a problem using the ‘Chemaxon Calculator’ component in PP to calculate the
number of H-Bond donors (HBD) and –acceptors (HBA). For a certain reason it was
quite helpful that the component is able to output not only integers but also
the distribution of HBA- and HBD-count at a certain pH. Therefore I am using
the ChemAxon_HBADistribution at pH 7.4 as the number of HBD.
I did some random testing to examine whether this component
gives reasonable results and it seems to work (although I was not able to
figure out every rule how the component classifies one group as an HBD and another not – is there a documentation about
today I experienced a very odd situation, where I found a molecule (see
attachment), for which the component calculated 32 HBD, whereas I have counted
only 8 HBD.
really see where the 32 HBD come from. Any guesses?
I might have found another issue with the Calculator component when I tried to understand how it works. I started with molecule 1 (see attachment). According to the component molecule 1 has three HBA (at pH 7). Subsequently I removed one of the oxygen atoms from the carboxylate group to see how many HBA do account for this particular (removed) atom (molecule 2). Molecule 2 now has only 2 HBA left. To be sure that none of the heteroatoms in the thiazole ring account for an HBA, I replaced the thiazole ring with a phenyl ring (molecule 3). Molecule 3 has the same number of HBA as molecule 2. So, this would mean the carbonyl oxygen formally accounts for two HBA, whereas the negatively oxygen accounts for one HBA.
But then I had a look at molecule 4 – it has only two HBA and I don't really see why?
My colleagues will answer soon to the calculation specific questions.
Meanwhile could you let us know the JChem version you are using ?
(so we can talk about the same algorithm)
In PP in the Components window under ChemAxon -> Utilities you can find a "Show ChemAxon Environment" component (actually it's a protocol).
The output should contain all relevant version information.
sorry for not specifying this information. This the output:
ChemAxon For Pipeline Pilot System Information
JChem version : 5.2.4
Component collection version : 1.5.1
JVM: Sun Microsystems Inc. Java HotSpot(TM) Server VM 1.5.0_07
I noticed something, which might actually turn out to be helpful to trace down the bug: As said before, the 'normal' structure gives an erroneous number of HBD (see 'aromatic.png').
After removing one double bond in the indole ring, the count of HBD is reduced from 32 to 8 (see 'non-aromatic.png')
This bug can occure in case of symmetric molecules sometimes. I fix it asap.
thanks for your reply. I thought it must have something to do with the symmetry in this molecule, since adding a methyl group fixes the problem, too!
What about the issue mentioned for molecule 4 in my second post. Am I wrong or should molecule 4 have three HBA?
What about the issue mentioned for molecule 4 in my second post.
Am I wrong or should molecule 4 have three HBA?
You are rigth there must be some additional bugs. We fix these bugs asap.
I attached a figure about the donor/acceptor site counts of the above mentioned 4 molecules.
Keto group has 2 acceptor sites and the "O-" anion also has 2 acceptor sites.
I considered the "lone pair electron of nitrogen" as acceptor site, as well.
Thanks for your reply Jozsi – makes sense now!
Just mail me if you'd be interested in more symmetric compounds for debugging. I've got a complete list of compounds having a four times higher HBD-count than I would expect, probably because of their symmetry.
Please attach a couple of symmetric structures which were badly handled by the 'HBDA' calculator.
Thank you in advance!
I attached some badly calculated compounds. I deliberately omitted more symmetric compounds and added some badly calculated non-symmetric compounds instead. (Please note: not all of the stereobonds depicted are correct).
If you're looking for more: here's a list of potentially(!) badly calculated compounds:
Thank you for the information.
I fixed the bug that is related with the bad HBDA prediction.
Fixed version will appear in 5.3