FMO DATABASE

FMODB ID: 9MG72

Calculation Name: 3CL3-A-Xray372

Preferred Name: NF-kappa-B essential modulator

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3CL3

Chain ID: A

ChEMBL ID: CHEMBL4967

UniProt ID: Q9Y6K9

Base Structure: X-ray

Registration Date: 2023-09-26

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	172
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1803898.309502
FMO2-HF: Nuclear repulsion	1734518.84977
FMO2-HF: Total energy	-69379.459732
FMO2-MP2: Total energy	-69579.485867

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-8.212	-4.269	0.137	-1.642	-2.438	0.004

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.007

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

Sort

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	4	TYR	0	-0.015	-0.018	3.493	-4.009	-1.620	0.032	-1.147	-1.275	0.006
4	A	5	GLU	-1	-0.945	-0.954	2.893	-4.846	-3.464	0.106	-0.466	-1.021	-0.002
5	A	6	VAL	0	0.053	0.017	4.346	0.349	0.521	-0.001	-0.029	-0.142	0.000
6	A	7	LEU	0	-0.011	-0.001	7.133	0.212	0.212	0.000	0.000	0.000	0.000
7	A	8	CYS	0	-0.067	-0.038	6.991	0.050	0.050	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.785	-0.877	8.580	-0.418	-0.418	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.006	0.009	10.585	0.053	0.053	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.036	0.014	12.107	0.024	0.024	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.785	0.872	9.184	0.445	0.445	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.863	0.926	14.123	0.350	0.350	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.030	-0.012	16.637	0.009	0.009	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.118	0.063	18.574	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.086	-0.046	22.058	0.011	0.011	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.845	-0.915	24.062	0.004	0.004	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.793	-0.891	21.278	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.835	0.912	19.031	0.019	0.019	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.714	-0.865	21.083	0.060	0.060	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.042	0.032	23.877	0.011	0.011	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.014	-0.023	17.619	0.013	0.013	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.036	-0.024	18.553	0.021	0.021	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.036	-0.002	21.473	0.012	0.012	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.026	-0.017	22.447	0.006	0.006	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.059	-0.034	17.509	0.013	0.013	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.075	-0.029	21.734	0.010	0.010	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.020	-0.012	20.119	0.012	0.012	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.021	0.015	22.168	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.014	-0.017	20.662	0.008	0.008	0.000	0.000	0.000	0.000
30	A	31	PRO	0	-0.010	0.000	24.661	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	32	GLN	0	-0.077	-0.046	25.778	0.000	0.000	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.018	0.040	20.728	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.027	-0.018	20.458	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.009	-0.003	15.171	0.021	0.021	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.003	0.002	15.341	0.025	0.025	0.000	0.000	0.000	0.000
36	A	37	GLN	0	0.079	0.043	15.951	0.030	0.030	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.012	0.017	15.520	0.029	0.029	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.013	-0.003	10.495	0.042	0.042	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.010	0.002	13.009	0.093	0.093	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.031	0.022	14.475	0.054	0.054	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.022	0.004	12.765	0.038	0.038	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.885	0.941	6.167	-1.274	-1.274	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.033	0.016	11.311	0.138	0.138	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.037	0.024	14.284	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.830	0.917	7.977	-0.845	-0.845	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.946	-0.991	9.645	1.395	1.395	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.879	-0.932	12.362	0.305	0.305	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.048	-0.017	13.722	-0.068	-0.068	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.916	0.971	14.815	-0.339	-0.339	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.010	0.009	12.888	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	52	THR	0	0.000	-0.005	13.009	0.079	0.079	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.023	0.010	11.367	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	54	PRO	0	0.040	-0.003	13.637	-0.034	-0.034	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.056	0.039	17.039	-0.026	-0.026	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.006	-0.001	12.873	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	57	ALA	0	0.014	0.009	16.117	-0.040	-0.040	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.717	-0.820	17.615	0.040	0.040	0.000	0.000	0.000	0.000
58	A	59	CYS	0	-0.008	0.005	18.464	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.032	0.016	15.265	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.062	-0.031	19.802	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.823	0.897	22.575	-0.036	-0.036	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.021	-0.006	21.612	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.032	0.015	23.736	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.725	0.815	20.062	0.080	0.080	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.828	0.884	20.365	0.032	0.032	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.824	-0.883	20.606	-0.136	-0.136	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.058	0.026	16.093	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.013	0.002	15.717	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.868	0.951	16.743	0.127	0.127	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.889	-0.942	15.945	-0.253	-0.253	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.051	-0.022	11.178	-0.073	-0.073	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.079	-0.029	11.297	-0.068	-0.068	0.000	0.000	0.000	0.000
73	A	74	HIS	0	-0.009	0.004	11.315	0.070	0.070	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.019	-0.010	15.321	0.033	0.033	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.799	-0.922	18.181	-0.082	-0.082	0.000	0.000	0.000	0.000
76	A	77	PRO	0	0.011	0.002	21.548	0.018	0.018	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.986	0.980	23.482	0.074	0.074	0.000	0.000	0.000	0.000
78	A	79	PHE	0	-0.032	-0.007	21.087	0.010	0.010	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.046	0.014	19.576	0.010	0.010	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.864	-0.915	23.541	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.884	0.928	26.756	0.047	0.047	0.000	0.000	0.000	0.000
82	A	83	HIS	0	-0.002	0.015	23.508	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.020	-0.013	23.490	0.009	0.009	0.000	0.000	0.000	0.000
84	A	85	ALA	0	-0.042	-0.006	26.933	0.005	0.005	0.000	0.000	0.000	0.000
85	A	86	GLY	0	-0.024	-0.008	29.445	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	THR	0	-0.070	-0.034	26.216	0.005	0.005	0.000	0.000	0.000	0.000
87	A	88	MET	0	-0.012	-0.001	28.862	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.008	-0.026	26.512	0.007	0.007	0.000	0.000	0.000	0.000
89	A	90	TYR	0	-0.040	-0.022	20.954	0.009	0.009	0.000	0.000	0.000	0.000
90	A	91	PHE	0	-0.033	-0.017	21.793	0.010	0.010	0.000	0.000	0.000	0.000
91	A	92	SER	0	0.020	-0.001	27.136	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	93	PRO	0	0.070	0.010	30.778	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	TYR	0	0.008	-0.007	32.316	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	95	GLN	0	0.050	0.044	25.945	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.002	-0.010	28.061	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.019	-0.028	30.978	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.028	-0.011	31.488	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.002	-0.001	26.721	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	HIS	0	-0.026	-0.014	30.641	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.007	-0.008	33.598	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.928	-0.998	29.654	0.020	0.020	0.000	0.000	0.000	0.000
102	A	103	GLY	0	-0.021	0.013	32.357	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.926	-0.958	32.910	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.076	-0.027	36.086	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	106	CYS	0	-0.038	-0.018	36.620	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.074	0.016	38.036	0.002	0.002	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.819	0.885	38.917	0.001	0.001	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.727	-0.840	39.886	0.005	0.005	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.091	0.045	34.564	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.940	0.962	38.411	0.009	0.009	0.000	0.000	0.000	0.000
111	A	112	SER	0	-0.001	0.010	40.220	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	LEU	0	0.043	0.023	37.124	0.001	0.001	0.000	0.000	0.000	0.000
113	A	114	ILE	0	-0.030	-0.002	35.732	0.002	0.002	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.046	-0.017	39.226	0.001	0.001	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.035	-0.032	42.786	0.001	0.001	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.037	-0.011	39.985	0.002	0.002	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.841	0.907	40.384	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.873	-0.899	41.418	0.023	0.023	0.000	0.000	0.000	0.000
119	A	120	THR	0	-0.019	-0.028	39.037	0.001	0.001	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.070	0.027	40.873	0.002	0.002	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.020	0.020	39.475	0.002	0.002	0.000	0.000	0.000	0.000
122	A	123	SER	0	-0.006	-0.021	35.983	0.003	0.003	0.000	0.000	0.000	0.000
123	A	124	ARG	1	0.891	0.939	33.913	-0.055	-0.055	0.000	0.000	0.000	0.000
124	A	125	SER	0	0.034	0.001	32.717	0.002	0.002	0.000	0.000	0.000	0.000
125	A	126	THR	0	-0.052	0.011	35.098	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	127	PRO	0	0.022	0.011	34.224	0.001	0.001	0.000	0.000	0.000	0.000
127	A	128	GLN	0	-0.020	-0.029	32.925	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	129	THR	0	0.005	-0.009	29.536	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	130	PHE	0	0.011	0.022	32.779	0.004	0.004	0.000	0.000	0.000	0.000
130	A	131	LEU	0	0.078	0.044	27.284	0.004	0.004	0.000	0.000	0.000	0.000
131	A	132	HIS	0	0.038	0.047	30.553	0.004	0.004	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.008	-0.011	31.486	0.004	0.004	0.000	0.000	0.000	0.000
133	A	134	VAL	0	0.029	0.002	32.143	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	TYR	0	0.034	0.024	28.757	0.001	0.001	0.000	0.000	0.000	0.000
135	A	136	CYS	0	-0.099	-0.041	31.907	0.003	0.003	0.000	0.000	0.000	0.000
136	A	137	MET	0	0.000	0.007	34.900	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.768	-0.862	31.332	0.076	0.076	0.000	0.000	0.000	0.000
138	A	139	ASN	0	-0.146	-0.085	31.307	0.007	0.007	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.095	-0.056	35.071	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.956	-0.974	37.709	0.061	0.061	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.050	-0.014	39.201	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.060	-0.023	35.940	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	144	GLY	0	0.075	0.043	35.147	0.004	0.004	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.044	-0.044	34.152	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	146	THR	0	-0.038	-0.028	36.708	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.867	-0.917	39.475	0.038	0.038	0.000	0.000	0.000	0.000
147	A	148	VAL	0	0.042	0.017	37.941	0.001	0.001	0.000	0.000	0.000	0.000
148	A	149	ASP	-1	-0.923	-0.977	40.651	0.027	0.027	0.000	0.000	0.000	0.000
149	A	150	ALA	0	0.045	0.023	41.443	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	151	LEU	0	-0.028	-0.019	37.093	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	152	MET	0	-0.035	-0.014	40.713	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	153	SER	0	-0.030	-0.001	43.695	-0.004	-0.004	0.000	0.000	0.000	0.000
153	A	154	MET	0	0.066	0.027	40.608	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	155	LEU	0	0.017	0.016	39.837	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	156	ARG	1	0.882	0.926	43.591	-0.024	-0.024	0.000	0.000	0.000	0.000
156	A	157	SER	0	-0.082	-0.029	45.390	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	158	LEU	0	-0.021	-0.014	41.417	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	159	SER	0	-0.056	-0.022	45.652	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	160	ARG	1	0.795	0.897	40.242	-0.006	-0.006	0.000	0.000	0.000	0.000
160	A	161	VAL	0	0.050	0.006	44.683	0.002	0.002	0.000	0.000	0.000	0.000
161	A	162	ASP	-1	-0.802	-0.881	43.501	0.008	0.008	0.000	0.000	0.000	0.000
162	A	163	LEU	0	0.039	0.026	39.087	0.001	0.001	0.000	0.000	0.000	0.000
163	A	164	GLN	0	0.027	0.034	42.155	0.003	0.003	0.000	0.000	0.000	0.000
164	A	165	ARG	1	0.874	0.922	44.290	-0.015	-0.015	0.000	0.000	0.000	0.000
165	A	166	GLN	0	0.051	0.032	40.297	0.001	0.001	0.000	0.000	0.000	0.000
166	A	167	VAL	0	0.032	0.029	38.636	0.002	0.002	0.000	0.000	0.000	0.000
167	A	168	GLN	0	0.036	0.013	40.693	0.001	0.001	0.000	0.000	0.000	0.000
168	A	169	THR	0	-0.139	-0.082	42.526	0.000	0.000	0.000	0.000	0.000	0.000
169	A	170	LEU	0	-0.048	-0.039	36.168	0.001	0.001	0.000	0.000	0.000	0.000
170	A	171	MET	0	-0.036	0.005	37.360	0.004	0.004	0.000	0.000	0.000	0.000
171	A	172	GLY	0	0.005	0.021	40.403	0.002	0.002	0.000	0.000	0.000	0.000
172	A	173	LEU	0	-0.026	-0.012	43.988	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)