A synchrotron radiation experiment and a large-scale simulation are indispensable for development new functional rubber materials in recent years. In this series of lectures, I will try to explain about an analysis of structure of filled rubber vulcanizates by cooperation of a synchrotron radiation experiment and a large-scale simulation. In this second article, I will discuss a large scale coarse-grained molecular dynamics simulation of end-modified styrene butadiene rubber compounds conducted on the K-computer. Filler aggregates are modeled by reverse Monte Carlo method from a part of ultra-small angle X-ray scattering data of rubber compounds obtained in the large-scale synchrotron radiation facility SPring-8. The difference of experimental stress-strain curves between end-modified SBR and non-modified SBR has been reproduced qualitatively by simulation. Behaviors of large strain region of experimental SS curves can be explained by the difference of maximum elongation of network chains due to the difference of number of bonds between filler in end-modified SBR and non-modified SBR. Difference of small strain region of experimental SS curves reveals to be due to the difference of structure of filler aggregates in end-modified SBR and non-modified SBR.