(Edit: I correct here the mistakes in my previous question. My title is not correct. Indeed, different compounds have different SMILES)
Different compounds (named with variants a, b, c, d …) differ by chirality at certain nodes (for example, a carbon going to the right in a, to the left in b, or a carbon to one place on a ring in a, or to another place in b).
Is there a standard naming that takes all these aspects into account ?
The SMILES format should be able to represent chirality information (e.g. the common L-isomer of alanine is C[C@H](C(=O)O)N and the D variant is C[C@@H](C(=O)O)N.)
The fact that the a/b/c/d variants are all the same except for chirality is expected, as those results are generated by the Foldit client from "racemic" SMILES provided by the library search. (SMILES without the chirality information, e.g. CC(C(=O)O)N for alanine. You can't go to 3D without picking a chirality, though, so we enumerate the chiralities and provide each as an option.)
If the SMILES provided in the info panel does not have the chirality information, that is unexpected. The structure->SMILES functionality should include chirality information. I'm not quite sure why it wouldn't.