Eli5 why is that an atom is 99,6 % empty space ?

Question

Eli5 why is that an atom is 99,6 % empty space ?

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Answer 1

Makes it awfully sound like the whole universe is a single atom in another universe which is also an atom in another universe and so on. Maybe that empty space isn’t so empty, maybe the matter that makes up that empty space isn’t visible to our eyes.