ATP chemical structure: phosphate groups with Oxygen anions or with OH groups?
in vivo : ATP with oxygen anions.
in vitro : Depends on pH of solution
IN VIVO :
DNA = Deoxy Ribonucleic Acid.
DNA is acidic , because its monomers contain three phosphates bound together and this so-called triphosphoric acid is extremely acidic.
In living organisms, DNA is always accompanied by histones(positively charged proteins) or sometimes by Mg+2 complexes. Therefore the dNMPs ( deoxyribo Nucleoside Mono Phosphates) that constitute the genetic material , are negatively charged .
For rNMPs (ribo Nucleoside Mono Phosphates) the negative charged form is also more preferable.
Generally speaking in living creatures , ATP = -4 , ADP = -3 , AMP = -2 charged.
(It is worth mentioning that Pi which is a by-product in cellular energetics is HPO4(-2). )
You can see in Molecular Cell Biology Lodish et al 8th ed section 12.1 that the overall reaction of cellular respiration is:

Notice the charges.
IMPORTANT : Sometimes during the metabolism of these compounds Proton(H+) may be added to oxygens of phosphate groups only because of the mechanism of the reaction which is temporary. But usually the charges are as I mentioned before.
IN VITRO :
If you purify ATP in a solution isolated from the cell, the number of acidic hydrogens attached to the molecule is related to the pH of solution. you can predict the molar concentration of each chemical species the same way you predict the [H3PO4] , [H2PO4 -] , [HPO4 2-] , [PO4 3-] , [H+] in a solution of H3PO4 and H2O (a typical analytical chemistry question) Either by a complex utilization of Henderson–Hasselbalch equation or by Charge and Mass equations.
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