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With the outstanding spatial resolution and sensitivity of the Atacama Large Millimeter/sub-millimeter Array (ALMA), molecular gas other than the abundant CO can be observed and resolved in circumstellar envelopes (CSEs) around evolved stars, such as the binary S-type Asymptotic Giant Branch (AGB) star W Aquilae. Aims. We aim to constrain the chemical composition of the CSE and determine the radial abundance distribution, the photospheric peak abundance, and isotopic ratios of a selection of chemically important molecular species in the innermost CSE of W Aql. 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