[Zinc-fans] Same IDs for molecules

[John J. Irwin]

Hi Lena

Thanks for your interest in ZINC.

Lena Dolghih wrote:
> Hi,
>
> 	I downloaded a subset of molecules in sdf, mol2 and smiles formats. 
> There are quite a few cases when both mol2 and sdf files have more then one 
> entry with the same name and ID. 
>   
Yes, different tautomers and protonation states have the same ZINC ID,
since a ZINC ID refers to a chemical substance, for which more than one
representation may be relevant.
> 	
> 	When i go back and search database for that ID, i get only one molecule.
> Also if i download the mol2 file for just that molecule (instead of downloading 
> the file with the whole subset) - i see only one entry.
>   
You have a chance to download the reference structure (pH 7.0)
separately from other pH ranges, if available. ZINC is a big database,
and I assure you I have not looked at each case individually. I am sure
there are many errors. If you would like to write me off the list with
ZINC IDs, what you see, and what you think you should see, I would be
glad to attempt to follow up and, if appropriate, put it right.

John

> If the two compounds with the same ID are tautomers then why do I not see both 
> of them when i download the file individually?
>
> Also, is there a way to pick just one? 
>
> lena
>
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