Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein-Ligand Interaction Research

We report for the first time the use of experimental electron density (ED) in the Protein Data Bank for modeling of noncovalent interactions (NCIs) for protein-ligand complexes. Our methodology is based on reduced electron density gradient (RDG) theory describing intermolecular NCIs 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 similar to 200,000 NCIs from over 12,000 protein-ligand complexes. We also demonstrated the usage of the database in the case of depicting amide-pi interactions in protein-ligand binding systems. In summary, the database provides details on experimentally observed NCIs for protein-ligand complexes and can support future studies including studies on rarely documented NCIs and the development of artificial intelligence models for protein-ligand binding prediction.