Simplified Molecular Input Line Entry System: Difference between revisions

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Revision as of 17:30, 1 November 2020

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For example, consider the [[amino acid]] [[alanine]]. One of its SMILES forms is <code>NC(C)C(=O)O</code>, more fully written as <code>N[CH](C)C(=O)O</code>. [[L-alanine|<small>L</small>-Alanine]], the more common [[enantiomer]], is written as <code>N[C@@H](C)C(=O)O</code> ([https://web.archive.org/web/20130704043108/http://www.daylight.com/daycgi/depict?4e5b434040485d28432943283d4f294f see depiction]). Looking from the nitrogen–carbon bond, the hydrogen (<code>H</code>), methyl (<code>C</code>), and carboxylate (<code>C(=O)O</code>) groups appear clockwise. <small>D</small>-Alanine can be written as <code>N[C@H](C)C(=O)O</code> ([https://web.archive.org/web/20130522072012/http://www.daylight.com/daycgi/depict?4e5b4340485d28432943283d4f294f see depiction]).

While the order isin which branches are specified in SMILES is normally unimportant, in this case it matters; swapping any two groups requires reversing the chirality indicator. If the branches are reversed so alanine is written as <code>NC(C(=O)O)C</code>, then the configuration also reverses; <small>L</small>-alanine is written as <code>N[C@H](C(=O)O)C</code> ([https://web.archive.org/web/20130522073747/http://www.daylight.com/daycgi/depict?4e5b434040485d2843283d4f294f2943 see depiction]). Other ways of writing it include <code>C[C@H](N)C(=O)O</code>, <code>OC(=O)[C@@H](N)C</code> and <code>OC(=O)[C@H](C)N</code>.

Normally, the first of the four bonds appears to the left of the carbon atom, but if the SMILES is written beginning with the chiral carbon, such as <code>C(C)(N)C(=O)O</code>, then all four are to the right, but the first to appear (the <code>[CH]</code> bond in this case) is used as the reference to order the following three: <small>L</small>-alanine may also be written <code>[C@@H](C)(N)C(=O)O</code>.