Table 2 Mean values averaged from the last 20 ns of 100 ns MD simulation of nonbonding interaction energy; combined from Coulomb and Van der Waals potential energies.

N	Ref.	Docking result (kcal/mol)	Distance to T790 (nm)	RMSD (nm)	Numcount	SASA (nm²)	Ligand–protein interaction energy (kcal/mol)	Hydrogen bond (number)
1	3a	− 10.2	0.25	0.21	2608	7.83	− 54.2	1.73
2	3b	− 11.0	0.81	0.27	1714	8.76	− 41.6	0.0
3	3c	− 9.2	2.36	0.35	1049	9.24	− 61.2	1.94
4	3d	− 10.7	0.28	0.12	2220	8.33	− 48.4	0.0
5	3e	− 10.6	0.82	0.14	1499	8.43	− 49.3	0.01
6	3f.	− 10.6	0.35	0.09	2094	7.92	− 61.5	1.46
7	3 g	− 10.9	0.29	0.12	1918	8.02	− 65.0	1.32
8	3 h	− 10.6	0.25	0.05	2677	7.81	− 79.9	1.54
9	3i	− 8.5	0.82	0.16	1260	7.22	− 40.0	0.07
10	3j	− 9.4	1.03	0.3	1230	8.54	− 31.1	0.44
11	3 k	− 9.4	0.84	0.31	1894	9.44	− 41.0	1.26
12	4a	− 9.8	0.65	0.24	1697	8.1	− 51.3	0.87
13	4b	− 10.1	0.86	0.3	1655	8.14	− 59.4	0.36
14	4c	− 10.1	0.56	0.26	1804	7.8	− 53.1	1.25
15	4d	− 10.3	1.77	0.35	1804	8.42	− 43.9	1.09
16	4f.	− 10.0	1.01	0.24	1168	7.59	− 49.4	0.03
17	4 g	− 10.2	0.69	0.27	2034	8.08	− 66.6	1.09
18	4 h	− 8.3	0.38	0.19	2145	8.17	− 53.8	0.66

A contact is counted when the distance from one ligand’s atom and one protein’s atom becomes smaller than 0.6 nm. Minimal distance from ligand to one of the most important residues T790 is shown. Averaging minimal distances to 10 locating residues are listed in Table S2 (SI file).
Significant values are in bold.

Quick links

Search