These files were fetched from the PDB using:
https://www.rcsb.org/pdb/download/downloadLigandFiles.do?ligandIdList=%s&structIdList=%s&instanceType=all&excludeUnobserved=false&includeHydrogens=false'%(lig,pdb)
(see fetch.py)
Then all but the first ligand was removed:
for i in *.sdf; do sed '/\$\$\$\$/q' $i -i; done

The pdb/lig identifiers used are in pdbs.txt

2c2t_39b.sdf was removed because the molecule is just crazy.

Exactly identical files are removed using 
./print_redundant.py | xargs git rm
