Figure 2. Molecular structure of the alanine dipeptide in the C_7eq and C_7ax isomers.

The Ramachandran dihedral angles φ and ψ define the conformation of the backbone. The peptide-bond dihedral angles Θ and ζ define the arrangement of the amide and carbonyl dipoles, relative to each other and the side-chain. The C_7eq metastable state is characterized by Φ = −1.41 rad, Ψ = 1.25 rad, Θ = −3.12 rad and ζ = 3.07 rad, while for C_7ax state Φ =1.26 rad, Ψ = −1.27 rad, Θ = 3.13 rad and ζ = −3.03 rad (after minimization in vacuum with the CHARMM22 force-field). All molecular graphics in the article were produced with VMD.⁶¹