This work gives a detailed analysis of a protein-ligand system. In this case, it is about an EUA drug, Paxlovid (Nirmatrelvir and Ritonavir) for treating early infection from SARS-Cov-2. The method can be used with any complex and is informative. Results from this type of analysis can be used to improve, via molecular modification, the binding of molecules, pharmacological properties, and also the identification of relevant conformations and their populations in different environments. Additionally, if a molecule is projected to be a covalent binder, then this type of analysis can be used together with the non-covalent analysis to modify it ahead of and including covalent binding to a better pharmaceutical.