923  "H1'"  UZL 19 
UZL "H2'"  H2  H 0 1 N N N 1.128  -7.843  9.530  1.722  0.694  2.405  "H2'"  UZL 20 
UZL HN41   H3  H 0 0 N N N -1.762 -3.391  8.946  5.347  -0.871 -1.237 HN41   UZL 21 
UZL HN42   H4  H 0 0 N N N -0.045 -3.391  9.174  5.759  -0.292 0.285  HN42   UZL 22 
UZL H1     H5  H 0 1 N N N -1.972 -9.623  9.961  -0.455 0.454  1.805  H1     UZL 23 
UZL H2     H6  H 0 1 N N N -1.833 -9.437  7.252  -0.344 1.181  -1.129 H2     UZL 24 
UZL HM21   H7  H 0 0 N N N -3.975 -12.101 8.527  -1.043 4.448  -0.010 HM21   UZL 25 
UZL HM22   H8  H 0 0 N N N -3.702 -10.463 9.212  0.012  3.463  -1.053 HM22   UZL 26 
UZL HM23   H9  H 0 0 N N N -3.921 -10.671 7.442  -1.753 3.418  -1.276 HM23   UZL 27 
UZL "H3'"  H10 H 0 1 N N N 0.583  -9.437  7.227  -2.440 0.307  -1.558 "H3'"  UZL 28 
UZL "H4'"  H11 H 0 1 N N N 0.376  -11.855 9.079  -2.860 -0.546 1.313  "H4'"  UZL 29 
UZL "HO3'" H12 H 0 0 N Y N 1.189  -11.502 6.341  -4.251 1.142  -0.242 "HO3'" UZL 30 
UZL "H5'"  H13 H 0 1 N N N 2.660  -11.493 8.390  -4.125 -1.484 -0.679 "H5'"  UZL 31 
UZL "H5''" H14 H 0 0 N N N 2.462  -10.941 10.089 -2.581 -2.124 -1.291 "H5''" UZL 32 
UZL "HO5'" H15 H 0 0 N N N 3.601  -9.392  8.768  -3.743 -3.729 0.043  "HO5'" UZL 33 
# 
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 
UZL "O3'" "C3'"  SING N N 1  
UZL "C3'" "C2'"  SING N N 2  
UZL "C3'" "C4'"  SING N N 3  
UZL "C2'" "O2'"  SING N N 4  
UZL "C2'" "C1'"  SING N N 5  
UZL "O2'" CM2    SING N N 6  
UZL "O5'" "C5'"  SING N N 7  
UZL O2    C2     DOUB N N 8  
UZL "C4'" "C5'"  SING N N 9  
UZL "C4'" "O4'"  SING N N 10 
UZL N3    C2     SING N N 11 
UZL N3    C4     DOUB N N 12 
UZL C2    N1     SING N N 13 
UZL N4    C4     SING N N 14 
UZL C4    C5     SING N N 15 
UZL N1    "C1'"  SING N N 16 
UZL N1    C6     SING N N 17 
UZL "C1'" "O4'"  SING N N 18 
UZL C5    C6     DOUB N N 19 
UZL C5    "H1'"  SING N N 20 
UZL C6    "H2'"  SING N N 21 
UZL N4    HN41   SING N N 22 
UZL N4    HN42   SING N N 23 
UZL "C1'" H1     SING N N 24 
UZL "C2'" H2     SING N N 25 
UZL CM2   HM21   SING N N 26 
UZL CM2   HM22   SING N N 27 
UZL CM2   HM23   SING N N 28 
UZL "C3'" "H3'"  SING N N 29 
UZL "C4'" "H4'"  SING N N 30 
UZL "O3'" "HO3'" SING N N 31 
UZL "C5'" "H5'"  SING N N 32 
UZL "C5'" "H5''" SING N N 33 
UZL "O5'" "HO5'" SING N N 34 
# 
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 
UZL InChI            InChI                1.06  "InChI=1S/C10H15N3O5/c1-17-8-7(15)5(4-14)18-9(8)13-3-2-6(11)12-10(13)16/h2-3,5,7-9,14-15H,4H2,1H3,(H2,11,12,16)/t5-,7-,8-,9-/m1/s1" 
UZL InChIKey         InChI                1.06  RFCQJGFZUQFYRF-ZOQUXTDFSA-N                                                                                                         
UZL SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N2C=CC(=NC2=O)N"                                                                                 
UZL SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](CO)O[CH]1N2C=CC(=NC2=O)N"                                                                                       
UZL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO)O"                                                                                 
UZL SMILES           "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=NC2=O)N)CO)O"                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           UZL 
_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        "4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      UZL 
_pdbx_chem_comp_synonyms.name         "4-azanyl-1-[(2R,3R,4R,5R)-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" 
_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 
UZL "Create component"         2023-02-17 PDBE 
UZL "Modify leaving atom flag" 2023-02-21 PDBE 
UZL "Initial release"          2023-03-01 RCSB 
# 
