FMO DATABASE

FMODB ID: 3JNJL

Calculation Name: 3FX0-A-Xray372

Preferred Name: NF-kappa-B essential modulator

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3FX0

Chain ID: A

ChEMBL ID: CHEMBL4967

UniProt ID: Q9Y6K9

Base Structure: X-ray

Registration Date: 2023-09-20

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	63
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-262568.695535
FMO2-HF: Nuclear repulsion	237407.522987
FMO2-HF: Total energy	-25161.172548
FMO2-MP2: Total energy	-25235.499559

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:267:LEU)

Summations of interaction energy for fragment #1(A:267:LEU)

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.
-7.753	-3.334	0.704	-2.088	-3.037	0.001

Interaction energy analysis for fragmet #1(A:267:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.033

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	269	GLN	0	-0.045	-0.022	3.543	-3.413	-0.411	-0.014	-1.478	-1.511	0.002
4	A	270	ALA	0	-0.028	-0.011	2.425	-0.856	-0.095	0.710	-0.468	-1.004	-0.001
5	A	271	GLU	-1	-0.879	-0.937	3.413	-2.073	-1.450	0.009	-0.133	-0.499	0.000
6	A	272	GLU	-1	-0.756	-0.880	5.237	-1.009	-0.976	-0.001	-0.009	-0.023	0.000
7	A	273	ALA	0	-0.114	-0.070	7.312	0.207	0.207	0.000	0.000	0.000	0.000
8	A	274	LEU	0	-0.078	-0.031	5.921	0.058	0.058	0.000	0.000	0.000	0.000
9	A	275	VAL	0	0.064	0.035	9.385	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	276	ALA	0	0.043	0.035	11.051	0.044	0.044	0.000	0.000	0.000	0.000
11	A	277	LYS	1	0.862	0.920	11.144	-0.493	-0.493	0.000	0.000	0.000	0.000
12	A	278	GLN	0	-0.006	-0.008	13.463	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	279	GLU	-1	-0.860	-0.922	15.274	0.021	0.021	0.000	0.000	0.000	0.000
14	A	280	VAL	0	-0.052	-0.045	17.220	0.001	0.001	0.000	0.000	0.000	0.000
15	A	281	ILE	0	-0.034	-0.005	15.895	0.006	0.006	0.000	0.000	0.000	0.000
16	A	282	ASP	-1	-0.819	-0.934	19.454	-0.068	-0.068	0.000	0.000	0.000	0.000
17	A	283	LYS	1	0.905	0.977	21.438	-0.104	-0.104	0.000	0.000	0.000	0.000
18	A	284	LEU	0	-0.071	-0.037	21.790	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	285	LYS	1	0.842	0.941	23.319	0.023	0.023	0.000	0.000	0.000	0.000
20	A	286	GLU	-1	-0.954	-0.976	24.914	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	287	GLU	-1	-0.893	-0.971	26.521	0.064	0.064	0.000	0.000	0.000	0.000
22	A	288	ALA	0	0.004	0.001	28.011	0.003	0.003	0.000	0.000	0.000	0.000
23	A	289	GLU	-1	-0.896	-0.942	28.265	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	290	GLN	0	0.028	0.016	31.678	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	291	HIS	0	-0.051	-0.033	31.120	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	292	LYS	1	0.903	0.959	32.811	0.000	0.000	0.000	0.000	0.000	0.000
27	A	293	ILE	0	0.055	0.033	35.613	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	294	VAL	0	0.000	0.007	38.055	0.000	0.000	0.000	0.000	0.000	0.000
29	A	295	MET	0	-0.028	-0.024	36.159	0.000	0.000	0.000	0.000	0.000	0.000
30	A	296	GLU	-1	-0.891	-0.934	38.473	0.003	0.003	0.000	0.000	0.000	0.000
31	A	297	THR	0	-0.038	-0.030	41.735	0.000	0.000	0.000	0.000	0.000	0.000
32	A	298	VAL	0	-0.003	0.008	42.182	0.000	0.000	0.000	0.000	0.000	0.000
33	A	299	PRO	0	0.002	-0.008	43.867	0.001	0.001	0.000	0.000	0.000	0.000
34	A	300	VAL	0	0.025	0.006	46.785	0.000	0.000	0.000	0.000	0.000	0.000
35	A	301	LEU	0	-0.004	-0.008	46.370	0.000	0.000	0.000	0.000	0.000	0.000
36	A	302	LYS	1	0.918	0.970	44.984	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	303	ALA	0	0.033	0.018	50.613	0.000	0.000	0.000	0.000	0.000	0.000
38	A	304	GLN	0	0.014	0.009	52.941	0.000	0.000	0.000	0.000	0.000	0.000
39	A	305	ALA	0	0.012	0.008	53.336	0.000	0.000	0.000	0.000	0.000	0.000
40	A	306	ASP	-1	-0.889	-0.950	53.668	0.018	0.018	0.000	0.000	0.000	0.000
41	A	307	ILE	0	0.005	0.008	56.410	0.000	0.000	0.000	0.000	0.000	0.000
42	A	308	TYR	0	0.048	0.035	57.182	0.000	0.000	0.000	0.000	0.000	0.000
43	A	309	LYS	1	0.836	0.927	55.767	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	310	ALA	0	0.005	-0.012	60.370	0.000	0.000	0.000	0.000	0.000	0.000
45	A	311	ASP	-1	-0.892	-0.946	62.367	0.010	0.010	0.000	0.000	0.000	0.000
46	A	312	PHE	0	-0.049	-0.027	63.404	0.000	0.000	0.000	0.000	0.000	0.000
47	A	313	GLN	0	-0.018	-0.025	62.008	0.000	0.000	0.000	0.000	0.000	0.000
48	A	314	ALA	0	0.005	0.018	66.092	0.000	0.000	0.000	0.000	0.000	0.000
49	A	315	GLU	-1	-0.865	-0.941	68.389	0.010	0.010	0.000	0.000	0.000	0.000
50	A	316	ARG	1	0.711	0.863	67.988	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	317	GLN	0	0.022	0.008	70.029	0.000	0.000	0.000	0.000	0.000	0.000
52	A	318	ALA	0	0.026	0.014	71.967	0.000	0.000	0.000	0.000	0.000	0.000
53	A	319	ARG	1	0.905	0.952	73.295	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	320	GLU	-1	-0.878	-0.942	72.690	0.015	0.015	0.000	0.000	0.000	0.000
55	A	321	LYN	0	0.014	-0.007	75.921	0.000	0.000	0.000	0.000	0.000	0.000
56	A	322	LEU	0	-0.078	-0.030	77.959	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	323	ALA	0	-0.073	-0.036	78.971	0.000	0.000	0.000	0.000	0.000	0.000
58	A	324	GLU	-1	-0.861	-0.911	80.718	0.011	0.011	0.000	0.000	0.000	0.000
59	A	325	LYS	1	0.891	0.936	82.382	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	326	LYS	1	0.841	0.909	83.955	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	327	GLU	-1	-0.842	-0.911	85.111	0.011	0.011	0.000	0.000	0.000	0.000
62	A	328	LEU	0	-0.026	-0.009	87.385	0.000	0.000	0.000	0.000	0.000	0.000
63	A	329	LEU	0	-0.021	0.005	88.555	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:267:LEU)