How does a neutron have more mass than a hydrogen atom's isotope (Specifically deuterium)? A hydrogen atom weighs 1.00794 u ± 0.00001 u. The mass of a neutron is slightly above it, at 1.00866491600(43) u‎. I'm wondering, how does a neutron weigh more than itself plus 2 extra particles, as we see in hydrogens weight? 
Edit: I was unaware that I should have mentioned the hydrogens isotope, deuterium, since hydrogen atoms do not have a neutron as Ghost pointed out in his answer below.
 A: Free neutrons are unstable, and decay to a proton, electron, and electron antineutrino with a half life of about 10 minutes. https://en.wikipedia.org/wiki/Neutron
In most cases, the electron escapes but the proton captures another electron from its environment, making a hydrogen atom composed of one proton, one electron (and no neutrons.) In some rare cases the electron fails to escape from the proton and the two particles become a hydrogen atom directly (in these cases all the excess energy is carried off by the antineutrino.) 
Given that the decay from a neutron to a hydrogen atom is spontaneous (releases energy) it is unsurprising that a neutron weighs more than a hydrogen atom, in accordance with the relativistic mass-energy relation E=mc^2.
A: There is a misconception in your question, specifically:

how does a neutron weigh more than itself plus 2 extra particles

It doesn't.
A hydrogen atom is composed only of a proton and an electron, but no neutron.  Hydrogen is shown diagrammatically shown below:

Image Source
If a neutron were included, then it becomes the isotope of hydrogen, deuterium, which 
according to the Commission of Isotopic Abundances and Atomic Weights, has an atomic mass greater than a neutron itself.
