multiple constraints

[albertma-evotec]

I try generate the linker with multiple constraints, e.g. this is my fragment pair
[L_6 0 0 1 1] * C ( = O ) N C 1 C C 1 . * C ( = O ) N C C ( C ) ( C ) C

One of the generated structures is this
CC(C)(C)CNC(=O)C1CCCN1C(=O)CCCn1cncn1

, in which it missed one of the original fragment.

I noticed that in the provided training data, there is not any pharmacophoric constraints. Do I need to generate a new set of training data and re-train the model?