also a molecule doesnt just have a single set of 3d coordinates. You have conformers, solvent effects that affect their conformation as well... Often in a biological system it can be a minor conformer shape that is the strongly binding one (case of taxol). If you want to compute physical properties such as NMR, VCD, ECD you need to optimize your molecules in a completely different way (quantum mechanic calculations of electron shells) than just with a simple mechanical modelling approach to just do docking... we are talking about a 1s calculation per molecule vs a 24h or more for a mid-sized molecule.