## Description

This dataset contains additional material related to the fitting for the article: "Cost-effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments" (preprint is available at [https://doi.org/10.26434/chemrxiv.8126912](https://doi.org/10.26434/chemrxiv.8126912)). It contains the final fitted atom-centered point charges and atom-centered isotropic dipole--dipole polarizabilities of all the standard amino acids including alternate protonation states and different N- and C-terminals, and the structures and electric potentials used in the parameter fitting. See [preprint](https://doi.org/10.26434/chemrxiv.8126912) regarding details of the fitting procedure and how the structures and electric potentials were produced.

## Files

This dataset contains the following files:
 - readme.txt
 - CP3.csv
 - fitting_data.zip

The *CP3.csv* file contains the final atom-centered point charges and atom-centered isotropic dipole--dipole
polarizabilities (both in au) of the standard amino-acid residues including alternate protonation states. Included
are also parameters for terminal residues where the N-terminal is charged, neutral, or terminated with an acetyl
group, and the C-terminal is either charged, neutral, or terminated with an N-methyl group. In each case, the residue
names are appended as follow (XXX is the residue name):
 - NXXX -- charged N-terminal
 - CXXX -- charged C-terminal
 - nXXX -- neutral N-terminal
 - cXXX -- neutral C-terminal
 - AXXX -- N-terminal is capped with an acetyl group
 - BXXX -- C-terminal is capped with an N-methyl group
Note that the file contains duplicates corresponding to some alternate residue and atom names that are used in
different programs. The file contains the following columns:
 - RESNAME -- residue name
 - ATOMTYPE -- atom type
 - q -- point charge
 - axx -- xx-component of polarizability
 - axy -- xy-component of polarizability
 - axz -- xz-component of polarizability
 - ayy -- yy-component of polarizability
 - ayz -- yz-component of polarizability
 - azz -- zz-component of polarizability
Since the polarizabilities are isotropic the xx-, yy-, and zz-components are equal and the others are zero.

The *fitting_data.zip* file contains directories named *AAA_XXX_BBB* where *AAA* and *BBB* are the N- and C-terminal
capping groups and *XXX* is the central amino-acid residue (see below for an explanation of the terminology used for
capping groups and residues). The directories contain files containing structures and electric potentials that were
used in the fitting procedure (see preprint for details). The structures are provided in XYZ format (file extension
*.xyz*) and the electric potentials in HDF5 format (where the file extension is *.h5*). The latter files are also
prepended with *EP_*. The files are numbered according to highest occurrence, starting from 1 as the most occurring.
The HDF5 files contain five fields:
 - "atom_coordinates" -- atom coordinates in au
 - "atom_numbers" -- atomic numbers (in the same order as the atom coordinates)
 - "atom_symbols" -- element symbols (in the same order as the atom coordinates)
 - "electric_potential" -- electric potential in au on a set of grid points
 - "grid_coordinates" -- coordinates in au of the grid points (in the same order as the electric potential)


## Terminology

AAA_XXX_BBB -- AAA an BBB are the N- and C-terminal capping groups and XXX is the central amino-acid residue

### Capping groups

Capping-group charges that are different from zero are indicated in square brackets.

ACE -- acetyl
NH2 -- amine
NH3 -- protonated amine [+1]
NME -- N-methyl
COOH -- carboxyl
COO -- carboxylate [-1]

### Amino-acid residues

Residue charges that are different from zero are indicated in square brackets.

ALA -- alanine
ARG -- arginine
ASP -- aspartate [-1]
ASH -- aspartic acid
ASN -- asparagine
CYS -- cysteine
CYD -- deprotonated cysteine [-1]
CYX -- disulfide-bonded cysteine (has an additional thiomethyl (SCH3) capping group)
GLU -- glutamate
GLH -- glutamic acid [-1]
GLN -- glutamine
GLY -- glycine
HIS -- protonated histidine [+1]
HID -- delta-protonated histidine
HIE -- epsilon-protonated histidine
ILE -- isoleucine
LEU -- leucine
LYS -- protonated lysine [+1]
LYD -- lysine
MET -- methionine
PHE -- phenylalanine
PRO -- proline
SER -- serine
THR -- threonine
TRP -- tryptophan
TYR -- tyrosine
VAL -- valine