FMO DATABASE

FMODB ID: 1791Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1147690.265309
FMO2-HF: Nuclear repulsion	1094396.637986
FMO2-HF: Total energy	-53293.627323
FMO2-MP2: Total energy	-53447.068809

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.
-5.279	0.907	5.332	-6.053	-5.464	-0.041

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 : 0.024 / q_NPA : -0.005

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	1.012	0.971	3.779	0.783	2.034	-0.008	-0.753	-0.490	0.004
4	A	478	PHE	0	-0.028	0.008	2.814	1.197	1.864	0.054	-0.173	-0.548	0.001
5	A	479	GLU	-1	-0.727	-0.889	2.429	-14.212	-10.111	5.287	-5.116	-4.271	-0.046
6	A	480	ASN	0	-0.022	-0.005	4.564	1.229	1.396	-0.001	-0.011	-0.155	0.000
7	A	481	ILE	0	-0.043	-0.014	7.459	0.476	0.476	0.000	0.000	0.000	0.000
8	A	482	ALA	0	0.011	0.012	7.280	0.320	0.320	0.000	0.000	0.000	0.000
9	A	483	GLU	-1	-0.802	-0.888	7.966	0.281	0.281	0.000	0.000	0.000	0.000
10	A	484	GLY	0	-0.026	0.001	10.307	0.150	0.150	0.000	0.000	0.000	0.000
11	A	485	LEU	0	-0.011	-0.016	12.366	0.100	0.100	0.000	0.000	0.000	0.000
12	A	486	ARG	1	0.839	0.893	10.676	0.167	0.167	0.000	0.000	0.000	0.000
13	A	487	ALA	0	0.014	0.018	14.436	0.067	0.067	0.000	0.000	0.000	0.000
14	A	488	LEU	0	-0.017	-0.008	16.448	0.033	0.033	0.000	0.000	0.000	0.000
15	A	489	LEU	0	-0.026	-0.013	15.910	0.018	0.018	0.000	0.000	0.000	0.000
16	A	490	ALA	0	-0.012	-0.001	18.667	0.023	0.023	0.000	0.000	0.000	0.000
17	A	491	ARG	1	0.760	0.866	20.384	0.214	0.214	0.000	0.000	0.000	0.000
18	A	492	SER	0	-0.018	0.000	23.059	0.009	0.009	0.000	0.000	0.000	0.000
19	A	493	HIS	0	0.000	0.008	23.839	0.005	0.005	0.000	0.000	0.000	0.000
20	A	494	VAL	0	-0.039	-0.032	24.381	0.001	0.001	0.000	0.000	0.000	0.000
21	A	495	GLU	-1	-0.870	-0.918	24.919	-0.131	-0.131	0.000	0.000	0.000	0.000
22	A	496	ARG	1	0.843	0.898	16.423	0.262	0.262	0.000	0.000	0.000	0.000
23	A	497	THR	0	-0.041	-0.035	23.405	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	498	THR	0	-0.031	-0.020	26.004	0.008	0.008	0.000	0.000	0.000	0.000
25	A	499	ASP	-1	-0.918	-0.949	29.295	-0.087	-0.087	0.000	0.000	0.000	0.000
26	A	500	GLU	-1	-0.872	-0.932	31.944	-0.126	-0.126	0.000	0.000	0.000	0.000
27	A	501	GLY	0	-0.016	0.003	28.219	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	502	THR	0	-0.007	0.002	27.974	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	503	TRP	0	-0.055	-0.041	22.108	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	504	VAL	0	0.100	0.042	27.601	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	505	ALA	0	0.001	0.025	26.664	0.006	0.006	0.000	0.000	0.000	0.000
32	A	506	GLY	0	0.034	-0.008	23.929	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	507	VAL	0	-0.027	-0.014	21.140	0.016	0.016	0.000	0.000	0.000	0.000
34	A	508	PHE	0	0.039	0.007	21.765	-0.045	-0.045	0.000	0.000	0.000	0.000
35	A	509	VAL	0	0.002	-0.001	18.016	0.019	0.019	0.000	0.000	0.000	0.000
36	A	510	TYR	0	0.035	0.002	20.839	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	511	GLY	0	0.017	0.017	22.161	0.009	0.009	0.000	0.000	0.000	0.000
38	A	512	GLY	0	0.004	0.002	20.014	-0.052	-0.052	0.000	0.000	0.000	0.000
39	A	513	SER	0	0.018	-0.001	17.913	0.018	0.018	0.000	0.000	0.000	0.000
40	A	514	LYS	1	1.060	1.017	16.635	0.543	0.543	0.000	0.000	0.000	0.000
41	A	515	THR	0	0.051	0.014	13.044	-0.078	-0.078	0.000	0.000	0.000	0.000
42	A	516	SER	0	-0.011	0.016	12.958	-0.154	-0.154	0.000	0.000	0.000	0.000
43	A	517	LEU	0	0.027	0.024	13.841	-0.110	-0.110	0.000	0.000	0.000	0.000
44	A	518	TYR	0	-0.019	0.003	8.435	-0.166	-0.166	0.000	0.000	0.000	0.000
45	A	519	ASN	0	-0.065	-0.056	8.430	-0.501	-0.501	0.000	0.000	0.000	0.000
46	A	520	LEU	0	0.064	0.038	9.400	-0.288	-0.288	0.000	0.000	0.000	0.000
47	A	521	ARG	1	0.887	0.964	12.061	0.957	0.957	0.000	0.000	0.000	0.000
48	A	522	ARG	1	0.900	0.955	4.987	2.983	2.983	0.000	0.000	0.000	0.000
49	A	523	GLY	0	0.044	0.013	8.020	-0.168	-0.168	0.000	0.000	0.000	0.000
50	A	524	THR	0	-0.003	-0.025	8.916	0.249	0.249	0.000	0.000	0.000	0.000
51	A	525	ALA	0	-0.019	-0.016	9.957	0.146	0.146	0.000	0.000	0.000	0.000
52	A	526	LEU	0	-0.062	-0.014	4.986	0.108	0.108	0.000	0.000	0.000	0.000
53	A	527	ALA	0	-0.007	-0.001	9.622	0.282	0.282	0.000	0.000	0.000	0.000
54	A	528	ILE	0	-0.052	-0.031	12.100	0.191	0.191	0.000	0.000	0.000	0.000
55	A	529	PRO	0	0.059	0.040	13.520	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	530	GLN	0	0.055	0.028	15.468	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	531	CYS	0	-0.035	0.013	15.912	0.005	0.005	0.000	0.000	0.000	0.000
58	A	532	ARG	1	0.917	0.961	17.764	0.374	0.374	0.000	0.000	0.000	0.000
59	A	533	LEU	0	-0.013	-0.007	13.439	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	534	THR	0	0.060	0.051	17.511	0.008	0.008	0.000	0.000	0.000	0.000
61	A	535	PRO	0	-0.011	-0.006	16.746	-0.099	-0.099	0.000	0.000	0.000	0.000
62	A	536	LEU	0	-0.041	-0.027	14.864	0.020	0.020	0.000	0.000	0.000	0.000
63	A	537	SER	0	0.022	0.022	18.312	0.033	0.033	0.000	0.000	0.000	0.000
64	A	538	ARG	1	0.863	0.908	22.010	0.295	0.295	0.000	0.000	0.000	0.000
65	A	539	LEU	0	0.017	0.024	24.765	0.011	0.011	0.000	0.000	0.000	0.000
66	A	540	PRO	0	0.075	0.058	27.440	0.002	0.002	0.000	0.000	0.000	0.000
67	A	541	PHE	0	-0.047	-0.028	30.915	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	542	GLY	0	0.026	0.015	33.401	0.000	0.000	0.000	0.000	0.000	0.000
69	A	543	MET	0	-0.039	-0.026	35.444	0.005	0.005	0.000	0.000	0.000	0.000
70	A	544	ALA	0	0.001	0.018	38.561	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	545	PRO	0	-0.013	-0.005	40.244	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	546	GLY	0	0.071	0.018	43.614	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	547	PRO	0	-0.053	-0.051	46.060	0.001	0.001	0.000	0.000	0.000	0.000
74	A	548	GLY	0	0.026	0.044	46.357	0.002	0.002	0.000	0.000	0.000	0.000
75	A	549	PRO	0	-0.032	0.007	44.154	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	550	GLN	0	0.061	0.007	41.011	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	551	PRO	0	-0.040	-0.022	37.212	0.003	0.003	0.000	0.000	0.000	0.000
78	A	552	GLY	0	0.034	0.013	39.417	0.003	0.003	0.000	0.000	0.000	0.000
79	A	553	PRO	0	0.048	0.000	37.139	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	554	LEU	0	0.019	0.012	34.688	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	555	ARG	1	0.904	0.980	33.643	0.155	0.155	0.000	0.000	0.000	0.000
82	A	556	GLU	-1	-0.812	-0.884	28.554	-0.293	-0.293	0.000	0.000	0.000	0.000
83	A	557	SER	0	-0.037	-0.033	28.342	0.001	0.001	0.000	0.000	0.000	0.000
84	A	558	ILE	0	0.006	-0.019	25.596	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	559	VAL	0	-0.029	0.000	24.178	-0.037	-0.037	0.000	0.000	0.000	0.000
86	A	560	CYS	0	-0.054	-0.029	20.170	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	561	TYR	0	0.032	-0.006	21.040	0.005	0.005	0.000	0.000	0.000	0.000
88	A	562	PHE	0	-0.021	-0.024	15.588	-0.062	-0.062	0.000	0.000	0.000	0.000
89	A	563	MET	0	0.022	0.026	19.757	0.017	0.017	0.000	0.000	0.000	0.000
90	A	564	VAL	0	-0.011	-0.002	17.737	-0.058	-0.058	0.000	0.000	0.000	0.000
91	A	565	PHE	0	0.045	0.025	20.034	0.033	0.033	0.000	0.000	0.000	0.000
92	A	566	LEU	0	-0.014	-0.028	20.338	-0.035	-0.035	0.000	0.000	0.000	0.000
93	A	567	GLN	0	0.071	0.032	23.504	0.023	0.023	0.000	0.000	0.000	0.000
94	A	568	THR	0	0.048	0.035	25.871	0.011	0.011	0.000	0.000	0.000	0.000
95	A	569	HIS	0	0.061	0.009	26.690	-0.028	-0.028	0.000	0.000	0.000	0.000
96	A	570	ILE	0	0.021	0.017	27.915	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	571	PHE	0	0.020	0.002	18.963	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	572	ALA	0	0.010	0.004	23.548	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	573	GLU	-1	-0.798	-0.890	24.255	-0.222	-0.222	0.000	0.000	0.000	0.000
100	A	574	VAL	0	0.005	0.007	21.679	-0.014	-0.014	0.000	0.000	0.000	0.000
101	A	575	LEU	0	-0.001	-0.005	17.252	-0.027	-0.027	0.000	0.000	0.000	0.000
102	A	576	LYS	1	0.751	0.855	20.347	0.174	0.174	0.000	0.000	0.000	0.000
103	A	577	ASP	-1	-0.765	-0.870	22.418	-0.239	-0.239	0.000	0.000	0.000	0.000
104	A	578	ALA	0	-0.009	0.012	18.189	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	579	ILE	0	0.009	-0.006	16.840	-0.035	-0.035	0.000	0.000	0.000	0.000
106	A	580	LYS	1	0.847	0.905	18.947	0.218	0.218	0.000	0.000	0.000	0.000
107	A	581	ASP	-1	-0.801	-0.887	21.026	-0.219	-0.219	0.000	0.000	0.000	0.000
108	A	582	LEU	0	-0.030	-0.007	13.292	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	583	VAL	0	-0.034	-0.028	16.860	-0.031	-0.031	0.000	0.000	0.000	0.000
110	A	584	MET	0	-0.004	0.012	18.747	0.020	0.020	0.000	0.000	0.000	0.000
111	A	585	THR	0	-0.005	0.006	18.582	0.012	0.012	0.000	0.000	0.000	0.000
112	A	586	LYS	1	0.770	0.895	14.243	0.475	0.475	0.000	0.000	0.000	0.000
113	A	587	PRO	0	0.069	0.028	17.282	0.024	0.024	0.000	0.000	0.000	0.000
114	A	588	ALA	0	0.043	0.038	19.443	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	589	PRO	0	-0.020	-0.035	18.298	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	590	THR	0	-0.001	-0.021	15.405	0.003	0.003	0.000	0.000	0.000	0.000
117	A	591	CYS	0	0.038	0.039	18.161	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	592	ASN	0	-0.040	-0.024	21.259	0.038	0.038	0.000	0.000	0.000	0.000
119	A	593	ILE	0	-0.088	-0.035	16.864	0.000	0.000	0.000	0.000	0.000	0.000
120	A	594	ARG	1	0.913	0.969	21.157	0.305	0.305	0.000	0.000	0.000	0.000
121	A	595	VAL	0	0.003	-0.011	21.397	-0.033	-0.033	0.000	0.000	0.000	0.000
122	A	596	THR	0	-0.030	-0.005	23.598	0.034	0.034	0.000	0.000	0.000	0.000
123	A	597	VAL	0	0.027	0.031	25.525	-0.027	-0.027	0.000	0.000	0.000	0.000
124	A	598	CYS	0	-0.067	-0.025	26.667	0.001	0.001	0.000	0.000	0.000	0.000
125	A	599	SER	0	0.028	0.002	28.324	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	600	PHE	0	-0.058	-0.041	26.238	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	601	ASP	-1	-0.905	-0.943	31.953	-0.154	-0.154	0.000	0.000	0.000	0.000
128	A	602	ASP	-1	-0.912	-0.953	35.122	-0.135	-0.135	0.000	0.000	0.000	0.000
129	A	603	GLY	0	-0.056	-0.022	31.213	0.000	0.000	0.000	0.000	0.000	0.000
130	A	604	VAL	0	-0.071	-0.038	27.104	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	605	ASP	-1	-0.912	-0.959	28.818	-0.192	-0.192	0.000	0.000	0.000	0.000
132	A	606	LEU	0	-0.084	-0.048	22.916	-0.012	-0.012	0.000	0.000	0.000	0.000
133	A	607	PRO	0	0.008	0.010	25.118	0.012	0.012	0.000	0.000	0.000	0.000
134	A	608	PRO	0	0.022	0.020	25.584	-0.018	-0.018	0.000	0.000	0.000	0.000
135	A	609	TRP	0	-0.031	-0.022	20.027	-0.020	-0.020	0.000	0.000	0.000	0.000
136	A	610	PHE	0	0.024	-0.004	24.913	0.015	0.015	0.000	0.000	0.000	0.000
137	A	611	PRO	0	-0.024	0.006	22.675	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:475:ASN)