Ring Represenations in SMILES

Cheminformatics Tutorials - Herong's Tutorial Examples

∟SMILES (Simplified Molecular-Input Line-Entry System)

∟Ring Represenations in SMILES

This section provides a quick introduction on ring represenations in SMILES. Append a numeric digit to the starting atom of a ring and close it with the numeric digit as the start atom.

How Rings Are Represented in SMILES? - Rings are represented in SMILES according to the following rules:

1. Append a numeric digit to the starting atom of a ring as its identifier. For example, "C6..." starts ring "6" at atom C.

2. Use the numeric digit associated to the ring to represent the starting atom to the closing bond to the last atom. For example, "...=6" closes ring "6" with a double bond.

Note that closing bond symbol can be omitted, if it is a single bond, or an aromatic bond with atoms in lower letters. For example, C1CCCCC1 is the same as C1CCCCC-1; c1ccccc1 is the same as c1ccccc:1.

3. A ring identifier can be re-used, if the identified ring is already closed. For example, O1CCCCC1N1CCCCC1 is the same as O1CCCCC1N2CCCCC2.

Note that rings can be nested represent multiple connected rings. For example, 'c1ccc2c(c1)c3ccccc3c4ccccc42' represents 4 connected rings as shown below:

Multiple Nested Rings Represented in SMILES

4. If single numerical digits are not enough to identify rings, double digits can used with a prefix of "%" symbol. For example, C60 molecule can represented in SMILES as:

C12=C3C4=C5C6=C1C7=C8C9=C1C%10=C%11C(=C29)C3=C2C3=C4C4=C5C5=C9C6=C7C6=C7C8
=C1C1=C8C%10=C%10C%11=C2C2=C3C3=C4C4=C5C5=C%11C%12=C(C6=C95)C7=C1C1=C%12C5
=C%11C4=C3C3=C5C(=C81)C%10=C23