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.
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.The original method and some later extensions are described briefly below. Where type definitions are not mutually exclusive, the atom is assigned the most specific type possible; for example, although a carboxylate carbon is also sp2-hybridized, it is assigned the Cac type. Since the categorizations in ChimeraX differ from those in the original method, the same type may appear in more than one row in the following table.
|C1–||C1||sp-hybridized carbon with formal negative charge (carbon monoxide)|
|N3+||N3+, Nox||sp3-hybridized nitrogen with formal positive charge|
|N3||N3||sp3-hybridized nitrogen, formally neutral|
|N2+||Npl||sp2-hybridized ring nitrogen bonded to three other atoms, formally positive|
|N2||Npl||sp2-hybridized nitrogen bonded to two other atoms, formally neutral (pyridine)|
|Npl||Npl||sp2-hybridized nitrogen bonded to three other atoms, formally neutral (amide, aniline)|
|Ng+||Ng+||resonance-equivalent nitrogen sharing formal positive charge (guanidinium, amidinium)|
|Ntr||Ntr||nitro group nitrogen|
|N1+||N1||sp-hybridized nitrogen bonded to two other atoms|
|Oar+||(none)||aromatic oxygen, formally positive (pyrylium)|
|Oar||(none)||aromatic oxygen, formally neutral|
|O3–||O–||possibly resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, N-oxide)|
|O2–||O–||resonance-equivalent terminal oxygen on planar center (carboxylate, nitro, nitrate)|
|O1+||(none)||sp-hybridized oxygen with formal positive charge (carbon monoxide)|
|O1||(none)||sp-hybridized oxygen (nitric oxide)|
|S3+||S3+||sp3-hybridized sulfur with formal positive charge|
|S3–||S2||terminal sulfur on tetrahedral center (thiophosphate)|
|Sac||Sac||sulfate, sulfonate, or sulfamate sulfur|
|Son||Sox||sulfone sulfur (>SO2)|
|Sxd||Sox||sulfoxide sulfur (>SO)|
|B||Bac, Box, B||boron|
|P3+||P3+||sp3-hybridized phosphorus with formal positive charge|
|Pac||Pac||phosphate, phosphonate, or phosphamate phosphorus|
|HC||HC||hydrogen bonded to carbon|
|DC||DC||deuterium bonded to carbon|
|(element symbol)||(element symbol)||atoms of elements not mentioned above|
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:
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:
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.
|Selected covalent bond radii (Å)|
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.