I think before anyone can make judgment on whether or not godmodding is occurring, you should list your character's weaknesses. Giving people one side of the story often leads to biased judgment.
But from what I can tell, if he has the power to manipulate atoms and molecules, then he's essentially manipulating matter, correct? Now, I pose some questions to you, and hopefully these will help determine whether or not god-modding is happening.
Can your character affect objects in motion? Are his abilities limited only to the material he has around him, or can he affect all matter? Can he affect matter generated by an adversary? Do any manipulation abilities cause bio-recoil? (As in, if he uses an electricity-based attack, is there any feedback from delivering said shock?)
Like I said, it will help people answer your question if you post your character's weaknesses.