Analyze ligand geometries using the Cambridge Structural Database (CSD)

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Written by Chase Webb 20190521

The generation of torsion angle distributions to determine conformational preference about single rotatable bonds is one of the most common uses of the CSD. This tutorial illustrates how Mogul, part of the CSD software can be used to rapidly determine the torsion angle preferences of substituted oxamides by inspecting occurrences of this motif in the CSD.

Source the current environment for CSD-2019 

source /nfs/soft/csd/csd-2019/env.csh

Open mogul it by running the following command: 

 /nfs/soft/csd/csd-2019/CSD_2019/bin/mogul

If prompted for the license, it lives here: 

/nfs/soft/csd/csd-2019/CSD_2019/csd_licence.dat

In the CCDC Mogul 1.8.1 interface, import smiles by clicking load, or draw the motif you are interested in assessing by clicking on the Draw button to bring up a drawing window.

Hit search to submit the query and you should find see a histogram of the reported torsion angles for your query.

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