The questions become: From where did this primal atom come and in what type of existence was the primal atom nestled?
It is only panentheism which has rational answers to these two questions, namely: The primal atom was created by its creator or in short, the primal atom was generated by the Creator of the physical universe.
As to what it was the primal atom was nestled before it exploded: The primal atom was nestled within its creator.