The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

TL;DR

This paper extends the EFMO method to treat covalently bonded fragments, achieving comparable accuracy to FMO and ab initio methods but with significantly improved computational efficiency for polypeptides and proteins.

Contribution

The authors develop and validate an extended EFMO method capable of handling covalently bonded fragments, providing accurate and faster electronic structure calculations.

Findings

Errors within 2 kcal/mol for RHF and MP2 energies

EFMO is 2-5 times faster than FMO

Optimized structures have RMSD around 0.4 Å

Abstract

We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 {\AA} for RHF and MP2, respectively.