OpenBabel [1] offers several functions including file format conversion, generation of 3D structures from smiles, and so on. In this article, we are going to generate multiple conformers of a ligand using OpenBabel.

We will use the command-line tool of OpenBabel.

Let’s say, we have an sdf file of a ligand and we want to generate 50 conformers in the same format. Then we will use the following command:

$ obabel -i sdf input.sdf -O conformers.sdf --conformer --nconf 50 --score rmsd --writeconformers

Generating low-energy conformers

If you want to get low-energy conformers for the ligand (input.sdf), then you can use the confab argument. For this, the input file must contain one or more 3D structures. Let’s generate 50 low-energy conformers using the confab argument.

$ obabel input.sdf -O conformers.sdf --confab --conf 50

You can also generate a confab report using the confabreport argument. This argument can also compare the conformers to the reference input structure as shown below:

$ obabel conformers.sdf -oconfabreport -xf input.sdf -xr 1.0

Here, -xr defines the RMSD value within which the conformers are to be compared to the reference (input) structure.

You can generate thousands of conformers depending upon your requirement.

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References

1. O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of cheminformatics, 3(1), 33.