Here is an example of how animated xyz files can be used to display the movement of atoms in a real chemical reaction. In this case it's the hydroxylation reaction of the enzyme p-hydroxybenzoate-3-hydroxylase (PHBH). This has been calculated using a QM/MM approach, which uses quantum mechanical (AM1) treatment of the small group of reacting atoms but molecular mechanical treatment of other atoms [Ref L. Ridder et al]. The calculation yields the x,y,z coordinates for the atoms undergoing the reaction, taken in small time steps along the reaction coordinate. These sets of coordinates are then combined together into a single xyz file which is then animated in Chime. It can be seen as the animation runs that the hydroxyl group is transferred from the flavin cofactor to the substrate, and that nearby tyrosine, proline and water groups interact with the transition state and so also play a role in the mechanism.
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