Nope, the base form of it is "있다", and "계시다" is the honorific form of "있다".
The ending "-(으)세요" is used to make a sentence into an imperative.
e.g.
계시다 + 세요 => 계세요.
드시다 + 세요 => 드세요.
However, "계세요" in "안녕히 계세요" is just a fixed expression when a guest leave like "안녕히 가세요", "어서오세요", etc.
\^o^/