Table 3 H-bond analysis of the MD simulations corresponding to the lowest binding energies for CMA and N-methylglucamine (abbreviated as NMG) in complexes with PPARα and/or RORα receptors.

Protein	Ligand	Program-Pose number	H-bond description	Occupancy, %
PPARα	CMA	CMA-Autodock4.2-3	O_C=O-Ser280(OH)	95
			O_COO-Ala333(NH)	60
			O_COO-Tyr334(NH)	22
	NMG	NMG-DOCK-1	O₃-His440(NE2)	16
			H_OH4-Gln277(OE1)	83
			N_NH-Cys276(O_C=O)	26
			H_OH2-Tyr464(NE2)	13
			N_NH-Ser280(OH)	12
RORα	CMA	CMA-DOCK-1	O_COO-Gln289(NH)	96
			O_C=O-Arg370(NH)	68
			O_COO-Tyr290(NH)	60
			O_COO-Arg370(NH2)	46
	NGM	NMG-Autodock4.2-3	N_NH-Glu329(COO)	95
			N_NH-Asp382(COO)	106
			H_OH4-Tyr380(O_C=O)	49
			H_OH-Lys326(O_C=O)	40
			H_OH-Glu329(O_C=O)	28
			H_OH1-Lys326(O_C=O)	24
			H_OH3-Tyr380(O_C=O)	20
			H_OH3-Glu329(O_C=O)	20

H-bonds with occupancies higher than 10% in the last 10 ns of the MD simulation are reported. In cases wherein an analyzed chemical group had identical atoms (like oxygen or hydrogen atoms in -COO or -NH2, respectively), the sum of the H-bond occupancies (corresponding to all types of H-bond) is provided, which can lead to a number higher than 100%. The number higher than 100%, however, still corresponds to a single type of the hydrogen bond in terms of the atoms participating in its establishment. For example, 106% of the N_NH-Asp382(COO) corresponds to a unique type of hydrogen bond established between one of the two hydrogen atoms bound to the nitrogen atom in N-methylglucamine and one of the two oxygen atoms from the carboxyl group of Asp382. Since the atoms of each of these pairs are completely equivalent and are only numbered differently in the simulation for technical reasons, providing any information where these atoms are distinguished, would be physically irrelevant. The four possible combinations making up this type of the hydrogen bond would contribute 25% of the sum for all the bonds in an MD simulation of the infinite length. For NGM: hydroxyl groups are abbreviated as OH, OH1, OH2, OH3, or OH4 from the closest to the most remote group in the carbon chain in relation to the amine-group.

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