Structure based on 5dlf

Ideal structure
Name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1h)-one
Formula: C11 H17 N2 O8 P
Weight: 336.235
SMILES: "COC1=NC(=O)N(C=C1C)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"
Spacial conformation based on PDB 5dlf.
Also present on 5dlg
RESIDUE   5DB     39
CONECT      P      4 OP1  O5'  OP2  OP3 
CONECT      OP1    2 P    H1  
CONECT      O5'    2 P    C5' 
CONECT      C5'    4 O5'  C4'  H2   H3  
CONECT      C4'    4 C5'  C3'  O4'  H4  
CONECT      C3'    4 C4'  O3'  C2'  H5  
CONECT      O3'    2 C3'  H6  
CONECT      C2'    4 C3'  C1'  H7   H8  
CONECT      C1'    4 C2'  O4'  N1   H9  
CONECT      O4'    2 C4'  C1' 
CONECT      N1     3 C1'  C6   C2  
CONECT      C6     3 N1   C5   H10 
CONECT      C5     3 C6   C7   C4  
CONECT      C7     4 C5   H11  H12  H13 
CONECT      C4     3 C5   N3   O4  
CONECT      N3     2 C4   C2  
CONECT      C2     3 N1   N3   O2  
CONECT      O2     1 C2  
CONECT      O4     2 C4   C1  
CONECT      OP2    1 P   
CONECT      C1     4 O4   H15  H16  H17 
CONECT      H1     1 OP1 
CONECT      H2     1 C5' 
CONECT      H3     1 C5' 
CONECT      H4     1 C4' 
CONECT      H5     1 C3' 
CONECT      H6     1 O3' 
CONECT      H7     1 C2' 
CONECT      H8     1 C2' 
CONECT      H9     1 C1' 
CONECT      H10    1 C6  
CONECT      H11    1 C7  
CONECT      H12    1 C7  
CONECT      H13    1 C7  
CONECT      H15    1 C1  
CONECT      H16    1 C1  
CONECT      H17    1 C1  
CONECT      OP3    2 P    H19 
CONECT      H19    1 OP3 
HET    5DB             39
HETNAM     5DB 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)
HETNAM   2 5DB -4-methoxy-5-methylpyrimidin-2(1H)-one
FORMUL      5DB    C11 H17 N2 O8 P1

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