Using the complete rate equation for the PP i-ATP exchange reaction at equilibrium, the dissociation constants of phenylalanine (10 −5 m), phenylalanine butyl ester (8 × 10 −5 m), benzyl alcohol (6 × 10 −4 m), phenylalaninol (2 × 10 −4 m), hydrocinnamic acid (3 × 10 −3 m) and glycine (>1 m) with the phenylalanyl-tRNA synthetase (Escherichia coli K12) were determined. Taking the model of Koshland (1962) for the estimation of the configurational free energy change due to proximity and orientation, and decomposing the process of binding into several thermodynamic steps, the contribution to binding of the benzyl group, glycine unit, protonated amino group, carboxylate group and joint interactions were estimated. The results are: (1) the standard free energy contributions for binding phenylalanine are benzyl group (−8.2 kcal/mol), glycine unit (−2.5 kcal/mol), protonated amino group (−0.8 kcal/mol) and carboxylate group (1 kcal/mol). (2) The standard free energy change due to the change in the interaction between the protonated amino group and carboxylate group when they are transferred from the aqueous environment to the enzyme environment is −2.7 kcal/mol. (3) A dissociation constant for glycine of 7.5 m is calculated without the hypothesis that a conformational change occurs in the enzyme when the benzyl unit of phenylalanine binds, permitting an interaction of the enzyme with the protonated amino and/or carboxylate groups. The detection of E·AA † † Abbreviations used: E·AA, E·PP, etc., the enzyme substrate complexes of AA, PP i, etc; I, inhibitor; E, an AA-tRNA synthetase; AAAMP, aminoacyl adenylate. and E·ATP shows that a sequential addition of substrates is not necessary for binding. A comparison of the dissociation constants of E·AA (10 −5 m), E·ATP (1.5 × 10 −3 m), E·PP (5.5 × 10 −4 m), E·I (8 × 10 −5 m) and the mixed complexes E·I·ATP (6 × 10 −8 m 2), E·I·PP (5 × 10 −8 m 2) and E·AA·PP (7 × 10 −9 m 2), with phenylalanine butyl ester as the inhibitor, indicates no strong interaction between the binding of ATP or PP i with the binding of phenylalanine.