Atom Types in ChimeraX

Atom types are classifications based on element and bonding environment. These assignments are used to identify functional groups and to set VDW radii. Like element symbols, ChimeraX atom types can be used in command-line specification or chosen from the Select menu.

ChimeraX uses atom and residue names, or if these are not “standard,” the coordinates of atoms, to determine connectivity and atom types. Errors in atom-type assignment may occur, especially in low-resolution structures and unusual functional groups.

For determination from coordinates, the algorithm and atom types are adapted from the program IDATM:

Determination of molecular topology and atomic hybridization states from heavy atom coordinates. Meng EC, Lewis RA. J Comput Chem. 1991 Sep;12(7):891-8.

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Atom-Type Identification Algorithm

Many experimentally determined structures of molecules do not include hydrogen atoms. IDATM uses the coordinates of nonhydrogen atoms (plus any hydrogens, if present) to determine the connectivity and hybridization states of atoms within molecules. This knowledge is essential for detailed molecular modeling. The algorithm is hierarchical; the “easiest” assignments are done first and used to aid subsequent assignments. The procedure can be divided into several stages:

1. Heavy Atom Valence (HAV). Elements are determined from atom names, and atoms are considered bonded if the distance between them is no greater than the sum of their covalent bond radii plus a tolerance of 0.4 Å. Atoms are sorted according to the number of nonhydrogen atoms they are bonded to; this will be referred to as heavy atom valence.
2. Fully Determined Atoms and Atoms With HAV > 1. The types of some atoms may already be fully determined at this stage; for example, HAV 4 carbons must be sp³-hybridized. Distinctions are also made based on the number of attached oxygens. The average of the three bond angles about each HAV 3 atom is calculated and used to assign the type of the central atom. The average bond angle has been found to be a reliable indicator of hybridization state. Only one bond angle is available for HAV 2 atoms, and this is a less reliable indicator; HAV 2 carbon and nitrogen atoms are assigned types based on the angle but are marked for further examination.
3. Atoms with HAV = 1. The only geometric information available for HAV 1 atoms is bond length. Types are assigned based on bond length and the type of the partner atom.
4. Resolution of Ambiguities and Identification of Charged Groups. Atoms tagged for further examination in the second stage are retyped, if necessary, using bond length information. Next, functional groups likely to be charged at physiological pH are identified: sp³-hybridized nitrogens bonded only to sp³-hybridized carbons and/or hydrogens are assigned a positively charged type; guanidinium groups are identified; carboxylate and nitro groups are identified. Finally, isolated sp²-hybridized carbons (bonded to only sp³-hybridized atoms) are retyped as sp³-hybridized carbons.

In ChimeraX, a few additional distinctions are made. Carbons that are sp²-hybridized and part of planar ring systems are given an aromatic type. Oxygens within aromatic rings are given an aromatic type. Geometric criteria are used to subdivide sp²-hybridized nitrogens into double-bonded (or aromatic) and non-double-bonded categories. Sulfone and sulfoxide sulfurs are given two different types rather than lumped into a single category, as are resonance-equivalent terminal oxygens sharing formal negative charge.

Some types depend on protonation states, and more information is used to determine the protonation states of groups with pKa values close to 7:

• When a phosphate group has three terminal oxygens (bonded only to the phosphorus), if one P–O bond is at least 0.05 Å longer than each of the others, that oxygen will be typed as O3 instead of O3–. A terminal O3 oxygen will be protonated if/when hydrogens are added, whereas terminal O3– oxygens will not.

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Covalent Bond Radii

Approximate covalent bond radii are used to identify bonds when connectivity is not specified in the input file, and to set default VDW radii for certain rarely encountered atom types.

A longer list, obtained many years ago from documentation from the Cambridge Crystallographic Data Centre, can be found in Table III of the paper cited above.