Abstract
The Protein Data Bank (PDB) contains a massive amount of experimental electron density (ED) data. Such data are traditionally used to determine atomic coordinates. We report for the first time the use of experimental ED in the PDB for modeling of noncovalent interactions (NCIs) for protein–ligand complexes. Our methodology is based on the reduced electron density gradient (RDG) theory describing intermolecular NCI by ED and its first derivative. We established a database named Experimental NCI Database (ExptNCI; http://ncidatabase.stonewise.cn/#/nci) containing ED saddle points, indicating ∼200,000 NCIs from over 12,000 protein–ligand complexes. The value of such data is demonstrated in a usage case of understanding amide–π interaction geometry in protein-ligand binding system by using the database to facilitate quantum mechanics-based potential energy landscape scan. In summary, the database provides details on experimentally observed NCIs for protein-ligand complexes, and can support future studies on rarely documented NCIs. The potential of fueling artificial intelligence algorithm development by using the database is also discussed.
Competing Interest Statement
The authors have declared no competing interest.