The strategy behind choosing the base pair step as the fundamental training unit is that any arbitrary DNA structure can be broken down into a sequence of overlapping base pair steps. A model that understands the features of every possible base pair step should be able to reasonably reconstruct the electron density for any DNA sequence. This training protocol is validated by comparing model predictions to quantum calculation in a test set of B-DNA structures. In the test set, arbitrary structures ranging from two to five base pairs in length were included (referred to as 2-mers, 3-mers, and so on). For 2-, 3-, and 4-mers, every possible combination of base pairs (10, 32, and 136 combinations, respectively) was included. For 5-mers, the sheer number of base pair combinations as well as the size of the structures makes exhaustive sampling costly. Therefore, we selectively sampled the 5-mer space using ten randomly generated base sequences. Table summarizes the contents of the test set (see the ESI † for details on the 5-mer base sequences which are located in Table ). We emphasize that the training and test sets are both based off of the B-form of DNA. We later demonstrate the ability of the model to extrapolate to other structural motifs such as A-and Z-DNA. To sample representative geometries of all base pair steps, molecular dynamics (MD) simulations were run with Amber 20 using the BSC1 force field. An initial 12mer B-DNA structure was placed in a periodic truncated octahedral box with a 10 Å buffer and solvated with TIP3P water. Mg 2+ counterions were added to neutralize the structure, and then an excess of Mg 2+ and Cl -at about 100 mmol/L were added to the simulation box. Since we are only interested in the dynamics of the central base pair step, restraints were added to keep intact the base pairs at both ends of the DNA.