FMO DATABASE

FMODB ID: L7JG9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1805067.10055
FMO2-HF: Nuclear repulsion	1735689.082741
FMO2-HF: Total energy	-69378.017809
FMO2-MP2: Total energy	-69578.239878

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.
-8.451	-4.594	0.111	-1.614	-2.353	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 : 0.025 / 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	-0.033	-0.032	3.436	-4.057	-1.640	0.035	-1.167	-1.285	0.006
4	A	5	GLU	-1	-0.960	-0.966	3.012	-4.755	-3.487	0.077	-0.418	-0.926	-0.002
5	A	6	VAL	0	0.079	0.030	4.400	0.246	0.418	-0.001	-0.029	-0.142	0.000
6	A	7	LEU	0	-0.006	-0.003	7.217	0.182	0.182	0.000	0.000	0.000	0.000
7	A	8	CYS	0	-0.076	-0.030	7.132	0.015	0.015	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.841	-0.934	8.638	-0.380	-0.380	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.012	0.010	10.636	0.038	0.038	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.021	0.008	12.178	0.015	0.015	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.842	0.916	9.386	0.278	0.278	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.885	0.948	14.616	0.276	0.276	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.029	-0.005	16.431	0.004	0.004	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.107	0.051	18.639	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.091	-0.054	22.121	0.012	0.012	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.812	-0.898	24.124	0.023	0.023	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.825	-0.912	21.252	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.814	0.919	19.346	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.734	-0.878	21.158	0.070	0.070	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.054	0.036	23.811	0.011	0.011	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.013	-0.018	17.724	0.011	0.011	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.040	-0.031	18.629	0.022	0.022	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.046	0.000	21.558	0.010	0.010	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.017	-0.020	22.596	0.005	0.005	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.072	-0.038	17.626	0.012	0.012	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.047	-0.009	21.824	0.007	0.007	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.041	-0.025	20.216	0.012	0.012	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.018	0.010	22.250	0.001	0.001	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.012	-0.016	20.922	0.008	0.008	0.000	0.000	0.000	0.000
30	A	31	PRO	0	-0.017	-0.005	24.733	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	32	GLN	0	-0.030	-0.016	25.860	0.002	0.002	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.048	0.050	20.833	0.000	0.000	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.021	-0.021	20.276	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.018	0.003	15.215	0.021	0.021	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.001	-0.001	15.395	0.029	0.029	0.000	0.000	0.000	0.000
36	A	37	GLN	0	0.061	0.012	16.003	0.030	0.030	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.017	0.024	15.472	0.028	0.028	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.009	-0.008	10.641	0.041	0.041	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.019	-0.004	13.080	0.093	0.093	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.038	0.028	14.536	0.050	0.050	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.025	0.005	12.790	0.036	0.036	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.913	0.934	6.155	-0.992	-0.992	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.062	0.029	11.387	0.131	0.131	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.024	0.024	14.378	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.827	0.920	7.777	-0.890	-0.890	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.987	-1.002	10.336	1.249	1.249	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.888	-0.939	12.362	0.301	0.301	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.065	-0.015	13.640	-0.069	-0.069	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.944	0.977	14.734	-0.332	-0.332	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.006	0.011	12.700	-0.043	-0.043	0.000	0.000	0.000	0.000
51	A	52	THR	0	0.013	-0.004	12.922	0.077	0.077	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.033	0.011	11.029	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	54	PRO	0	0.009	-0.017	13.555	-0.034	-0.034	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.051	0.043	16.941	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.002	-0.006	12.737	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	57	ALA	0	0.009	0.012	16.117	-0.037	-0.037	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.721	-0.819	17.615	0.044	0.044	0.000	0.000	0.000	0.000
58	A	59	CYS	0	0.005	-0.005	18.545	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.035	0.022	15.220	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.044	-0.027	19.802	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.813	0.891	22.575	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.021	-0.008	21.723	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.038	0.021	23.819	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.734	0.840	20.194	0.058	0.058	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.886	0.927	20.365	0.030	0.030	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.826	-0.886	20.130	-0.118	-0.118	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.059	0.026	16.046	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.022	-0.002	15.718	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.890	0.958	16.657	0.109	0.109	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.912	-0.945	15.912	-0.238	-0.238	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.050	-0.019	11.513	-0.063	-0.063	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.083	-0.030	11.289	-0.066	-0.066	0.000	0.000	0.000	0.000
73	A	74	HIS	0	0.011	0.011	11.090	0.063	0.063	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.018	-0.013	15.229	0.030	0.030	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.833	-0.922	18.074	-0.087	-0.087	0.000	0.000	0.000	0.000
76	A	77	PRO	0	0.014	-0.003	21.391	0.017	0.017	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.962	0.971	23.375	0.071	0.071	0.000	0.000	0.000	0.000
78	A	79	PHE	0	-0.066	-0.027	20.758	0.009	0.009	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.044	0.010	20.047	0.009	0.009	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.906	-0.950	23.419	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.941	0.952	26.918	0.043	0.043	0.000	0.000	0.000	0.000
82	A	83	HIS	0	-0.010	0.013	22.940	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.001	-0.004	23.513	0.008	0.008	0.000	0.000	0.000	0.000
84	A	85	ALA	0	-0.040	-0.003	26.801	0.005	0.005	0.000	0.000	0.000	0.000
85	A	86	GLY	0	-0.030	-0.011	29.317	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	THR	0	-0.050	-0.033	26.324	0.003	0.003	0.000	0.000	0.000	0.000
87	A	88	MET	0	-0.033	-0.008	28.762	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.007	-0.015	26.311	0.007	0.007	0.000	0.000	0.000	0.000
89	A	90	TYR	0	-0.035	-0.020	20.336	0.014	0.014	0.000	0.000	0.000	0.000
90	A	91	PHE	0	-0.026	-0.016	21.953	0.010	0.010	0.000	0.000	0.000	0.000
91	A	92	SER	0	0.018	0.010	27.049	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	93	PRO	0	0.069	0.010	30.691	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	94	TYR	0	0.021	0.036	32.196	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	95	GLN	0	0.046	0.031	26.032	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	96	LEU	0	0.006	-0.010	28.041	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.031	-0.042	31.050	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.017	-0.009	31.312	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.005	-0.008	26.851	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	HIS	0	-0.023	-0.024	30.729	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.002	-0.005	33.685	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.974	-1.027	30.266	0.027	0.027	0.000	0.000	0.000	0.000
102	A	103	GLY	0	0.006	0.029	32.433	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.933	-0.965	32.991	0.000	0.000	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.102	-0.042	35.873	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	106	CYS	0	-0.041	-0.028	36.697	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.073	0.010	38.102	0.002	0.002	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.896	0.936	38.988	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.759	-0.851	39.878	0.010	0.010	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.073	0.037	34.839	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.927	0.956	38.485	0.002	0.002	0.000	0.000	0.000	0.000
111	A	112	SER	0	-0.004	0.008	40.289	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	LEU	0	0.048	0.027	37.117	0.001	0.001	0.000	0.000	0.000	0.000
113	A	114	ILE	0	-0.037	-0.011	35.863	0.002	0.002	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.041	-0.016	39.298	0.001	0.001	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.053	-0.041	42.856	0.001	0.001	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.048	-0.006	40.127	0.002	0.002	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.921	0.963	40.464	-0.022	-0.022	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.930	-0.941	41.487	0.028	0.028	0.000	0.000	0.000	0.000
119	A	120	THR	0	-0.015	-0.030	39.290	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.080	0.034	40.944	0.002	0.002	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.005	0.011	39.551	0.002	0.002	0.000	0.000	0.000	0.000
122	A	123	SER	0	0.000	-0.007	36.151	0.003	0.003	0.000	0.000	0.000	0.000
123	A	124	ARG	1	0.904	0.947	33.923	-0.061	-0.061	0.000	0.000	0.000	0.000
124	A	125	SER	0	0.006	-0.009	32.540	0.001	0.001	0.000	0.000	0.000	0.000
125	A	126	THR	0	-0.008	0.029	35.161	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	127	PRO	0	-0.021	-0.016	34.294	0.001	0.001	0.000	0.000	0.000	0.000
127	A	128	GLN	0	-0.001	-0.019	32.932	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	129	THR	0	0.000	0.009	29.764	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	130	PHE	0	0.028	0.029	32.853	0.004	0.004	0.000	0.000	0.000	0.000
130	A	131	LEU	0	0.105	0.046	27.368	0.004	0.004	0.000	0.000	0.000	0.000
131	A	132	HIS	0	0.008	0.032	30.774	0.005	0.005	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.007	-0.012	31.563	0.004	0.004	0.000	0.000	0.000	0.000
133	A	134	VAL	0	0.034	0.004	32.254	0.001	0.001	0.000	0.000	0.000	0.000
134	A	135	TYR	0	0.000	0.007	29.071	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	CYS	0	-0.101	-0.075	31.988	0.002	0.002	0.000	0.000	0.000	0.000
136	A	137	MET	0	-0.005	0.008	34.978	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.803	-0.895	31.177	0.084	0.084	0.000	0.000	0.000	0.000
138	A	139	ASN	0	-0.101	-0.046	31.762	0.006	0.006	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.100	-0.064	35.151	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.952	-0.973	37.792	0.062	0.062	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.055	-0.014	39.280	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.044	-0.003	35.839	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	144	GLY	0	0.070	0.036	35.236	0.003	0.003	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.052	-0.056	34.165	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	146	THR	0	-0.034	-0.020	36.799	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.902	-0.953	39.567	0.041	0.041	0.000	0.000	0.000	0.000
147	A	148	VAL	0	0.044	0.030	38.153	0.001	0.001	0.000	0.000	0.000	0.000
148	A	149	ASP	-1	-0.893	-0.958	40.740	0.033	0.033	0.000	0.000	0.000	0.000
149	A	150	ALA	0	0.067	0.035	41.524	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	151	LEU	0	-0.045	-0.027	37.164	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	152	MET	0	-0.040	-0.022	40.800	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	153	SER	0	-0.041	-0.006	43.783	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	154	MET	0	0.075	0.029	40.757	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	155	LEU	0	0.029	0.018	40.033	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	156	ARG	1	0.907	0.948	43.676	-0.025	-0.025	0.000	0.000	0.000	0.000
156	A	157	SER	0	-0.096	-0.032	45.419	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	158	LEU	0	-0.015	-0.008	41.466	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	159	SER	0	-0.055	-0.024	45.732	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	160	ARG	1	0.837	0.933	40.464	-0.010	-0.010	0.000	0.000	0.000	0.000
160	A	161	VAL	0	0.036	0.001	44.769	0.002	0.002	0.000	0.000	0.000	0.000
161	A	162	ASP	-1	-0.834	-0.913	43.992	0.011	0.011	0.000	0.000	0.000	0.000
162	A	163	LEU	0	0.039	0.022	39.379	0.001	0.001	0.000	0.000	0.000	0.000
163	A	164	GLN	0	0.005	0.012	42.243	0.002	0.002	0.000	0.000	0.000	0.000
164	A	165	ARG	1	0.857	0.918	44.379	-0.017	-0.017	0.000	0.000	0.000	0.000
165	A	166	GLN	0	0.076	0.059	40.302	0.002	0.002	0.000	0.000	0.000	0.000
166	A	167	VAL	0	0.043	0.034	38.848	0.002	0.002	0.000	0.000	0.000	0.000
167	A	168	GLN	0	0.049	0.022	40.783	0.001	0.001	0.000	0.000	0.000	0.000
168	A	169	THR	0	-0.135	-0.080	42.506	-0.001	-0.001	0.000	0.000	0.000	0.000
169	A	170	LEU	0	-0.059	-0.044	36.159	0.000	0.000	0.000	0.000	0.000	0.000
170	A	171	MET	0	-0.043	0.004	37.049	0.003	0.003	0.000	0.000	0.000	0.000
171	A	172	GLY	0	0.012	0.025	40.404	0.001	0.001	0.000	0.000	0.000	0.000
172	A	173	LEU	0	-0.034	-0.020	43.901	0.000	0.000	0.000	0.000	0.000	0.000

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