Energy crystal of matrix is found in the Elona+ mod of Elona. If you had the Gem stone of Mani before you imported your game into Elona+, that item will transform into this. It can also be dropped randomly, most probably from machine type enemies.
The item works the same as the old Gem stone of mani, which means it is a reusuable Rod of Alchemy. It can be used once every 24 hours.
It can be obtained as a random loot by slaying Metamorphose enemies (a 1% chance).
The item sprite ID for the gem is 657 (Row 19, Column 30) using the item sprite zero-based position system. It is a god jewel, without tint.