How does InChI deal with the many equivalent ways of arranging bonds and charges in delocalized structures?
When computing atom numbers (during canonicalization), bond orders and charge positions are ignored. Electron density and pi-electrons are important for descibing a large portion of interesting chemistry but they can be ignored here as they are not important for naming. This does not introduce ambiguity as long as all H-atoms are accounted for. InChI only uses bond orders for perceiving stereochemistry ((Z)- vs (E)- but-2-ene, for example) and mobile H. It only stores the net charge, without regard to position. Note that the above InChI does not contain any information on the double bond position or charges.
