@ahmed jehanzeb
The certificate that used for Federation Trust are different from the certificate that binding in IIS. It is a separate certificate which only used for Federation Trust don't need assigned IIS services.
The certificate that binding in IIS is used for service which based on IIS, such as OWA, ECP etc. This certificate need contain the domain name and FQDN of your organization in it(Such domain.name, FQDN like: mail.domain.com/autodiscover.domain.com, it decided by which URL that you used to access OWA)
Here is the detailed information about the certificate that used for Federation Trust: Use the Shell to create and configure a federation trust
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