Table 2. Mean Intramolecular Distances for the CLY Constructs from Discrete Molecular Dynamics.

Distances are reported in nanometers (nm). <V_c> is the RMS distance between the eCFP chromophore and the linker N-terminus. <V_y> is the RMS distance between the eYFP chromophore and the linker C-terminus. <R_c> is the RMS distance between the two chromophores. <R_e> is the RMS end-to-end distance for the linker. Model <R_e> is the calculated end-to-end distance for the linker using a published geometrical model to relate the interchromophore separation to the linker end-to-end distance as $\langle R_e\rangle =\sqrt{\left(\langle V_c^2\rangle +\langle V_y^2\rangle +\langle R_c^2\rangle \right)}$ [26]. This geometrical calculation using these parameters does not recover the observed RMS end-to-end distance for the linker.

Parameter	CLY1	CLY5
<Vc>	2.0 ± 0.1	2.0 ± 0.1
<Vy>	2.2 ± 0.1	2.4± 0.1
<Rc>	5.2± 1.5	6.2 ± 1..8
<Re>	3.1 ± 1.0	4.4 ± 15
Model <Re>	4.4	5.6