Quantum mechanical calculations are now sufficiently advanced that they can be used in a practical way to answer certain structural questions in biology. These calculations are particularly valuable for the positioning of protons, and the orientation of water. Water can be found in X-ray structures as a blob of electron density, but the length and strength of hydrogen bonds is not known, and the orientation of the hydrogens can at best be inferred from neighboring groups. However, these uncertain properties can be critical in understanding the behavior of a protein. Cooperative effects in hydrogen bonding are important; hydrogen bonds are modified as to length and strength by neighboring hydrogen bonds. We have found this effect to be equivalent to more than ± 2 k_BT, compared to the TIP3P potential, at room temperature. This has implications for the accuracy of molecular dynamics simulations of water in protein clefts, where the hydration cannot be assumed to be ergodic on the time scale of the simulation. Water wires are similarly not easily found in X-ray or NMR structures, but can be seen in quantum calculations. Water can also play a role in certain complexes, such as those between phosphate and arginine, as well as in modifying salt bridges in proteins. Examples of the use of QM calculations to understand structure, including water wires near a peptide, and the gating of an ion channel, will be discussed. Possible future extensions, to allow other functional calculations, including pK values, will also be briefly considered.