Stereogram of a typical initial quantum region for carbinolamine formation mediated by an active site water.

<p>The large purple “atoms” are the link hydrogens, proxies for the classical mechanics sites covalently bonded to the quantum region. The atomic coordinates for this figure were taken directly from one of the Protein Data Bank (PDB) files for the quantum atoms written at the beginning of each QM/MM run. Molecular graphics in this and other similar figures were prepared with MOLSCRIPT <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031377#pone.0031377-Kraulis1" target="_blank">[37]</a> and Raster3D <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031377#pone.0031377-Merritt1" target="_blank">[38]</a>.