Table 1. Matrix of Global Distance Test (GDT) Results Showing % Similarity of the Unliganded GR Crystal Structure and CONCOORD Generated Structures Using a 1 Å Cutoff.

structure	unliganded GRa	CONCOORD 1	CONCOORD 2	CONCOORD 3	CONCOORD 4	CONCOORD 5	CONCOORD 6	CONCOORD 7	CONCOORD 8
unliganded GRa	100	28.15	29.577	20.079	17.667	26.427	19.193	16.683	23.228
CONCOORD 1	28.15	100	20.472	16.093	32.677	14.124	14.665	17.224	20.276
CONCOORD 2	29.577	20.471	100	23.278	21.555	28.593	11.86	10.433	22.195
CONCOORD 3	20.079	16.093	23.278	100	12.894	10.531	17.372	13.829	13.484
CONCOORD 4	17.667	32.677	21.555	12.894	100	17.52	8.563	14.075	16.978
CONCOORD 5	26.427	14.124	28.593	10.531	17.52	100	11.811	7.136	33.612
CONCOORD 6	19.193	14.665	11.86	17.372	8.563	11.811	100	14.764	10.974
CONCOORD 7	16.683	17.224	10.433	13.829	14.075	7.136	14.764	100	11.614
CONCOORD 8	23.228	20.276	22.195	13.484	16.978	33.612	10.974	11.614	100

^aThe crystal structure (PDB 1ZUW)⁸ of GR bound to d-glutamate was used as the initial structure. d-Glutamate was deleted from the structure, and the unliganded GR form was subjected to a 20 ns MD simulation. The low energy structure from the production phase of the MD simulation was used as the seed structure for the CONCOORD method of structural sampling. The aggregate of the structures in Table 1 represent a crude model for the apo GR ensemble. YASARA’s CONCOORD utility was used to generate structures which sample the conformational space of the GR structure.²¹ A GDT using a 1 Å cutoff was then performed on a structural superpose of the ensemble of the unliganded GR crystal structure and the CONCOORD generated structures. The GDT assesses the quality of superpose of two structures within a defined distance, providing the percentage of superposed atoms (Method S10).