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The above image is a cross-eye stereo pair showing the hydrogen-bond interactions of nicotinamide adenine dinucleotide in complex with mannitol dehydrogenase (PDB entry 1lj8). The ligand is depicted in gold, with nearby interacting protein side chains and backbone in translucent purple and water in dark blue. Chimera's FindHBond extension was used to determine the hydrogen bonds, using angle and distance criteria specific to each atom type. Atom types, in turn, were determined by heavy-atom element types and bond distances and angles. This allows characterization of ligands without other a priori knowledge.
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