X-ray emission was discovered in comet Hyakutake (C/1996 B2) by the Röntgen satellite in 1996, and these emissions were attributed to the excitation of high charge state solar wind ions due to electron capture from cometary molecules or atoms. Using the plasma flow in the coma of Hyakutake calculated by a three-dimensional adaptive magnetohydrodynamic model, the density distribution of solar wind ions in the coma and the resulting x-ray emission were computed. The calculated High Resolution Imager count rate of 4.4 per second and the spatial distribution of the x-ray emission agree with the observations. A detailed energy spectrum of cometary x-rays is predicted in the 80 to 2000 electronvolt energy range. Cometary x-rays present a sensitive tool to monitor cometary activity and solar wind ion composition.