Compare torsion drive results between C and O linker of specific structure #qcportal #souyakuAC2021

I wrote a Japanese post about PAM/NAM about mGlu family yesterday. As I mentioned that, small difference of molecules makes big difference of these conformations. I tried to check it with ETKDGv2 method which is implemented in RDKit. The approach is based on Molecular Mechanics(MM) so I would like to check it not only but also QM.

Fortunately we can use really useful open source data set named QCArchive ;)

If reader has interest the activity, I recommend to check following URL.

In this post, I would like to show an example to use the data source. At first, qcportal installation is required but it’s really easy. You can install it via conda, just type ‘conda( ormamba) install -c conda-forge qcportal’.

After the installation, we can use the data base. So let’s use it. QCPortal provides lots of data source and I used torsion drive data set which is provided from Roche in this post. There is no same structures which were described in yesterday. So I searched DB again and found Ph-CH2-Ph and Ph-O-Ph from different data source.

And I found that both molecule energy profile is similar. So following results it’s difficult to describe big difference of mGlu profile of my previous post.

Thinking molecules from 3D structure is very important task for molecular design. We can use molecular model and lots of CADD tools conveniently recently. So let’s view 3D molecules rather than 2D ;)

QCArchive provides lots of data so I recommend to use it for chemoinformatics tasks. And I would like to thank the useful tools developer !

I uploaded my code on gist. And all figures will render in following link

Some plots aren’t rendered in following site (gist).

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view raw qc_portal.ipynb hosted with ❤ by GitHub

May this Christmas bring more happy memories and joy to you and your family.


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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