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The phrase "atom that was" is correct and usable in written English.
It can be used in contexts discussing a specific atom in a past state or condition, often in scientific or metaphorical discussions.
Example: "The atom that was once part of the molecule has now been isolated for further study."
Alternatives: "atom previously" or "atom that existed".
Exact(5)
Forty years later Isaac Newton expressed a typical 18th-century view of the atom that was similar to that of Democritus, Gassendi, and Boyle.
+1 for each atom that was merged with another atom due to positional overlap.
Another atom that was off is the hydroxyl hydrogen atom of Thr118 in 1muw.
This is noteworthy because the POCl3 starting material contains one oxygen atom that was expected to remain bonded to the P atom, preventing the formation of P18O4.
An atom that was both a hydrogen-bond donor and an acceptor ('polar' atom, according to the PATTY algorithm) was treated as 0.5 donor and 0.5 acceptor.
Similar(55)
Two optical isomers are possible for every carbon atom that is bonded to four different groups.
A dotted list is a list that has a terminating atom that is not the empty list.
Sometimes we have a very electronegative atom that's going to take more of its equal share of electron density.
For all ligands, every atom that is capable of making a hydrogen bond does so with either protein or solvent.
For each bit, it is determined whether there exists a query atom that is covered by the bit information.
By aliphatic hydroxylation reaction, we mean a hydroxylation of the carbon atom that is not included in the aromatic rings.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com