FMO DATABASE

FMODB ID: 39QKL

Calculation Name: 3BRV-A-Xray372

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

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3BRV

Chain ID: A

ChEMBL ID: CHEMBL1991

UniProt ID: O14920

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	39
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-133782.118745
FMO2-HF: Nuclear repulsion	117869.456705
FMO2-HF: Total energy	-15912.662041
FMO2-MP2: Total energy	-15958.922174

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:705:SER)

Summations of interaction energy for fragment #1(A:705:SER)

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.
-11.696	-5.798	1.364	-2.704	-4.558	0.019

Interaction energy analysis for fragmet #1(A:705:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.028

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	707	GLU	-1	-0.924	-0.967	2.797	-3.401	-0.697	0.320	-1.241	-1.784	0.007
4	A	708	LEU	0	-0.003	0.012	2.380	-6.530	-3.736	1.044	-1.361	-2.477	0.012
5	A	709	VAL	0	-0.025	-0.012	3.934	-1.172	-0.772	0.000	-0.102	-0.297	0.000
6	A	710	ALA	0	-0.020	-0.006	6.227	-0.168	-0.168	0.000	0.000	0.000	0.000
7	A	711	GLU	-1	-0.912	-0.968	7.363	-0.214	-0.214	0.000	0.000	0.000	0.000
8	A	712	ALA	0	-0.018	-0.001	8.658	-0.130	-0.130	0.000	0.000	0.000	0.000
9	A	713	HIS	0	0.017	0.009	10.619	-0.057	-0.057	0.000	0.000	0.000	0.000
10	A	714	ASN	0	0.014	-0.003	11.969	-0.030	-0.030	0.000	0.000	0.000	0.000
11	A	715	LEU	0	-0.020	-0.006	12.040	-0.043	-0.043	0.000	0.000	0.000	0.000
12	A	716	CYS	0	-0.033	-0.014	13.730	-0.034	-0.034	0.000	0.000	0.000	0.000
13	A	717	THR	0	0.046	0.041	16.500	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	718	LEU	0	-0.040	-0.023	16.917	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	719	LEU	0	-0.011	-0.010	18.893	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	720	GLU	-1	-0.955	-0.982	19.829	0.115	0.115	0.000	0.000	0.000	0.000
17	A	721	ASN	0	-0.026	-0.028	22.276	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	722	ALA	0	-0.009	0.018	23.547	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	723	ILE	0	0.001	-0.012	23.931	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	724	GLN	0	-0.025	-0.017	26.529	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	725	ASP	-1	-0.886	-0.948	28.195	0.037	0.037	0.000	0.000	0.000	0.000
22	A	726	THR	0	-0.008	0.001	29.111	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	727	VAL	0	-0.081	-0.020	30.246	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	728	ARG	1	0.853	0.913	32.467	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	729	GLU	-1	-0.932	-0.960	33.871	0.012	0.012	0.000	0.000	0.000	0.000
26	A	730	GLN	0	-0.067	-0.031	35.664	0.001	0.001	0.000	0.000	0.000	0.000
27	A	731	ASP	-1	-0.908	-0.970	36.881	0.025	0.025	0.000	0.000	0.000	0.000
28	A	732	GLN	0	-0.075	-0.008	38.984	0.000	0.000	0.000	0.000	0.000	0.000
29	A	733	SER	0	0.047	0.002	41.388	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	734	PHE	0	0.051	-0.001	43.862	0.000	0.000	0.000	0.000	0.000	0.000
31	A	735	THR	0	-0.060	0.005	46.749	0.000	0.000	0.000	0.000	0.000	0.000
32	A	736	ALA	0	-0.022	-0.001	46.945	0.000	0.000	0.000	0.000	0.000	0.000
33	A	737	LEU	0	-0.033	-0.008	48.632	0.000	0.000	0.000	0.000	0.000	0.000
34	A	738	ASP	-1	-0.853	-0.913	51.281	0.010	0.010	0.000	0.000	0.000	0.000
35	A	739	TRP	0	-0.048	-0.060	50.515	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	740	SER	0	-0.030	-0.022	56.279	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	741	TRP	0	-0.005	-0.002	55.683	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	742	LEU	0	-0.050	-0.016	56.455	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	743	GLN	0	-0.066	-0.020	60.980	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:705:SER)