FMO DATABASE

FMODB ID: LNLN9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-262485.685031
FMO2-HF: Nuclear repulsion	237323.740227
FMO2-HF: Total energy	-25161.944804
FMO2-MP2: Total energy	-25236.162338

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.
-4.304	-0.959	1.313	-1.79	-2.869	-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 : 0.024 / q_NPA : -0.010

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	-0.042	-0.031	3.477	-1.200	0.973	-0.010	-0.978	-1.185	0.001
4	A	270	ALA	0	-0.044	-0.018	2.324	-0.267	0.254	1.321	-0.674	-1.168	-0.002
5	A	271	GLU	-1	-0.839	-0.917	3.936	-2.176	-1.525	0.002	-0.138	-0.516	0.000
6	A	272	GLU	-1	-0.809	-0.903	5.485	-1.036	-1.036	0.000	0.000	0.000	0.000
7	A	273	ALA	0	-0.069	-0.029	7.090	0.274	0.274	0.000	0.000	0.000	0.000
8	A	274	LEU	0	-0.034	-0.026	5.109	0.172	0.172	0.000	0.000	0.000	0.000
9	A	275	VAL	0	0.041	0.029	8.748	0.108	0.108	0.000	0.000	0.000	0.000
10	A	276	ALA	0	0.040	0.024	11.236	0.090	0.090	0.000	0.000	0.000	0.000
11	A	277	LYS	1	0.873	0.915	11.064	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	278	GLN	0	-0.031	-0.010	13.214	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	279	GLU	-1	-0.868	-0.933	14.867	-0.128	-0.128	0.000	0.000	0.000	0.000
14	A	280	VAL	0	-0.059	-0.030	17.031	0.029	0.029	0.000	0.000	0.000	0.000
15	A	281	ILE	0	-0.032	-0.016	15.966	0.019	0.019	0.000	0.000	0.000	0.000
16	A	282	ASP	-1	-0.817	-0.902	18.887	-0.184	-0.184	0.000	0.000	0.000	0.000
17	A	283	LYS	1	0.766	0.872	20.983	0.041	0.041	0.000	0.000	0.000	0.000
18	A	284	LEU	0	-0.031	-0.028	21.247	0.012	0.012	0.000	0.000	0.000	0.000
19	A	285	LYS	1	0.789	0.893	23.038	0.112	0.112	0.000	0.000	0.000	0.000
20	A	286	GLU	-1	-0.880	-0.922	24.801	-0.084	-0.084	0.000	0.000	0.000	0.000
21	A	287	GLU	-1	-0.797	-0.890	26.584	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	288	ALA	0	0.003	0.004	27.613	0.006	0.006	0.000	0.000	0.000	0.000
23	A	289	GLU	-1	-0.881	-0.940	27.647	-0.086	-0.086	0.000	0.000	0.000	0.000
24	A	290	GLN	0	-0.007	-0.007	30.884	0.004	0.004	0.000	0.000	0.000	0.000
25	A	291	HIS	0	-0.040	-0.028	31.498	0.005	0.005	0.000	0.000	0.000	0.000
26	A	292	LYS	1	0.854	0.922	33.011	0.053	0.053	0.000	0.000	0.000	0.000
27	A	293	ILE	0	0.005	0.009	35.070	0.002	0.002	0.000	0.000	0.000	0.000
28	A	294	VAL	0	0.018	0.011	37.777	0.002	0.002	0.000	0.000	0.000	0.000
29	A	295	MET	0	-0.027	-0.010	35.704	0.002	0.002	0.000	0.000	0.000	0.000
30	A	296	GLU	-1	-0.836	-0.912	37.508	-0.040	-0.040	0.000	0.000	0.000	0.000
31	A	297	THR	0	-0.039	-0.025	41.155	0.002	0.002	0.000	0.000	0.000	0.000
32	A	298	VAL	0	-0.001	0.007	41.844	0.002	0.002	0.000	0.000	0.000	0.000
33	A	299	PRO	0	-0.023	-0.015	43.531	0.002	0.002	0.000	0.000	0.000	0.000
34	A	300	VAL	0	0.023	0.012	46.523	0.001	0.001	0.000	0.000	0.000	0.000
35	A	301	LEU	0	0.014	0.006	45.874	0.001	0.001	0.000	0.000	0.000	0.000
36	A	302	LYS	1	0.929	0.967	45.152	0.010	0.010	0.000	0.000	0.000	0.000
37	A	303	ALA	0	0.042	0.025	50.180	0.001	0.001	0.000	0.000	0.000	0.000
38	A	304	GLN	0	0.009	0.001	52.460	0.001	0.001	0.000	0.000	0.000	0.000
39	A	305	ALA	0	0.006	0.006	52.963	0.001	0.001	0.000	0.000	0.000	0.000
40	A	306	ASP	-1	-0.901	-0.954	53.045	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	307	ILE	0	-0.021	-0.007	55.980	0.001	0.001	0.000	0.000	0.000	0.000
42	A	308	TYR	0	0.041	0.026	56.827	0.000	0.000	0.000	0.000	0.000	0.000
43	A	309	LYS	1	0.827	0.925	55.561	0.005	0.005	0.000	0.000	0.000	0.000
44	A	310	ALA	0	0.010	0.002	60.123	0.001	0.001	0.000	0.000	0.000	0.000
45	A	311	ASP	-1	-0.871	-0.939	62.088	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	312	PHE	0	-0.039	-0.019	63.131	0.001	0.001	0.000	0.000	0.000	0.000
47	A	313	GLN	0	-0.036	-0.036	61.769	0.000	0.000	0.000	0.000	0.000	0.000
48	A	314	ALA	0	-0.002	0.006	65.717	0.000	0.000	0.000	0.000	0.000	0.000
49	A	315	GLU	-1	-0.873	-0.949	68.020	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	316	ARG	1	0.748	0.871	68.047	0.000	0.000	0.000	0.000	0.000	0.000
51	A	317	GLN	0	0.013	0.005	70.026	0.000	0.000	0.000	0.000	0.000	0.000
52	A	318	ALA	0	0.018	0.017	72.009	0.000	0.000	0.000	0.000	0.000	0.000
53	A	319	ARG	1	0.952	0.970	73.301	0.000	0.000	0.000	0.000	0.000	0.000
54	A	320	GLU	-1	-0.893	-0.937	72.767	0.001	0.001	0.000	0.000	0.000	0.000
55	A	321	LYN	0	-0.002	-0.025	75.849	0.000	0.000	0.000	0.000	0.000	0.000
56	A	322	LEU	0	-0.081	-0.029	77.825	0.000	0.000	0.000	0.000	0.000	0.000
57	A	323	ALA	0	-0.014	-0.014	78.940	0.000	0.000	0.000	0.000	0.000	0.000
58	A	324	GLU	-1	-0.842	-0.901	80.393	0.000	0.000	0.000	0.000	0.000	0.000
59	A	325	LYS	1	0.923	0.951	81.982	0.003	0.003	0.000	0.000	0.000	0.000
60	A	326	LYS	1	0.786	0.878	83.878	0.000	0.000	0.000	0.000	0.000	0.000
61	A	327	GLU	-1	-0.840	-0.900	84.781	0.001	0.001	0.000	0.000	0.000	0.000
62	A	328	LEU	0	-0.040	-0.015	86.923	0.000	0.000	0.000	0.000	0.000	0.000
63	A	329	LEU	0	-0.048	-0.003	88.306	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)