Data Set "Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions"

<p>This data set accompanies the publication "Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions" by Johannes Vornweg and Christoph R. Jacob (TU Braunschweig, Germany)&nbsp;</p> <p>It contains the following files:</p> <p><br>Directory 1_structures:</p> <p>&nbsp; &nbsp; PDB files of all structures used for the test calculations.&nbsp;<br>&nbsp; &nbsp; The PDB files correspond to the protonated structures obtained&nbsp;<br>&nbsp; &nbsp; as described in the main text.</p> <p><br>Directory 02_figure_scripts:</p> <p>&nbsp; &nbsp; Jupyter Notebook for generating all plots included in the manuscript,&nbsp;<br>&nbsp; &nbsp; including raw numerical data.</p> <p><br>Directory 03_input_scripts:</p> <p>&nbsp; &nbsp; - min_congrad.mdp: input file for partial optimization of protonated&nbsp;<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;protein--ligand complexes with Gromacs</p> <p>&nbsp; &nbsp; PyADF input scripts:</p> <p>&nbsp; &nbsp; - sp_single.pyadf: single-point calculations of separate protein and ligand<br>&nbsp; &nbsp; - sp_complex.pyadf: single-point calculation of protein-ligand complex<br>&nbsp; &nbsp; - mfccmbe3.pyadf: MFCC and MFCC-MBE(2) calculations of P-L interaction energy</p> <p>&nbsp; &nbsp; These scripts can be used with PyADF v1.5 (DOI: 10.5281/zenodo.13236550)</p>