Structure based on 4rt2

Ideal structure
Name: 2'-deoxy-5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine
Formula: C11 H20 N3 O12 P3
Weight: 479.211
SMILES: "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)N[P](O)(O)=O)O2)C(=O)NC1=O"
Spacial conformation based on PDB 4rt2
RESIDUE   N6T     49
CONECT      O4     1 C4  
CONECT      C4     3 O4   C5   N3  
CONECT      C5     3 C4   C7   C6  
CONECT      C7     4 C5   H1   H2   H3  
CONECT      C6     3 C5   N1   H4  
CONECT      N3     3 C4   C2   H5  
CONECT      C2     3 N3   O2   N1  
CONECT      O2     1 C2  
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  C3A 
CONECT      O1A    2 PA   H14 
CONECT      O2A    1 PA  
CONECT      C3A    4 PA   PB   H15  H16 
CONECT      PB     4 C3A  O1B  O2B  N3B 
CONECT      O1B    1 PB  
CONECT      O2B    2 PB   H17 
CONECT      N3B    3 PB   PG   H18 
CONECT      PG     4 N3B  O2G  O1G  O3G 
CONECT      O2G    1 PG  
CONECT      O1G    2 PG   H19 
CONECT      O3G    2 PG   H20 
CONECT      H1     1 C7  
CONECT      H2     1 C7  
CONECT      H3     1 C7  
CONECT      H4     1 C6  
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 O1A 
CONECT      H15    1 C3A 
CONECT      H16    1 C3A 
CONECT      H17    1 O2B 
CONECT      H18    1 N3B 
CONECT      H19    1 O1G 
CONECT      H20    1 O3G 
HET    N6T             49
HETNAM     N6T 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)
HETNAM   2 N6T phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine
FORMUL      N6T    C11 H20 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