FMO DATABASE

FMODB ID: V5Z41

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	OptAll
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	-653708.431969
FMO2-HF: Nuclear repulsion	617829.383624
FMO2-HF: Total energy	-35879.048345
FMO2-MP2: Total energy	-35985.198545

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.
1.804	-1.743	2.88	4.397	-3.731	-0.007

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 : -0.021 / q_NPA : -0.012

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	0.081	0.055	2.620	8.602	4.526	2.823	4.434	-3.181	-0.010
4	A	301	SER	0	0.063	0.020	3.807	-2.879	-2.599	0.056	0.016	-0.352	0.003
5	A	302	THR	0	-0.047	-0.033	5.825	-0.666	-0.666	0.000	0.000	0.000	0.000
6	A	303	SER	0	0.010	-0.021	3.669	-1.299	-1.050	0.001	-0.053	-0.198	0.000
7	A	304	ASP	-1	-0.833	-0.879	6.502	0.548	0.548	0.000	0.000	0.000	0.000
8	A	305	ILE	0	-0.002	-0.026	7.875	-0.217	-0.217	0.000	0.000	0.000	0.000
9	A	306	LEU	0	0.011	0.012	11.002	-0.076	-0.076	0.000	0.000	0.000	0.000
10	A	307	HIS	0	-0.011	-0.002	10.875	-0.184	-0.184	0.000	0.000	0.000	0.000
11	A	308	ARG	1	0.794	0.913	9.672	-1.048	-1.048	0.000	0.000	0.000	0.000
12	A	309	MET	0	0.013	0.025	13.875	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	310	VAL	0	-0.029	-0.026	16.671	0.051	0.051	0.000	0.000	0.000	0.000
14	A	311	ILE	0	-0.027	0.009	19.339	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	312	HIS	0	0.022	0.016	22.106	0.014	0.014	0.000	0.000	0.000	0.000
16	A	313	VAL	0	0.000	-0.010	23.810	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	314	PHE	0	0.006	0.003	26.008	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	315	SER	0	-0.009	-0.016	28.019	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	316	LEU	0	0.036	-0.002	29.717	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	317	GLN	0	-0.048	-0.018	31.420	0.000	0.000	0.000	0.000	0.000	0.000
21	A	318	GLN	0	0.008	0.004	28.953	0.003	0.003	0.000	0.000	0.000	0.000
22	A	319	MET	0	-0.023	0.005	31.800	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	320	THR	0	-0.004	-0.009	27.565	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	321	ALA	0	0.031	0.014	27.654	0.006	0.006	0.000	0.000	0.000	0.000
25	A	322	HIS	0	-0.034	-0.009	22.859	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	323	LYS	1	0.848	0.914	20.523	-0.215	-0.215	0.000	0.000	0.000	0.000
27	A	324	ILE	0	-0.024	-0.004	18.264	0.032	0.032	0.000	0.000	0.000	0.000
28	A	325	TYR	0	0.018	0.000	14.675	0.005	0.005	0.000	0.000	0.000	0.000
29	A	326	ILE	0	-0.037	-0.009	14.113	0.084	0.084	0.000	0.000	0.000	0.000
30	A	327	HIS	0	0.005	-0.015	10.398	-0.079	-0.079	0.000	0.000	0.000	0.000
31	A	328	SER	0	0.012	-0.018	13.489	-0.103	-0.103	0.000	0.000	0.000	0.000
32	A	329	TYR	0	0.009	0.009	14.301	-0.081	-0.081	0.000	0.000	0.000	0.000
33	A	330	ASN	0	-0.015	0.006	11.815	0.032	0.032	0.000	0.000	0.000	0.000
34	A	331	THR	0	0.027	0.009	15.508	-0.036	-0.036	0.000	0.000	0.000	0.000
35	A	332	ALA	0	0.056	0.017	19.055	0.023	0.023	0.000	0.000	0.000	0.000
36	A	333	THR	0	-0.036	-0.006	19.641	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	334	ILE	0	0.052	0.032	14.316	0.002	0.002	0.000	0.000	0.000	0.000
38	A	335	PHE	0	0.027	0.008	17.495	0.012	0.012	0.000	0.000	0.000	0.000
39	A	336	HIS	1	0.882	0.928	19.734	-0.222	-0.222	0.000	0.000	0.000	0.000
40	A	337	GLU	-1	-0.854	-0.921	16.819	0.341	0.341	0.000	0.000	0.000	0.000
41	A	338	LEU	0	-0.043	-0.023	13.864	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	339	VAL	0	0.042	0.018	17.973	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	340	TYR	0	-0.028	0.026	19.838	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	341	LYS	1	0.949	0.969	12.912	-0.496	-0.496	0.000	0.000	0.000	0.000
45	A	342	GLN	0	-0.047	-0.008	18.396	-0.044	-0.044	0.000	0.000	0.000	0.000
46	A	343	THR	0	0.000	-0.026	21.414	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	344	LYS	1	0.829	0.913	21.548	-0.212	-0.212	0.000	0.000	0.000	0.000
48	A	345	ILE	0	0.033	0.030	24.985	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	346	ILE	0	0.037	0.015	25.023	0.020	0.020	0.000	0.000	0.000	0.000
50	A	347	SER	0	0.024	-0.005	21.594	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	348	SER	0	-0.015	-0.007	24.699	0.003	0.003	0.000	0.000	0.000	0.000
52	A	349	ASN	0	-0.002	0.004	28.050	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	350	GLN	0	-0.011	0.001	23.243	0.002	0.002	0.000	0.000	0.000	0.000
54	A	351	GLU	-1	-0.886	-0.943	28.861	0.112	0.112	0.000	0.000	0.000	0.000
55	A	352	LEU	0	-0.031	-0.017	26.607	0.008	0.008	0.000	0.000	0.000	0.000
56	A	353	ILE	0	-0.009	-0.008	30.703	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	354	TYR	0	0.003	-0.019	30.303	0.007	0.007	0.000	0.000	0.000	0.000
58	A	355	GLU	-1	-0.837	-0.903	33.151	0.113	0.113	0.000	0.000	0.000	0.000
59	A	356	GLY	0	-0.006	0.004	36.187	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	357	ARG	1	0.917	0.955	36.740	-0.095	-0.095	0.000	0.000	0.000	0.000
61	A	358	ARG	1	0.970	0.995	34.532	-0.094	-0.094	0.000	0.000	0.000	0.000
62	A	359	LEU	0	-0.025	-0.009	28.472	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	360	VAL	0	-0.017	-0.014	31.063	0.006	0.006	0.000	0.000	0.000	0.000
64	A	361	LEU	0	-0.016	-0.012	25.804	0.002	0.002	0.000	0.000	0.000	0.000
65	A	362	GLU	-1	-0.759	-0.838	26.283	0.173	0.173	0.000	0.000	0.000	0.000
66	A	363	PRO	0	0.028	-0.006	24.021	0.017	0.017	0.000	0.000	0.000	0.000
67	A	364	GLY	0	0.019	0.010	21.899	0.026	0.026	0.000	0.000	0.000	0.000
68	A	365	ARG	1	0.774	0.858	22.049	-0.167	-0.167	0.000	0.000	0.000	0.000
69	A	366	LEU	0	0.012	0.007	18.311	0.025	0.025	0.000	0.000	0.000	0.000
70	A	367	ALA	0	0.044	0.022	18.085	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	368	GLN	0	-0.014	-0.037	18.706	-0.058	-0.058	0.000	0.000	0.000	0.000
72	A	369	HIS	0	-0.038	-0.019	21.406	-0.028	-0.028	0.000	0.000	0.000	0.000
73	A	370	PHE	0	0.014	0.014	22.288	-0.020	-0.020	0.000	0.000	0.000	0.000
74	A	371	PRO	0	0.000	0.009	25.540	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	372	LYS	1	0.866	0.939	25.060	-0.197	-0.197	0.000	0.000	0.000	0.000
76	A	373	THR	0	0.036	0.030	25.291	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	374	THR	0	-0.047	-0.050	26.857	0.010	0.010	0.000	0.000	0.000	0.000
78	A	375	GLU	-1	-0.810	-0.903	25.606	0.194	0.194	0.000	0.000	0.000	0.000
79	A	376	GLU	-1	-0.862	-0.910	29.004	0.134	0.134	0.000	0.000	0.000	0.000
80	A	377	ASN	0	-0.106	-0.052	31.041	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	378	PRO	0	0.028	0.023	28.254	0.012	0.012	0.000	0.000	0.000	0.000
82	A	379	ILE	0	-0.030	-0.023	25.892	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	380	PHE	0	0.025	0.006	28.193	0.008	0.008	0.000	0.000	0.000	0.000
84	A	381	VAL	0	-0.039	-0.022	26.640	0.004	0.004	0.000	0.000	0.000	0.000
85	A	382	VAL	0	0.020	0.006	30.125	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	383	SER	0	-0.013	-0.013	31.633	0.007	0.007	0.000	0.000	0.000	0.000
87	A	384	LEU	0	-0.026	-0.020	32.474	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	385	GLU	-1	-0.881	-0.919	32.414	0.098	0.098	0.000	0.000	0.000	0.000
89	A	386	ARG	1	0.922	0.965	34.986	-0.079	-0.079	0.000	0.000	0.000	0.000

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