Observance of the commandments of a Jew who does not believe in God and the commandments

peace.

I saw in the Rabbi’s class in the Halacha and Reality series that one can come to him with the argument that a Jew who does not believe in why he is desecrating Shabbat because halachic facts can obligate a Jew who does not believe. The Rabbi said in another class that someone who does not believe in God and the commandments, even if he performs a mitzvah – he should put on tefillin, joining the minyan is not considered to have fulfilled it. So if from the point of view of the mitzvah he cannot fulfill it, because he does not believe in it, how can one come to him with the demand that he fulfill certain mitzvahs (not to desecrate Shabbat).
thanks