Atom types are classifications based on element and bonding environment. Atom type assignments are used in functional group identification, hydrogen addition, and hydrogen bond identification, and to determine VDW radii.
Chimera 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. Atom type assignments can be displayed as labels (for example, with Actions... Label... IDATM type) and changed with the command setattr.
The algorithm and atom types discerned are adapted from the program IDATM; for a detailed description of IDATM and validation testing, please see
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 atom types and algorithm, including extensions of the original method, 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 Chimera differ from those in the original method, the same type may appear in more than one row in the following table.
|IDATM atom type||description|
|N3+||N3+||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 (trigonal planar; 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|
|O3–||O–||resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, etc.)|
|O2–||O–||resonance-equivalent terminal oxygen on planar center (carboxylate, nitro, nitrate)|
|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||Box||other oxidized boron|
|B||B||other boron (not oxidized)|
|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|
Brief descriptions of the original algorithm and further steps added during implementation in Chimera are given here.
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 Chimera, 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: