FMO DATABASE

FMODB ID: 52QZZ

Calculation Name: 4EFO-A-Xray372

Preferred Name: Serine/threonine-protein kinase TBK1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4EFO

Chain ID: A

ChEMBL ID: CHEMBL5408

UniProt ID: Q9UHD2

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-652467.587702
FMO2-HF: Nuclear repulsion	616589.008566
FMO2-HF: Total energy	-35878.579135
FMO2-MP2: Total energy	-35984.734754

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:298:PRO)

Summations of interaction energy for fragment #1(A:298:PRO)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
14.319	0.083999999999999	9.214	10.157	-5.137	-0.019

Interaction energy analysis for fragmet #1(A:298:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.003

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	300	GLY	0	0.085	0.036	2.539	19.429	5.233	9.137	9.684	-4.626	-0.022
4	A	301	SER	0	0.028	-0.002	3.328	-0.678	-0.856	0.078	0.483	-0.383	0.003
5	A	302	THR	0	-0.002	-0.027	6.450	-0.472	-0.472	0.000	0.000	0.000	0.000
6	A	303	SER	0	0.014	0.011	4.411	-1.614	-1.475	-0.001	-0.010	-0.128	0.000
7	A	304	ASP	-1	-0.826	-0.909	6.562	0.630	0.630	0.000	0.000	0.000	0.000
8	A	305	ILE	0	-0.017	-0.026	8.185	-0.378	-0.378	0.000	0.000	0.000	0.000
9	A	306	LEU	0	0.016	0.008	11.134	-0.135	-0.135	0.000	0.000	0.000	0.000
10	A	307	HIS	0	-0.026	0.008	11.278	-0.225	-0.225	0.000	0.000	0.000	0.000
11	A	308	ARG	1	0.863	0.946	10.407	-1.227	-1.227	0.000	0.000	0.000	0.000
12	A	309	MET	0	-0.010	0.018	14.312	-0.084	-0.084	0.000	0.000	0.000	0.000
13	A	310	VAL	0	-0.023	-0.029	17.421	0.058	0.058	0.000	0.000	0.000	0.000
14	A	311	ILE	0	-0.032	0.003	20.040	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	312	HIS	0	0.013	0.008	22.464	0.018	0.018	0.000	0.000	0.000	0.000
16	A	313	VAL	0	0.005	0.003	24.054	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	314	PHE	0	0.004	0.000	26.330	0.004	0.004	0.000	0.000	0.000	0.000
18	A	315	SER	0	-0.004	-0.025	27.913	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	316	LEU	0	0.052	0.008	29.790	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	317	GLN	0	-0.033	-0.011	31.655	0.002	0.002	0.000	0.000	0.000	0.000
21	A	318	GLN	0	0.017	0.022	28.955	0.003	0.003	0.000	0.000	0.000	0.000
22	A	319	MET	0	-0.025	0.009	31.984	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	320	THR	0	-0.016	-0.030	27.585	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	321	ALA	0	0.028	0.016	27.886	0.001	0.001	0.000	0.000	0.000	0.000
25	A	322	HIS	0	-0.008	0.022	22.693	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	323	LYS	1	0.954	0.987	20.863	-0.313	-0.313	0.000	0.000	0.000	0.000
27	A	324	ILE	0	-0.018	-0.010	18.379	0.035	0.035	0.000	0.000	0.000	0.000
28	A	325	TYR	0	0.004	-0.005	15.036	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	326	ILE	0	-0.031	-0.015	14.480	0.054	0.054	0.000	0.000	0.000	0.000
30	A	327	HIS	0	0.013	0.012	10.105	-0.078	-0.078	0.000	0.000	0.000	0.000
31	A	328	SER	0	0.063	0.011	13.492	-0.117	-0.117	0.000	0.000	0.000	0.000
32	A	329	TYR	0	-0.003	-0.014	13.994	-0.068	-0.068	0.000	0.000	0.000	0.000
33	A	330	ASN	0	-0.036	-0.005	11.999	0.050	0.050	0.000	0.000	0.000	0.000
34	A	331	THR	0	0.040	0.018	15.347	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	332	ALA	0	0.057	0.022	18.681	0.031	0.031	0.000	0.000	0.000	0.000
36	A	333	THR	0	-0.040	-0.018	19.575	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	334	ILE	0	0.027	0.022	14.339	0.007	0.007	0.000	0.000	0.000	0.000
38	A	335	PHE	0	0.033	0.009	17.558	0.026	0.026	0.000	0.000	0.000	0.000
39	A	336	HIS	1	0.884	0.921	19.656	-0.179	-0.179	0.000	0.000	0.000	0.000
40	A	337	GLU	-1	-0.893	-0.932	16.366	0.253	0.253	0.000	0.000	0.000	0.000
41	A	338	LEU	0	-0.044	-0.031	13.897	0.014	0.014	0.000	0.000	0.000	0.000
42	A	339	VAL	0	0.030	0.018	17.865	0.003	0.003	0.000	0.000	0.000	0.000
43	A	340	TYR	0	-0.003	0.023	19.995	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	341	LYS	1	0.911	0.954	13.103	-0.557	-0.557	0.000	0.000	0.000	0.000
45	A	342	GLN	0	-0.062	-0.043	18.609	-0.030	-0.030	0.000	0.000	0.000	0.000
46	A	343	THR	0	0.011	0.004	21.524	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	344	LYS	1	0.887	0.948	21.238	-0.226	-0.226	0.000	0.000	0.000	0.000
48	A	345	ILE	0	0.031	0.038	25.041	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	346	ILE	0	0.025	0.003	25.237	0.016	0.016	0.000	0.000	0.000	0.000
50	A	347	SER	0	0.050	0.009	22.041	0.003	0.003	0.000	0.000	0.000	0.000
51	A	348	SER	0	-0.024	-0.013	25.019	0.003	0.003	0.000	0.000	0.000	0.000
52	A	349	ASN	0	0.030	0.016	28.346	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	350	GLN	0	-0.038	-0.006	23.297	0.006	0.006	0.000	0.000	0.000	0.000
54	A	351	GLU	-1	-0.918	-0.948	28.926	0.094	0.094	0.000	0.000	0.000	0.000
55	A	352	LEU	0	-0.037	-0.019	26.436	0.009	0.009	0.000	0.000	0.000	0.000
56	A	353	ILE	0	0.015	0.011	30.702	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	354	TYR	0	-0.019	-0.031	30.868	0.008	0.008	0.000	0.000	0.000	0.000
58	A	355	GLU	-1	-0.840	-0.915	33.353	0.113	0.113	0.000	0.000	0.000	0.000
59	A	356	GLY	0	-0.012	-0.003	36.437	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	357	ARG	1	0.940	0.972	36.985	-0.089	-0.089	0.000	0.000	0.000	0.000
61	A	358	ARG	1	0.979	0.994	34.474	-0.077	-0.077	0.000	0.000	0.000	0.000
62	A	359	LEU	0	-0.029	-0.016	28.521	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	360	VAL	0	-0.023	-0.023	31.261	0.003	0.003	0.000	0.000	0.000	0.000
64	A	361	LEU	0	-0.029	-0.012	25.332	0.000	0.000	0.000	0.000	0.000	0.000
65	A	362	GLU	-1	-0.803	-0.885	25.811	0.114	0.114	0.000	0.000	0.000	0.000
66	A	363	PRO	0	0.048	0.005	24.035	0.016	0.016	0.000	0.000	0.000	0.000
67	A	364	GLY	0	0.028	-0.005	21.662	0.019	0.019	0.000	0.000	0.000	0.000
68	A	365	ARG	1	0.837	0.927	21.899	-0.132	-0.132	0.000	0.000	0.000	0.000
69	A	366	LEU	0	-0.007	-0.003	18.315	0.020	0.020	0.000	0.000	0.000	0.000
70	A	367	ALA	0	0.060	0.029	18.129	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	368	GLN	0	-0.036	-0.035	18.375	-0.037	-0.037	0.000	0.000	0.000	0.000
72	A	369	HIS	0	-0.048	-0.024	21.206	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	370	PHE	0	-0.032	-0.010	22.307	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	371	PRO	0	-0.015	0.002	25.313	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	372	LYS	1	0.961	0.980	25.495	-0.174	-0.174	0.000	0.000	0.000	0.000
76	A	373	THR	0	0.028	0.040	25.677	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	374	THR	0	-0.017	-0.019	27.386	0.011	0.011	0.000	0.000	0.000	0.000
78	A	375	GLU	-1	-0.906	-0.963	27.257	0.233	0.233	0.000	0.000	0.000	0.000
79	A	376	GLU	-1	-0.909	-0.956	29.442	0.168	0.168	0.000	0.000	0.000	0.000
80	A	377	ASN	0	-0.092	-0.037	31.489	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	378	PRO	0	0.016	0.014	28.959	0.010	0.010	0.000	0.000	0.000	0.000
82	A	379	ILE	0	-0.025	-0.022	26.087	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	380	PHE	0	0.013	0.000	28.695	0.010	0.010	0.000	0.000	0.000	0.000
84	A	381	VAL	0	-0.039	-0.030	26.607	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	382	VAL	0	0.031	0.012	29.986	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	383	SER	0	0.014	0.004	31.735	0.003	0.003	0.000	0.000	0.000	0.000
87	A	384	LEU	0	-0.025	-0.012	32.629	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	385	GLU	-1	-1.004	-0.989	33.019	0.085	0.085	0.000	0.000	0.000	0.000
89	A	386	ARG	1	0.954	0.978	34.937	-0.074	-0.074	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:298:PRO)