<b>Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical </b><b>calculation database for large biomolecules </b>

• DOI: 10.1273/cbij.19.5
• Publication Date: 2019-03-22T20:22:48Z
• Authors: Chiduru Watanabe; Hirofumi Watanabe; Yoshio Okiyama; Daisuke Takaya; Kaori Fukuzawa; Shigenori Tanaka; Teruki Honma
• Keywords: Fragment molecular orbital

We developed an automated FMO calculation protocol (Auto-FMO protocol) to calculate huge numbers of protein and ligand complexes, such as drug discovery targets, by ab initio method. The performs not only calculations but also pre-processing input structures homology modeling missing atoms subsequent MM-based optimization, well post-processing results. In addition, QM/MM optimization complex structures, conformational searches in solvent, MM-PBSA/GBSA can be optionally carried out. this paper, for 149 X-ray estrogen receptor α p38 MAP kinase were performed at the K computer in-house PC cluster server using Auto-FMO protocol. To demonstrate usefulness protocol, we compared binding interaction energies with those manually prepared data. most cases, data calculated showed reasonable agreement Further improvement is necessary treatment ionization tautomerization structure preparation stage, because some outlier observed due these issues. provides a powerful tool deal complexes design, construction database (http://drugdesign.riken.jp/FMODB/) released 2019.