Let's say you want to simulate three carbon atoms with near perfect accuracy (not considering constituent quarks, radiative effects, or relativistic effects). We'll remove the BO approximation though. So that's 2^(3 atoms * 3 coordinates * 3*12 particles) = 2^324. That's more than the number of particles in the universe. A classical computer that can handle that is simply not gonna happen. And that's just three atoms.
My naive implementation ended up being something like O(n!) in the number of lines, due to combinations/permutations. That's because I created a 3D representation as large as the dimensions of the graph that was drawn, and tried arranging the blocks in every possible combination and seeing which one matched the hand drawn lines when projected to 2D.
If each cube in that 3D space represents a bit, then even a 4x4x4 space has 2^64 (18 quintillion) possibilities. So you could draw a few overlapping blocks, but add one more and the iPhone would freeze for several minutes. Add a few more and it wouldn't finish on a human timescale!
I ended up getting around it with a hill climbing algorithm that tried toggling blocks and keeping the result that most closely matched the projection, with a certain amount of fanout up to N entries. It was basically a primitive genetic algorithm. It actually worked great even on relatively large graphs, because humans tend to draw them as a sheet where all of the blocks are next to one another on a diagonal.
It's not perfect and really falls down if a line's out of place (think M.C. Escher) but it's worth playing around with. The client is a teacher, so if you purchase the app, the money will go to a good cause.
Simulating classical systems results in slow downs that are only polynomially with respect to system size while quantum systems slow exponentially. Consider that a quantum system of n qubits would require a classical system able to cope with 2^n bits. But you might be right since there is a (remote) possibility that classical systems can efficiently simulate quantum systems. However, it is generally believed that quantum computers are more powerful than classical but not strong enough to solve NP-complete problems.