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Hydrogen Bonding Interactions of Covalently Bonded Fluorine Atoms:  From Crystallographic Data to a New Angular Function in the GRID Force Field

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journal contribution
posted on 07.10.2004, 00:00 authored by Emanuele Carosati, Simone Sciabola, Gabriele Cruciani
Through the years the GRID force field has been tuned to fit experimental observations in crystal structures. This paper describes the determination of the hydrogen bonding pattern for organic fluorines based on an exhaustive inspection of the Protein Data Bank. All the PDB complexes, whose protein structures have cocrystallized fluorine-containing ligands, were examined and geometrically inspected. By applying statistics, the hydrogen bonding geometry was described as a distribution function of the angle at the fluorine:  a new specific angular function was consequently defined and inserted in the program GRID to estimate the effect of fluorine hydrogen bonds on the ligand−protein binding. All the fluorine-containing ligands collected from the PDB were docked within their corresponding protein binding sites:  introducing the fluorine hydrogen bonding contribution improves the results of the docking experiments in terms of accuracy and ranking.