Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method

The fragment molecular orbital (FMO) method enables quantum mechanical calculations for macromolecules by dividing the target into fragments. However, most calculations, even for metalloproteins, have been performed by removing metal ions from the structures registered in the Protein Data Bank (PDB)...

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Veröffentlicht in:	Chem-Bio Informatics Journal 2023/07/20, Vol.23, pp.14-25
Hauptverfasser:	Kato, Koichiro, Yamamoto, Ami, Watanabe, Chiduru, Fukuzawa, Kaori
Format:	Artikel
Sprache:	eng
Schlagworte:	Atomic charge FMO calculation Fragmentation Mg2+ ions Model Core Potential PIEDA Zn2+ ions
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description	The fragment molecular orbital (FMO) method enables quantum mechanical calculations for macromolecules by dividing the target into fragments. However, most calculations, even for metalloproteins, have been performed by removing metal ions from the structures registered in the Protein Data Bank (PDB). For more realistic and useful calculations, FMO calculations must be performed without removing the metal ions. In this study, we discuss the results obtained from FMO calculations performed using 6-31G* and model core potentials (MCPs) for metal proteins containing Zn and Mg ions. Subsequently, we analyze the differences in atomic charges and interactions.
doi_str_mv	10.1273/cbij.23.14
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subjects	Atomic charge FMO calculation Fragmentation Mg2+ ions Model Core Potential PIEDA Zn2+ ions
title	Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method
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