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Ensemble refinement of six protein–ligand crystal structures indicates a much larger flexibility of some amino-acid side chains and ligand groups than is suggested by standard crystallographic refinement. Molecular-dynamics simulations and automatic generation of alternative conformations confirm the high flexibility of these groups, indicating that ensemble refinement can be used to identify such flexible groups., Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein–ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein–ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and R free values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.

No interconversion has been found to occur on the NMR time scale between the structural arrangements found in the solid state. The σ, π motion of the vinyl group does not cause a cis-trans interconversion of the terminal hydrogens in [HOs3(CO)10(CHCH2)] which simply takes place by alternating the π-electron cloud to opposite osmium centres. The 1H chemical shift of the =C moieties is a useful probe to assess the coordination mode of the vinyl ligand. In [HOs3(CO)10(CPhC(H)Ph)], a trigonal twist process has been shown to occur at the Os(CO)4 unit. For the same unit 2Jc−c trans have been obtained for all the reported derivatives and their magnitude is almost unchanged along the series. Further Jcc information has been obtained from a sample of [HOs3(CO)10(CHCH2)] C-13 labelled in the vinyl ligand.