Structure based on 4oio

Ideal structure
Name: 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
Formula: C10 H18 N3 O13 P3
Weight: 481.184
SMILES: "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O"
Spacial conformation based on PDB 4oio.
Also present in other 14 PDB entries.
RESIDUE   2TM     47
CONECT      O5'    2 C5'  PA  
CONECT      C5'    4 O5'  C4'  H1   H2  
CONECT      C4'    4 C5'  O4'  C3'  H3  
CONECT      O4'    2 C4'  C1' 
CONECT      C3'    4 C4'  O3'  C2'  H4  
CONECT      O3'    2 C3'  H5  
CONECT      C2'    4 C3'  O2'  C1'  H6  
CONECT      O2'    2 C2'  H7  
CONECT      C1'    4 O4'  C2'  N1   H8  
CONECT      C5     3 C6   C4   H9  
CONECT      C6     3 C5   N1   H10 
CONECT      N1     3 C1'  C6   C2  
CONECT      C2     3 N1   N3   O2  
CONECT      N3     2 C2   C4  
CONECT      C4     3 C5   N3   N4  
CONECT      O3G    2 PG   H11 
CONECT      PG     4 O3G  O1G  O2G  O3B 
CONECT      O1G    1 PG  
CONECT      O2G    2 PG   H12 
CONECT      O3B    2 PG   PB  
CONECT      PB     4 O3B  O1B  O2B  C1  
CONECT      O1B    2 PB   H13 
CONECT      O2B    1 PB  
CONECT      PA     4 O5'  O1A  O2A  C1  
CONECT      O1A    1 PA  
CONECT      O2A    2 PA   H14 
CONECT      N4     3 C4   H15  H16 
CONECT      O2     1 C2  
CONECT      C1     4 PB   PA   H17  H18 
CONECT      H1     1 C5' 
CONECT      H2     1 C5' 
CONECT      H3     1 C4' 
CONECT      H4     1 C3' 
CONECT      H5     1 O3' 
CONECT      H6     1 C2' 
CONECT      H7     1 O2' 
CONECT      H8     1 C1' 
CONECT      H9     1 C5  
CONECT      H10    1 C6  
CONECT      H11    1 O3G 
CONECT      H12    1 O2G 
CONECT      H13    1 O1B 
CONECT      H14    1 O2A 
CONECT      H15    1 N4  
CONECT      H16    1 N4  
CONECT      H17    1 C1  
CONECT      H18    1 C1  
HET    2TM             47
HETNAM     2TM 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]
HETNAM   2 2TM methyl}phosphoryl]cytidine
FORMUL      2TM    C10 H18 N3 O13 P3

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