Improve various docs things

Input submission checklist

[ ] created a directory for each system based on the template directory
[ ] 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
[ ] added a PDB file with the protein named protein.pdb
[ ] removed any cofactors from the PDB file and placed them in cofactors.sdf
[ ] kept cystallographic waters and metals in the PDB file
[ ] tested the PDB and, if available, cofactors.sdf file using the input validation script
[ ] 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

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