How to understand the structure of the interesting graph obtained from the group?

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Let $G = A_5$ and $H < G$ is subgroup of $A_5$ generated by $(12)(34)$, and $(125)$.

Define graph $\Gamma$ by a vertex set is element of $G$ and elements $x$ and $y$ adjacent if $|H^x \cap H^y| = 1$. We obtain a regular graph with valency $36$.

I computed with SAGE some other properties of this graph:

Order of ${\rm Aut}(\Gamma)$ is $4492687491149384908800000000000 = 2^{43} \cdot 3^{21}\cdot 5^{11}$ and act vertex, edge and arc transitive. ${\rm Aut}(\Gamma)$ has a trivial solvable radical and $|{\rm Soc}({\rm Aut}(\Gamma))| = 2^{30} \cdot 3^{20} \cdot 5^{10}$, hence ${\rm Soc}({\rm Aut}(\Gamma)) = A_6^{10}$

$\Gamma$ has diameter $2$ and spectrum $\{36^1, 6^4, 0^{50}, -12^5\}$.

Let $u, w \in \Gamma$, then $$ |\Gamma(u) \cap \Gamma(w)| = \begin{cases} 18 & \text{if u and v adjacent } \\ 36 & \text{if u and v non adjacent and } \Gamma(u)=\Gamma(v) \\ 24 & \text{if u and v non adjacent and } \Gamma(u) \ne \Gamma(v)\\ \end{cases} $$ Hence if $M$ djacency matrix of the graph, then $M^2 = 18M+24A+36B+36I$, where $A, B$$01$-matrix and $M+A+B+I=J$ ($I$ - identity matrix and $J$ - all one matrix)

Let $D=\Gamma(u)$, is local graph, then ${\rm Spec}(D) = \{18^1, 6^1, 0^{32}, -12^2\}$ and $\bar D = C_6 ⊠ K_6$ (strong product)

Can you say something more about this graph? I saw a question about a similar graph, but only his automorphism group was discussed there.

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Without computing it explicitly, given some of the data that you've given, this is almost certainly the lexicographic product of the complement of the Petersen graph $\overline{P}$, with an edgeless graph on $6$ vertices.

(In other words, you take $\overline{P}$, each vertex becomes $6$ vertices, and every edge a $K_{6,6}$.)

You could build this with Sage and check for isomorphism.

Here is my train of thought: since some vertices have the same open neighbourhood and the graph is vertex-transitive, it must be a lexicographic product with an edgeless graph. Given the socle, I guessed there are $10$ blocks of size $6$.

The quotient then has order $10$ and valency $6$. It's automorphism group has order the one you started with, divided by $(6!)^{10}$, which is $120$. The complement is $3$-valent with automorphism group of order $120$. In particular, it is connected, and since $3$ divides the order, must be arc-transitive, and the only possibility is $P$.

In particular, this means the group is isomorphic to $(S_6)^{10}\rtimes S_5$ where $S_5$ acts as on unordered pairs.