In Injustice, Supes womps him in round one, then Captain Atom comes back and has a slight edge in round two. Supes seems to be holding back, having something of an emotional break.
Pre-52 Supes and Captain Atom fought a couple of time iirc, and Supes won pretty much every encounter. Although, Pre-52, Captain Atom does become Monarch who is a universal being.
New 52, last I saw Captain Atom, he probably would lose to current New 52 Supes. However, Captain Atom did see his future self, which was like an omnipotent being.
Honestly, I think Captain Atom and Martian Manhunter should be DC's most powerful characters. Supes should be able to hang with either for a bit, but those guys have so many abilities.
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