obabel add SMILES stereocenter @/@@ to achiral unsaturated spiro compounds

[e-kwsm]

Environment Information

Open Babel version: 3.1.1
Operating system and version: Debian 12.5

Expected Behavior

openbabel yields SMILES without chirality for spiro[4.4]nonatetraene: C1=CC2(C=C1)C=CC=C2.

Actual Behavior

openbabel thinks the spiro center is chiral: C1=C[C@]2(C=C1)C=CC=C2, while it works successfully for spiro[2.2]pentadiene, C1=CC21C=C2, spiro[3.3]heptane, C1CC2(C1)CCC2, and spiro[4.4]nonane, C1CCC2(C1)CCCC2.

I checked all of the combinations of (cyclopropane, cyclopropene, cyclopentane, and cyclopentadiene), and found that spiro[2.4]heptatriene is also misclassified as chiral: C1=C[C@]2(C=C1)C=C2.

Steps to Reproduce

<?xml version="1.0" encoding="UTF-8"?>
<molecule xmlns="http://www.xml-cml.org/schema">
  <atomArray>
    <atom id="a1" elementType="C" x3="0" y3="0" z3="0"/>
    <atom id="a2" elementType="C" x3="-0.94" y3="-1.2" z3="0"/>
    <atom id="a3" elementType="C" x3="-2.258" y3="-0.707" z3="0"/>
    <atom id="a4" elementType="C" x3="-2.258" y3="0.707" z3="0"/>
    <atom id="a5" elementType="C" x3="-0.94" y3="1.2" z3="0"/>
    <atom id="a6" elementType="C" x3="0.94" y3="0" z3="-1.2"/>
    <atom id="a7" elementType="C" x3="2.258" y3="0" z3="-0.707"/>
    <atom id="a8" elementType="C" x3="2.258" y3="0" z3="0.707"/>
    <atom id="a9" elementType="C" x3="0.94" y3="0" z3="1.2"/>
    <atom id="a10" elementType="H" x3="-0.650" y3="-2.230" z3="0"/>
    <atom id="a11" elementType="H" x3="-3.137" y3="-1.316" z3="0"/>
    <atom id="a12" elementType="H" x3="-3.137" y3="1.316" z3="0"/>
    <atom id="a13" elementType="H" x3="-0.650" y3="2.230" z3="0"/>
    <atom id="a14" elementType="H" x3="0.650" y3="0" z3="-2.230"/>
    <atom id="a15" elementType="H" x3="3.137" y3="0" z3="-1.316"/>
    <atom id="a16" elementType="H" x3="3.137" y3="0" z3="1.3168"/>
    <atom id="a17" elementType="H" x3="0.650" y3="0" z3="2.230"/>
  </atomArray>
  <bondArray>
    <bond atomRefs2="a1 a2" order="1"/>
    <bond atomRefs2="a2 a3" order="2"/>
    <bond atomRefs2="a3 a4" order="1"/>
    <bond atomRefs2="a4 a5" order="2"/>
    <bond atomRefs2="a1 a5" order="1"/>
    <bond atomRefs2="a1 a6" order="1"/>
    <bond atomRefs2="a6 a7" order="2"/>
    <bond atomRefs2="a7 a8" order="1"/>
    <bond atomRefs2="a8 a9" order="2"/>
    <bond atomRefs2="a1 a9" order="1"/>
    <bond atomRefs2="a2 a10" order="1"/>
    <bond atomRefs2="a3 a11" order="1"/>
    <bond atomRefs2="a4 a12" order="1"/>
    <bond atomRefs2="a5 a13" order="1"/>
    <bond atomRefs2="a6 a14" order="1"/>
    <bond atomRefs2="a7 a15" order="1"/>
    <bond atomRefs2="a8 a16" order="1"/>
    <bond atomRefs2="a9 a17" order="1"/>
  </bondArray>
</molecule>

Save above as spiro.cml.

$ obabel spiro.cml -o can
C1=C[C@]2(C=C1)C=CC=C2
$ obabel spiro.cml -o mol | obabel -i mol -o can
1 molecule converted
C1=C[C@]2(C=C1)C=CC=C2	
1 molecule converted

Also,

$ obabel '-:C1=C[C@]2(C=C1)C=CC=C2' -o can 
C1=C[C@]2(C=C1)C=CC=C2	
1 molecule converted
$ obabel '-:C1=C[C@@]2(C=C1)C=CC=C2' -o can
C1=C[C@]2(C=C1)C=CC=C2	
1 molecule converted
$ obabel '-:C1=CC2(C=C1)C=CC=C2' -o can 
C1=CC2(C=C1)C=CC=C2	
1 molecule converted
$ obabel '-:C1C[C@@]2(CC1)CCCC2' -o can
C1CCC2(C1)CCCC2	
1 molecule converted

[nbehrnd]

@e-kwsm Complementary observation: entry VS001, spiro[4.5]dec-2-ene in the cipvalidationsuite compiled by Robert Hanson et al. equally is assigned by them by the SMILES string C1[C@]2(CCCC1)CC=CC2. However, the submission of their 3D .sdf file to Open Babel (version 3.1.1 by Jan 10 2024 in Debian 13/trixie)

$ obabel VS001.sdf -ocan
C1CCC2(CC1)CC=CC2	VS001
1 molecule converted
$ obabel -:"C1[C@]2(CCCC1)CC=CC2" -ocan
C1CCC2(CC1)CC=CC2	
1 molecule converted

drops the @. The compilation of 300 structures may contain additional entries worth to test.

Hanson, R. M.; Musacchio, S.; Mayfield, J. W.; Vainio, M. J.; Yerin, A.; Redkin, D. Algorithmic Analysis of Cahn–Ingold–Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. J. Chem. Inf. Model. 2018, 58 (9), 1755–1765. https://doi.org/10.1021/acs.jcim.8b00324.