Skip to main content
. Author manuscript; available in PMC: 2021 Apr 23.
Published in final edited form as: J Chem Theory Comput. 2021 Feb 9;17(3):1842–1857. doi: 10.1021/acs.jctc.0c01148

Figure 1.

Figure 1.

Schematic of the coarse-grained representation in IsRNA1 model and the structural variables used in the energy functions for canonical base-pairing interactions. (A) The backbone is defined by two beads P and S located at the P and C4’ atoms, respectively, and (B-D) the purine and pyrimidine bases are represented by three and two beads positioned at the center-of-mass of the grouped heavy atoms, respectively. Three canonical base-pairing interactions are accurately described by the combined covalent energy functions based on the selected reaction coordinates: (B) G-C base pair with ϕ1 = ϕ(RC − GO − GN− CN) and ϕ2 = ϕ(GN − GO − CN − Yc), (C) A-U base pair with ϕ1 = ϕ(RC − Ac − AN − UO) and ϕ2 = ϕ(AC − AN − UO − YC), and (D) G-U base pair with ϕ1 = ϕ(RC − GO − GN − UO) and ϕ2 = ϕ(GN − GO − UO − YC).