But that's not how the systems work?? The programmes come up with a whole bunch of different molecules based on the input. The programme isn't broken, the method is, and it won't be good until the issues with it are fixed.

Also, there really is no reason why it can't be the same team doing both these things, they're not isolated groups of people (and if they are, then there's a high chance they're not doing good science)

They haven't done anything to address any of those issues. Making another AI or virtual 'hit' tool for pharmacologically active molecule fragments is literally not what is needed due to the aforementioned issues. It's well known in the field that this is not an effective approach.

But like I said, they've done this before and it didn't work then. They've done nothing to address those previous issues.

They've literally tried this before and it's not that simple. First of all synthesizing the molecules aren't always simple, and then you have to get them into the cells and make sure they stay intact in the cells. Then even if you do, they don't always have the predicted effect.