Parametrization and validation of the nonbonded dummy model for Zn²⁺. (A) Geometry of the nonbonded dummy model. The central ZND site (magenta) is surrounded by six dummy sites DM (gray) forming a rigid octahedral shell. ZND-DM distances were maintained at 0.9 Å. Each DM particle carries a charge of δ⁺ = +0.35e and the central ZND particle carries −0.10e for a total charge of +2e. ZND and DM particles participate in van der Waals interactions. The approximate van der Waals radii of the ZND and DM particles are shown in the space-filling representation. (B) Results from the genetic algorithm parameter search. The Lennard-Jones parameters for the van der Waals interactions of the ZND and DM particles were optimized using a genetic algorithm to reproduce the Zn²⁺ HFE at standard conditions of −1,955 kJ/mol and the IOD of 2.08 Å in simulations with water. The optimization ran through six iterations, at which point it reproduced the experimental values within 1% and 0.3%, respectively. (C) Zn dummy model in water. The RDF for the Zn (ZND)-water oxygen distance, g(r), and its integral, N(r), show the first peak at the target IOD and the experimental number of water molecules in the first hydration shell, n₁ = 6. (D) Validation with MD simulations of β-1,3-1,4-endoglucanase (PDB accession no. 1U0A, resolution 1.64 Å). The Zn binding site (with ZN 5005) is located in a dimer interface between chains A and C and formed by HHDD residues. (E) Binding site RMSDs of the three repeat simulations of 1U0A as time series and distribution over all repeat simulations (computed as a KDE) where the trajectory frames were superimposed on the same residues that the RMSDs was calculated for: backbone of the protein (N, C, C_α, and O atoms for all protein residues in blue), backbone and side chain heavy atoms of the coordinating residues (Asp161, His145 on chains A and C, orange and labeled residues), and coordinating atoms only (O_δ1/O_δ2 for Asp161, N_ε or N_δ for His145 on chains A and C in green and labeled atoms). (F) Radial distribution of the distances of coordinating atoms (O and N) in 1U0A to the Zn ion (measured to the ZND center). Distributions were computed for each simulation repeat separately and averaged. The solid line shows the mean with bands, which are barely visible, indicating the SD. The dashed vertical lines mark the distances in the crystal structure. (G) Validation with MD simulations of stromelysin-1 (PDB accession no. 2USN, resolution 2.2 Å). The Zn binding site (with ZN 258) is formed by HHHD residues. (H) Binding site RMSDs of the three repeat simulations of 2USN, as in E: specifically, backbone and side chain atoms for His69, His84, His97, and Asp71; or N_ε or N_δ for the three His residues and O_δ1/O_δ2 for Asp71. (I) Radial distribution of the distances of coordinating O and N atoms in 2USN, as in F. (J) Validation with MD simulations of δ' subunit of E. coli clamp-loader complex (PDB accession no. 1A5T, resolution 2.2 Å). The Zn binding site (with ZN 501) is formed by CCCC residues. (K) Binding site RMSDs of the three repeat simulations of 1A5T, as in E: specifically, backbone and side chain atoms for Cys50, Cys59, Cys62, and Cys65; or the C_γ of these four Cys residues. (L) Radial distribution of the distances of coordinating S atoms in 1A5T, otherwise as in F.