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  • The conformational energy of a peptide can be expressed in Equation 1. ##EQU1## where Etot is the total conformational energy of the protein, the Q's are the charges on the ith and jth atoms; Rij is the distance between the ith and jth atoms, D is the dielectric constant, ??ij and ??ij are the lowest non-bonded (Lennard-Jones) energy and the distance at this lowest energy between atoms i and j in
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