The main protease will also be too large for your software since it's a few hundred times the size of the molecule you've drawn. The structure you've posted does however look like it might be an inhibitor for a protease. i.e it's a small molecule you stuff into one of the much larger bits of protein machinery that the virus uses to function, and hope it jams it up. Researchers throw thousands of different inhibitors like this at viral proteins to quite literally see what sticks. It is not part of the virus - it is one of a vast number of possible molecules people are using to try and use as a drug to treat it. You are fundamentally misunderstanding this if you think this is the thing that is mutating. This paper has the structure of the main protease of Covid in figure 2, and a close up of the working site they're trying to block in figure 3. https://science.sciencemag.org/content/368/6489/409 Hmm - the structures in Figure 1 of some of their potential inhibitors bear some resemblance to what you drew, although they're not identical. Is this where you got this from?