azabicyclo is not recognized in IAPUC

[sky1ove]

In this case, the iupac name is (1R,5R,6R)-3-((S)-7-(8-ethyl-7-fluoro-3-hydroxynaphthalen-1-yl)-6,8-difluoro-2-(((2R,7aS)-2- fluorohexahydro-1H-pyrrolizin-7a-yl)methoxy)quinazolin-4-yl)-3-azabicyclo[3.2.1]octan-6-ol

It cannot recognize azabicyclo and convert to smiles. There's no problems with this iupac name.

[dan2097]

The error it's giving is due to it being unable to assign each stereochemistry description to a distinct stereocenter.

Assuming the structure is intended to be:

C(C)C=1C(=CC=C2C=C(C=C(C12)C1=C(C=C2C(=NC(=NC2=C1F)OC[C@]12CCCN2C[C@@H](C1)F)N1C[C@H]2C[C@H]([C@@H](C1)C2)O)F)O)F

There are 5 stereocenters, 3 on the 3-azabicyclo[3.2.1]octan-6-ol and 2 on the pyrrolizin. It looks possible that the (S) is intended to describe axial chirality where the naphthalene connects to the quinazoline. OPSIN does not currently support axial chirality.

e.g. (1R,5R,6R)-3-(7-(8-ethyl-7-fluoro-3-hydroxynaphthalen-1-yl)-6,8-difluoro-2-(((2R,7aS)-2- fluorohexahydro-1H-pyrrolizin-7a-yl)methoxy)quinazolin-4-yl)-3-azabicyclo[3.2.1]octan-6-ol is interpreted

[sky1ove]

Thanks for the clarification. That makes sense. Do you know when OPSIN will support axial chirality or if there’s any software that support this kind of IUPAC-structures conversion?

On Sun, Aug 27, 2023 at 5:00 PM Daniel Lowe @.***> wrote:

The error it's giving is due to it being unable to assign each stereochemistry description to a distinct stereocenter.

Assuming the structure is intended to be:

C(C)C=1C(=CC=C2C=C(C=C(C12)C1=C(C=C2C(=NC(=NC2=C1F)OC[C@]12CCCN2C[C@@@.**@.(C@@HC2)O)F)O)F

There are 5 stereocenters, 3 on the 3-azabicyclo[3.2.1]octan-6-ol and 2 on the pyrrolizin. It looks possible that the (S) is intended to describe axial chirality where the naphthalene connects to the quinazoline. OPSIN does not currently support axial chirality.

e.g. (1R,5R,6R)-3-(7-(8-ethyl-7-fluoro-3-hydroxynaphthalen-1-yl)-6,8-difluoro-2-(((2R,7aS)-2- fluorohexahydro-1H-pyrrolizin-7a-yl)methoxy)quinazolin-4-yl)-3-azabicyclo[3.2.1]octan-6-ol is interpreted

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[dan2097]

Do you know when OPSIN will support axial chirality

Probably not for awhile as it's relatively rarely besides with BINAP compounds

if there’s any software that support this kind of IUPAC-structures conversion

ChemDraw appears to support this conversion (https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html) as indicated by the hatched bond it puts on the quinazoline ring. I'm not familiar enough with this nomenclature to say whether this should be a wedge or a hatched bond.