--- title: "How to Resolve the Stereochemistry of a Monomer" slug: "how-to-resolve-the-stereochemistry-of-a-monomer" status: "new" updated: 2026-11-03T16:08:17Z published: 2026-11-03T16:08:17Z canonical: "docs.discngine.com/how-to-resolve-the-stereochemistry-of-a-monomer" --- > ## Documentation Index > Fetch the complete documentation index at: https://docs.discngine.com/llms.txt > Use this file to discover all available pages before exploring further. # 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](/public/docs/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. 1. On the **Monomers** page, click **New monomer** and fill in the definition as for any monomer. See [How to Create or Edit a Monomer](/public/docs/how-to-create-or-edit-a-monomer). 2. 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| ``` 3. 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. 4. 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. 1. Open the unknown monomer, Phx1, from the **Monomers** page. 2. 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 ``` 3. Fill in the **Symbol**, which must be new, and the **Name**. 4. 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. 5. Write the method and the confidence in **Stereo comment**, for example `Configuration assigned by X-ray on the HCl salt, batch 2026-10`. 6. 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 Register the racemate with an *and* group, `|&1:10|` on the same example. No label applies. 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. ## Related - [Enhanced Stereochemistry](/public/docs/enhanced-stereochemistry): what the groups, the label and the link mean. - [How to Create or Edit a Monomer](/public/docs/how-to-create-or-edit-a-monomer): the rest of the form. - [How to Import Monomers in Bulk](/public/docs/how-to-import-monomers-in-bulk): the `ISOMER_LABEL` and `RESOLVED_FROM` columns do the same from a file.