Add prepared systems by JB

All pass the validation script

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:

[ ] 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] 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

For IRAK4, the charged ligands were kept and the neutral ligands discarded.

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