FMO DATABASE

FMODB ID: MNM4Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-407831.789624
FMO2-HF: Nuclear repulsion	372716.264847
FMO2-HF: Total energy	-35115.524778
FMO2-MP2: Total energy	-35219.291722

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.
-15.175	-14.626	11.737	-6.102	-6.185	-0.056

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 : -0.003 / q_NPA : -0.020

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	-0.825	-0.906	3.157	-1.562	0.433	0.004	-0.916	-1.083	0.001
4	B	262	ASP	-1	-0.823	-0.904	1.849	-14.759	-17.118	11.681	-4.992	-4.330	-0.057
5	B	263	LEU	0	-0.015	0.003	3.198	0.655	1.568	0.052	-0.194	-0.772	0.000
6	B	264	LYS	1	0.825	0.894	6.083	-0.017	-0.017	0.000	0.000	0.000	0.000
7	B	265	GLN	0	0.003	0.005	7.545	0.202	0.202	0.000	0.000	0.000	0.000
8	B	266	GLN	0	-0.035	-0.025	6.044	0.166	0.166	0.000	0.000	0.000	0.000
9	B	267	LEU	0	-0.017	0.003	10.130	0.011	0.011	0.000	0.000	0.000	0.000
10	B	268	GLN	0	-0.020	-0.026	11.975	-0.048	-0.048	0.000	0.000	0.000	0.000
11	B	269	GLN	0	0.010	0.008	13.464	0.039	0.039	0.000	0.000	0.000	0.000
12	B	270	ALA	0	-0.024	-0.017	14.478	-0.017	-0.017	0.000	0.000	0.000	0.000
13	B	271	GLU	-1	-0.919	-0.953	16.183	0.186	0.186	0.000	0.000	0.000	0.000
14	B	272	GLU	-1	-0.915	-0.956	18.136	0.115	0.115	0.000	0.000	0.000	0.000
15	B	273	ALA	0	-0.015	-0.010	18.955	-0.015	-0.015	0.000	0.000	0.000	0.000
16	B	274	LEU	0	-0.064	-0.037	18.768	-0.012	-0.012	0.000	0.000	0.000	0.000
17	B	275	VAL	0	-0.006	0.007	22.061	-0.017	-0.017	0.000	0.000	0.000	0.000
18	B	276	ALA	0	0.058	0.029	23.912	-0.011	-0.011	0.000	0.000	0.000	0.000
19	B	277	LYS	1	0.888	0.935	22.061	-0.248	-0.248	0.000	0.000	0.000	0.000
20	B	278	GLN	0	0.014	0.009	26.216	-0.015	-0.015	0.000	0.000	0.000	0.000
21	B	279	GLU	-1	-0.864	-0.927	28.186	0.106	0.106	0.000	0.000	0.000	0.000
22	B	280	VAL	0	-0.047	-0.018	29.510	-0.009	-0.009	0.000	0.000	0.000	0.000
23	B	281	ILE	0	-0.028	-0.020	27.986	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	282	ASP	-1	-0.815	-0.904	31.825	0.117	0.117	0.000	0.000	0.000	0.000
25	B	283	LYS	1	0.824	0.899	34.117	-0.094	-0.094	0.000	0.000	0.000	0.000
26	B	284	LEU	0	-0.033	-0.018	33.097	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	285	LYS	1	0.772	0.876	31.664	-0.132	-0.132	0.000	0.000	0.000	0.000
28	B	286	GLU	-1	-0.944	-0.964	37.765	0.072	0.072	0.000	0.000	0.000	0.000
29	B	287	GLU	-1	-0.796	-0.893	38.608	0.080	0.080	0.000	0.000	0.000	0.000
30	B	288	ALA	0	-0.047	-0.026	39.840	-0.004	-0.004	0.000	0.000	0.000	0.000
31	B	289	GLU	-1	-0.841	-0.904	41.751	0.068	0.068	0.000	0.000	0.000	0.000
32	B	290	GLN	0	-0.053	-0.028	44.228	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	291	HIS	0	-0.012	-0.016	42.625	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	292	ASN	0	-0.052	-0.035	43.861	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	293	ILE	0	0.027	0.016	47.468	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	294	VAL	0	-0.029	-0.005	49.331	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	295	MET	0	-0.019	0.010	47.932	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	296	GLU	-1	-0.905	-0.959	51.216	0.052	0.052	0.000	0.000	0.000	0.000
39	B	297	THR	0	-0.072	-0.051	53.717	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	298	VAL	0	0.005	0.011	53.118	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	299	PRO	0	-0.015	-0.014	54.962	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	300	VAL	0	0.022	0.016	57.920	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	301	LEU	0	0.026	0.009	58.162	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	302	LYS	1	0.774	0.873	59.459	-0.041	-0.041	0.000	0.000	0.000	0.000
45	B	303	ALA	0	0.045	0.019	61.449	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	304	GLN	0	-0.008	-0.011	63.879	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	305	ALA	0	-0.013	0.003	64.227	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	306	ASP	-1	-0.854	-0.911	63.973	0.037	0.037	0.000	0.000	0.000	0.000
49	B	307	ILE	0	-0.008	0.000	67.101	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	308	TYR	0	0.051	0.029	68.184	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	309	LYS	1	0.887	0.944	68.522	-0.032	-0.032	0.000	0.000	0.000	0.000
52	B	310	ALA	0	-0.030	-0.017	71.370	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	311	ASP	-1	-0.847	-0.933	73.155	0.027	0.027	0.000	0.000	0.000	0.000
54	B	312	PHE	0	-0.019	-0.012	74.523	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	313	GLN	0	-0.030	-0.017	72.798	0.000	0.000	0.000	0.000	0.000	0.000
56	B	314	ALA	0	0.002	0.007	76.949	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	315	GLU	-1	-0.883	-0.939	79.179	0.021	0.021	0.000	0.000	0.000	0.000
58	B	316	ARG	1	0.815	0.911	78.236	-0.024	-0.024	0.000	0.000	0.000	0.000
59	B	317	GLN	0	0.027	0.013	81.140	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	318	ALA	0	0.002	0.002	82.838	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	319	ARG	1	0.933	0.952	83.010	-0.021	-0.021	0.000	0.000	0.000	0.000
62	B	320	GLU	-1	-0.840	-0.910	83.453	0.021	0.021	0.000	0.000	0.000	0.000
63	B	321	LYS	1	0.916	0.942	84.786	-0.022	-0.022	0.000	0.000	0.000	0.000
64	B	322	LEU	0	-0.046	-0.012	88.981	0.000	0.000	0.000	0.000	0.000	0.000
65	B	323	ALA	0	0.008	0.003	90.370	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	324	GLU	-1	-0.897	-0.950	90.940	0.017	0.017	0.000	0.000	0.000	0.000
67	B	325	LYS	1	0.922	0.959	92.082	-0.018	-0.018	0.000	0.000	0.000	0.000
68	B	326	LYS	1	0.809	0.901	95.038	-0.016	-0.016	0.000	0.000	0.000	0.000
69	B	327	GLU	-1	-0.806	-0.893	95.698	0.015	0.015	0.000	0.000	0.000	0.000
70	B	328	LEU	0	0.039	0.031	97.849	0.000	0.000	0.000	0.000	0.000	0.000
71	B	329	LEU	0	-0.052	-0.043	98.342	0.000	0.000	0.000	0.000	0.000	0.000
72	B	330	GLN	0	-0.017	-0.001	100.981	0.000	0.000	0.000	0.000	0.000	0.000
73	B	331	GLU	-1	-0.907	-0.949	101.411	0.014	0.014	0.000	0.000	0.000	0.000
74	B	332	GLN	0	-0.035	-0.025	102.688	0.000	0.000	0.000	0.000	0.000	0.000
75	B	333	LEU	0	-0.021	0.000	105.377	0.000	0.000	0.000	0.000	0.000	0.000
76	B	334	GLU	-1	-0.822	-0.906	105.709	0.013	0.013	0.000	0.000	0.000	0.000
77	B	335	GLN	0	-0.023	-0.001	108.408	0.000	0.000	0.000	0.000	0.000	0.000
78	B	336	LEU	0	0.009	0.003	109.864	0.000	0.000	0.000	0.000	0.000	0.000
79	B	337	GLN	0	-0.005	-0.009	109.609	0.000	0.000	0.000	0.000	0.000	0.000
80	B	338	ARG	1	0.893	0.945	108.619	-0.012	-0.012	0.000	0.000	0.000	0.000
81	B	339	GLU	-1	-0.831	-0.884	114.103	0.011	0.011	0.000	0.000	0.000	0.000
82	B	340	TYR	0	0.006	-0.010	115.703	0.000	0.000	0.000	0.000	0.000	0.000
83	B	341	SER	0	-0.011	-0.025	116.710	0.000	0.000	0.000	0.000	0.000	0.000
84	B	342	LYS	1	0.782	0.870	117.009	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	343	LEU	0	-0.037	0.001	119.403	0.000	0.000	0.000	0.000	0.000	0.000
86	B	344	LYS	1	0.876	0.952	120.815	-0.010	-0.010	0.000	0.000	0.000	0.000

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