The Guiding Principle of Chiral Innovative drugs clearly stipulates that "the direct method for determination of molecular configuration of chiral drugs is single crystal X-ray structure analysis". For general chiral innovative drugs, single-crystal X-ray diffraction structure analysis results are also required. Since chiral crystals have anomalously scattered signals to X-rays, the Flack coefficient can be calculated by measuring the anomalously scattered signals, and then the molecular configuration can be obtained. Compared with other analytical methods for analyzing chirality, X-ray single crystal diffraction is more direct and reliable.

In addition to small molecule drug crystal structure, another major use of X-ray single crystal diffractionis to resolve the complex structure of drug precursor molecules and target proteins. In modern drug discovery methods, we can obtain the structure of the target protein, as well as the complex structure of the small molecule precursor drug and the target protein, and clearly see the mode of action of small molecule drugs. Structure-based drug design, with the help of computers, has become very clear and straightforward. Therefore, high-throughput screening, virtual screening, structure-based drug design, and optimization of lead compounds have become common techniques for small molecule drug discovery. These technologies have been very successful and are still being enriched and developed today.