Structure based on 364d

Ideal structure
Name: 5'-o-thiophosphonocytidine
Formula: C9 H14 N3 O7 P S
Weight: 339.262
SMILES: "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(S)=O)[CH](O)[CH]2O"
Spacial conformation based on PDB 364d
RESIDUE   1SC     35
CONECT      O3P    2 P    HO3P
CONECT      P      4 O3P  O1P  O5'  S   
CONECT      O1P    1 P   
CONECT      O5'    2 P    C5' 
CONECT      C5'    4 O5'  C4'  H5'1 H5'2
CONECT      C4'    4 C5'  O4'  C3'  H4' 
CONECT      O4'    2 C4'  C1' 
CONECT      C3'    4 C4'  O3'  C2'  H3' 
CONECT      O3'    2 C3'  HO3'
CONECT      C2'    4 C3'  O2'  C1'  H2' 
CONECT      O2'    2 C2'  HO2'
CONECT      C1'    4 O4'  C2'  N1   H1' 
CONECT      N1     3 C1'  C2   C6  
CONECT      C2     3 N1   O2   N3  
CONECT      O2     1 C2  
CONECT      N3     2 C2   C4  
CONECT      C4     3 N3   N4   C5  
CONECT      N4     3 C4   HN41 HN42
CONECT      C5     3 C4   C6   H5  
CONECT      C6     3 N1   C5   H6  
CONECT      S      2 P    HS  
CONECT      HO3P   1 O3P 
CONECT      H5'1   1 C5' 
CONECT      H5'2   1 C5' 
CONECT      H4'    1 C4' 
CONECT      H3'    1 C3' 
CONECT      HO3'   1 O3' 
CONECT      H2'    1 C2' 
CONECT      HO2'   1 O2' 
CONECT      H1'    1 C1' 
CONECT      HN41   1 N4  
CONECT      HN42   1 N4  
CONECT      H5     1 C5  
CONECT      H6     1 C6  
CONECT      HS     1 S   
END   
HET    1SC             35
HETNAM     1SC 5'-O-THIOPHOSPHONOCYTIDINE
FORMUL      1SC    C9 H14 N3 O7 P1 S1

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uses Jmol, developed by the Jmol Development Team (color reference)
OCA© by Jaime Prilusky, 1996-2004,2006,2010,2014
Bioinformatics Unit
Weizmann Institute of Science