Prepared input files for t4l and mcl1

[vgapsys]

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

Summary of changes

Capped C-term in t4l and mcl1 Consistently renumbered protein atoms

Licensing agreement

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

[hannahbaumann]

Thank you @vgapsys for your PR! This generally looks great, I just noticed that only the C-termini are capped, while the N-termini are uncapped and charged. Was it better to leave those uncapped? Or would it be possible to add a cap there as well to be consistent within the benchmark set?

[vgapsys]

This is based on the instructions: https://industrybenchmarks2024.readthedocs.io/en/latest/public/input_preparation.html#capping-proteins

[hannahbaumann]

@vgapsys you're right! I just added a suggestion for a brief bullet point in the preparation instruction as a future reference, please let me know if you agree and we can merge this PR! Thank you!

[vgapsys]

I am fine with the change, but I do not know whether the current termini are the actual beginning of the construct (actually, which construct are we thinking of: x-ray structure or the one in the affinity assay?). I left the N-terms uncapped to keep the setup consistent with the initial structures provided by Schrodinger

[hannahbaumann]

Thanks @vgapsys , I changed the suggestion!