FMOE: Preprocessing and Visualizing library of Fragment Molecular Orbital Method for Molecular Operating Environment

Abstract

Fragment Molecular Orbital (FMO) method, developed by Kitaura et. al., is an approach to perform ab-initio quantum chemistry calculation for large molecule such as protein or nucleic acid by splitting covalent bonds. In addition, a more detailed analysis can be performed by Pair Interaction Energy Decomposition Analysis (PIEDA) that divides the interaction energy between fragments into its components. FMO method is implemented by GAMESS, ABINIT-MP, and PAICS. ABINIT-MP can perform fragmentation protein and nucleic acid automatically. However, manual fragmentation should be performed when calculating the system contains a large legend or performing detailed PIEDA (e.g. Analyzing interaction energy components of functional groups). The current fragmentation interface of ABINIT-MP requires selecting all atoms in fragments and it is more complicated than necessary. Thus, we developed the library for Molecular Operating Environment (MOE) to perform fragmentation the system and analyzing the FMO calculation result. It makes the entire of FMO workflow conclude in MOE.