FMO DATABASE

FMODB ID: 94GL2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-133973.45028
FMO2-HF: Nuclear repulsion	118060.27306
FMO2-HF: Total energy	-15913.17722
FMO2-MP2: Total energy	-15959.370944

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.
-5.167	0.176	2.046	-2.784	-4.603	0.015

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 : 0.024 / 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	707	GLU	-1	-0.930	-0.961	3.314	-0.949	1.791	0.068	-1.275	-1.532	0.008
4	A	708	LEU	0	0.016	0.013	2.262	-4.787	-2.610	1.977	-1.387	-2.766	0.007
5	A	709	VAL	0	-0.026	-0.007	3.600	-0.650	-0.224	0.001	-0.122	-0.305	0.000
6	A	710	ALA	0	0.001	0.000	6.116	0.428	0.428	0.000	0.000	0.000	0.000
7	A	711	GLU	-1	-0.957	-0.979	7.627	0.919	0.919	0.000	0.000	0.000	0.000
8	A	712	ALA	0	0.015	0.005	8.136	-0.047	-0.047	0.000	0.000	0.000	0.000
9	A	713	HIS	0	0.030	0.024	9.922	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	714	ASN	0	0.010	0.004	11.892	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	715	LEU	0	-0.007	-0.003	11.424	0.013	0.013	0.000	0.000	0.000	0.000
12	A	716	CYS	0	-0.060	-0.031	13.405	0.003	0.003	0.000	0.000	0.000	0.000
13	A	717	THR	0	0.029	0.004	16.010	0.011	0.011	0.000	0.000	0.000	0.000
14	A	718	LEU	0	-0.042	-0.021	16.473	0.015	0.015	0.000	0.000	0.000	0.000
15	A	719	LEU	0	-0.018	0.002	18.499	0.009	0.009	0.000	0.000	0.000	0.000
16	A	720	GLU	-1	-0.936	-0.975	19.831	-0.144	-0.144	0.000	0.000	0.000	0.000
17	A	721	ASN	0	-0.070	-0.039	21.512	0.005	0.005	0.000	0.000	0.000	0.000
18	A	722	ALA	0	0.054	0.032	23.237	0.004	0.004	0.000	0.000	0.000	0.000
19	A	723	ILE	0	-0.031	-0.007	23.876	0.005	0.005	0.000	0.000	0.000	0.000
20	A	724	GLN	0	0.016	0.007	26.103	0.006	0.006	0.000	0.000	0.000	0.000
21	A	725	ASP	-1	-0.876	-0.945	27.884	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	726	THR	0	-0.016	-0.016	28.255	0.005	0.005	0.000	0.000	0.000	0.000
23	A	727	VAL	0	-0.102	-0.048	30.106	0.002	0.002	0.000	0.000	0.000	0.000
24	A	728	ARG	1	0.808	0.897	32.322	0.029	0.029	0.000	0.000	0.000	0.000
25	A	729	GLU	-1	-0.918	-0.968	33.598	0.004	0.004	0.000	0.000	0.000	0.000
26	A	730	GLN	0	-0.054	-0.030	34.932	0.001	0.001	0.000	0.000	0.000	0.000
27	A	731	ASP	-1	-0.862	-0.911	36.532	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	732	GLN	0	-0.108	-0.035	38.143	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	733	SER	0	0.000	-0.013	40.908	0.004	0.004	0.000	0.000	0.000	0.000
30	A	734	PHE	0	0.067	0.012	42.943	0.000	0.000	0.000	0.000	0.000	0.000
31	A	735	THR	0	-0.042	-0.010	46.298	0.000	0.000	0.000	0.000	0.000	0.000
32	A	736	ALA	0	-0.023	-0.001	46.298	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	737	LEU	0	-0.035	-0.008	48.245	0.000	0.000	0.000	0.000	0.000	0.000
34	A	738	ASP	-1	-0.784	-0.877	50.668	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	739	TRP	0	-0.018	-0.021	49.917	0.002	0.002	0.000	0.000	0.000	0.000
36	A	740	SER	0	-0.073	-0.054	55.826	0.001	0.001	0.000	0.000	0.000	0.000
37	A	741	TRP	0	-0.048	-0.028	54.556	0.001	0.001	0.000	0.000	0.000	0.000
38	A	742	LEU	0	-0.049	-0.017	55.754	0.001	0.001	0.000	0.000	0.000	0.000
39	A	743	GLN	0	-0.080	-0.028	60.245	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)