Figure 2.

This diagram explains energy terms used in Eq. 1 including the (A) self-energy, (B) two-body energy, and (C) three-body energy. The induced dipole vectors for three side-chain oxygen atoms in wild-type PCNA are shown in the absence of Lys¹⁰⁷ (left) and in its presence (right). A vector length of 7 Å corresponds to 1 Debye. Changes in induced dipole direction and magnitude reflect the AMOEBA electronic polarization response to the total electrostatic field, which results in polarization energy that is not pairwise. For this example, the three-body energy is 1.55 kcal/mol.