QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery

Journal of Chemical Theory and Computation vol. 19  p. 1261-1275  DOI: 10.1021/acs.jctc.2c01172  Published: 2023-01-25 


Jinzhe Zeng [ ] , Yujun Tao [ ] , Timothy J. Giese [ ] , Darrin M. York [ ]

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Abstract

<p>We report QD&pi;-v1.0 for modeling the internal energy of drug molecules containing H, C, N, and O atoms. The QD&pi; model is in the form of a quantum mechanical/machine learning potential correction (QM/&Delta;-MLP) that uses a fast third-order self-consistent density-functional tight-binding (DFTB3/3OB) model that is corrected to a quantitatively high-level of accuracy through a deep-learning potential (DeepPot-SE). The model has the advantage that it is able to properly treat electrostatic interactions and handle changes in charge/protonation states. The model is trained against reference data computed at the &omega;B97X/6-31G* level (as in the ANI-1x data set) and compared to several other approximate semiempirical and machine learning potentials (ANI-1x, ANI-2x, DFTB3, MNDO/d, AM1, PM6, GFN1-xTB, and GFN2-xTB). The QD&pi; model is demonstrated to be accurate for a wide range of intra- and intermolecular interactions (despite its intended use as an internal energy model) and has shown to perform exceptionally well for relative protonation/deprotonation energies and tautomers. An example application to model reactions involved in RNA strand cleavage catalyzed by protein and nucleic acid enzymes illustrates QD&pi; has average errors less than 0.5 kcal/mol, whereas the other models compared have errors over an order of magnitude greater. Taken together, this makes QD&pi; highly attractive as a potential force field model for drug discovery.</p>