A computing system is provided, including a processor configured to, during a training phase, provide a training data set, including a pre-transformation molecular graph and post-transformation energy parameter value representing an energy change in a molecular system following an energy transformation. The pre-transformation graph includes a plurality of normal nodes connected by edges representing a distance and a bond between a pair of the normal nodes. The processor is further configured to encode structural information in each pre-transformation molecular graph as learnable embeddings, the structural information describing the relative positions of the atoms represented by the normal nodes. The structural information includes an edge encoding representing a type of bond between a pair of normal nodes in each pre-transformation molecular graph, and a spatial encoding representing a shortest path distance along the edges between a pair of normal nodes in each pre-transformation molecular graph.