There was no atom - the universe was much, much smaller than a hydrogen atom at the moment of the Big Bang. The first atom didn't exist for several hundred thousand years after the Big Bang.
The big impediment to most people's understanding is this idea of "before" and "outside" the Big Bang. Space and time only came into existence with the Big Bang, so it's pointless to ask when and where the Big Bang occurred, or what happened "before" it.
As moondoong said, the laws of physics can be traced backwards almost to the very moment of the Big Bang, but just before we get there, the laws break down because they cannot handle such small distances and times (the so-called Planck Epoch). At that point, time and space start to lose meaning anyway so whatever happened between the Big Bang and the moment the laws of physics start to work is a pointless question.
Plenty of room in there for God, if you choose to invoke God as the cause of the Big Bang. Physics can't say what caused the Big Bang, at least until we have developed a theory of quantum gravity.
