It is called unfulffiled conditional.
If he had come here yesterday at 5PM, , he might have seen his sister.
Context is more important to explain any sentence.
Suppose His sister was waiting for her brother at the Railway station.The train started exactly at 5 PM.He camea after 5M.So He did not see his sister.
The sentence implies that he came after 5 PM yesterday.
atimplies specific time so it does not mean that he came before 5 PM.
If we use the preposition
it implies that he came before 5 PM.
So I think that the preposition
by is preferrable in the context
Here the condition of his coming yesterday at 5Pm was not fulfilled.
so his chances of seeing his sister did not happen.
In other words, the sentence means
he did not come yesterday at 5 PM so he did not see his sister.
The past perfect form in the if clause tells that the incident did
not happen if it is positive.
Look at the sentence given below:
If he had not helped me, I would have been in trouble
Since the if clause is negative, it means that the incident happened.
So the above sentence means:
He had helped me so I was out of trouble.