@GianmarcoLuchetti Thanks for joining

I see that the features that you use as atomic number; atomic mass; Van der Waals atomic radius; atom degree; atom degree including Hs; valence; formal charge; hybridization; aromaticity; total number of Hs; radical electrons; is in ring; atom is chiral center; chirality.

Can you please comment on the requirement for the features related to chirality, if you are interested in Hbond donor/acceptor capabilities only?

@HemanthHaridas Of course! I use two features related to chirality, number 13 which returns an output of the type 0 if the atom in question is symmetric and 1 if it is asymmetric. Number 14 on the other hand, in case it is an asymmetric carbon goes to specify whether it has a configuration of type R (1) or S (2).

Are you trying to use this in an ML model? If yes, have you checked the correlation between the output and the features that you use? Like if they are correlated, anticorrelated or not correlated?

That's right we are doing a ML project, our samples are molecules experimented on the IDO1 enzyme, the correlation with the output then comes directly from the experimental data

Ok. But my question was slightly different. I was asking about the correlation between lets say total number of Hs and the Hbond donor capacity.

Sorry I didn't understand that correctly! The chosen features are not all used for the purpose of figuring out whether an atom will be acceptor/donor, but the ultimate goal is to get the most accurate mathematical description possible for that atom. So there in between you will find features that have nothing to do with hydrogen bonds (like chirality), but that can be very important in biological activity

Ok. Thanks for the clarification.

Are you sure nitro group is not an acceptor? Because we do observe Hbonding interactions between NH and NO2 in MD simulations.

I have read in several articles that the nitro group (as well as the sulfone) can be an H-bond acceptor, but still very weak. Do you have any articles on this, I would be curious to investigate further

These two are my papers Paper 1 and Paper 2 where we observe strong Hbonding interactions between NH and CO groups. We also observed some cases of hydrogen bond NH and NH2 groups also.

Regarding Hbond interactions between NH and NO2, you can check papers about Hachimoji DNA. They have NO2 groups as part of the molecular skeleton and are pretty stable

thanks for your contribution and helpfulness, I'll get to reading the papers!

Thanks for your clarifications. I myself have not worked on Chemoinformatics (but would love to). Do you have any references for that?