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I think of it this way: An negatively charged electron farther from the nucleus must be of higher energy in order to resist the pull of the positively charged nucleus. Therefore, an electron closer to the nucleus is of lower energy.
Another way to think of it is that a greater amount of energy is required to free an electron from the inner shell rather than an electron from the outer shell. Because of this, electrons in the outer shell have a higher (potential) energy compared to those in the inner shell.
I don't know if this is correct, but I explain it to myself in this way: The closer an electron is to the nucleus, the greater energy it needs to resist the positive charge of the nucleus. Because the energy of an electron is negative (-), so the greater the "absolute value" of its energy, the lower its energy is.
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