Molecular fragmentation tool for quantum chemical torsion scan #open_force_field #RDKit

As many reader knows that quantum chemical(QC) calculations are useful and important to determine conformational distributions of small molecules. Because chemists design molecule with not only 2D information but also 3D information. However, computational cost of QC calculation is higher than molecular mechanics(MM) calculations.

Last year, Prof. John D Chodera’s group published useful approach for QC torsion scanning. The article can be freely accessible from bioRxiv!

Their approach divides molecule to piece of fragments with Wiberg Bond Order (WBO), as an indicator. And also define functional groups with SMARTS which should be kept during fragmentation steps.

Whole steps of fragmentation is shown in Fig 3.

Wiberg bond order is a measure of electron population overlap between two atoms. More details are described in the document.

The fragmentation approach results are show in Fig9-11. It seems that the approach isn’t always optimal but it works well in many cases.

Fortunately they shared the code on github! When the article was published, initial version of fragmenter supports only OpenEye toolkit as Tookit however, recent version of fragmenter supports rdkit so, you can use fragmenter without OETK it means that you can run the code on you private PC ;)

Fragmenter has function for molecular fragmentation and depict the result like below(Following image came from OE depict so I can’t render the image from my PC).

As you can see, depict function can highlight bonds of result fragments. I tried it RDKit version and worked fine however I would like to render WBO on the depiction. So I forked the code and modified some parts of the code.

New version of rdkit has lots of drawing options and it can render bond annotation if you add ‘bondNote’. Greg wrote nice blog post about rdkit drawing options.

URL of My github repo is here

I added simple molecule example notebook to show_bond_order branch.

By using the branch code, depict function can render fragment with WBO.

In summary fragmenter is useful tool for QC torsion scan and rdkit new drawing code is nice tool for visualize molecule ;)


Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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