| B3LYP | Becke-Lee-Yang-Parr |
| CC-Hept | Coiled Coil-Heptamer |
| CC-Hept-Cys-His-Glu | Coiled Coil-Heptamer-Cysteine-Histidine-Glutamate |
| CpHMD | Constant pH Molecular Dynamics |
| DFT | Density Functional Theory |
| FES | Free Energy Surfaces |
| GAFF | General Amber Force Field |
| MD | Molecular Dynamics |
| ONIOM | Our own N-layered Integrated MO and MM |
| pNPA | Para-NitroPhenylAcetate |
| QMMM | Quantum Mechanics/Molecular Mechanics |
| RESP | Restrained ElectroStatic Potential |
| RMSD | Root Mean Square Deviation |
| ZPE | Zero Point Energy |
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