Let $Δ$ be a $3$-dimensional lattice polytope containing exactly one interior lattice point. We give a simple combinatorial formula for computing the stringy $E$-function of the $3$-dimensional canonical toric Fano variety $X_Δ$ associated with the polytope $Δ$. Using the stringy Libgober-Wood identity and our formula, we generalize the well-known combinatorial identity $\sum_{θ\preceq Δ\atop \dim (θ) =1} v(θ) \cdot v(θ^*) = 24$ holding in the case of $3$-dimensional reflexive polytopes $Δ$.