jc_Standardize and tautomerise option

Hi,





I am trying to standardize all molecules before they are saved to the database in order to be able to get the correct results when we run a jc_compare. So I run

Code:

select jc_Standardize('C\C(Cl)=C(/C)c1ccc(cc1)C2CCC(O)=C2N', 'sep=! config:dearomatize..dehydrogenize..expand..tautomerize..aromatize!cleaningTemplate:select ''null'' from dual!outFormat:cxsmiles') from dual

I get CC(Cl)=C(C)c1ccc(cc1)C2CCC(=O)C2. The CIS / TRANS Chirality is lost.





If I run the same statement without "tautomerize", I get C\C(Cl)=C(/C)c1ccc(cc1)C2CCC(O)=C2N back, the CIS / TRANS is no longer lost, but I will fail to identify both molecules as idendical with jc_compare

Code:

select * from dual where jc_compare ('CC(Cl)=C(C)c1ccc(cc1)C2CCC(=O)C2N', 'CC(Cl)=C(C)c1ccc(cc1)C2CCC(O)=C2N', 't:e') = 1

I also also tried to run the same molecule with Tautomerize only and get the same result. Cis / trans is lost.

Code:

select jc_Standardize('C\C(Cl)=C(/C)c1ccc(cc1)C2CCC(O)=C2N', 'config:tautomerize') from dual

I have tried to understand why the stereochemistry is lost.


I have run the Tautomers in Marvin Sketch and noticed that CC(Cl)C(=C)C1=CC=C(C=C1)C2CC=C(O)C2N is generated. But in order to generate this Tautomer, we need to remove one H from CH3.


To confirm whether this was possible, I have calculated the pKa on this molecule and the pKa of that H is not mentioned, which means it is outside of the range specified (-50, 50).





Is this a bug with the "tautomerize"?


What other options are available to generate a unique molecule for 2 tautomers? My output format needs to be cxsmiles.





Thanks


Catherine





PS I amusing JChem 3.2.6

Hi,





We are examining the problem and will get back to you soon.





Zsolt

There is a bug in the "tautomerize" action. We will correct it ASAP.





Zsolt