Wolfram Language

Generating Atomic Coordinates

The Wolfram Language is able to generate 3D structures for molecules based only on the chemical graph. This example shows how to generate 100 random conformations for adenosine and find the lowest-energy structure.

Generate a list of 100 molecules with different randomly generated coordinates.

Visualize the molecules as closely packed together as possible.

Find the force-field energy for the different conformations.

Now optimize the energy conformations using the MMFF force field. Note that the energy spread is smaller and the overall energies have decreased.

Use TakeSmallestBy to find the molecule with the lowest-energy conformation.

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