Table 3.

Intramolecular hydrogen bond between O7 and O8 in clindamycin (observed only in WT–CLY trajectories) and intermolecular hydrogen bonds between clindamycin and nucleotides occurring over 10% of total simulation time

Sim. type		Donor	Acceptor	% of sim.	D ⋯ A	D-H ⋯ A
and number		(D)	(A)	time	[Å]	[°]
WT–CLY	1	CLY:O7	CLY:O8	54	2.74 ± 0.06	158.9 ± 3.1
	2			13
	3			36
	1	A2059:N6	CLY:O4	29	3.05 ± 0.04	155.1 ± 1.1
	2			34
	3			58
	1	CLY:O4	A2059:N1	23	2.91 ± 0.01	158.6 ± 1.9
	2			35
	3			27
MUT–CLY	1	G2058:N1	CLY:O4	27	3.02 ± 0.02	146.0 ± 2.8
	2			29
	3			25
	1	CLY:O4	G2058:O6	82	2.71 ± 0.03	158.2 ± 2.2
	2			87
	3			78
	1	A2059:N6	CLY:O6	74	3.11 ± 0.04	152.9 ± 1.2
	2			86
	3			84
	1	CLY:O6	A2059:N1	38	2.90 ± 0.02	157.8 ± 0.9
	2			64
	3			40
	1	CLY:O7	A2503:O2’	86	2.79 ± 0.01	161.3 ± 1.3
	2			96
	3			92
	1	CLY:N1	G2505:O’4	61	3.51 ± 0.03	158.4 ± 0.9
	2			92
	3			82

The simulation types are listed in Table 1. For atom names see Figs. 1 and 2