It can be read off the The Elliott configuration - a $5$-coloring of $K6$ - that $S_6$ has an exotic $S_5$ subgroup (it's not a point stabilizer) which I will call $X_5 = \langle (1\;3\;6\;4\;5), (1\;2)(3\;6)(4\;5) \rangle$.

How can I prove that there are exactly 6 conjugates of $X_5$?
I thought that I could use orbit-stabilizer theorem with $G = S_6$ acting on itself by conjugation, then the number of conjugates of $X_5$ is $|G|/|N_{G}(X_5)|$.. but I don't know how to compute the denominator.
Denote $c = [G : N_G(X_5)]$. By Lagrange's theorem $c = 1, 2, 3$ or $6$. The only non-trivial proper normal subgroup of $S_6$ is $A_6$, so $c$ cannot be $1$. For the same reason $c$ cannot be $3$, because otherwise $N_G(X_5)$ would contain the kernel of a homomorphism $G \rightarrow S_3$. Also, $c$ cannot be $2$ because then $N_G(X_5) = A_6$, but $S_5$ does not embed into $A_6$. The only possibility is $c = 6$.