Standardization rule - enol

<Transformation ID="enol" Structure="[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]"/>





I have an original structure (see MOL below) sent through different standardization programs. See the attached file for three different results obtained using JChem Standardizer (triggered by the above enol rule), an in-house program that does not have this rule, and PubChem (http://pubchem.ncbi.nlm.nih.gov/standardize/standardize.cgi).





I consulted with some chemists in my company, nobody likes the PubChem output, so let's forget about that. People here think the second output is more correct at physiological pHs. Not being a chemist myself, I wonder if you can check the original enol rule and see wether rule needs to be patched based on this example?





Thanks


==================


MY_TEST


NSMI2MOL 1 1.00000 0.00000 0





21 22 0 0 0 0 1 V2000


2.3743 2.8674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.3743 3.6736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.0240 4.0571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.7127 3.6736 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


3.7127 2.8753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.0240 2.4839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.0005 1.7717 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0


3.6814 1.5525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.8067 0.8638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.2431 0.3785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


4.4954 0.6290 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0


4.2450 2.0534 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


4.3389 2.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.0318 4.7928 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


1.7169 4.0571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.0360 3.6658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.0360 2.8674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.7169 2.4839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.7169 1.7325 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


0.3785 2.4917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


1.7247 4.7850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


1 6 1 0 0 0 0


1 18 1 0 0 0 0


1 2 1 0 0 0 0


2 3 1 0 0 0 0


3 4 1 0 0 0 0


4 5 1 0 0 0 0


5 6 1 0 0 0 0


6 7 1 0 0 0 0


7 8 1 0 0 0 0


8 9 1 0 0 0 0


9 10 1 0 0 0 0


9 11 1 0 0 0 0


8 12 2 0 0 0 0


5 13 1 0 0 0 0


3 14 2 0 0 0 0


2 15 2 0 0 0 0


15 16 1 0 0 0 0


16 17 1 0 0 0 0


17 18 1 0 0 0 0


18 19 1 0 0 0 0


17 20 1 0 0 0 0


15 21 1 0 0 0 0


M END

Standardizer is for the canonicalization of functional groups. This is independent from the physiological form at a given pH. The transform action in the rules does not consider any pH, it just transforms all enols to oxo forms. A uniform representation is usually preferred for database standardization.





Would you like to convert the compounds in your database into their major formats at a given pH? Sometimes more than one forms are present, and your data will depend on the prediction quality. Anyway, at pH 7.4, your amino group is probably protonated (charged).