How to Resolve the Stereochemistry of a Monomer

This guide shows how to register a monomer whose stereochemistry is not fully known, how to register two separated fractions that cannot yet be told apart, and how to register the assigned form later while keeping the link to the unknown it came from. It uses Phx1, a 1-methyl-indazolyl glycine with one unknown centre, and bhPX7, a pair of separated epimers, as the worked examples.

Prerequisites: the Manager or Administrator role in Biotoolkit Monomers. Read Enhanced Stereochemistry first if or1, &1 and isomer label are new to you.

One field per monomer

An isomer label belongs to one monomer. Two separated fractions are two registrations, A on one and B on the other, never A and B in one field.

Case 1: one fraction, configuration unknown

You hold a product you know to be a single enantiomer, without knowing which one.

On the Monomers page, click New monomer and fill in the definition as for any monomer. See How to Create or Edit a Monomer.
In SMILES or molfile, write the SMILES with the wedge as drawn and an or group on the centre, as a CXSMILES block. The number after the colon is the 0-based index of the atom in your SMILES:
```
C[n]1[n]cc2cc(ccc12)[C@@H](N([*:1]))C([*:2])=O |o1:10|
```
Click Preview. The drawing carries the label or1 on the centre. The Isomer label field appears as soon as the structure holds an or group; leave it empty, a single fraction has nothing to be told apart from.
Set the cap groups and click Create.

The monomer is registered with the unknown in its key, so it does not collide with the absolute forms of the same drawing.

Case 2: two fractions, not yet assigned

A separation gave two flasks with the same drawing. Register them the same day, one after the other:

Field	Flask 1	Flask 2
Symbol	`bhPX7A`	`bhPX7B`
SMILES or molfile	`CC1(C)CN(CCN([:1]))C(=O)[C@@H]1CC([:2])=O \\|o1:10\\|`	the same
Isomer label	`A`	`B`

The second registration is accepted because the uniqueness rule compares the structure and the label. Leaving the label empty on the second one is refused as a duplicate of the first.

Case 3: registering the assigned form

The configuration of Phx1, or of bhPX7A, is now established. Register the assigned form as a new monomer, linked to the unknown.

Open the unknown monomer, Phx1, from the Monomers page.
Click Duplicate and resolve stereo. The button is offered only on a monomer whose structure carries an or or and group. The form reopens in create mode with everything copied from Phx1 except the symbol and the name, Resolved from set to Phx1 and locked, and the structure without its stereo block:
```
C[n]1[n]cc2cc(ccc12)[C@@H](N([*:1]))C([*:2])=O
```
Fill in the Symbol, which must be new, and the Name.
Edit the structure if the assignment is the mirror of the drawing: [C@H] in place of [C@@H]. Leave it as it is when the drawing was right.
Write the method and the confidence in Stereo comment, for example Configuration assigned by X-ray on the HCl salt, batch 2026-10.
Click Preview, check the drawing shows no or1 any more, set the cap groups, then click Create.

The service checks that the new structure is one of the isomers Phx1 stands for, then writes the monomer. Back on its page, the Stereo resolution region shows the link to Phx1, and the Stereo analysis region lists each centre with its label in Phx1 and in the new monomer, the configuration (same or inverted) and the verdict. Phx1 itself now lists the new monomer under Resolved into.

For bhPX7A, do the same from bhPX7A; the copy carries no label, because the assigned form has no or group left. When bhPX7B is resolved later to the same configuration as bhPX7A's child, the registration goes through and a warning names both: two labels on one drawing are expected to resolve to mirror images. Check which assignment is wrong before relying on either.

Messages that stop the creation

Resolved from 'Phx1': not the same molecular graph once stereo is removed … The skeleton or the attachment points differ from the source. Only stereo labels may change on a resolution.
Resolved from 'Phx1': atom 10 (C) is absolute in the parent and inverted here. A centre that was already settled on the source has been flipped.
Resolved from 'Phx1': the same stereo statement as the parent: nothing is resolved, this is a duplicate, not a resolution. The stereo block was left as it was. Remove it, or settle at least one group.
Monomer with this structure is already registered: Phx3. The assigned form already exists, under another symbol: the resolution was done before. Open that monomer.
An isomer label ('A') is only allowed on a structure that carries an OR enhanced-stereo group … A label was typed on a resolved structure. Clear it.

Case 4: a racemate

Later, from Duplicate and resolve stereo on the racemate, either:

register one enantiomer you isolated and identified: structure without the block, the wedge as assigned, a new symbol; or
register two fractions separated but not yet identified: two copies that keep the centre unknown, |o1:10|, with labels A and B, each resolved from the racemate. Turning &1 into or1 counts as a resolution, and the labels keep the two apart.

Editing a resolved monomer or its source

The Resolved from field is read-only once set. The link is changed by registering a new monomer, not by editing it.
The Stereo comment stays editable, and empties the note when cleared.
The structure of a source that has resolved children is frozen: the edit is refused and names the children. Register the corrected structure as a new monomer, or retire the children first.
Retiring the source is allowed. Its children keep the link, shown as retired, and still open its version history.

Enhanced Stereochemistry: what the groups, the label and the link mean.
How to Create or Edit a Monomer: the rest of the form.
How to Import Monomers in Bulk: the ISOMER_LABEL and RESOLVED_FROM columns do the same from a file.