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I think it's just a matter of convention. From what I've read though, at least in the realm of electrostatics, potential energy is usually the work that must be done to move an object a certain distance. if the potential energy is negative, it's entirely possible that it means that no work has to be done for the two atoms to move together.
This is because the charges on both the atoms are different i.e. one is positive and the other is negative. When using the equation to calculate Ep, you are multiplying both the charges on the atoms (q1.q2/r^2). Since multiplying a negative by a positive, will always give you a negative answer, Ep is negative for attractive forces (as the charges have to be opposite for attraction to occur.
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