Standard amino acids:

All standard amino acids are referred to using their 3 letter codes.

Note that specific protonation states for residues with titratable side chains can be specified, and are referred to with the following codes:

ASH: neutral ASP

GLH: neutral GLU

LYN: neutral LYS

ARN: neutral ARG

HID: neutral HIS, protonated at delta position

HIE: neutral HIS, protonated at epsilon position

HIP: positively charge HIS (protonated at both positions)

TYM: negatively charged TYR

CYM: negatively charged CYS

The disulfide-bonded version of CYS is CYX.

By default, the terminal residues are charged (positively charged amino group on N-terminus; negatively charged carboxylate on C-terminus). These residues have an appended letter to distinguish them, "B" for the N-terminus ("beginning"), and "E" for C-terminus ("ending"), e.g., ALAB and ALAE for terminal alanines.

Nonstandard amino acids

SEP: phosphorylated serine

TPO: phosphorylated threonine

PTR: phosphorylated tyrosine

ASQ: phosphorylated Asp

NLE: norleucine (frequently used non-natural)

AIB: aminobutyric acid

MSE: seleno-methionine

HYP: hydroxyproline

MMO: N-methyl Arg

D amino acids

DAL: D-Ala

DVA: D-Val

DLE: D-Leu

DLY: D-Lys

DTY: D-Tyr

DTR: D-Trp

Monoatomic ions

NA: sodium (1+)

K: potassium (1+)

CA: calcium (2+)

MG: magnesium (2+)

FE: iron (3+)

ZN: zinc (2+)

CO: cobalt (2+)

CL: chloride (1-)

Capping groups:

There are a variety of options for terminating the chain.

ACE: acetyl (N-terminus)

NMA: N-methyl amide (C-terminus)

PCA: pyroglutamic acid (N-terminus)

NH2: amide cap (N-terminus; like NMA, except without the methyl)

ASA: aspartic aldehyde (C-terminus; ASP, but with aldehyde terminus)

Note that the common capping groups ACE, NH2, and NMA create an additional peptide bond. PCA is somewhat more exotic, and results from a GLU side chain forming a cyclic amide with the N-terminus. All of the listed caps create a neutral terminus.

Common ligands:

Many ligands are now supported, in fact most ligands found in the PDB have been atomtyped. Some common ones include HEM (heme) and COA (acetyl CoA). There are about 3000 others. Naming conventions are intended to match those approved by the PDB, i.e., 3-letter codes, which can be found in databases such as HIC-UP.