data_RY
# 
_chem_comp.id                                    RY 
_chem_comp.name                                  
;5'-3,6-dihydrocytidylic acid
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H16 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-09-06 
_chem_comp.pdbx_modified_date                    2018-10-26 
_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                        325.212 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     RY 
_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        6MCF 
_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 
RY P      P1  P 0 1 N N N 32.896 6.856  -5.847 -4.067 -1.071 0.048  P      RY 1  
RY "C5'"  C1  C 0 1 N N N 30.597 5.982  -4.718 -2.130 0.726  -0.352 "C5'"  RY 2  
RY "O5'"  O1  O 0 1 N N N 32.002 6.244  -4.634 -2.798 -0.195 0.512  "O5'"  RY 3  
RY "C4'"  C2  C 0 1 N N R 30.220 4.708  -5.495 -0.974 1.387  0.402  "C4'"  RY 4  
RY "O4'"  O2  O 0 1 N N N 30.772 3.540  -4.893 0.033  0.407  0.709  "O4'"  RY 5  
RY "C3'"  C3  C 0 1 N N S 28.695 4.437  -5.549 -0.314 2.459  -0.486 "C3'"  RY 6  
RY "O3'"  O3  O 0 1 N N N 28.104 4.707  -6.821 -0.398 3.743  0.135  "O3'"  RY 7  
RY "C2'"  C4  C 0 1 N N R 28.598 2.927  -5.226 1.162  2.006  -0.595 "C2'"  RY 8  
RY "O2'"  O4  O 0 1 N N N 27.700 2.186  -6.044 2.047  3.123  -0.502 "O2'"  RY 9  
RY "C1'"  C5  C 0 1 N N R 30.032 2.466  -5.441 1.309  1.078  0.638  "C1'"  RY 10 
RY N1     N1  N 0 1 N N N 30.349 1.152  -4.818 2.390  0.111  0.430  N1     RY 11 
RY C2     C6  C 0 1 N N N 30.522 0.027  -5.633 2.303  -0.823 -0.538 C2     RY 12 
RY O2     O5  O 0 1 N N N 30.355 0.028  -6.845 1.311  -0.853 -1.242 O2     RY 13 
RY N3     N2  N 0 1 N N N 30.838 -1.142 -5.077 3.276  -1.718 -0.748 N3     RY 14 
RY C4     C7  C 0 1 N N N 30.973 -1.285 -3.797 4.443  -1.765 -0.001 C4     RY 15 
RY N4     N3  N 0 1 N N N 31.297 -2.455 -3.318 5.402  -2.730 -0.289 N4     RY 16 
RY C5     C8  C 0 1 N N N 30.748 -0.198 -2.910 4.661  -0.901 0.989  C5     RY 17 
RY C6     C9  C 0 1 N N N 30.446 1.012  -3.455 3.598  0.140  1.270  C6     RY 18 
RY OP1    O6  O 0 1 N N N 32.002 7.206  -6.975 -3.717 -1.840 -1.167 OP1    RY 19 
RY OP2    O7  O 0 1 N N N 33.735 7.954  -5.302 -4.477 -2.087 1.227  OP2    RY 20 
RY OP3    O8  O 0 1 N Y N 33.875 5.682  -6.362 -5.305 -0.093 -0.273 OP3    RY 21 
RY "H5''" H1  H 0 0 N N N 30.119 6.839  -5.215 -1.740 0.193  -1.220 "H5''" RY 22 
RY "H5'"  H2  H 0 1 N N N 30.206 5.886  -3.694 -2.833 1.491  -0.681 "H5'"  RY 23 
RY "H4'"  H3  H 0 1 N N N 30.589 4.808  -6.526 -1.343 1.840  1.322  "H4'"  RY 24 
RY "H3'"  H4  H 0 1 N N N 28.197 5.011  -4.754 -0.781 2.479  -1.471 "H3'"  RY 25 
RY H1     H5  H 0 1 N N N 27.173 4.521  -6.784 0.002  4.457  -0.381 H1     RY 26 
RY "H2'"  H6  H 0 1 N N N 28.338 2.809  -4.164 1.332  1.453  -1.520 "H2'"  RY 27 
RY "HO2'" H7  H 0 0 N N N 27.705 1.275  -5.776 1.930  3.778  -1.204 "HO2'" RY 28 
RY "H1'"  H8  H 0 1 N N N 30.217 2.399  -6.523 1.485  1.664  1.540  "H1'"  RY 29 
RY H3     H9  H 0 1 N N N 30.976 -1.936 -5.669 3.159  -2.367 -1.459 H3     RY 30 
RY H41    H10 H 0 1 N N N 31.362 -2.401 -2.322 5.251  -3.363 -1.009 H41    RY 31 
RY H42    H11 H 0 1 N N N 30.598 -3.124 -3.571 6.221  -2.770 0.229  H42    RY 32 
RY H5     H12 H 0 1 N N N 30.814 -0.328 -1.840 5.571  -0.939 1.571  H5     RY 33 
RY H6     H13 H 0 1 N N N 31.224 1.713  -3.120 4.053  1.125  1.168  H6     RY 34 
RY H2     H14 H 0 1 N N N 29.475 1.314  -3.036 3.287  0.025  2.309  H2     RY 35 
RY H4     H15 H 0 1 N N N 33.562 8.754  -5.784 -5.236 -2.648 1.016  H4     RY 36 
RY H7     H16 H 0 1 N N N 33.670 5.471  -7.265 -5.588 0.443  0.480  H7     RY 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 
RY OP1   P      DOUB N N 1  
RY O2    C2     DOUB N N 2  
RY "O3'" "C3'"  SING N N 3  
RY "O2'" "C2'"  SING N N 4  
RY P     OP2    SING N N 5  
RY P     "O5'"  SING N N 6  
RY C2    N3     SING N N 7  
RY C2    N1     SING N N 8  
RY "C3'" "C4'"  SING N N 9  
RY "C3'" "C2'"  SING N N 10 
RY "C4'" "O4'"  SING N N 11 
RY "C4'" "C5'"  SING N N 12 
RY "C1'" "C2'"  SING N N 13 
RY "C1'" "O4'"  SING N N 14 
RY "C1'" N1     SING N N 15 
RY N3    C4     SING N N 16 
RY N1    C6     SING N N 17 
RY "C5'" "O5'"  SING N N 18 
RY C4    N4     SING N N 19 
RY C4    C5     DOUB N N 20 
RY C6    C5     SING N N 21 
RY P     OP3    SING N N 22 
RY "C5'" "H5''" SING N N 23 
RY "C5'" "H5'"  SING N N 24 
RY "C4'" "H4'"  SING N N 25 
RY "C3'" "H3'"  SING N N 26 
RY "O3'" H1     SING N N 27 
RY "C2'" "H2'"  SING N N 28 
RY "O2'" "HO2'" SING N N 29 
RY "C1'" "H1'"  SING N N 30 
RY N3    H3     SING N N 31 
RY N4    H41    SING N N 32 
RY N4    H42    SING N N 33 
RY C5    H5     SING N N 34 
RY C6    H6     SING N N 35 
RY C6    H2     SING N N 36 
RY OP2   H4     SING N N 37 
RY OP3   H7     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 
RY SMILES           ACDLabs              12.01 "P(O)(OCC1OC(C(C1O)O)N2CC=C(NC2=O)N)(O)=O"                                                                                                          
RY InChI            InChI                1.03  "InChI=1S/C9H16N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1,4,6-8,13-14H,2-3,10H2,(H,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" 
RY InChIKey         InChI                1.03  NWPXZYGTNOANAA-XVFCMESISA-N                                                                                                                         
RY SMILES_CANONICAL CACTVS               3.385 "NC1=CCN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N1"                                                                                      
RY SMILES           CACTVS               3.385 "NC1=CCN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N1"                                                                                            
RY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1C=C(NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N"                                                                                      
RY SMILES           "OpenEye OEToolkits" 2.0.6 "C1C=C(NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N"                                                                                                        
# 
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 
RY "SYSTEMATIC NAME" ACDLabs              12.01 
;5'-3,6-dihydrocytidylic acid
;
RY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-1,4-dihydropyrimidin-3-yl)-3,4-bis(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 
RY "Create component" 2018-09-06 RCSB 
RY "Initial release"  2018-10-31 RCSB 
# 
