As Islander2 says.
When thinking about these things, I always find it easier to think about the case with the throttle partly closed. That way, there is some real "sucking" going on. The engine is trying to suck air in from the inlet manifold, and the throttle, being partly closed, prevents the air from being completely replaced, hence a manifold pressure which is lower than atmospheric pressure.
The slower the engine turns, the less it sucks air out of the manifold, therefore the higher (and closer to atmospheric pressure) the manifold pressure. As an extreme, when you stop the engine the manifold pressure goes right up to atmospheric pressure.
(The same is, of course, true with the throttle open, but I find it harder to visualise with the throttle open.)
FFF
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