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. 2018 Jun 9;46(13):6528–6543. doi: 10.1093/nar/gky490

Table 4.

Geometry parameters of the U14(N3)/A17(OP2) and C14+(N3)/A17(OP2) H-bonds in the optimized structures

N3–H3 bond and interatomic distances (in Å)
N3–H3 H3/OP2 N3/OP2
Methoda MM QM/MM MM QM/MM MM QM/MM
System
2n0j_wt 1.011 1.034 1.86 1.84 2.86 2.87
2n0j_wt_K+ 1.010 1.036 1.78 1.75 2.76 2.77
2n0j_C14+ 1.010 1.047 1.78 1.65 2.73 2.66
Methoda MM QM
System
Uracil base (reference) 1.004 1.017
Cytosine+ base (reference) 1.003 1.017

aMethod used to perform the optimization: MM—molecular mechanics (bsc0χOL3); QM—TPSS-D3; QM/MM—TPSS-D3 in the QM part of the system and bsc0χOL3 in the MM part of the system. The reference MM and QM optimizations of isolated bases were performed in continuum solvent as implemented in AMBER (40,74) and in COSMO model (75), respectively. All other calculations (QM/MM and MM of the complete NSR) were performed in explicit SPC/E solvent.