Table 1.

Hydrogen-bonding pairs observed in both 35 and 14mer RNA aptamers complexed with FMN

Simulation
Hydrogen bond	Average length (Å)	Average angle (°)
1	1.96	163
2	2.23	162
Experimental (NMR)
1	2.11	160
2	2.14	136

Hydrogen bonding data for the 35mer are based on the NMR structure (PDB code 1FMN, first structure). Hydrogen-bonding analysis for the 14mer was performed using the PTRAJ program of AMBER 7. Cutoff distance between heavy atoms is 4.0 Å. Cutoff donor-hydrogen-acceptor angle is 120°. In both cases, hydrogen bond 1 corresponds to that between atom HN3 of FMN and atom N7 of adenine 13 (adenine 26 in the 35mer); hydrogen bond 2 corresponds to that between atom O2 of FMN and atom HN6 of adenine 13 (adenine 26 in the 35mer).