Since it's about an atom's day, the main character is the atom. But there could also be other atoms or molecules that it interacts with as secondary characters. For instance, if the atom is a carbon atom, it might interact with oxygen atoms during a combustion reaction, and those oxygen atoms could be considered important secondary characters in the story.
The atom is the central character. However, depending on the context of the story, other entities could also be seen as important characters. If the story is set in a biological system, then the molecules that the atom is a part of, like proteins or DNA, could be like supporting characters. And the ions or other small particles that the atom exchanges electrons with or has electrostatic interactions with could also play significant roles in the atom's day - to - day 'life' as described in the story.