Structure based on 3rjh

Ideal structure
Name: 2'-deoxy-5'-o-[(s)-{difluoro[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine
Formula: C10 H16 F2 N3 O12 P3
Weight: 501.165
SMILES: "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)C(F)(F)[P](O)(=O)O[P](O)(O)=O)O2"
Spacial conformation based on PDB 3rjh.
Also present in other 7 PDB entries.
RESIDUE   6CF     46
CONECT      N1     3 C2   C6   C1' 
CONECT      P1     4 O1A  O2A  C3A  O5' 
CONECT      C2     3 N1   O2   N3  
CONECT      O2     1 C2  
CONECT      P2     4 O1B  O2B  C3A  O3B 
CONECT      N3     2 C2   C4  
CONECT      P3     4 O1G  O2G  O3B  O3G 
CONECT      C4     3 N3   N4   C5  
CONECT      N4     3 C4   HN4  HN4A
CONECT      C5     3 C4   C6   H5  
CONECT      C6     3 N1   C5   H6  
CONECT      C1'    4 N1   C2'  O4'  H1' 
CONECT      F1A    1 C3A 
CONECT      O1A    2 P1   HO1A
CONECT      O1B    1 P2  
CONECT      O1G    2 P3   HO1G
CONECT      C2'    4 C1'  C3'  H2'  H2'A
CONECT      F2A    1 C3A 
CONECT      O2A    1 P1  
CONECT      O2B    2 P2   HO2B
CONECT      O2G    2 P3   HO2G
CONECT      C3'    4 C2'  O3'  C4'  H3' 
CONECT      O3'    2 C3'  HO3'
CONECT      C3A    4 P1   P2   F1A  F2A 
CONECT      O3B    2 P2   P3  
CONECT      O3G    1 P3  
CONECT      C4'    4 C3'  O4'  C5'  H4' 
CONECT      O4'    2 C1'  C4' 
CONECT      C5'    4 C4'  O5'  H5'  H5'A
CONECT      O5'    2 P1   C5' 
CONECT      HN4    1 N4  
CONECT      HN4A   1 N4  
CONECT      H5     1 C5  
CONECT      H6     1 C6  
CONECT      H1'    1 C1' 
CONECT      HO1A   1 O1A 
CONECT      HO1G   1 O1G 
CONECT      H2'    1 C2' 
CONECT      H2'A   1 C2' 
CONECT      HO2B   1 O2B 
CONECT      HO2G   1 O2G 
CONECT      H3'    1 C3' 
CONECT      HO3'   1 O3' 
CONECT      H4'    1 C4' 
CONECT      H5'    1 C5' 
CONECT      H5'A   1 C5' 
HET    6CF             46
HETNAM     6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)p
HETNAM   2 6CF hosphoryl]methyl}(hydroxy)phosphoryl]cytidine
FORMUL      6CF    C10 H16 F2 N3 O12 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