Analyze ligand geometries using the Cambridge Structural Database (CSD)

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 interface 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

You can save a copy in your home directory so that you are not prompted for the location every time you use the CSD.

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.