Attachment Points and CAP Groups

A monomer is not a molecule but a fragment of one: it has open bonds where it joins its neighbours. This article explains how those bonds, the attachment points or R-groups, are written in a SMILES, what a cap group is, and why the service insists on both.

A monomer is a residue, not a free molecule

Alanine as a free amino acid is C[C@H](N)C(=O)O. Inside a peptide it has lost a hydrogen from its amine and a hydroxyl from its carboxylic acid, and it is bonded to two neighbours instead. The monomer registered in the library is that residue, with the two open bonds marked:

C[C@H](N[*:1])C([*:2])=O

Each [*:n] is a dummy atom standing for a bond to something else. The number is the R-group label: R1 and R2 here. HELM connects monomers by naming the R-groups on each side, so R2 of one residue bonds to R1 of the next.

The conventions behind the numbers

The numbers are a convention, not a chemical fact, and the tools that build sequences rely on it.

Polymer type	Monomer type	`R1`	`R2`	`R3`
`PEPTIDE`	`Backbone`	Amine nitrogen, N-terminal side	Carbonyl carbon, C-terminal side	Side chain, when the residue can branch, such as the epsilon amine of lysine or the thiol of cysteine
`PEPTIDE`	`Branch`	Bond to the backbone residue's `R3`
`RNA`	`Backbone` sugar	5' oxygen, to the previous phosphate	3' oxygen, to the next phosphate	1' carbon, to the base
`RNA`	`Backbone` phosphate	To the 3' of the previous sugar	To the 5' of the next sugar
`RNA`	`Branch` base	Bond to the sugar's `R3`
`CHEM`	`Undefined`	Free choice, but numbered from `R1` without gaps

Labels run from R1 to R25. They must start at R1 and increase without a gap: a monomer with R1 and R3 but no R2 is rejected.

Notations the service accepts

The service normalises every structure to the [*:n] form, and that is the form it shows when you reopen a monomer. It also reads:

Notation	Example	Where you meet it
Atom map on a dummy atom, `[*:n]`	`C[C@H](N[:1])C([:2])=O`	The recommended form, used by the import file and the form.
CXSMILES R-labels	`C[C@H](N[])C([])=O \\|$;;;_R1;;_R2$\\|`	Exported by chemistry toolkits; the label block after the `\\|` names each dummy atom.
Folded cap atom, `[H:1]`, `[OH:2]`	`C[C@H](N[H:1])C([OH:2])=O`	The original Pistoia HELM monomer library. The cap atom itself carries the map number.

[R1] as a bracket atom, and an unnumbered [*], are not attachment points. The first is not valid SMILES for the service; the second is a dummy atom with no label and is rejected with Number of R-Groups in Attachmentlist is NOT equal to number of R-Groups in Smiles.

Cap groups: what sits on an unused attachment point

An attachment point that is not bonded to a neighbour still has to be something. The cap group is the small group that completes the valence there: for a peptide backbone, a hydrogen on R1 gives the free amine, and a hydroxyl on R2 gives the free carboxylic acid. The cap is what the toolkit adds when it draws or computes a monomer at the end of a chain, or on its own.

The service stores the cap group as a name from a controlled vocabulary, and turns it into chemistry with a SMILES template where {n} is the R-group number. The public vocabulary is the one the HELM toolkit ships, and every organisation shares it:

Cap group	Template	Chemistry it completes
`H`	`[*:{n}][H]`	An amine, a thiol, an alcohol, an alkyl chain end. The default.
`OH`	`O[*:{n}]`	A carboxylic acid on `R2` of an amino acid, a phosphate oxygen.
`NH2`	`N[*:{n}]`	A C-terminal amide, a guanidine or amine attached through its carbon.
`Azide`	`[*:{n}]N=[N+]=[N-]`	An azido handle for click chemistry.
`Ethynyl`	`[*:{n}]C#C`	A terminal alkyne, the other partner of a click reaction.

Any other cap, such as a halide end (Br, Cl, I) or a vinyl end (Ethenyl), is a cap group of the organisation that uses it, described in the next section.

Cap groups are written in the import file as R1:H;R2:OH and chosen from a selector per attachment point on the form. A cap outside the vocabulary is rejected with the list of valid values, never silently replaced: substituting a hydroxyl for an unknown cap would store a different molecule without anyone noticing.

Your organisation's vocabulary

The vocabulary a curator sees is the public one plus the cap groups your organisation adds. An administrator manages them on the Cap groups page: see How to Manage Your Organisation's Cap Groups.

A private cap group belongs to your organisation alone. Its symbol is valid in your monomers and imports, and unknown to every other organisation, which rejects it like any cap outside its vocabulary.
A private cap group never takes the symbol of a public one. OH means the public hydroxyl for every organisation; a cap of another structure gets a symbol of its own. The reason is in the next section: public monomers name their caps by symbol.
Symbols are compared whatever the case. oh, OH and Oh name the same cap group, so an organisation cannot hold two cap groups that differ only by case, nor a private oh beside the public OH.

A cap is copied into your monomers

When one of your organisation's monomers is saved, the service stores each cap group by its symbol, together with the atoms the template gave it. The cap group is not looked up again when that monomer is read. Two consequences follow:

changing a cap group's template leaves your monomers already registered as they were. Only the monomers written afterwards, or edited and saved again, take the new template;
retiring a cap group never alters the structure of your monomers.

Public monomers are the exception. They name their cap groups without storing the atoms, and are read with the public cap groups. That is why a private cap group cannot take a public symbol: a private OH would cap every public monomer that ends on OH with another structure, for your organisation only, and the public catalogue would no longer be the same molecules for everyone.

Retired, not deleted

There are two ways for an organisation to stop using a cap group, and the difference matters:

Deactivating it keeps the cap group, unused. It leaves the form and imports refuse it, but it can be switched back on, and the monomers that name it still name something that exists.
Deleting it removes the cap group. That is allowed only when none of the organisation's monomers uses it. Otherwise those monomers would name a cap group that exists nowhere, and a cap group created later under the same symbol, with a different template, would silently give their name another structure.

So a cap group that monomers use is retired by deactivating it, and deleted only once nothing uses it.

Why a wrong cap matters

The cap decides the molecule that tools compute from your monomer when the attachment point is free:

R2:H on an amino acid makes its free form an aldehyde, and the molecular weight and logP of every peptide ending on it are wrong;
R1:OH on an amino acid makes the N-terminus a hydroxylamine;
a cap chosen on the wrong side of a multi-atom template, such as writing the azide as if it were a single atom, gives a pentavalent carbon.

The cap does not change how the monomer bonds inside a chain. Two monomers with the same skeleton and different caps are the same residue in the middle of a sequence, and different molecules at its ends.

How to Create or Edit a Monomer: where the caps are set on the form.
How to Manage Your Organisation's Cap Groups: add, deactivate or delete a cap group.
Canonical SMILES and Duplicate Detection: why a change of cap counts as a change of the monomer.