FMO DATABASE

FMODB ID: JQMQ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-262836.599897
FMO2-HF: Nuclear repulsion	237676.236255
FMO2-HF: Total energy	-25160.363643
FMO2-MP2: Total energy	-25234.758863

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.
-7.788	-3.289	0.726	-2.091	-3.136	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 : -0.026 / q_NPA : -0.043

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	-0.014	-0.005	3.543	-3.493	-0.456	-0.015	-1.480	-1.542	0.002
4	A	270	ALA	0	-0.040	-0.020	2.424	-0.792	-0.027	0.731	-0.465	-1.032	-0.001
5	A	271	GLU	-1	-0.922	-0.960	3.411	-2.218	-1.581	0.011	-0.137	-0.511	0.000
6	A	272	GLU	-1	-0.788	-0.900	5.218	-1.045	-0.985	-0.001	-0.009	-0.051	0.000
7	A	273	ALA	0	-0.115	-0.080	7.299	0.254	0.254	0.000	0.000	0.000	0.000
8	A	274	LEU	0	-0.091	-0.041	6.080	0.077	0.077	0.000	0.000	0.000	0.000
9	A	275	VAL	0	0.086	0.055	9.233	-0.047	-0.047	0.000	0.000	0.000	0.000
10	A	276	ALA	0	0.035	0.033	11.033	0.058	0.058	0.000	0.000	0.000	0.000
11	A	277	LYS	1	0.864	0.914	11.448	-0.377	-0.377	0.000	0.000	0.000	0.000
12	A	278	GLN	0	0.038	-0.008	13.359	-0.042	-0.042	0.000	0.000	0.000	0.000
13	A	279	GLU	-1	-0.879	-0.929	15.045	-0.036	-0.036	0.000	0.000	0.000	0.000
14	A	280	VAL	0	-0.057	-0.049	17.174	0.007	0.007	0.000	0.000	0.000	0.000
15	A	281	ILE	0	-0.038	0.016	15.543	0.012	0.012	0.000	0.000	0.000	0.000
16	A	282	ASP	-1	-0.843	-0.945	19.136	-0.099	-0.099	0.000	0.000	0.000	0.000
17	A	283	LYS	1	0.927	0.986	21.355	-0.079	-0.079	0.000	0.000	0.000	0.000
18	A	284	LEU	0	-0.081	-0.048	22.060	0.000	0.000	0.000	0.000	0.000	0.000
19	A	285	LYS	1	0.934	1.011	22.990	0.051	0.051	0.000	0.000	0.000	0.000
20	A	286	GLU	-1	-0.949	-0.976	24.732	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	287	GLU	-1	-0.906	-0.975	27.163	0.044	0.044	0.000	0.000	0.000	0.000
22	A	288	ALA	0	0.005	0.001	27.930	0.005	0.005	0.000	0.000	0.000	0.000
23	A	289	GLU	-1	-1.002	-1.047	28.607	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	290	GLN	0	0.031	0.030	31.498	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	291	HIS	0	-0.049	-0.030	31.179	0.000	0.000	0.000	0.000	0.000	0.000
26	A	292	LYS	1	0.911	0.980	31.700	0.009	0.009	0.000	0.000	0.000	0.000
27	A	293	ILE	0	0.050	0.014	35.469	0.000	0.000	0.000	0.000	0.000	0.000
28	A	294	VAL	0	0.005	0.022	37.872	0.001	0.001	0.000	0.000	0.000	0.000
29	A	295	MET	0	-0.053	-0.026	35.904	0.001	0.001	0.000	0.000	0.000	0.000
30	A	296	GLU	-1	-0.873	-0.910	38.893	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	297	THR	0	-0.019	-0.039	41.601	0.000	0.000	0.000	0.000	0.000	0.000
32	A	298	VAL	0	-0.016	0.006	42.339	0.001	0.001	0.000	0.000	0.000	0.000
33	A	299	PRO	0	-0.007	-0.020	43.732	0.001	0.001	0.000	0.000	0.000	0.000
34	A	300	VAL	0	0.033	0.013	46.695	0.000	0.000	0.000	0.000	0.000	0.000
35	A	301	LEU	0	0.000	-0.009	46.473	0.000	0.000	0.000	0.000	0.000	0.000
36	A	302	LYS	1	0.895	0.963	44.739	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	303	ALA	0	0.050	0.026	50.535	0.000	0.000	0.000	0.000	0.000	0.000
38	A	304	GLN	0	0.025	0.012	52.493	0.000	0.000	0.000	0.000	0.000	0.000
39	A	305	ALA	0	-0.003	0.004	53.277	0.000	0.000	0.000	0.000	0.000	0.000
40	A	306	ASP	-1	-0.942	-0.978	53.734	0.014	0.014	0.000	0.000	0.000	0.000
41	A	307	ILE	0	-0.005	-0.001	56.345	0.000	0.000	0.000	0.000	0.000	0.000
42	A	308	TYR	0	0.048	0.042	57.294	0.000	0.000	0.000	0.000	0.000	0.000
43	A	309	LYS	1	0.908	0.958	56.173	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	310	ALA	0	-0.005	-0.015	60.310	0.000	0.000	0.000	0.000	0.000	0.000
45	A	311	ASP	-1	-0.884	-0.941	62.309	0.007	0.007	0.000	0.000	0.000	0.000
46	A	312	PHE	0	-0.050	-0.030	63.278	0.000	0.000	0.000	0.000	0.000	0.000
47	A	313	GLN	0	-0.019	-0.025	61.676	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	314	ALA	0	0.007	0.022	66.044	0.000	0.000	0.000	0.000	0.000	0.000
49	A	315	GLU	-1	-0.874	-0.944	68.324	0.007	0.007	0.000	0.000	0.000	0.000
50	A	316	ARG	1	0.818	0.927	67.613	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	317	GLN	0	0.037	0.015	69.979	0.000	0.000	0.000	0.000	0.000	0.000
52	A	318	ALA	0	0.028	0.016	71.928	0.000	0.000	0.000	0.000	0.000	0.000
53	A	319	ARG	1	0.882	0.942	73.282	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	320	GLU	-1	-0.967	-1.001	72.479	0.012	0.012	0.000	0.000	0.000	0.000
55	A	321	LYN	0	0.113	0.051	75.836	0.000	0.000	0.000	0.000	0.000	0.000
56	A	322	LEU	0	-0.136	-0.057	77.906	0.000	0.000	0.000	0.000	0.000	0.000
57	A	323	ALA	0	-0.087	-0.047	78.989	0.000	0.000	0.000	0.000	0.000	0.000
58	A	324	GLU	-1	-0.904	-0.940	80.678	0.009	0.009	0.000	0.000	0.000	0.000
59	A	325	LYS	1	0.917	0.951	82.348	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	326	LYS	1	0.937	0.972	83.844	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	327	GLU	-1	-0.938	-0.976	84.722	0.009	0.009	0.000	0.000	0.000	0.000
62	A	328	LEU	0	-0.038	-0.015	87.291	0.000	0.000	0.000	0.000	0.000	0.000
63	A	329	LEU	0	-0.026	0.003	88.378	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)