Solar wind (SW) charge exchange (CX) is an important mechanism responsible for X-ray emissions in comets’ coma and many other astrophysical environments. By incorporating the experimentally derived total cross sections and the tested state-selectivity models into the Kronos program, we generate X-ray spectra in H-like and fully stripped C, N, O, etc. ions charge exchange collision with atomic H. Using these data, we revisit the fitting of Chandra X-ray data of Comet C/1999 S4 by considering the typical solar wind collision energies of 0.8 keV/u and 3 keV/u, respectively. Our results are in an excellent agreement with the astrophysical observation. We find that charge exchange between C5 +, 6 +, N6 +, 7 +, O7 +, 8 + and H significantly contributes to the comet’s spectrum ranging from 300 eV to 800 eV for both slow and fast solar wind ions, where N7 + abundance is underestimated in previous studies.