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A key requirement for the correct interpretation of high resolution X ray spectra is that transition energies are known with high accuracy and precision. We investigate the K shell features of Ne, CO2, and SF6 gases, by measuring their photo ion yield spectra at the BESSY II synchrotron facility simultaneously with the 1s np fluorescence emission of He like ions produced in the Polar X EBIT. Accurate ab initio calculations of transitions in these ions provide the basis of the calibration. While the CO2 result agrees well with previous measurements, the SF6 spectrum appears shifted by amp; 8764;0.5 eV, about twice the uncertainty of the earlier results. Our result for Ne shows a large departure from earlier results, but may suffer from larger systematic effects than our other measurements. The molecular spectra agree well with our results of time dependent density functional theory. We find that the statistical uncertainty allows calibrations in the desired range of 1 10 meV, however, systematic contributions still limit the uncertainty to amp; 8764;40 100 meV, mainly due to the temporal stability of the monochromator energy scale. Combining our absolute calibration technique with a relative energy calibration technique such as photoelectron energy spectroscopy will be necessary to realize its full potential of achieving uncertainties as low as 1 10 meV