In this paper (e.g. doi:10.1021/cs500093h and other applied QM/MM studies), it is demonstrated several transition states, intermediates, and products of given set of biomolecules (several residues, metal ions, and its substrates). What makes me it is interesting is that they depicted carefully the lose and gain of the atoms on each molecules. I have seen on some places that the showed bonds can be reproduced from some molecular docking softwares (e.g. Schrodinger Maestro, etc.) but it would be also interesting if a software could also draw the electron flow arrows (reaction mechanism) for each states. I have seen some research papers about docking studies before but they only depicted the bonds without giving any information of whether an atom had newly made or unreactive (the paper I cited clearly showed the lose of hydrogen and the bond forming on intermediate state).
How do they model the states? Is it that we have to manually draw the molecules on each states and put the protonated/deprotonated and dissociated/bonded forms combinatorically for the states and we evaluate the energy for each of these scenarios? Or the softwares could also make and break those bonds automatically and showed the energy for each of them? Which software? On the cited paper, I can not find any specific line that mentioning this and I am curious with the line on the paper, stated "the QM/MM boundaries crossed carbon-carbon bonds, and hydrogen atoms were used as “link” atoms". Is this one?