The ResonateBond command reverses the changes made by KekulizeBond: Bonds between selected atoms are scanned for patterns of alternating single/double bonds and replaced by the proper resonance form.

Two typical examples:

• Deprotonated carboxyl groups: If one oxygen makes a double bond and the other one a single bond, ResonateBond will change the order of both bonds to 1.5 (shown in red).
• Aromatic rings like benzene: If conjugated single/double bonds are present, ResonateBond will make all bonds identical (bond order 1.5).

Note: the choices that have to be made by the ResonateBond command are ambiguous if hydrogen atoms are missing. In such a case it is better to just retype the bonds, which also considers the pH dependency of missing hydrogen atoms.

The ResonateBond command is especially useful after loading molecules in a format that does not support fractional bond orders (e.g. mol2), since it makes sure that chemically equivalent atoms are also perceived as such - which is in turn important for commands like Sup or RMSD which flip chemically equivalent atoms to minimize RMSDs.

More details about fractional bond orders can be found here .

ResonateBond all,all

Replace alternating single/double bonds with the corresponding fractional bond order, e.g. 1.5 in benzene rings.

ResonateBond CZ Res Arg,NE NH? Res Arg

Make sure that the bond orders between atoms CZ and NE,NH1,NH2 in arginines are 1.33.