Hi Chandan - thanks for your post. I am going to move it to the Hyperlynx community where it will receive greater visibility by other Hyperlynx users. Where you have posted it is for general community questions and suggestions.
HyperLynx PI is really optimized for analysis of the PCB. What you want to do is more of a general purpose simulator task. From the point of view of HyperLynx PI, you probably want to focus on the low-frequency decoupling of the PCB. Does Xilinx provide any power noise or impedance recommendations for frequency bands of interest?
If you want to see the impedance including the package and die, you need to run a few extra steps. Create a LineSim schematic of the package, on-package capacitance, and die. Extract S parameters of this network at the pins.
Export the power plane pair (for example VDD and VSS) for analysis into LineSim. Assign the extracted S parameters of the component to the appropriate component pins and run the decoupling analysis in LineSim.