FMO DATABASE

FMODB ID: MV3RZ

Calculation Name: 3BRT-B-Xray372

Preferred Name: Inhibitor of nuclear factor kappa B kinase alpha subunit

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3BRT

Chain ID: B

ChEMBL ID: CHEMBL3476

UniProt ID: O15111

Base Structure: X-ray

Registration Date: 2023-06-21

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-282230.720296
FMO2-HF: Nuclear repulsion	255416.9521
FMO2-HF: Total energy	-26813.768196
FMO2-MP2: Total energy	-26889.632104

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(B:49:GLU)

Summations of interaction energy for fragment #1(B:49:GLU)

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.
-34.67	-29.215	10.143	-6.056	-9.543	0.003

Interaction energy analysis for fragmet #1(B:49:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.925 / q_NPA : -0.967

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	B	51	LEU	0	0.065	0.031	1.737	-13.075	-11.485	5.844	-3.177	-4.257	0.015
4	B	52	GLN	0	0.033	0.004	1.958	-3.821	-0.468	4.296	-2.716	-4.933	-0.012
5	B	53	ARG	1	0.980	1.001	3.929	-37.784	-37.272	0.003	-0.163	-0.353	0.000
6	B	54	CYS	0	0.004	-0.003	5.901	-4.273	-4.273	0.000	0.000	0.000	0.000
7	B	55	LEU	0	-0.019	-0.011	5.945	-3.196	-3.196	0.000	0.000	0.000	0.000
8	B	56	GLU	-1	-0.922	-0.954	7.934	22.577	22.577	0.000	0.000	0.000	0.000
9	B	57	GLU	-1	-0.885	-0.947	9.925	18.910	18.910	0.000	0.000	0.000	0.000
10	B	58	ASN	0	-0.034	-0.012	11.302	-2.208	-2.208	0.000	0.000	0.000	0.000
11	B	59	GLN	0	-0.001	-0.008	12.606	-2.344	-2.344	0.000	0.000	0.000	0.000
12	B	60	GLU	-1	-0.858	-0.924	13.807	16.798	16.798	0.000	0.000	0.000	0.000
13	B	61	LEU	0	-0.029	-0.008	15.218	-1.299	-1.299	0.000	0.000	0.000	0.000
14	B	62	ARG	1	0.799	0.892	15.519	-18.517	-18.517	0.000	0.000	0.000	0.000
15	B	63	ASP	-1	-0.898	-0.948	18.138	14.850	14.850	0.000	0.000	0.000	0.000
16	B	64	ALA	0	-0.014	-0.004	20.205	-0.790	-0.790	0.000	0.000	0.000	0.000
17	B	65	ILE	0	0.003	-0.009	21.738	-0.717	-0.717	0.000	0.000	0.000	0.000
18	B	66	ARG	1	0.896	0.948	18.587	-15.188	-15.188	0.000	0.000	0.000	0.000
19	B	67	GLN	0	-0.006	0.021	24.672	-0.820	-0.820	0.000	0.000	0.000	0.000
20	B	68	SER	0	0.057	0.019	26.245	-0.579	-0.579	0.000	0.000	0.000	0.000
21	B	69	ASN	0	-0.011	-0.012	26.945	-0.524	-0.524	0.000	0.000	0.000	0.000
22	B	70	GLN	0	-0.021	0.001	29.001	-0.083	-0.083	0.000	0.000	0.000	0.000
23	B	71	ILE	0	0.012	0.015	29.781	-0.366	-0.366	0.000	0.000	0.000	0.000
24	B	72	LEU	0	0.021	0.009	31.009	-0.348	-0.348	0.000	0.000	0.000	0.000
25	B	73	ARG	1	0.928	0.958	30.372	-9.821	-9.821	0.000	0.000	0.000	0.000
26	B	74	GLU	-1	-0.830	-0.895	35.154	8.202	8.202	0.000	0.000	0.000	0.000
27	B	75	ARG	1	0.793	0.844	36.188	-8.351	-8.351	0.000	0.000	0.000	0.000
28	B	76	CYS	0	-0.052	-0.026	37.046	-0.211	-0.211	0.000	0.000	0.000	0.000
29	B	77	GLU	-1	-0.931	-0.952	39.596	7.398	7.398	0.000	0.000	0.000	0.000
30	B	78	GLU	-1	-0.842	-0.890	41.172	7.235	7.235	0.000	0.000	0.000	0.000
31	B	79	LEU	0	-0.016	-0.017	41.384	-0.204	-0.204	0.000	0.000	0.000	0.000
32	B	80	LEU	0	-0.020	-0.004	43.644	-0.181	-0.181	0.000	0.000	0.000	0.000
33	B	81	HIS	0	-0.028	-0.039	44.678	-0.273	-0.273	0.000	0.000	0.000	0.000
34	B	82	PHE	0	0.009	0.020	47.086	-0.175	-0.175	0.000	0.000	0.000	0.000
35	B	83	GLN	0	-0.028	-0.029	46.478	-0.048	-0.048	0.000	0.000	0.000	0.000
36	B	84	ALA	0	-0.020	-0.001	49.968	-0.137	-0.137	0.000	0.000	0.000	0.000
37	B	85	SER	0	0.055	0.021	51.759	-0.095	-0.095	0.000	0.000	0.000	0.000
38	B	86	GLN	0	-0.023	-0.005	51.949	-0.156	-0.156	0.000	0.000	0.000	0.000
39	B	87	ARG	1	0.881	0.948	54.213	-5.759	-5.759	0.000	0.000	0.000	0.000
40	B	88	GLU	-1	-0.872	-0.938	55.286	5.594	5.594	0.000	0.000	0.000	0.000
41	B	89	GLU	-1	-0.909	-0.938	57.523	5.217	5.217	0.000	0.000	0.000	0.000
42	B	90	LYS	1	0.934	0.964	58.489	-5.483	-5.483	0.000	0.000	0.000	0.000
43	B	91	GLU	-1	-0.955	-0.984	59.594	5.230	5.230	0.000	0.000	0.000	0.000
44	B	92	PHE	0	0.032	0.008	61.936	-0.144	-0.144	0.000	0.000	0.000	0.000
45	B	93	LEU	0	0.017	-0.003	61.612	-0.120	-0.120	0.000	0.000	0.000	0.000
46	B	94	MET	0	-0.051	-0.043	61.742	-0.092	-0.092	0.000	0.000	0.000	0.000
47	B	95	CYS	0	-0.014	0.010	66.169	-0.096	-0.096	0.000	0.000	0.000	0.000
48	B	96	LYS	1	0.932	0.983	67.514	-4.712	-4.712	0.000	0.000	0.000	0.000
49	B	97	PHE	0	0.016	0.002	66.152	-0.092	-0.092	0.000	0.000	0.000	0.000
50	B	98	GLN	0	-0.059	-0.024	68.943	-0.125	-0.125	0.000	0.000	0.000	0.000
51	B	99	GLU	-1	-0.928	-0.971	72.101	4.374	4.374	0.000	0.000	0.000	0.000
52	B	100	ALA	0	-0.010	-0.007	73.339	-0.072	-0.072	0.000	0.000	0.000	0.000
53	B	101	ARG	1	0.907	0.967	73.515	-4.334	-4.334	0.000	0.000	0.000	0.000
54	B	102	LYS	1	0.992	0.992	75.510	-4.263	-4.263	0.000	0.000	0.000	0.000
55	B	103	LEU	0	-0.051	-0.015	77.982	-0.069	-0.069	0.000	0.000	0.000	0.000
56	B	104	VAL	0	0.037	0.005	78.277	-0.058	-0.058	0.000	0.000	0.000	0.000
57	B	105	GLU	-1	-0.930	-0.971	78.799	4.039	4.039	0.000	0.000	0.000	0.000
58	B	106	ARG	1	0.900	0.935	81.225	-3.932	-3.932	0.000	0.000	0.000	0.000
59	B	107	LEU	0	-0.037	-0.009	82.818	-0.048	-0.048	0.000	0.000	0.000	0.000
60	B	108	GLY	0	-0.008	0.010	85.316	-0.043	-0.043	0.000	0.000	0.000	0.000
61	B	109	LEU	0	-0.039	-0.004	86.738	-0.068	-0.068	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:49:GLU)