FMO DATABASE

FMODB ID: YZ722

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	OptHSide
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	-652927.291826
FMO2-HF: Nuclear repulsion	617048.316705
FMO2-HF: Total energy	-35878.975121
FMO2-MP2: Total energy	-35985.12644

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.
10.628	-3.678	9.019	10.93	-5.642	-0.017

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 : -0.055 / q_NPA : -0.005

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

Sort

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	0.082	0.042	2.480	17.622	2.957	8.932	10.624	-4.891	-0.021
4	A	301	SER	0	0.054	0.012	3.648	-2.313	-2.369	0.068	0.421	-0.433	0.004
5	A	302	THR	0	-0.045	-0.048	6.133	-0.565	-0.565	0.000	0.000	0.000	0.000
6	A	303	SER	0	0.010	0.008	3.005	-2.216	-1.801	0.019	-0.115	-0.318	0.000
7	A	304	ASP	-1	-0.818	-0.872	6.082	0.925	0.925	0.000	0.000	0.000	0.000
8	A	305	ILE	0	-0.005	-0.022	8.124	-0.318	-0.318	0.000	0.000	0.000	0.000
9	A	306	LEU	0	0.020	0.013	11.083	-0.113	-0.113	0.000	0.000	0.000	0.000
10	A	307	HIS	0	-0.023	-0.006	10.947	-0.236	-0.236	0.000	0.000	0.000	0.000
11	A	308	ARG	1	0.840	0.951	9.782	-1.110	-1.110	0.000	0.000	0.000	0.000
12	A	309	MET	0	0.001	0.020	14.149	-0.086	-0.086	0.000	0.000	0.000	0.000
13	A	310	VAL	0	-0.025	-0.026	16.855	0.045	0.045	0.000	0.000	0.000	0.000
14	A	311	ILE	0	-0.028	0.003	19.429	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	312	HIS	0	0.020	0.017	22.072	0.008	0.008	0.000	0.000	0.000	0.000
16	A	313	VAL	0	0.010	0.002	23.968	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	314	PHE	0	0.002	-0.003	26.073	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	315	SER	0	-0.006	-0.014	27.882	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	316	LEU	0	0.044	0.005	29.742	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	317	GLN	0	-0.029	-0.008	31.622	0.000	0.000	0.000	0.000	0.000	0.000
21	A	318	GLN	0	0.013	0.006	29.313	0.002	0.002	0.000	0.000	0.000	0.000
22	A	319	MET	0	-0.017	0.012	32.013	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	320	THR	0	-0.003	-0.008	27.587	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	321	ALA	0	0.012	0.010	27.564	0.005	0.005	0.000	0.000	0.000	0.000
25	A	322	HIS	0	-0.020	-0.001	22.556	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	323	LYS	1	0.848	0.926	20.415	-0.223	-0.223	0.000	0.000	0.000	0.000
27	A	324	ILE	0	-0.020	-0.010	18.191	0.024	0.024	0.000	0.000	0.000	0.000
28	A	325	TYR	0	0.017	0.001	14.476	0.007	0.007	0.000	0.000	0.000	0.000
29	A	326	ILE	0	-0.037	-0.019	14.223	0.050	0.050	0.000	0.000	0.000	0.000
30	A	327	HIS	0	-0.009	-0.015	10.427	-0.123	-0.123	0.000	0.000	0.000	0.000
31	A	328	SER	0	0.033	-0.013	13.669	-0.122	-0.122	0.000	0.000	0.000	0.000
32	A	329	TYR	0	0.013	0.007	14.512	-0.079	-0.079	0.000	0.000	0.000	0.000
33	A	330	ASN	0	-0.029	0.002	12.213	0.031	0.031	0.000	0.000	0.000	0.000
34	A	331	THR	0	0.043	0.017	15.796	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	332	ALA	0	0.065	0.028	19.168	0.022	0.022	0.000	0.000	0.000	0.000
36	A	333	THR	0	-0.040	-0.019	19.969	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	334	ILE	0	0.034	0.025	14.448	0.002	0.002	0.000	0.000	0.000	0.000
38	A	335	PHE	0	0.035	0.011	17.649	0.008	0.008	0.000	0.000	0.000	0.000
39	A	336	HIS	1	0.893	0.931	19.739	-0.215	-0.215	0.000	0.000	0.000	0.000
40	A	337	GLU	-1	-0.874	-0.926	16.626	0.304	0.304	0.000	0.000	0.000	0.000
41	A	338	LEU	0	-0.045	-0.029	13.944	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	339	VAL	0	0.030	0.018	17.974	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	340	TYR	0	0.002	0.028	19.935	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	341	LYS	1	0.934	0.968	13.189	-0.424	-0.424	0.000	0.000	0.000	0.000
45	A	342	GLN	0	-0.045	-0.032	18.466	-0.041	-0.041	0.000	0.000	0.000	0.000
46	A	343	THR	0	0.008	-0.001	21.633	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	344	LYS	1	0.831	0.917	21.529	-0.184	-0.184	0.000	0.000	0.000	0.000
48	A	345	ILE	0	0.024	0.036	25.123	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	346	ILE	0	0.032	0.009	25.258	0.018	0.018	0.000	0.000	0.000	0.000
50	A	347	SER	0	0.054	0.011	22.028	0.000	0.000	0.000	0.000	0.000	0.000
51	A	348	SER	0	-0.007	-0.004	25.029	0.002	0.002	0.000	0.000	0.000	0.000
52	A	349	ASN	0	-0.013	-0.004	28.332	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	350	GLN	0	-0.020	-0.005	23.328	0.007	0.007	0.000	0.000	0.000	0.000
54	A	351	GLU	-1	-0.910	-0.951	28.987	0.106	0.106	0.000	0.000	0.000	0.000
55	A	352	LEU	0	-0.037	-0.016	26.572	0.006	0.006	0.000	0.000	0.000	0.000
56	A	353	ILE	0	0.013	0.007	30.765	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	354	TYR	0	-0.008	-0.022	30.407	0.007	0.007	0.000	0.000	0.000	0.000
58	A	355	GLU	-1	-0.824	-0.897	33.142	0.119	0.119	0.000	0.000	0.000	0.000
59	A	356	GLY	0	-0.015	-0.005	36.135	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	357	ARG	1	0.933	0.971	36.812	-0.098	-0.098	0.000	0.000	0.000	0.000
61	A	358	ARG	1	0.973	0.992	34.775	-0.092	-0.092	0.000	0.000	0.000	0.000
62	A	359	LEU	0	-0.030	-0.014	28.850	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	360	VAL	0	-0.022	-0.022	31.563	0.003	0.003	0.000	0.000	0.000	0.000
64	A	361	LEU	0	-0.026	-0.010	25.836	0.001	0.001	0.000	0.000	0.000	0.000
65	A	362	GLU	-1	-0.761	-0.845	26.480	0.171	0.171	0.000	0.000	0.000	0.000
66	A	363	PRO	0	0.039	-0.001	24.347	0.018	0.018	0.000	0.000	0.000	0.000
67	A	364	GLY	0	0.017	-0.003	22.131	0.025	0.025	0.000	0.000	0.000	0.000
68	A	365	ARG	1	0.794	0.891	22.415	-0.170	-0.170	0.000	0.000	0.000	0.000
69	A	366	LEU	0	0.001	-0.005	18.709	0.022	0.022	0.000	0.000	0.000	0.000
70	A	367	ALA	0	0.060	0.031	18.369	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	368	GLN	0	-0.030	-0.042	18.762	-0.053	-0.053	0.000	0.000	0.000	0.000
72	A	369	HIS	0	-0.053	-0.037	21.482	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	370	PHE	0	-0.012	0.000	22.635	-0.021	-0.021	0.000	0.000	0.000	0.000
74	A	371	PRO	0	-0.001	0.007	25.574	0.001	0.001	0.000	0.000	0.000	0.000
75	A	372	LYS	1	0.885	0.950	24.836	-0.221	-0.221	0.000	0.000	0.000	0.000
76	A	373	THR	0	0.044	0.039	25.369	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	374	THR	0	-0.046	-0.054	26.825	0.011	0.011	0.000	0.000	0.000	0.000
78	A	375	GLU	-1	-0.808	-0.909	25.947	0.200	0.200	0.000	0.000	0.000	0.000
79	A	376	GLU	-1	-0.871	-0.912	28.831	0.147	0.147	0.000	0.000	0.000	0.000
80	A	377	ASN	0	-0.106	-0.057	30.918	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	378	PRO	0	0.020	0.017	28.551	0.012	0.012	0.000	0.000	0.000	0.000
82	A	379	ILE	0	-0.026	-0.020	26.038	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	380	PHE	0	0.004	-0.005	28.505	0.006	0.006	0.000	0.000	0.000	0.000
84	A	381	VAL	0	-0.030	-0.022	26.559	0.003	0.003	0.000	0.000	0.000	0.000
85	A	382	VAL	0	0.021	0.005	30.021	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	383	SER	0	0.027	0.008	31.830	0.006	0.006	0.000	0.000	0.000	0.000
87	A	384	LEU	0	-0.014	-0.008	32.589	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	385	GLU	-1	-0.994	-0.985	32.725	0.082	0.082	0.000	0.000	0.000	0.000
89	A	386	ARG	1	0.939	0.973	34.971	-0.072	-0.072	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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