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<div style="margin:0 0 10px 0;"><b>I have an interesting question reguarding NH2 attached to cyclic rings in topology files. I have seen them represented in a somewhat SP3 state, where the hydrogens are held as if there were almost 3, rather than two. I have also seen them artificially flatened with an improper dihedral, which allows them to rotate around the N-C bond. My question is which is correct, and if they are given an improper dihedral how would this effect the energy calculations. These do commonly occure such as nucletides, but mostly I refer to small molecules with gnerated topologies. I have looked up in chem liturature and found in empirical studies they do indeed remain flatened in reguard to the plane of the ring, rotating around the bond, however in chemistry text and papers treeting them in reactions, etc, they are in an SP3 state?</b></div>
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<div style="margin:0 0 10px 0;"><b>Stephan Watkins</b></div>
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