Structure based on 3d8y

Ideal structure
Name: 5'-deoxy-5'-piperidin-1-ylthymidine
Formula: C15 H23 N3 O4
Weight: 309.361
SMILES: "CC1=CN([CH]2C[CH](O)[CH](CN3CCCCC3)O2)C(=O)NC1=O"
Spacial conformation based on PDB 3d8y
RESIDUE   T3S     45
CONECT      C21    4 C22  N26  H21  H21A
CONECT      C22    4 C21  C23  H22  H22A
CONECT      C23    4 C22  C24  H23  H23A
CONECT      C24    4 C23  C25  H24  H24A
CONECT      C25    4 C24  N26  H25  H25A
CONECT      N26    3 C21  C25  C5' 
CONECT      C5'    4 N26  C4'  H5'  H5'A
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'  C1'  H2'  H2'A
CONECT      C1'    4 O4'  C2'  N1   H1' 
CONECT      N1     3 C1'  C6   C2  
CONECT      C6     3 N1   C5   H6  
CONECT      C5     3 C6   C5M  C4  
CONECT      C5M    4 C5   H5M  H5MA H5MB
CONECT      C4     3 C5   O4   N3  
CONECT      O4     1 C4  
CONECT      N3     3 C4   C2   HN3 
CONECT      C2     3 N1   N3   O2  
CONECT      O2     1 C2  
CONECT      H21    1 C21 
CONECT      H21A   1 C21 
CONECT      H22    1 C22 
CONECT      H22A   1 C22 
CONECT      H23    1 C23 
CONECT      H23A   1 C23 
CONECT      H24    1 C24 
CONECT      H24A   1 C24 
CONECT      H25    1 C25 
CONECT      H25A   1 C25 
CONECT      H5'    1 C5' 
CONECT      H5'A   1 C5' 
CONECT      H4'    1 C4' 
CONECT      H3'    1 C3' 
CONECT      HO3'   1 O3' 
CONECT      H2'    1 C2' 
CONECT      H2'A   1 C2' 
CONECT      H1'    1 C1' 
CONECT      H6     1 C6  
CONECT      H5M    1 C5M 
CONECT      H5MA   1 C5M 
CONECT      H5MB   1 C5M 
CONECT      HN3    1 N3  
END   
HET    T3S             45
HETNAM     T3S 5'-deoxy-5'-piperidin-1-ylthymidine
FORMUL      T3S    C15 H23 N3 O4

This OCA MONOMER page
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