The phrase "atomic clash" is correct and usable in written English.
It can be used in contexts discussing conflicts or confrontations that are significant or impactful, often in a metaphorical sense.
Example: "The two rival factions engaged in an atomic clash that would determine the future of their society."
Alternatives: "nuclear confrontation" or "cataclysmic conflict".
With regard to the atomic clashes of H-atoms with others, it is observed that the absolute number of atomic clashes involving non-polar H-atoms is much higher than the number of clashes made by polar H-atoms; this is because non-polar H-atoms are mostly located in the hydrophobic core, which is usually tightly packed [39], and thus have a higher chance to clash with other atoms.
The number of atomic clashes between the predicted H-atoms and other atoms for all the 37 high resolution structures are shown in Fig. 4 and the average values are summarized in Table 5.
The number of atomic clashes between the added H-atoms and other heavy atoms is an another important evaluation criterion to assess the quality of hydrogen addition algorithms [36].
On average, for all the H-atoms, the experimental structures have the lowest average number of atomic clashes, i.e. Nall = 1.48.
Although the interactions with binding sites improve, the changes are very small, except for the reduction in atomic clashes.
Programs available as of this writing are very fast and reasonably accurate, as measured by deviations of side-chain dihedral angles; however, often due to multiple atomic clashes, they produce structures with high positive energies.
The interactions measured in YASARA include the number of atomic clashes (bumps), the number and total energy of hydrogen bonds, and the number and strength of hydrophobic contacts, π-π interactions, and cation-π interactions.
This is problematic in applications where the energy values are important, for example when placing small molecules in docking applications; the relatively small binding energy of the small molecule is drowned by the large energy due to atomic clashes that hampers finding the lowest energy state of the docked ligand.
It has been reported that the length of bonds between hydrogen and heavy atoms are systematically underestimated in X-ray diffraction [39], [40]; this may be partially the reason why there are still some atomic clashes in the experimental structures.
Therefore, the ID-loop was manually rebuilt, to avoid atomic clashes.
