Convert SMILES reaction to xyz with correct atom order

Hi,

I have a SMILES string describing a reaction, for example: OOCCC=O>>O=CCC=O.O

I would like to create 3D structures of the reactants and products in an xyz format and save them with the atoms in the correct order, since I am interested in feeding these structures to quantum chemical software later on. Ideally, I would like to be able to do all of this from the command line.

I know that it is possible in Marvin Sketch to create an automatic atom mapping, which would give the following SMILES (with explicit hydrogens):

[H:12][O:6][O:5][C:4]([H:10])([H:11])[C:3]([H:8])([H:9])[C:2]([H:7])=[O:1]>>[H:11][C:4](=[O:5])[C:3]([H:9])([H:8])[C:2]([H:7])=[O:1].[H:12][O:6][H:10]

From this, I would then like to create two xyz files in which the atom mapping is retained as the order of atoms on each line, i.e., H12 for the reactant is on the same line as H12 for the products, and so on.

Is it possible to do this from the command line using "molconvert" and "cxcalc" commands?

Hi,

there is no way to do that. The export is based on the atom indexes, not on the atom mapping.

Janos