Structure based on 4ir1

Ideal structure
Name: 5'-o-[(r)-hydroxy{[(r)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
Formula: C10 H18 N3 O13 P3
Weight: 481.184
SMILES: "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"
Spacial conformation based on PDB 4ir1.
Also present in other 26 PDB entries.
RESIDUE   1FZ     47
CONECT      O2     1 C2  
CONECT      O4     1 C4  
CONECT      C4     3 O4   C5   N3  
CONECT      C5     3 C4   C6   C5M 
CONECT      C6     3 C5   N1   H1  
CONECT      C5M    4 C5   H2   H3   H4  
CONECT      N3     3 C4   C2   H5  
CONECT      C2     3 O2   N3   N1  
CONECT      N1     3 C6   C2   C1' 
CONECT      C1'    4 N1   C2'  O4'  H6  
CONECT      C2'    4 C1'  C3'  H7   H8  
CONECT      C3'    4 C2'  O3'  C4'  H9  
CONECT      O3'    2 C3'  H10 
CONECT      O4'    2 C1'  C4' 
CONECT      C4'    4 C3'  O4'  C5'  H11 
CONECT      C5'    4 C4'  O5'  H12  H13 
CONECT      O5'    2 C5'  PA  
CONECT      PA     4 O5'  O1A  O2A  N3A 
CONECT      O1A    1 PA  
CONECT      O2A    2 PA   H14 
CONECT      N3A    3 PA   PB   H15 
CONECT      PB     4 N3A  O1B  O2B  O3B 
CONECT      O1B    2 PB   H16 
CONECT      O2B    1 PB  
CONECT      O3B    2 PB   PG  
CONECT      PG     4 O3B  O1G  O3G  O2G 
CONECT      O1G    2 PG   H17 
CONECT      O3G    1 PG  
CONECT      O2G    2 PG   H18 
CONECT      H1     1 C6  
CONECT      H2     1 C5M 
CONECT      H3     1 C5M 
CONECT      H4     1 C5M 
CONECT      H5     1 N3  
CONECT      H6     1 C1' 
CONECT      H7     1 C2' 
CONECT      H8     1 C2' 
CONECT      H9     1 C3' 
CONECT      H10    1 O3' 
CONECT      H11    1 C4' 
CONECT      H12    1 C5' 
CONECT      H13    1 C5' 
CONECT      H14    1 O2A 
CONECT      H15    1 N3A 
CONECT      H16    1 O1B 
CONECT      H17    1 O1G 
CONECT      H18    1 O2G 
HET    1FZ             47
HETNAM     1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]
HETNAM   2 1FZ amino}phosphoryl]thymidine
FORMUL      1FZ    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