FMO DATABASE

FMODB ID: LZJQ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-133797.459885
FMO2-HF: Nuclear repulsion	117884.45425
FMO2-HF: Total energy	-15913.005635
FMO2-MP2: Total energy	-15959.206402

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.
-5.627	-0.039	1.33	-2.662	-4.256	0.014

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 : 0.005 / q_NPA : 0.001

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	-0.923	-0.960	3.042	-1.584	1.651	0.114	-1.538	-1.811	0.010
4	A	708	LEU	0	0.006	0.009	2.300	-4.416	-2.469	1.215	-1.024	-2.138	0.004
5	A	709	VAL	0	-0.023	-0.010	3.638	-0.684	-0.278	0.001	-0.100	-0.307	0.000
6	A	710	ALA	0	-0.008	-0.003	6.140	0.349	0.349	0.000	0.000	0.000	0.000
7	A	711	GLU	-1	-0.940	-0.974	7.757	0.829	0.829	0.000	0.000	0.000	0.000
8	A	712	ALA	0	0.002	0.008	8.472	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	713	HIS	0	0.026	0.018	10.222	0.011	0.011	0.000	0.000	0.000	0.000
10	A	714	ASN	0	0.015	0.000	12.126	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	715	LEU	0	-0.017	-0.008	11.795	0.013	0.013	0.000	0.000	0.000	0.000
12	A	716	CYS	0	-0.039	-0.020	13.583	0.007	0.007	0.000	0.000	0.000	0.000
13	A	717	THR	0	0.028	0.028	16.308	0.004	0.004	0.000	0.000	0.000	0.000
14	A	718	LEU	0	-0.040	-0.027	16.947	0.014	0.014	0.000	0.000	0.000	0.000
15	A	719	LEU	0	-0.013	-0.006	18.635	0.009	0.009	0.000	0.000	0.000	0.000
16	A	720	GLU	-1	-0.946	-0.980	19.978	-0.156	-0.156	0.000	0.000	0.000	0.000
17	A	721	ASN	0	-0.034	-0.032	22.133	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	722	ALA	0	0.003	0.022	23.380	0.006	0.006	0.000	0.000	0.000	0.000
19	A	723	ILE	0	-0.006	-0.008	24.061	0.005	0.005	0.000	0.000	0.000	0.000
20	A	724	GLN	0	-0.012	-0.009	26.277	0.006	0.006	0.000	0.000	0.000	0.000
21	A	725	ASP	-1	-0.890	-0.944	28.034	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	726	THR	0	-0.016	-0.014	28.581	0.005	0.005	0.000	0.000	0.000	0.000
23	A	727	VAL	0	-0.074	-0.022	30.399	0.002	0.002	0.000	0.000	0.000	0.000
24	A	728	ARG	1	0.850	0.906	32.395	0.034	0.034	0.000	0.000	0.000	0.000
25	A	729	GLU	-1	-0.933	-0.964	33.718	0.002	0.002	0.000	0.000	0.000	0.000
26	A	730	GLN	0	-0.078	-0.037	35.335	0.001	0.001	0.000	0.000	0.000	0.000
27	A	731	ASP	-1	-0.904	-0.948	36.493	-0.028	-0.028	0.000	0.000	0.000	0.000
28	A	732	GLN	0	-0.082	-0.017	38.784	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	733	SER	0	0.043	0.008	41.153	0.004	0.004	0.000	0.000	0.000	0.000
30	A	734	PHE	0	0.052	0.000	43.302	0.000	0.000	0.000	0.000	0.000	0.000
31	A	735	THR	0	-0.061	-0.015	46.555	0.001	0.001	0.000	0.000	0.000	0.000
32	A	736	ALA	0	-0.013	0.002	46.751	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	737	LEU	0	-0.030	-0.002	48.671	0.000	0.000	0.000	0.000	0.000	0.000
34	A	738	ASP	-1	-0.809	-0.882	51.038	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	739	TRP	0	-0.045	-0.045	50.206	0.002	0.002	0.000	0.000	0.000	0.000
36	A	740	SER	0	-0.050	-0.040	55.931	0.001	0.001	0.000	0.000	0.000	0.000
37	A	741	TRP	0	-0.022	-0.017	55.096	0.001	0.001	0.000	0.000	0.000	0.000
38	A	742	LEU	0	-0.058	-0.022	56.094	0.001	0.001	0.000	0.000	0.000	0.000
39	A	743	GLN	0	-0.066	-0.018	60.598	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)