FMO DATABASE

FMODB ID: LNLY9

Calculation Name: 4BWN-B-Xray372

Preferred Name: NF-kappa-B essential modulator

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4BWN

Chain ID: B

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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-406472.007698
FMO2-HF: Nuclear repulsion	371357.682853
FMO2-HF: Total energy	-35114.324845
FMO2-MP2: Total energy	-35218.112858

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(B:259:GLN)

Summations of interaction energy for fragment #1(B:259:GLN)

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.
-16.209	-11.67	6.776	-5.565	-5.752	-0.053

Interaction energy analysis for fragmet #1(B:259:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.003

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	B	261	GLU	-1	-0.946	-0.999	3.400	-2.206	-0.323	-0.006	-0.852	-1.026	0.003
4	B	262	ASP	-1	-0.834	-0.910	2.000	-15.132	-13.009	6.781	-4.623	-4.281	-0.056
5	B	263	LEU	0	-0.018	-0.012	3.753	0.994	1.527	0.001	-0.090	-0.445	0.000
6	B	264	LYS	1	0.928	0.968	6.223	-0.260	-0.260	0.000	0.000	0.000	0.000
7	B	265	GLN	0	-0.003	0.000	8.025	0.101	0.101	0.000	0.000	0.000	0.000
8	B	266	GLN	0	-0.020	-0.011	6.507	-0.003	-0.003	0.000	0.000	0.000	0.000
9	B	267	LEU	0	-0.020	0.005	10.512	0.021	0.021	0.000	0.000	0.000	0.000
10	B	268	GLN	0	0.008	-0.007	12.270	-0.041	-0.041	0.000	0.000	0.000	0.000
11	B	269	GLN	0	0.007	0.009	13.758	0.068	0.068	0.000	0.000	0.000	0.000
12	B	270	ALA	0	-0.014	-0.013	14.868	-0.024	-0.024	0.000	0.000	0.000	0.000
13	B	271	GLU	-1	-0.956	-0.979	16.396	0.226	0.226	0.000	0.000	0.000	0.000
14	B	272	GLU	-1	-0.904	-0.947	18.288	0.198	0.198	0.000	0.000	0.000	0.000
15	B	273	ALA	0	-0.018	-0.014	19.411	-0.021	-0.021	0.000	0.000	0.000	0.000
16	B	274	LEU	0	-0.043	-0.028	19.056	-0.012	-0.012	0.000	0.000	0.000	0.000
17	B	275	VAL	0	0.002	0.015	22.417	-0.020	-0.020	0.000	0.000	0.000	0.000
18	B	276	ALA	0	0.027	0.013	24.084	-0.014	-0.014	0.000	0.000	0.000	0.000
19	B	277	LYS	1	0.901	0.940	23.363	-0.306	-0.306	0.000	0.000	0.000	0.000
20	B	278	GLN	0	-0.002	0.004	26.471	-0.010	-0.010	0.000	0.000	0.000	0.000
21	B	279	GLU	-1	-0.850	-0.922	28.269	0.145	0.145	0.000	0.000	0.000	0.000
22	B	280	VAL	0	-0.084	-0.025	29.475	-0.010	-0.010	0.000	0.000	0.000	0.000
23	B	281	ILE	0	-0.062	-0.036	28.364	-0.009	-0.009	0.000	0.000	0.000	0.000
24	B	282	ASP	-1	-0.882	-0.965	32.135	0.142	0.142	0.000	0.000	0.000	0.000
25	B	283	LYS	1	0.863	0.942	34.290	-0.129	-0.129	0.000	0.000	0.000	0.000
26	B	284	LEU	0	-0.034	-0.031	33.557	-0.006	-0.006	0.000	0.000	0.000	0.000
27	B	285	LYS	1	0.937	0.964	33.927	-0.148	-0.148	0.000	0.000	0.000	0.000
28	B	286	GLU	-1	-0.922	-0.947	37.959	0.093	0.093	0.000	0.000	0.000	0.000
29	B	287	GLU	-1	-0.873	-0.928	40.100	0.110	0.110	0.000	0.000	0.000	0.000
30	B	288	ALA	0	-0.036	-0.024	40.240	-0.005	-0.005	0.000	0.000	0.000	0.000
31	B	289	GLU	-1	-0.924	-0.958	42.179	0.082	0.082	0.000	0.000	0.000	0.000
32	B	290	GLN	0	0.003	-0.003	44.378	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	291	HIS	0	-0.008	-0.022	42.828	-0.008	-0.008	0.000	0.000	0.000	0.000
34	B	292	ASN	0	0.010	0.000	43.993	-0.004	-0.004	0.000	0.000	0.000	0.000
35	B	293	ILE	0	0.047	0.043	47.870	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	294	VAL	0	-0.030	-0.012	49.588	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	295	MET	0	-0.058	-0.007	48.201	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	296	GLU	-1	-0.938	-0.963	51.515	0.065	0.065	0.000	0.000	0.000	0.000
39	B	297	THR	0	-0.064	-0.053	53.859	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	298	VAL	0	0.013	0.016	54.004	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	299	PRO	0	-0.027	-0.019	55.115	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	300	VAL	0	0.016	0.015	58.098	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	301	LEU	0	0.015	-0.002	58.571	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	302	LYS	1	0.831	0.913	59.950	-0.053	-0.053	0.000	0.000	0.000	0.000
45	B	303	ALA	0	0.032	0.009	61.796	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	304	GLN	0	0.000	-0.001	64.104	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	305	ALA	0	-0.008	0.007	64.833	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	306	ASP	-1	-0.878	-0.934	64.868	0.047	0.047	0.000	0.000	0.000	0.000
49	B	307	ILE	0	0.006	0.003	67.738	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	308	TYR	0	0.047	0.022	68.986	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	309	LYS	1	0.898	0.966	68.739	-0.043	-0.043	0.000	0.000	0.000	0.000
52	B	310	ALA	0	-0.028	-0.015	71.929	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	311	ASP	-1	-0.847	-0.919	73.752	0.035	0.035	0.000	0.000	0.000	0.000
54	B	312	PHE	0	0.005	-0.002	75.199	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	313	GLN	0	-0.072	-0.058	73.492	0.000	0.000	0.000	0.000	0.000	0.000
56	B	314	ALA	0	0.015	0.017	77.514	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	315	GLU	-1	-0.904	-0.951	79.674	0.028	0.028	0.000	0.000	0.000	0.000
58	B	316	ARG	1	0.890	0.947	77.211	-0.034	-0.034	0.000	0.000	0.000	0.000
59	B	317	GLN	0	0.034	0.018	81.678	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	318	ALA	0	0.001	-0.004	83.349	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	319	ARG	1	0.979	0.987	84.149	-0.029	-0.029	0.000	0.000	0.000	0.000
62	B	320	GLU	-1	-0.943	-0.976	84.240	0.028	0.028	0.000	0.000	0.000	0.000
63	B	321	LYS	1	0.911	0.958	85.559	-0.028	-0.028	0.000	0.000	0.000	0.000
64	B	322	LEU	0	-0.046	-0.016	89.570	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	323	ALA	0	-0.022	-0.025	90.845	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	324	GLU	-1	-0.897	-0.945	91.509	0.023	0.023	0.000	0.000	0.000	0.000
67	B	325	LYS	1	0.939	0.969	92.939	-0.024	-0.024	0.000	0.000	0.000	0.000
68	B	326	LYS	1	0.934	0.975	95.597	-0.022	-0.022	0.000	0.000	0.000	0.000
69	B	327	GLU	-1	-0.864	-0.929	96.110	0.021	0.021	0.000	0.000	0.000	0.000
70	B	328	LEU	0	0.014	0.022	98.201	0.000	0.000	0.000	0.000	0.000	0.000
71	B	329	LEU	0	-0.063	-0.058	99.817	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	330	GLN	0	-0.036	-0.006	101.344	0.000	0.000	0.000	0.000	0.000	0.000
73	B	331	GLU	-1	-0.878	-0.934	101.882	0.019	0.019	0.000	0.000	0.000	0.000
74	B	332	GLN	0	-0.068	-0.038	103.526	0.000	0.000	0.000	0.000	0.000	0.000
75	B	333	LEU	0	-0.026	-0.009	106.002	0.000	0.000	0.000	0.000	0.000	0.000
76	B	334	GLU	-1	-0.907	-0.954	106.369	0.018	0.018	0.000	0.000	0.000	0.000
77	B	335	GLN	0	-0.009	-0.021	109.046	0.000	0.000	0.000	0.000	0.000	0.000
78	B	336	LEU	0	0.008	0.008	110.506	0.000	0.000	0.000	0.000	0.000	0.000
79	B	337	GLN	0	-0.017	-0.014	110.078	0.000	0.000	0.000	0.000	0.000	0.000
80	B	338	ARG	1	0.945	0.983	109.601	-0.017	-0.017	0.000	0.000	0.000	0.000
81	B	339	GLU	-1	-0.887	-0.950	114.443	0.015	0.015	0.000	0.000	0.000	0.000
82	B	340	TYR	0	0.004	-0.003	116.315	0.000	0.000	0.000	0.000	0.000	0.000
83	B	341	SER	0	-0.014	-0.023	117.804	0.000	0.000	0.000	0.000	0.000	0.000
84	B	342	LYS	1	0.809	0.922	117.466	-0.015	-0.015	0.000	0.000	0.000	0.000
85	B	343	LEU	0	-0.025	-0.006	120.571	0.000	0.000	0.000	0.000	0.000	0.000
86	B	344	LYS	1	0.908	0.981	121.421	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:259:GLN)