Methods for small molecule drug design using neural networks with two or more output heads, wherein one head, a sequence head, is trained to generate the sequence of a small molecule drug, and another head, a structure head, is trained to generate the structure of the small molecule drug; and wherein the neural network is configured to accept a representation of a specified condition as input, and output a representation of a small molecule drug's sequence and structure. The structure head and sequence head each have their own loss functions, and the weights of the neural network body are shared, and jointly updated during training. Non-limiting examples of specified input conditions include representations of associated proteins and/or sets of properties of the desired output small molecule drug. Some embodiments of the invention include for the design and synthesis of effective small molecule drug ligands.