A coordinate matrix is just a set of coordinates of N vertices or nodes.
So the points (1,2), (3,4), (5,6) are stored as:
\begin{pmatrix} 1 & 2\\ 3 & 4\\ 5 & 6 \end{pmatrix}
It's adjacency matrix is roughly:
\begin{pmatrix} 0 & 2.82 & 5.66\\ 2.82 & 0 & 2.82\\ 5.66 & 2.82 & 0 \end{pmatrix}...