But on the other side there are other directions in which a small push can put the nuclei under the influences of forces that move it further in that direction. The effective mass will be low in those directions. Let us step back even a bit further and look at how one can think of protein recognition. The lock-key metaphor is often used. The protein is like a key that recognizes the substrate in lock-key fashion.
Many weak interactions contribute.
So if molecules are big enough to have surface properties they can recognize each other, provided that at the same time they are small enough to explore each other's shapes through Brownian search. The conformational-electronic interaction described above makes this Brownian search more effective. There is a flaw in the above metaphor, connected with the idea of search. This is the docking problem. Docking requires dynamics.