FMO DATABASE

FMODB ID: 98YZ2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-407175.683644
FMO2-HF: Nuclear repulsion	372060.421528
FMO2-HF: Total energy	-35115.262117
FMO2-MP2: Total energy	-35219.031531

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.
-14.787	-15.672	13.501	-6.603	-6.013	-0.057

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 : -0.005 / q_NPA : -0.023

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	-0.821	-0.922	3.267	-1.605	0.251	-0.002	-0.833	-1.021	0.002
4	B	262	ASP	-1	-0.841	-0.911	1.807	-14.655	-17.957	13.500	-5.677	-4.521	-0.059
5	B	263	LEU	0	-0.018	-0.004	3.786	0.991	1.552	0.003	-0.093	-0.471	0.000
6	B	264	LYS	1	0.835	0.909	6.250	-0.001	-0.001	0.000	0.000	0.000	0.000
7	B	265	GLN	0	-0.008	-0.004	7.940	0.151	0.151	0.000	0.000	0.000	0.000
8	B	266	GLN	0	-0.038	-0.026	6.179	0.126	0.126	0.000	0.000	0.000	0.000
9	B	267	LEU	0	-0.023	0.003	10.553	0.046	0.046	0.000	0.000	0.000	0.000
10	B	268	GLN	0	-0.010	-0.026	12.298	-0.038	-0.038	0.000	0.000	0.000	0.000
11	B	269	GLN	0	0.007	0.012	13.807	0.048	0.048	0.000	0.000	0.000	0.000
12	B	270	ALA	0	-0.019	-0.015	14.861	-0.016	-0.016	0.000	0.000	0.000	0.000
13	B	271	GLU	-1	-0.919	-0.952	16.428	0.174	0.174	0.000	0.000	0.000	0.000
14	B	272	GLU	-1	-0.909	-0.947	18.316	0.116	0.116	0.000	0.000	0.000	0.000
15	B	273	ALA	0	-0.013	-0.014	19.374	-0.015	-0.015	0.000	0.000	0.000	0.000
16	B	274	LEU	0	-0.047	-0.027	19.243	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	275	VAL	0	-0.004	0.011	22.517	-0.014	-0.014	0.000	0.000	0.000	0.000
18	B	276	ALA	0	0.035	0.017	24.086	-0.010	-0.010	0.000	0.000	0.000	0.000
19	B	277	LYS	1	0.904	0.944	22.895	-0.232	-0.232	0.000	0.000	0.000	0.000
20	B	278	GLN	0	-0.004	0.001	26.586	-0.011	-0.011	0.000	0.000	0.000	0.000
21	B	279	GLU	-1	-0.859	-0.929	28.358	0.101	0.101	0.000	0.000	0.000	0.000
22	B	280	VAL	0	-0.067	-0.019	29.527	-0.008	-0.008	0.000	0.000	0.000	0.000
23	B	281	ILE	0	-0.056	-0.037	28.462	-0.007	-0.007	0.000	0.000	0.000	0.000
24	B	282	ASP	-1	-0.814	-0.921	32.279	0.109	0.109	0.000	0.000	0.000	0.000
25	B	283	LYS	1	0.834	0.922	34.377	-0.091	-0.091	0.000	0.000	0.000	0.000
26	B	284	LEU	0	-0.033	-0.027	33.451	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	285	LYS	1	0.838	0.916	32.242	-0.122	-0.122	0.000	0.000	0.000	0.000
28	B	286	GLU	-1	-0.936	-0.956	38.051	0.069	0.069	0.000	0.000	0.000	0.000
29	B	287	GLU	-1	-0.828	-0.904	39.173	0.078	0.078	0.000	0.000	0.000	0.000
30	B	288	ALA	0	-0.032	-0.023	40.284	-0.004	-0.004	0.000	0.000	0.000	0.000
31	B	289	GLU	-1	-0.847	-0.910	42.219	0.064	0.064	0.000	0.000	0.000	0.000
32	B	290	GLN	0	-0.040	-0.023	44.458	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	291	HIS	0	-0.013	-0.024	42.935	-0.005	-0.005	0.000	0.000	0.000	0.000
34	B	292	ASN	0	-0.037	-0.026	44.159	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	293	ILE	0	0.029	0.028	47.947	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	294	VAL	0	-0.030	-0.010	49.619	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	295	MET	0	-0.036	0.001	48.076	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	296	GLU	-1	-0.910	-0.953	51.478	0.050	0.050	0.000	0.000	0.000	0.000
39	B	297	THR	0	-0.071	-0.054	53.930	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	298	VAL	0	0.006	0.010	53.558	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	299	PRO	0	-0.010	-0.013	55.101	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	300	VAL	0	0.009	0.013	58.049	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	301	LEU	0	0.016	0.002	58.446	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	302	LYS	1	0.787	0.885	59.662	-0.040	-0.040	0.000	0.000	0.000	0.000
45	B	303	ALA	0	0.040	0.012	61.635	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	304	GLN	0	0.000	-0.003	64.034	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	305	ALA	0	-0.003	0.009	64.584	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	306	ASP	-1	-0.862	-0.918	64.519	0.035	0.035	0.000	0.000	0.000	0.000
49	B	307	ILE	0	0.003	0.002	67.563	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	308	TYR	0	0.052	0.023	68.588	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	309	LYS	1	0.876	0.943	68.660	-0.031	-0.031	0.000	0.000	0.000	0.000
52	B	310	ALA	0	-0.025	-0.016	71.741	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	311	ASP	-1	-0.840	-0.919	73.570	0.026	0.026	0.000	0.000	0.000	0.000
54	B	312	PHE	0	-0.007	-0.006	74.834	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	313	GLN	0	-0.038	-0.026	73.238	0.000	0.000	0.000	0.000	0.000	0.000
56	B	314	ALA	0	0.000	0.007	77.243	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	315	GLU	-1	-0.896	-0.947	79.482	0.021	0.021	0.000	0.000	0.000	0.000
58	B	316	ARG	1	0.837	0.916	77.921	-0.024	-0.024	0.000	0.000	0.000	0.000
59	B	317	GLN	0	0.006	0.009	81.412	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	318	ALA	0	0.012	0.002	83.075	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	319	ARG	1	0.930	0.961	83.493	-0.021	-0.021	0.000	0.000	0.000	0.000
62	B	320	GLU	-1	-0.840	-0.921	83.686	0.021	0.021	0.000	0.000	0.000	0.000
63	B	321	LYS	1	0.928	0.960	85.251	-0.021	-0.021	0.000	0.000	0.000	0.000
64	B	322	LEU	0	-0.037	-0.011	89.313	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	323	ALA	0	-0.004	-0.013	90.542	0.000	0.000	0.000	0.000	0.000	0.000
66	B	324	GLU	-1	-0.906	-0.950	91.211	0.017	0.017	0.000	0.000	0.000	0.000
67	B	325	LYS	1	0.929	0.962	92.818	-0.018	-0.018	0.000	0.000	0.000	0.000
68	B	326	LYS	1	0.801	0.899	95.310	-0.016	-0.016	0.000	0.000	0.000	0.000
69	B	327	GLU	-1	-0.796	-0.885	95.621	0.015	0.015	0.000	0.000	0.000	0.000
70	B	328	LEU	0	0.021	0.023	97.891	0.000	0.000	0.000	0.000	0.000	0.000
71	B	329	LEU	0	-0.058	-0.051	99.031	0.000	0.000	0.000	0.000	0.000	0.000
72	B	330	GLN	0	-0.035	-0.015	101.141	0.000	0.000	0.000	0.000	0.000	0.000
73	B	331	GLU	-1	-0.871	-0.929	101.665	0.014	0.014	0.000	0.000	0.000	0.000
74	B	332	GLN	0	-0.064	-0.037	103.473	0.000	0.000	0.000	0.000	0.000	0.000
75	B	333	LEU	0	-0.019	-0.003	105.707	0.000	0.000	0.000	0.000	0.000	0.000
76	B	334	GLU	-1	-0.869	-0.934	105.697	0.013	0.013	0.000	0.000	0.000	0.000
77	B	335	GLN	0	-0.012	-0.004	108.737	0.000	0.000	0.000	0.000	0.000	0.000
78	B	336	LEU	0	0.004	0.005	110.200	0.000	0.000	0.000	0.000	0.000	0.000
79	B	337	GLN	0	-0.008	-0.009	109.740	0.000	0.000	0.000	0.000	0.000	0.000
80	B	338	ARG	1	0.947	0.979	109.406	-0.012	-0.012	0.000	0.000	0.000	0.000
81	B	339	GLU	-1	-0.840	-0.908	114.188	0.011	0.011	0.000	0.000	0.000	0.000
82	B	340	TYR	0	0.007	-0.001	116.027	0.000	0.000	0.000	0.000	0.000	0.000
83	B	341	SER	0	-0.032	-0.040	117.034	0.000	0.000	0.000	0.000	0.000	0.000
84	B	342	LYS	1	0.790	0.885	117.157	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	343	LEU	0	-0.031	-0.004	120.190	0.000	0.000	0.000	0.000	0.000	0.000
86	B	344	LYS	1	0.898	0.978	121.225	-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)