Mutations in CIC channel proteins may cause serious functional changes and even diseases. The function of CIC proteins mainly manifests as Cl- transport, which is related to the binding free energies of chloride ions. Therefore, the influence of a mutation on CIC function can be studied by investigating the mutational effect on the binding free energies of chloride ions. The present study provides quantitative and systematic investigations on the influences of residue mutations on the electrostatic binding free energies in Escherichia coli CIC (EcCIC) proteins, using all-atom molecular dynamics simulations. It was found that the change of the electrostatic binding free energy decreases linearly with the increase of the residue-chloride ion distance for a mutation. This work reveals how changes in the charge of a mutated residue and in the distance between the mutated residue and the binding site govern the variations in the electrostatic binding free energies and therefore influence the transport of chloride ions and conduction in EcCIC. This work would facilitate our understanding of the mutational effects on transport of chloride ions and functions of CIC proteins and provide a guideline to estimate which residue mutations will have great influences on CIC functions.