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

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 Å for RHF and MP2, respectively.

本研究将有效碎片分子轨道法（effective fragment molecular orbital method，EFMO）拓展至处理含共价键连接的碎片体系。针对包含蛋白质在内的多肽体系，本研究将EFMO的计算精度与FMO及传统从头算电子结构方法进行了对比。对于中性多肽，RHF与MP2方法的能量误差均在2 kcal/mol以内；对于带电多肽，该误差则处于6 kcal/mol以内，精度与FMO相当，但计算速度提升2至5倍。对于蛋白质体系，其能量误差同样与FMO的计算结果相差仅数千卡每摩尔。本研究还开发了适配EFMO的RHF与MP2梯度算法。与从头算方法相比，经EFMO优化得到的结构，其均方根偏差（Root Mean Square Deviation，RMSD）在RHF与MP2水平下分别为0.40和0.44 Å。