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Figure 1 | Journal of Cheminformatics

Figure 1

From: Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes

Figure 1

Three examples for VMRs with alternative hydrogen positions and free electron pairs. Primary alcohols (A) are considered as rotatable and the associated hydrogen atom can occupy any position on the orbit around the oxygen atom. Three exemplary orientations are shown. Cyclic secondary amines (B) can either be protonated and positively charged or neutral. In the latter case the hydrogen atom can occupy two distinct positions. The imidazole ring (C) can either occur as one of the two different tautomeric species or in its ionized form. In contrast to the other examples the VMR contains multiple atoms in this case.

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