The molecule Nirmatrelvir is not very strongly non-covalently interacting with the relevant Mpro cavity to inhibit viral replication of SARS-Cov-2 virus, due to a score per atom of 2.0. It does have 2 important features: 1) it has separated anchor points of high interaction with the Mpro protein which attract it in an orientation to 2) covalently bind via a thionate reaction with CYS 145, generating a thioidinate adduct. Then these high interaction anchor points are maintained after binding. The energy gained in covalent binding is 7.1 kcal. Using atomic interaction distribution analysis, the highest binding conformational mode pre-covalently is shown atomically to be similar in interaction to the post-covalent binding. The hydrogen bonding across the amino acids, although maintaining 2 aminos out of the sets in contributing hydrogen bonds, is different. These features are relevant in determining stability and lifetime of the covalently bound molecule, Nirmatrelvir. In addition, it is noticed that there are interesting points in the molecule in possible alteration of the overall non-covalent binding and possible pharmacological properties.