The side chains and rotamers
were adjusted with knowledge-based potentials, simulated annealing with explicit solvent, and small equilibration simulations using YASARA's refinement protocol .
The isomers of lysine 113 in Air-AAR1-Like and lysine 132 in Air-CCAPR1-Like were adjusted using Dunbrack's list of rotamers
All the rotamers
of DHBAs are presented in Supplementary Material available online at https://doi.org/10.1155/2017/5936239 (Figures S1-S6).
The poor ramachandran outliers and rotamers
were removed by utilizing WinCoot  tool.
4 in which the influence of the THF ring's orientation on the potential energy of the rotamers
[sup.1]H NMR (CD[Cl.sub.3]): (Rotamers
1:1) 51.06 and 1.13 (t, J = 7.2 Hz, 3H, C[H.sub.3]), 2.95 (s, 3H, C[H.sub.3]), 3.29 and 3.35 (q, J = 7.2 Hz, 2H, C[H.sub.2]), 4.03 and 4.06 (s, 2H, C[H.sub.2]), 7.17 and 7.18 (dd, J = 9.5, 1.9 Hz, 1H), 7.38 and 7.39 (d, J = 8.4 Hz, 2H), 7.56 (dd, J = 9.5, 0.8 Hz, 1h), 7.8 (d, J= 8.4 Hz, 2H), 8.21 and 8.23 (J = 1.8, 0.8 Hz, 1H).
The topics include macromolecules and Chimera, algorithms dealing with distance, structure overlap and alignment, and rotamers
and side-chain conformation.
In the present investigation, we have calculated the static and dynamic electronic (hyper)polarizabilities of the most stable conformations of 2,2' -bithiophene in the gas phase, aiming to identify physicochemical properties useful to discriminate the different rotamers
. The frequency-dependent first-order hyperpolarizabilities were obtained for the SHG and EOPE NLO processes at the typical experimental wavelength of the Nd:YAG laser (1064 nm).
Andersen, "Isolation and identification of flavonoids, including flavone rotamers
, from the herbal drug (hawthorn)," Phytochemical Analysis, vol.
Pratt, "High resolution [S.sub.1] [left arrow] [S.sub.0] fluorescence excitation spectra of hydroquinone--distinguishing the cis and trans rotamers
by their nuclear spin statistical weights," The Journal of Chemical Physics, vol.
The density for Br2' is weaker than that for Br4', likely due to different rotamers
of the second ring, which would maintain the position of Br4' but reposition Br2' in multiple orientations.