It’s not clear what result (answer set) you expected.

From a syntax point of view, your second approach looks more “correct” if that makes sense:

It assigns for each protein/1 a choice/4 with 3x food/1.

But it does not define any specific relationship among those 3x food/1, e.g. these 3x food/1 can be the same, and can be the same across different proteins, as there are no further rules defined.

(Your first approach allows an empty answer set as result. While you assign a choice/4 for any combination of protein/1 and 3x food/1.)

I recommend you to check previous stackoverflow posts on Clingo as well as some introductional pdfs on that topic to better understand to the syntax and “logic”.

Good luck!