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Even at 500Da or less, it's much, much larger than that.

You may be interested in the work of Jean-Louis Reymond's group, who have done more or less exactly what you suggest: https://gdb.unibe.ch/downloads/

GDB-11, with 11 heavy atoms, has 26.4M structures (110.9M stereoisomers -- molecules aren't 2D). Going up to 13 gives you 970M molecules. Going up to 17 (still mostly below 250Da) is 166,400M.

There's a lot of space up there below 500Da.

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Also note that that only includes organic molecules. There's another 85-ish natural elements in the periodic table that could be important, but is much harder to synthesize or compute.

Although including heavier elements can blow past 500 Da pretty easily.

The heavier elements start acting more like continuous systems and less like quanta legos, as you get more and more states per eV. Transition metals and lanthanides don't get their own combinatoric explosion until literal sticks are stuck on the smooth balls in coordination chemistry.

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