FMO DATABASE

FMODB ID: 72GYK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-282873.417269
FMO2-HF: Nuclear repulsion	256058.769866
FMO2-HF: Total energy	-26814.647403
FMO2-MP2: Total energy	-26890.4523

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.
-91.142	-90.87	24.326	-10.146	-14.453	0.132

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 : -0.837 / q_NPA : -0.931

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	0.011	0.000	1.833	-32.344	-34.942	18.894	-8.196	-8.101	0.091
4	B	52	GLN	0	-0.024	-0.019	2.048	-31.856	-29.454	5.427	-1.735	-6.094	0.040
5	B	53	ARG	1	0.896	0.943	4.179	-45.844	-45.376	0.005	-0.215	-0.258	0.001
6	B	54	CYS	0	-0.010	-0.002	5.889	-6.299	-6.299	0.000	0.000	0.000	0.000
7	B	55	LEU	0	-0.015	-0.012	6.139	-5.522	-5.522	0.000	0.000	0.000	0.000
8	B	56	GLU	-1	-0.921	-0.960	8.089	23.760	23.760	0.000	0.000	0.000	0.000
9	B	57	GLU	-1	-0.831	-0.899	10.135	24.047	24.047	0.000	0.000	0.000	0.000
10	B	58	ASN	0	-0.051	-0.018	11.306	-3.084	-3.084	0.000	0.000	0.000	0.000
11	B	59	GLN	0	0.033	0.011	12.608	-2.802	-2.802	0.000	0.000	0.000	0.000
12	B	60	GLU	-1	-0.882	-0.940	13.768	18.509	18.509	0.000	0.000	0.000	0.000
13	B	61	LEU	0	-0.018	-0.001	15.406	-1.526	-1.526	0.000	0.000	0.000	0.000
14	B	62	ARG	1	0.840	0.902	14.896	-20.713	-20.713	0.000	0.000	0.000	0.000
15	B	63	ASP	-1	-0.810	-0.892	18.555	15.614	15.614	0.000	0.000	0.000	0.000
16	B	64	ALA	0	-0.014	0.002	20.305	-0.896	-0.896	0.000	0.000	0.000	0.000
17	B	65	ILE	0	-0.004	-0.008	21.751	-0.846	-0.846	0.000	0.000	0.000	0.000
18	B	66	ARG	1	0.811	0.885	18.041	-16.706	-16.706	0.000	0.000	0.000	0.000
19	B	67	GLN	0	-0.030	0.007	24.721	-0.918	-0.918	0.000	0.000	0.000	0.000
20	B	68	SER	0	0.093	0.033	26.315	-0.525	-0.525	0.000	0.000	0.000	0.000
21	B	69	ASN	0	-0.045	-0.028	26.502	-0.695	-0.695	0.000	0.000	0.000	0.000
22	B	70	GLN	0	-0.020	0.007	28.989	-0.111	-0.111	0.000	0.000	0.000	0.000
23	B	71	ILE	0	0.025	0.014	30.110	-0.414	-0.414	0.000	0.000	0.000	0.000
24	B	72	LEU	0	0.020	0.014	30.788	-0.360	-0.360	0.000	0.000	0.000	0.000
25	B	73	ARG	1	0.924	0.961	30.662	-10.276	-10.276	0.000	0.000	0.000	0.000
26	B	74	GLU	-1	-0.819	-0.887	35.155	8.565	8.565	0.000	0.000	0.000	0.000
27	B	75	ARG	1	0.759	0.818	36.468	-8.708	-8.708	0.000	0.000	0.000	0.000
28	B	76	CYS	0	-0.062	-0.035	36.876	-0.222	-0.222	0.000	0.000	0.000	0.000
29	B	77	GLU	-1	-0.929	-0.950	39.559	7.753	7.753	0.000	0.000	0.000	0.000
30	B	78	GLU	-1	-0.833	-0.888	41.174	7.636	7.636	0.000	0.000	0.000	0.000
31	B	79	LEU	0	-0.022	-0.011	41.999	-0.221	-0.221	0.000	0.000	0.000	0.000
32	B	80	LEU	0	-0.001	0.002	43.785	-0.199	-0.199	0.000	0.000	0.000	0.000
33	B	81	HIS	0	-0.023	-0.032	44.737	-0.306	-0.306	0.000	0.000	0.000	0.000
34	B	82	PHE	0	-0.002	0.015	47.092	-0.184	-0.184	0.000	0.000	0.000	0.000
35	B	83	GLN	0	-0.026	-0.026	46.171	-0.050	-0.050	0.000	0.000	0.000	0.000
36	B	84	ALA	0	-0.012	0.003	49.942	-0.148	-0.148	0.000	0.000	0.000	0.000
37	B	85	SER	0	0.044	0.021	51.749	-0.099	-0.099	0.000	0.000	0.000	0.000
38	B	86	GLN	0	-0.029	-0.014	52.018	-0.145	-0.145	0.000	0.000	0.000	0.000
39	B	87	ARG	1	0.806	0.891	54.185	-5.865	-5.865	0.000	0.000	0.000	0.000
40	B	88	GLU	-1	-0.886	-0.943	55.124	5.789	5.789	0.000	0.000	0.000	0.000
41	B	89	GLU	-1	-0.899	-0.936	57.533	5.327	5.327	0.000	0.000	0.000	0.000
42	B	90	LYS	1	0.928	0.955	58.546	-5.653	-5.653	0.000	0.000	0.000	0.000
43	B	91	GLU	-1	-0.869	-0.929	59.826	5.398	5.398	0.000	0.000	0.000	0.000
44	B	92	PHE	0	0.022	0.011	61.927	-0.150	-0.150	0.000	0.000	0.000	0.000
45	B	93	LEU	0	0.020	-0.002	61.572	-0.127	-0.127	0.000	0.000	0.000	0.000
46	B	94	MET	0	-0.049	-0.031	62.261	-0.088	-0.088	0.000	0.000	0.000	0.000
47	B	95	CYS	0	-0.069	-0.026	66.162	-0.107	-0.107	0.000	0.000	0.000	0.000
48	B	96	LYS	1	0.883	0.929	67.562	-4.793	-4.793	0.000	0.000	0.000	0.000
49	B	97	PHE	0	0.025	0.010	65.836	-0.100	-0.100	0.000	0.000	0.000	0.000
50	B	98	GLN	0	-0.046	-0.021	69.603	-0.139	-0.139	0.000	0.000	0.000	0.000
51	B	99	GLU	-1	-0.833	-0.895	71.099	4.526	4.526	0.000	0.000	0.000	0.000
52	B	100	ALA	0	-0.004	0.000	73.364	-0.077	-0.077	0.000	0.000	0.000	0.000
53	B	101	ARG	1	0.849	0.918	74.420	-4.397	-4.397	0.000	0.000	0.000	0.000
54	B	102	LYS	1	0.984	0.988	75.871	-4.369	-4.369	0.000	0.000	0.000	0.000
55	B	103	LEU	0	-0.058	-0.016	78.001	-0.072	-0.072	0.000	0.000	0.000	0.000
56	B	104	VAL	0	0.040	0.005	78.303	-0.060	-0.060	0.000	0.000	0.000	0.000
57	B	105	GLU	-1	-0.870	-0.927	79.105	4.139	4.139	0.000	0.000	0.000	0.000
58	B	106	ARG	1	0.906	0.944	81.213	-4.024	-4.024	0.000	0.000	0.000	0.000
59	B	107	LEU	0	-0.031	-0.007	82.537	-0.050	-0.050	0.000	0.000	0.000	0.000
60	B	108	GLY	0	-0.008	0.008	85.353	-0.045	-0.045	0.000	0.000	0.000	0.000
61	B	109	LEU	0	-0.036	-0.001	86.862	-0.070	-0.070	0.000	0.000	0.000	0.000

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