Preparation for SHP2 and MCL1 Protein and Ligand Sets

Protein and Ligand Prep for OpenFE Industry Benchmark for SHP2 and MCL1 sets.

Input submission checklist

[X ] created a directory for each system based on the template directory
[X] named and placed the directory with the following pattern: input_structures/prepared_structures/<set_name>/<system_name>

For each submitted directory:

[X] filled in system preparation details in the PREPARATION_DETAILS.md file
[X] added a PDB file with the protein named protein.pdb
[x] removed any cofactors from the PDB file and placed them in cofactors.sdf
[X] did not re-protonate the residues, but left protonation state of the protein unchanged
[X] kept cystallographic waters and metals in the PDB file
[X] tested the PDB and, if available, cofactors.sdf file using the input validation script
[X] copied over the ligands SDF file to a file named ligands.sdf and removed any duplicate binding modes or protonation states, keeping the more favorable state

Added protein and ligand files to SHP2 and MCL1 directories.

[ ] I agree to release these inputs under the combined MIT and CCBY SA 4.0 licenses of this repository