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ChargeCalculator:Theoretical background

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EEM is an empirical method developed as a cost-effective alternative to quantum mechanics (QM) based methods, as it enables the determination of atomic charges that are sensitive to the molecule's topology and three-dimensional structure. EEM has been successfully applied to zeolites, small organic molecules, polypeptides and proteins.
ACC implements one classical EEM formalism, along with two additional modifications. We give a brief description of each below. Please refer to the literature [[20,32-45]] for a more in-depth description of EEM and a few examples of applications [[44(e.g.,46-50]]<ref name="Ionescu_2013"/><ref name="Svobodova_2013"/>).
While in the ''EEM Cutoff'' method ACC generates one fragment for each atom in the molecule, this further approximation generates fragments only for a subset of atoms. The algorithm by which this subset of atoms is obtained ensures that each atom in the molecule will eventualy contribute to at least one fragment. In other words, the entire volume of the molecule is covered, and the method is thus termed ''EEM Cutoff Cover''.
In ''EEM Cutoff Cover'', the subset of fragment generating atoms is obtained in such a way that:
* no two atoms in this subset are connected to each other
* each atom in the molecule has at least one neighbor (within two bonds) included in this subset.
''EEM Cutoff Cover'' has also proven robust and sufficiently accurate (RMSD less than 0.003e compared to the ''EEM Cutoff Cover'' of comparable cutoff radius), and is the method of choice for biomolecular complexes of tens of thousands of atoms and higher.
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<ref name="Ionescu_2013">Ionescu C-M, Geidl S, Svobodová Vareková R, Koca J. Rapid Calculation of Accurate Atomic Charges For Proteins via the Electronegativity Equalization Method. J. Chem. Inf. Model., 2013, 53 (10), pp 2548-2558. DOI: 10.1021/ci400448n</ref>
<ref name="Svobodova_2013">Svobodová Vareková R, Geidl S, Ionescu C-M, Skrehota O, Bouchal T, Sehnal D, Abagyan R, Koca J. Predicting pKa values from EEM atomic charges. J. Cheminf. 2013, 5, 18.</ref>

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