FMO DATABASE

FMODB ID: V5Y31

Calculation Name: 5WMF-A-Xray372

Preferred Name: Epstein-Barr nuclear antigen 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5WMF

Chain ID: A

ChEMBL ID: CHEMBL1293281

UniProt ID: P03211

Base Structure: X-ray

Registration Date: 2023-06-22

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1147109.262649
FMO2-HF: Nuclear repulsion	1093816.331797
FMO2-HF: Total energy	-53292.930852
FMO2-MP2: Total energy	-53446.390781

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:475:ASN)

Summations of interaction energy for fragment #1(A:475:ASN)

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.
2.789	8.683	3.079	-4.457	-4.517	-0.025

Interaction energy analysis for fragmet #1(A:475:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.075 / q_NPA : 0.024

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	477	LYS	1	0.997	0.958	3.779	0.616	1.783	-0.007	-0.730	-0.430	0.004
4	A	478	PHE	0	-0.008	0.010	3.482	0.543	0.955	0.002	-0.073	-0.342	0.000
5	A	479	GLU	-1	-0.753	-0.898	2.611	-2.011	2.138	3.085	-3.645	-3.589	-0.029
6	A	480	ASN	0	-0.024	-0.002	4.573	0.842	1.008	-0.001	-0.009	-0.156	0.000
7	A	481	ILE	0	-0.073	-0.027	7.461	0.315	0.315	0.000	0.000	0.000	0.000
8	A	482	ALA	0	0.015	0.011	7.316	0.201	0.201	0.000	0.000	0.000	0.000
9	A	483	GLU	-1	-0.842	-0.934	7.857	0.696	0.696	0.000	0.000	0.000	0.000
10	A	484	GLY	0	-0.048	-0.010	10.309	0.058	0.058	0.000	0.000	0.000	0.000
11	A	485	LEU	0	-0.008	-0.017	12.195	0.050	0.050	0.000	0.000	0.000	0.000
12	A	486	ARG	1	0.903	0.953	10.744	-0.260	-0.260	0.000	0.000	0.000	0.000
13	A	487	ALA	0	0.014	0.018	14.443	0.031	0.031	0.000	0.000	0.000	0.000
14	A	488	LEU	0	-0.034	-0.012	16.451	0.008	0.008	0.000	0.000	0.000	0.000
15	A	489	LEU	0	-0.011	-0.014	16.060	0.008	0.008	0.000	0.000	0.000	0.000
16	A	490	ALA	0	-0.018	-0.004	18.665	0.011	0.011	0.000	0.000	0.000	0.000
17	A	491	ARG	1	0.773	0.876	20.389	0.061	0.061	0.000	0.000	0.000	0.000
18	A	492	SER	0	-0.011	0.004	23.066	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	493	HIS	0	0.003	0.008	23.847	0.016	0.016	0.000	0.000	0.000	0.000
20	A	494	VAL	0	-0.049	-0.034	24.341	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	495	GLU	-1	-0.877	-0.923	24.931	0.037	0.037	0.000	0.000	0.000	0.000
22	A	496	ARG	1	0.870	0.919	16.742	-0.077	-0.077	0.000	0.000	0.000	0.000
23	A	497	THR	0	-0.048	-0.042	23.600	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	498	THR	0	0.034	0.031	25.982	0.002	0.002	0.000	0.000	0.000	0.000
25	A	499	ASP	-1	-0.908	-0.947	29.269	0.060	0.060	0.000	0.000	0.000	0.000
26	A	500	GLU	-1	-0.944	-0.975	31.917	0.027	0.027	0.000	0.000	0.000	0.000
27	A	501	GLY	0	-0.018	-0.001	28.189	0.000	0.000	0.000	0.000	0.000	0.000
28	A	502	THR	0	-0.016	-0.002	27.950	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	503	TRP	0	-0.055	-0.041	21.992	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	504	VAL	0	0.089	0.039	27.584	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	505	ALA	0	0.006	0.025	26.551	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	506	GLY	0	0.047	0.001	23.921	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	507	VAL	0	-0.020	-0.009	21.056	0.000	0.000	0.000	0.000	0.000	0.000
34	A	508	PHE	0	0.022	0.003	21.766	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	509	VAL	0	0.003	-0.002	18.011	0.000	0.000	0.000	0.000	0.000	0.000
36	A	510	TYR	0	0.014	-0.002	20.850	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	511	GLY	0	0.019	0.018	22.180	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	512	GLY	0	0.011	0.004	20.041	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	513	SER	0	0.008	-0.007	18.118	0.004	0.004	0.000	0.000	0.000	0.000
40	A	514	LYS	1	1.058	1.018	16.738	0.238	0.238	0.000	0.000	0.000	0.000
41	A	515	THR	0	0.038	0.006	13.064	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	516	SER	0	-0.015	0.005	12.986	-0.077	-0.077	0.000	0.000	0.000	0.000
43	A	517	LEU	0	0.017	0.015	13.866	-0.056	-0.056	0.000	0.000	0.000	0.000
44	A	518	TYR	0	-0.035	-0.002	8.527	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	519	ASN	0	0.006	-0.015	9.024	-0.104	-0.104	0.000	0.000	0.000	0.000
46	A	520	LEU	0	0.043	0.030	9.416	-0.161	-0.161	0.000	0.000	0.000	0.000
47	A	521	ARG	1	0.910	0.974	12.069	0.345	0.345	0.000	0.000	0.000	0.000
48	A	522	ARG	1	0.897	0.953	5.578	0.808	0.808	0.000	0.000	0.000	0.000
49	A	523	GLY	0	0.034	0.009	8.023	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	524	THR	0	0.000	-0.016	8.920	0.186	0.186	0.000	0.000	0.000	0.000
51	A	525	ALA	0	-0.020	-0.018	9.966	0.096	0.096	0.000	0.000	0.000	0.000
52	A	526	LEU	0	-0.048	-0.009	4.924	0.057	0.057	0.000	0.000	0.000	0.000
53	A	527	ALA	0	-0.014	-0.006	9.603	0.181	0.181	0.000	0.000	0.000	0.000
54	A	528	ILE	0	-0.070	-0.031	12.115	0.085	0.085	0.000	0.000	0.000	0.000
55	A	529	PRO	0	0.044	0.029	13.746	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	530	GLN	0	0.037	0.005	15.442	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	531	CYS	0	-0.024	0.022	15.788	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	532	ARG	1	0.940	0.975	17.743	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	533	LEU	0	-0.018	-0.011	13.615	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	534	THR	0	0.049	0.053	17.500	0.011	0.011	0.000	0.000	0.000	0.000
61	A	535	PRO	0	-0.014	-0.016	16.745	-0.040	-0.040	0.000	0.000	0.000	0.000
62	A	536	LEU	0	-0.030	-0.021	14.666	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	537	SER	0	0.032	0.023	18.318	0.017	0.017	0.000	0.000	0.000	0.000
64	A	538	ARG	1	0.903	0.955	22.017	0.122	0.122	0.000	0.000	0.000	0.000
65	A	539	LEU	0	0.006	0.016	24.776	0.009	0.009	0.000	0.000	0.000	0.000
66	A	540	PRO	0	0.087	0.073	27.452	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	541	PHE	0	-0.040	-0.025	30.930	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	542	GLY	0	0.020	0.012	33.417	0.002	0.002	0.000	0.000	0.000	0.000
69	A	543	MET	0	-0.050	-0.029	35.460	0.003	0.003	0.000	0.000	0.000	0.000
70	A	544	ALA	0	0.002	0.042	38.580	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	545	PRO	0	-0.016	-0.030	40.266	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	546	GLY	0	0.069	0.018	43.635	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	547	PRO	0	-0.051	-0.055	46.144	0.000	0.000	0.000	0.000	0.000	0.000
74	A	548	GLY	0	0.022	0.048	46.411	0.002	0.002	0.000	0.000	0.000	0.000
75	A	549	PRO	0	-0.019	0.010	44.081	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	550	GLN	0	0.073	0.009	40.776	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	551	PRO	0	-0.041	-0.010	37.170	0.001	0.001	0.000	0.000	0.000	0.000
78	A	552	GLY	0	0.031	-0.005	39.429	0.002	0.002	0.000	0.000	0.000	0.000
79	A	553	PRO	0	0.047	-0.003	37.158	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	554	LEU	0	0.033	0.020	34.703	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	555	ARG	1	0.898	0.980	33.652	0.072	0.072	0.000	0.000	0.000	0.000
82	A	556	GLU	-1	-0.880	-0.938	28.345	-0.116	-0.116	0.000	0.000	0.000	0.000
83	A	557	SER	0	-0.038	-0.031	28.236	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	558	ILE	0	0.009	-0.019	25.574	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	559	VAL	0	-0.028	-0.004	24.200	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	560	CYS	0	-0.047	-0.027	20.137	0.003	0.003	0.000	0.000	0.000	0.000
87	A	561	TYR	0	0.040	0.004	21.065	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	562	PHE	0	-0.031	-0.036	15.604	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	563	MET	0	0.019	0.013	19.762	0.001	0.001	0.000	0.000	0.000	0.000
90	A	564	VAL	0	-0.011	0.003	17.514	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	565	PHE	0	0.040	0.021	20.027	0.006	0.006	0.000	0.000	0.000	0.000
92	A	566	LEU	0	-0.004	-0.027	20.221	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	567	GLN	0	0.074	0.040	23.490	0.003	0.003	0.000	0.000	0.000	0.000
94	A	568	THR	0	0.042	0.032	25.857	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	569	HIS	0	0.070	0.013	26.679	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	570	ILE	0	0.034	0.021	27.771	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	571	PHE	0	0.019	0.004	18.992	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	572	ALA	0	0.020	0.002	23.565	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	573	GLU	-1	-0.839	-0.904	24.254	-0.070	-0.070	0.000	0.000	0.000	0.000
100	A	574	VAL	0	0.021	0.017	21.757	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	575	LEU	0	-0.003	-0.006	17.254	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	576	LYS	1	0.766	0.871	20.351	0.043	0.043	0.000	0.000	0.000	0.000
103	A	577	ASP	-1	-0.826	-0.919	22.428	-0.090	-0.090	0.000	0.000	0.000	0.000
104	A	578	ALA	0	-0.042	-0.009	18.188	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	579	ILE	0	0.004	-0.003	16.837	-0.032	-0.032	0.000	0.000	0.000	0.000
106	A	580	LYS	1	0.936	0.945	18.959	0.086	0.086	0.000	0.000	0.000	0.000
107	A	581	ASP	-1	-0.780	-0.872	20.968	-0.101	-0.101	0.000	0.000	0.000	0.000
108	A	582	LEU	0	-0.049	-0.016	13.340	-0.021	-0.021	0.000	0.000	0.000	0.000
109	A	583	VAL	0	-0.055	-0.044	17.058	-0.038	-0.038	0.000	0.000	0.000	0.000
110	A	584	MET	0	-0.011	0.004	18.758	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	585	THR	0	-0.038	-0.003	18.321	0.001	0.001	0.000	0.000	0.000	0.000
112	A	586	LYS	1	0.865	0.942	13.284	0.406	0.406	0.000	0.000	0.000	0.000
113	A	587	PRO	0	0.066	0.027	17.245	0.022	0.022	0.000	0.000	0.000	0.000
114	A	588	ALA	0	0.042	0.041	19.443	-0.021	-0.021	0.000	0.000	0.000	0.000
115	A	589	PRO	0	-0.034	-0.039	18.248	-0.019	-0.019	0.000	0.000	0.000	0.000
116	A	590	THR	0	-0.010	-0.023	15.614	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	591	CYS	0	0.050	0.035	18.192	0.005	0.005	0.000	0.000	0.000	0.000
118	A	592	ASN	0	-0.039	-0.021	21.289	0.029	0.029	0.000	0.000	0.000	0.000
119	A	593	ILE	0	-0.093	-0.033	16.992	0.007	0.007	0.000	0.000	0.000	0.000
120	A	594	ARG	1	0.916	0.965	21.180	0.152	0.152	0.000	0.000	0.000	0.000
121	A	595	VAL	0	0.002	-0.001	21.521	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	596	THR	0	-0.042	-0.029	23.610	0.013	0.013	0.000	0.000	0.000	0.000
123	A	597	VAL	0	0.025	0.036	25.529	-0.009	-0.009	0.000	0.000	0.000	0.000
124	A	598	CYS	0	-0.072	-0.025	26.557	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	599	SER	0	0.056	0.013	28.320	0.003	0.003	0.000	0.000	0.000	0.000
126	A	600	PHE	0	-0.070	-0.041	26.396	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	601	ASP	-1	-0.910	-0.945	31.945	-0.026	-0.026	0.000	0.000	0.000	0.000
128	A	602	ASP	-1	-0.906	-0.951	35.116	-0.014	-0.014	0.000	0.000	0.000	0.000
129	A	603	GLY	0	-0.063	-0.027	31.199	0.003	0.003	0.000	0.000	0.000	0.000
130	A	604	VAL	0	-0.071	-0.037	27.048	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	605	ASP	-1	-0.915	-0.964	28.800	0.002	0.002	0.000	0.000	0.000	0.000
132	A	606	LEU	0	-0.089	-0.047	23.035	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	607	PRO	0	0.014	0.014	25.039	0.006	0.006	0.000	0.000	0.000	0.000
134	A	608	PRO	0	0.021	0.025	25.557	0.003	0.003	0.000	0.000	0.000	0.000
135	A	609	TRP	0	-0.025	-0.025	20.056	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	610	PHE	0	0.024	-0.002	24.881	0.007	0.007	0.000	0.000	0.000	0.000
137	A	611	PRO	0	-0.030	0.003	22.764	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:475:ASN)