Simulations of radiation damage in single molecule imaging using a X-ray free electron laser use atomic rates calculated in the lowest order. We investigate the difference in ion yield predictions using Hartree-Fock and Hartree-Fock-Slater pproximations for light and heavy elements of biological significance... The results show that for the biologically abundant elements of the second and third rows of the periodic table both approximations agree to about 6%. For the heavier elements beyond the fourth row the discrepancy rices to 11% for the range of the pulse parameters covered in this work. Presented analysis can be used for an error estimation in a wide range of ab initio simulations of the X-ray pulse interaction with biological molecules. We also discuss other atomic structure effects and show that their account has considerably smaller effect on the ion yields of respective elements compared to the choice of the approximation. (read more)