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How does CDD count the # of hydrogen bond acceptors on molecules?

You're looking at Lipinski properties of your compounds. You don't understand how the number of hydrogen bond acceptors is counted. It does not appear to simply be the sum of N's and O's in the molecule as was your understanding of how they're counted. 

H-bond donors and acceptors are being calculated according to the general rule, while the Lipinski violations are only counted based on oxygen and nitrogen.

Acceptor atoms are defined to have a lone-pair electron. 

Donor atoms are connected with at least one H atom. 

CDD displays the default value for the major protonation form at physiological pH. However, for the Lipinski Rule of 5  violations, only oxygen and nitrogen are counted, and that is what CDD takes into consideration despite the counts you see.