Pull-off forces were measured between a silica colloid attached to an atomic force microscope (AFM) cantilever and three homopolymer surfaces representing constituents of extracellular polymeric substances (EPS). The pull-off forces were −0.84 (±0.16), −0.68 (±0.15), and −2.37 (±0.31) nN as measured in water for dextran, phosphorylated dextran, and poly-l-lysine, respectively. Molecular orbital and density functional theory methods (DFT) were applied to analyze the measured pull-off forces using dimer clusters representing interactions between the three polymers and silica surfaces. Binding energies for each dimer were calculated with basis set superposition error (BSSE) and interpolated using corrections for silica surface hydroxyl density and silica charge density. The binding energies were compared with the normalized pull-off forces with the effective silica surface area contacting the polymer surfaces. The predicted binding energies at a −0.064 C/m2 silica surface charge density corresponding to circum-neutral pH were −0.055, −0.029, and −0.338 × 10−18 J/nm2 for the dimers corresponding to the silica surface with dextran, phosphorylated dextran, and poly-l-lysine, respectively. Polarizable continuum model (PCM) calculations with different solvents, silanol vibrational frequency calculations, and orbital interaction analysis based on natural bonding orbital (NBO) showed that phosphate groups formed stronger H-bonds with neutral silanols than hydroxyl and amino functional groups of polymers, implying that phosphate containing polymers would play important roles in EPS binding to silica surfaces.