To reproduce this, download a shared solution including bonus and submit it to the library. This one wont get the bonus, which makes it impossible to evolve it.
It's also visible on starting ligand (I don't know if this one is valid).
There is a way to get the bonus.
Work on a new computer (where you never loaded this compound).
Save the compound.
Add an atom anywhere on the compound before to submit it to the server.
Download the right compound again: If the library returned it, you'll get the bonus.
This is definitely a frustrating bug. Getting an exact match should give the bonus straight away.
It would appear that you have to submit the pose with the added/changed atom first, before ever submitting the target pose, or you still don't get the bonus. Sigh.
@"Bruno Kestemont" – I'm not seeing the behavior. I downloaded your Shared with Scientists solution labeled 111a (Score 20030) and loaded it on my local client. When first loaded, it does not get the compound bonus (this is expected, as the compound library bonus is based on the results you have downloaded to your local client).
I have to submit the compound to the compound library search, and that gives back results that have both a "Entry Query: Exact Match" and a "Entry 1a:Exact Match" – The former is always expected, and simply means that the current molecule is the same molecule you submitted to the compound library search. It does not mean that you should get a library bonus. The latter (being a numbered result) means that the current ligand is found in the search results, and thus means you should get the compound library bonus for that ligand.
HOWEVER, due to internal technical details, the objectives are only recalculated when the structure changes. This means that just getting back the search result isn't enough to change the score of the downloaded solution. You'll need to make some small change to the solution (e.g. shake/wiggle/pull of a sidechain/etc.) in order for the objective values to be recalcuated. When I do that with your solution, I do see that I get the compound library bonus, as expected.
Thanks for the tip. It happens that I don't get the Entry 1a:Exact Match, but I have to verify again if the structure was really correct (it's possible that small changes don't return an equal library compound if it doesn't fit). There are some other strange returns but I've to investigate it further, better learn to use the tool.