ATB | Functional Group

cyclohexane `cyclohexane` Carbon frameworks

Definition

anchor: one occurrence is one distinct set of these atoms. Unhighlighted atoms must be present but are not part of the group. Atoms are written as the pattern requires them: OH, NH₂ and O⁻ mean exactly those hydrogens and that charge. The note beside each atom gives its number in the table and, for a carbon, what its letter alone does not: sp3, sp2 or sp from the number of its connections, or aromatic / aliphatic where the pattern requires one (no note: either will do). Lower-case letters are aromatic atoms; * is any atom, a any aromatic atom.

#	Atom	Conditions
1 anchor	carbon (non-aromatic)	in a ring
2 anchor	carbon (non-aromatic)	in a ring
3 anchor	carbon (non-aromatic)	in a ring
4 anchor	carbon (non-aromatic)	in a ring
5 anchor	carbon (non-aromatic)	in a ring
6 anchor	carbon (non-aromatic)	in a ring

Bonds: 1–2 single; 2–3 single; 3–4 single; 4–5 single; 5–6 single; 1–6 single.

Anchor atoms: 1, 2, 3, 4, 5, 6. An environment is a SMARTS pattern that must (or must not) match around the atom, beginning at it; it is shown as written.

SMARTS: [C;R]1-[C;R]-[C;R]-[C;R]-[C;R]-[C;R]-1

Ring condition: the matched atoms must form one of the molecule’s smallest rings (its smallest set of smallest rings); the outer envelope of a fused or bridged system does not count.

Matched with RDKit’s substructure matcher on the molecule with implicit hydrogens and RDKit’s default aromaticity model, in the most aromatic resonance form.

Precedence

No group takes precedence over it.

The comparison is with every match of the other group before any precedence is applied, so the result does not depend on the order in which groups are tried.

Examples

Each is a test of the definition, checked on every change to it: the stated count must be found exactly. Each counted occurrence is highlighted in its own colour.

n = 1 C1CCCCC1

n = 1 CC1CCCCC1

n = 1 O=C1CCCCC1

n = 2 C1CCC(C2CCCCC2)CC1

n = 2 C1CCC2CCCCC2C1

n = 1 C1CCC2CCCC2C1

n = 3 C1CC2CCC1CC2

n = 1 C[C@]12CC[C@H]3[C@@H](CCc4cc(O)ccc43)[C@@H]1CC[C@@H]2O

Near misses

Molecules this group must not be found in (n = 0), also tested on every change. “Matched instead” names a group that takes precedence over this one there: this group’s pattern fits, at the grey atoms, but those lie inside the other group’s match. “Groups found” are simply the groups this molecule has; they did not replace this one.

n = 0 c1ccccc1

Groups found: benzene ring

n = 0 C1=CCCCC1

Groups found: alkene

n = 0 C1CCOCC1

Groups found: ether (aliphatic)

n = 0 C1CCCC1

Groups found: cyclopentane

n = 0 C1CC2CCC1C2

Groups found: cyclopentane

n = 0 c1ccc2c(c1)CCCC2

Groups found: benzene ring

In the ATB

2,063 annotated compounds have it;
56 of them have experimental reference data;
44 are monofunctional: this is their only group, once (rings count as groups, so a phenol is not).

The annotated compounds are those with experimental reference data plus small, neutral organic compounds (up to 12 heavy atoms), not every ATB molecule. Through the API: GET /api/v1/molecules?functional_group=cyclohexane.

Annotation scheme 2.