Step 3: Analysis of QM-calculation Results
After the calculation process has finished and the result files generated for MFCC, each result file is analyzed by GridMol automatically to examine and assemble the results to obtain the assembled system’s properties (e.g., energy). The total energy is approximated using Eq. (1):
\(E=\sum_{i}^{N}{(E_{fragi-lig}}-E_{\text{fragi}}-E_{\text{lig}})-\sum_{i=1}^{N-1}{(E_{capi-lig}}-E_{\text{capi}}-E_{\text{lig}})\)(1)
where E is the interaction energy between large molecules (e.g., a protein and a ligand), Efragi-lig, Efragi, and Elig are the energy of fragment−ligand molecules and fragments and ligands, respectively, and Ecapi-lig, Ecapi, and Elig represent the contributions of caps and ligands.
For FMO, the total energy of the system can be written as eq. (2)
\(E=\sum_{i=1}^{N}E_{i}+\sum_{i>j}^{N}{(E_{\text{ij}}}-E_{i}-E_{j})+\sum_{i>j>k}^{N}{\{(E_{\text{ijk}}}-E_{i}-E_{j}-E_{k})-(E_{\text{ij}}-E_{i}-E_{j})-(E_{\text{jk}}-E_{j}-E_{k})-(E_{\text{ki}}-E_{k}-E_{i})\}+\ldots\)(2)
where Ei, Eij, Eijkrepresent monomer, dimer, and trimer energies, which can be obtained from GAMESS output file for FMO2 and FMO3 calculations.