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I don't know how it can help train whatever 'CNN' stands for (i'm guessing not the news network, but something Neural Network?) Yet there are vast sources of various ("pictures") representations of small molecules all over the internet; from line-drawings, 2d stick models[1] to those providing rotation to space filling models[2]. As a very personal aside, neural networks are just a means of doing curve fitting without necessary learning anything.

[1] https://en.wikipedia.org/wiki/Morphine

[2] https://www.cancerquest.org/patients/drug-reference/morphine

It stands for convolutional neural network, which is a NN architecture that works well on image data. They use CNN's in object detection and other computer vision related tasks.

Chemception/Chemnet do just that with OK performance. https://arxiv.org/abs/1706.06689 https://arxiv.org/abs/1712.02734

it has been done here: https://arxiv.org/abs/1712.02734