FMO DATABASE

FMODB ID: M938Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1806107.339953
FMO2-HF: Nuclear repulsion	1736726.638905
FMO2-HF: Total energy	-69380.701048
FMO2-MP2: Total energy	-69580.575799

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.
-6.983	-2.793	0.151	-1.774	-2.566	0.006

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 : 0.064 / q_NPA : 0.021

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	0.010	-0.012	3.159	-4.495	-1.657	0.101	-1.375	-1.564	0.007
4	A	5	GLU	-1	-0.949	-0.949	3.090	-3.773	-2.558	0.051	-0.380	-0.886	-0.001
5	A	6	VAL	0	0.060	0.023	4.649	0.621	0.758	-0.001	-0.019	-0.116	0.000
6	A	7	LEU	0	-0.015	0.003	6.899	0.280	0.280	0.000	0.000	0.000	0.000
7	A	8	CYS	0	-0.045	-0.035	6.965	0.117	0.117	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.805	-0.879	8.761	-0.436	-0.436	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.019	0.001	10.739	0.080	0.080	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.008	-0.006	12.040	0.031	0.031	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.832	0.905	9.098	0.524	0.524	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.853	0.918	13.976	0.359	0.359	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.004	0.005	16.176	0.014	0.014	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.012	0.005	18.666	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.045	-0.039	21.295	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.841	-0.923	23.696	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.769	-0.888	21.136	-0.044	-0.044	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.834	0.919	19.487	0.042	0.042	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.708	-0.818	21.108	0.044	0.044	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.036	0.022	23.655	0.011	0.011	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.012	-0.015	17.514	0.012	0.012	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.039	-0.021	18.163	0.023	0.023	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.018	0.008	21.335	0.014	0.014	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.033	-0.006	22.347	0.006	0.006	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.039	-0.039	17.027	0.014	0.014	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.064	-0.025	21.259	0.013	0.013	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.029	-0.012	19.949	0.008	0.008	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.012	0.009	21.845	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.032	-0.021	20.371	0.007	0.007	0.000	0.000	0.000	0.000
30	A	31	PRO	0	0.018	0.012	24.357	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	32	GLN	0	-0.072	-0.062	25.713	0.002	0.002	0.000	0.000	0.000	0.000
32	A	33	PRO	0	-0.026	0.028	20.687	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.022	-0.034	20.167	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.048	0.006	15.139	0.017	0.017	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.011	0.009	15.195	0.015	0.015	0.000	0.000	0.000	0.000
36	A	37	GLN	0	0.064	0.052	15.727	0.028	0.028	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.023	0.029	15.366	0.033	0.033	0.000	0.000	0.000	0.000
38	A	39	ILE	0	-0.002	-0.010	10.299	0.037	0.037	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.002	0.002	12.349	0.099	0.099	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.033	0.019	14.443	0.066	0.066	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.002	-0.011	12.533	0.039	0.039	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.843	0.915	5.953	-1.240	-1.240	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.037	0.020	11.201	0.129	0.129	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.044	0.021	14.255	0.028	0.028	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.843	0.929	7.983	-0.769	-0.769	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.878	-0.945	9.168	1.410	1.410	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.823	-0.868	12.199	0.287	0.287	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.029	-0.019	13.286	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.836	0.896	14.323	-0.328	-0.328	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.018	0.007	13.048	-0.053	-0.053	0.000	0.000	0.000	0.000
51	A	52	THR	0	0.011	-0.002	12.684	0.063	0.063	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.016	0.000	11.036	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	54	PRO	0	0.033	0.005	13.276	-0.042	-0.042	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.049	0.044	16.816	-0.026	-0.026	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.013	0.009	12.658	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	57	ALA	0	0.038	0.013	15.837	-0.038	-0.038	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.748	-0.832	17.437	0.039	0.039	0.000	0.000	0.000	0.000
58	A	59	CYS	0	-0.046	-0.020	18.080	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.006	-0.002	15.086	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.042	-0.020	19.583	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.831	0.900	22.499	-0.031	-0.031	0.000	0.000	0.000	0.000
62	A	63	ALA	0	0.024	0.022	21.739	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.019	0.017	23.877	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.738	0.843	19.767	0.098	0.098	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.812	0.835	19.988	0.034	0.034	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.800	-0.861	20.224	-0.146	-0.146	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.035	0.016	15.748	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.024	-0.007	15.427	-0.033	-0.033	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.837	0.907	16.462	0.147	0.147	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.845	-0.910	16.041	-0.238	-0.238	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.065	-0.031	10.912	-0.067	-0.067	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.072	-0.032	11.179	-0.077	-0.077	0.000	0.000	0.000	0.000
73	A	74	HIS	0	-0.011	0.009	11.349	0.073	0.073	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.017	-0.006	14.863	0.035	0.035	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.780	-0.909	17.630	-0.076	-0.076	0.000	0.000	0.000	0.000
76	A	77	PRO	0	0.009	-0.003	21.270	0.017	0.017	0.000	0.000	0.000	0.000
77	A	78	ARG	1	1.004	0.993	22.915	0.070	0.070	0.000	0.000	0.000	0.000
78	A	79	PHE	0	-0.032	0.014	20.781	0.008	0.008	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.033	0.016	18.858	0.011	0.011	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.827	-0.873	23.234	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.828	0.892	26.000	0.046	0.046	0.000	0.000	0.000	0.000
82	A	83	HIS	0	0.021	0.017	23.286	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.040	-0.022	22.923	0.009	0.009	0.000	0.000	0.000	0.000
84	A	85	ALA	0	-0.026	0.000	26.797	0.003	0.003	0.000	0.000	0.000	0.000
85	A	86	GLY	0	-0.024	-0.007	29.216	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	THR	0	-0.067	-0.036	25.543	0.005	0.005	0.000	0.000	0.000	0.000
87	A	88	MET	0	-0.025	-0.011	28.502	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.013	-0.027	26.133	0.005	0.005	0.000	0.000	0.000	0.000
89	A	90	TYR	0	-0.035	-0.035	20.672	0.008	0.008	0.000	0.000	0.000	0.000
90	A	91	PHE	0	-0.012	-0.009	21.404	0.010	0.010	0.000	0.000	0.000	0.000
91	A	92	SER	0	0.017	-0.007	26.776	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	93	PRO	0	0.051	0.000	30.407	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	TYR	0	0.007	-0.011	31.934	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	95	GLN	0	0.041	0.041	25.753	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.005	-0.003	27.776	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.016	-0.022	30.794	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.020	-0.005	31.155	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	99	LEU	0	0.006	-0.007	26.528	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	HIS	0	-0.046	-0.023	30.528	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	101	VAL	0	-0.006	-0.011	33.393	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.895	-0.972	29.504	0.011	0.011	0.000	0.000	0.000	0.000
102	A	103	GLY	0	-0.027	0.003	31.936	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.879	-0.915	32.451	-0.009	-0.009	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.042	-0.006	35.757	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	106	CYS	0	-0.050	-0.015	36.536	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.049	-0.001	37.814	0.002	0.002	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.843	0.897	38.711	0.003	0.003	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.695	-0.827	39.779	0.001	0.001	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.052	0.028	34.186	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.940	0.958	38.137	0.014	0.014	0.000	0.000	0.000	0.000
111	A	112	SER	0	-0.012	0.005	40.213	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	LEU	0	0.045	0.025	36.810	0.001	0.001	0.000	0.000	0.000	0.000
113	A	114	ILE	0	0.003	0.026	35.851	0.002	0.002	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.042	-0.022	39.310	0.002	0.002	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.035	-0.029	42.965	0.001	0.001	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.016	-0.011	39.759	0.002	0.002	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.847	0.926	40.264	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.841	-0.903	41.105	0.018	0.018	0.000	0.000	0.000	0.000
119	A	120	THR	0	-0.045	-0.040	38.760	0.001	0.001	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.047	0.011	40.512	0.002	0.002	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.003	0.010	39.548	0.002	0.002	0.000	0.000	0.000	0.000
122	A	123	SER	0	0.030	0.005	35.833	0.003	0.003	0.000	0.000	0.000	0.000
123	A	124	ARG	1	0.866	0.919	33.588	-0.047	-0.047	0.000	0.000	0.000	0.000
124	A	125	SER	0	0.023	0.011	32.282	0.001	0.001	0.000	0.000	0.000	0.000
125	A	126	THR	0	-0.032	0.010	34.495	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	127	PRO	0	0.020	0.023	34.122	0.000	0.000	0.000	0.000	0.000	0.000
127	A	128	GLN	0	-0.018	-0.030	32.110	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	129	THR	0	-0.014	-0.047	29.483	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	130	PHE	0	-0.012	-0.006	32.611	0.004	0.004	0.000	0.000	0.000	0.000
130	A	131	LEU	0	0.051	0.034	27.124	0.004	0.004	0.000	0.000	0.000	0.000
131	A	132	HIS	0	0.018	0.038	30.233	0.003	0.003	0.000	0.000	0.000	0.000
132	A	133	TRP	0	0.027	0.002	31.342	0.004	0.004	0.000	0.000	0.000	0.000
133	A	134	VAL	0	-0.002	0.000	32.300	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	TYR	0	0.065	0.037	28.215	0.001	0.001	0.000	0.000	0.000	0.000
135	A	136	CYS	0	-0.102	-0.047	31.931	0.003	0.003	0.000	0.000	0.000	0.000
136	A	137	MET	0	0.007	0.009	34.960	0.000	0.000	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.792	-0.878	31.225	0.067	0.067	0.000	0.000	0.000	0.000
138	A	139	ASN	0	-0.129	-0.079	30.939	0.007	0.007	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.097	-0.049	34.926	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.947	-0.962	37.475	0.056	0.056	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.047	-0.018	38.861	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.060	-0.042	36.233	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	144	GLY	0	0.064	0.041	34.918	0.005	0.005	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.044	-0.035	33.703	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	146	THR	0	-0.023	-0.012	36.224	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.851	-0.915	39.266	0.033	0.033	0.000	0.000	0.000	0.000
147	A	148	VAL	0	0.051	0.016	38.065	0.001	0.001	0.000	0.000	0.000	0.000
148	A	149	ASP	-1	-0.798	-0.898	40.711	0.021	0.021	0.000	0.000	0.000	0.000
149	A	150	ALA	0	0.063	0.035	41.110	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	151	LEU	0	-0.007	0.004	36.976	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	152	MET	0	-0.066	-0.027	40.638	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	153	SER	0	-0.008	-0.012	43.682	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	154	MET	0	0.032	0.029	40.440	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	155	LEU	0	-0.001	0.007	39.669	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	156	ARG	1	0.757	0.860	43.450	-0.022	-0.022	0.000	0.000	0.000	0.000
156	A	157	SER	0	-0.067	-0.036	45.128	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	158	LEU	0	-0.034	-0.020	40.966	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	159	SER	0	-0.043	-0.020	45.372	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	160	ARG	1	0.721	0.832	40.072	-0.001	-0.001	0.000	0.000	0.000	0.000
160	A	161	VAL	0	0.033	-0.008	44.370	0.002	0.002	0.000	0.000	0.000	0.000
161	A	162	ASP	-1	-0.793	-0.870	43.217	0.004	0.004	0.000	0.000	0.000	0.000
162	A	163	LEU	0	0.031	0.027	38.422	0.001	0.001	0.000	0.000	0.000	0.000
163	A	164	GLN	0	0.016	0.025	41.798	0.003	0.003	0.000	0.000	0.000	0.000
164	A	165	ARG	1	0.852	0.926	44.050	-0.012	-0.012	0.000	0.000	0.000	0.000
165	A	166	GLN	0	0.024	0.021	39.925	0.001	0.001	0.000	0.000	0.000	0.000
166	A	167	VAL	0	0.077	0.031	38.498	0.002	0.002	0.000	0.000	0.000	0.000
167	A	168	GLN	0	0.027	0.013	40.540	0.001	0.001	0.000	0.000	0.000	0.000
168	A	169	THR	0	-0.095	-0.053	42.278	-0.001	-0.001	0.000	0.000	0.000	0.000
169	A	170	LEU	0	-0.032	-0.027	35.953	0.001	0.001	0.000	0.000	0.000	0.000
170	A	171	MET	0	-0.020	0.009	37.221	0.004	0.004	0.000	0.000	0.000	0.000
171	A	172	GLY	0	-0.019	0.011	39.984	0.002	0.002	0.000	0.000	0.000	0.000
172	A	173	LEU	0	-0.051	-0.034	43.383	-0.001	-0.001	0.000	0.000	0.000	0.000

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