Make protein-ligand example charge-neutral

[mattwthompson]

Description

Resolves #1136

Checklist

• Make final system in protein-ligand example charge-neutral
• Add tests
• Lint
• Update docstrings

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.38%. Comparing base (07c8611) to head (763366a).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1175   +/-   ##
=======================================
  Coverage   93.38%   93.38%           
=======================================
  Files          70       70           
  Lines        6036     6036           
=======================================
  Hits         5637     5637           
  Misses        399      399           

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