S4. Quantum-mechanical calculations
We have developed methods to obtain accurate structures of active sites of proteins by a combination of experimental and quantum-mechanical (QM) methods. It was first developed using experimental raw-data (structure factors) from X-ray crystallography .
Later, it was extended to use experimental data also from NMR or EXAFS measurements [2,3] and we currently work with a similar method for neutron-diffraction data. In essence, we replace the molecular mechanics (MM) potential employed in these methods to supplement the experimental data with more accurate QM calculations for a small but interesting part of the protein.
Thereby, we can actually improve structures obtained with standard methods .
Moreover, we can interpret the structures , deducing the oxidation state of the metal or the protonation state of protein ligands [6,7], or to detect photoreduction or disorder in the experimental data [8,9].
This information is often essential for the theoretical modelling of the protein.