FMO DATABASE

FMODB ID: ZV5JN

Calculation Name: 2X5Y-A-Xray372

Preferred Name: Zinc finger CCCH-type antiviral protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2X5Y

Chain ID: A

ChEMBL ID: CHEMBL4295879

UniProt ID: Q7Z2W4

Base Structure: X-ray

Registration Date: 2023-09-23

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	171
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1940141.913089
FMO2-HF: Nuclear repulsion	1869763.701477
FMO2-HF: Total energy	-70378.211612
FMO2-MP2: Total energy	-70584.053272

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:726:LYS)

Summations of interaction energy for fragment #1(A:726:LYS)

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.
-43.305	-34.02	5.026	-5.518	-8.793	-0.052

Interaction energy analysis for fragmet #1(A:726:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.926 / q_NPA : 0.951

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	728	TYR	0	0.015	0.014	2.318	-6.860	-1.192	3.019	-3.074	-5.612	-0.018
4	A	729	LYS	1	0.955	0.981	2.529	12.376	15.733	2.009	-2.420	-2.946	-0.034
5	A	730	LEU	0	0.001	-0.004	4.119	6.073	6.255	-0.001	-0.013	-0.168	0.000
6	A	731	SER	0	-0.044	-0.027	6.115	-1.497	-1.497	0.000	0.000	0.000	0.000
7	A	732	GLU	-1	-0.925	-0.965	9.048	-21.355	-21.355	0.000	0.000	0.000	0.000
8	A	733	ILE	0	-0.023	-0.002	11.570	0.375	0.375	0.000	0.000	0.000	0.000
9	A	734	HIS	0	0.057	0.026	15.019	0.380	0.380	0.000	0.000	0.000	0.000
10	A	735	HIS	0	0.082	0.015	17.912	-0.227	-0.227	0.000	0.000	0.000	0.000
11	A	736	LEU	0	-0.006	0.000	20.499	0.589	0.589	0.000	0.000	0.000	0.000
12	A	737	HIS	0	0.003	0.023	19.457	0.569	0.569	0.000	0.000	0.000	0.000
13	A	738	PRO	0	0.075	0.017	21.567	-0.088	-0.088	0.000	0.000	0.000	0.000
14	A	739	GLU	-1	-0.845	-0.891	17.097	-18.144	-18.144	0.000	0.000	0.000	0.000
15	A	740	TYR	0	0.039	0.034	17.502	0.082	0.082	0.000	0.000	0.000	0.000
16	A	741	VAL	0	0.026	0.007	19.741	0.178	0.178	0.000	0.000	0.000	0.000
17	A	742	ARG	1	0.981	0.995	20.595	14.416	14.416	0.000	0.000	0.000	0.000
18	A	743	VAL	0	-0.013	-0.001	17.904	0.278	0.278	0.000	0.000	0.000	0.000
19	A	744	SER	0	0.028	0.002	21.126	0.155	0.155	0.000	0.000	0.000	0.000
20	A	745	GLU	-1	-0.982	-0.983	22.605	-10.893	-10.893	0.000	0.000	0.000	0.000
21	A	746	HIS	0	-0.033	-0.014	22.853	0.605	0.605	0.000	0.000	0.000	0.000
22	A	747	PHE	0	0.012	0.001	21.002	0.269	0.269	0.000	0.000	0.000	0.000
23	A	748	LYS	1	0.989	0.981	23.835	12.611	12.611	0.000	0.000	0.000	0.000
24	A	749	ALA	0	0.011	0.027	26.727	0.545	0.545	0.000	0.000	0.000	0.000
25	A	750	SER	0	-0.036	-0.020	27.163	0.360	0.360	0.000	0.000	0.000	0.000
26	A	751	MET	0	-0.092	-0.019	23.423	0.421	0.421	0.000	0.000	0.000	0.000
27	A	752	LYS	1	0.892	0.932	27.418	9.986	9.986	0.000	0.000	0.000	0.000
28	A	753	ASN	0	-0.001	0.003	29.833	0.128	0.128	0.000	0.000	0.000	0.000
29	A	754	PHE	0	0.036	0.024	24.326	-0.101	-0.101	0.000	0.000	0.000	0.000
30	A	755	LYS	1	0.898	0.967	23.223	12.753	12.753	0.000	0.000	0.000	0.000
31	A	756	ILE	0	-0.037	-0.031	18.435	-0.408	-0.408	0.000	0.000	0.000	0.000
32	A	757	GLU	-1	-0.843	-0.904	17.415	-14.679	-14.679	0.000	0.000	0.000	0.000
33	A	758	LYS	1	0.866	0.930	11.672	21.724	21.724	0.000	0.000	0.000	0.000
34	A	759	ILE	0	0.035	0.026	14.387	0.021	0.021	0.000	0.000	0.000	0.000
35	A	760	LYS	1	0.891	0.950	7.775	32.170	32.170	0.000	0.000	0.000	0.000
36	A	761	LYS	1	0.913	0.945	11.050	20.843	20.843	0.000	0.000	0.000	0.000
37	A	762	ILE	0	-0.041	-0.023	7.582	-3.998	-3.998	0.000	0.000	0.000	0.000
38	A	763	GLU	-1	-0.954	-0.974	7.451	-26.377	-26.377	0.000	0.000	0.000	0.000
39	A	764	ASN	0	0.023	-0.014	6.853	-3.772	-3.772	0.000	0.000	0.000	0.000
40	A	765	SER	0	0.100	0.040	8.108	1.606	1.606	0.000	0.000	0.000	0.000
41	A	766	GLU	-1	-0.902	-0.940	7.771	-23.261	-23.261	0.000	0.000	0.000	0.000
42	A	767	LEU	0	-0.065	-0.036	9.993	1.911	1.911	0.000	0.000	0.000	0.000
43	A	768	LEU	0	0.000	0.000	12.034	1.536	1.536	0.000	0.000	0.000	0.000
44	A	769	ASP	-1	-0.891	-0.936	13.860	-17.143	-17.143	0.000	0.000	0.000	0.000
45	A	770	LYS	1	0.897	0.946	12.840	19.317	19.317	0.000	0.000	0.000	0.000
46	A	771	PHE	0	0.001	0.005	16.488	1.015	1.015	0.000	0.000	0.000	0.000
47	A	772	THR	0	-0.017	-0.020	17.601	0.983	0.983	0.000	0.000	0.000	0.000
48	A	773	TRP	0	0.001	0.006	19.869	0.813	0.813	0.000	0.000	0.000	0.000
49	A	774	LYS	1	0.945	0.976	21.149	12.624	12.624	0.000	0.000	0.000	0.000
50	A	775	LYS	1	0.911	0.952	21.563	14.064	14.064	0.000	0.000	0.000	0.000
51	A	776	SER	0	-0.053	-0.015	24.157	0.669	0.669	0.000	0.000	0.000	0.000
52	A	777	GLN	0	-0.058	-0.040	25.608	0.718	0.718	0.000	0.000	0.000	0.000
53	A	778	MET	0	-0.065	-0.023	25.982	0.177	0.177	0.000	0.000	0.000	0.000
54	A	779	LYS	1	0.886	0.959	28.371	9.763	9.763	0.000	0.000	0.000	0.000
55	A	780	GLU	-1	-0.815	-0.886	26.358	-10.687	-10.687	0.000	0.000	0.000	0.000
56	A	781	GLU	-1	-0.872	-0.945	24.427	-12.869	-12.869	0.000	0.000	0.000	0.000
57	A	782	GLY	0	-0.032	-0.012	22.512	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	783	LYS	1	0.907	0.958	23.513	11.654	11.654	0.000	0.000	0.000	0.000
59	A	784	LEU	0	0.008	-0.004	19.073	-0.522	-0.522	0.000	0.000	0.000	0.000
60	A	785	LEU	0	-0.014	0.003	20.854	0.686	0.686	0.000	0.000	0.000	0.000
61	A	786	PHE	0	-0.016	-0.016	19.912	-1.081	-1.081	0.000	0.000	0.000	0.000
62	A	787	TYR	0	-0.030	-0.032	17.066	0.121	0.121	0.000	0.000	0.000	0.000
63	A	788	ALA	0	0.037	0.013	17.547	-1.145	-1.145	0.000	0.000	0.000	0.000
64	A	789	THR	0	-0.001	-0.004	14.477	0.211	0.211	0.000	0.000	0.000	0.000
65	A	790	SER	0	0.052	0.037	16.310	-0.249	-0.249	0.000	0.000	0.000	0.000
66	A	791	ARG	1	0.827	0.867	11.346	19.742	19.742	0.000	0.000	0.000	0.000
67	A	792	ALA	0	-0.025	-0.006	11.365	-2.408	-2.408	0.000	0.000	0.000	0.000
68	A	793	TYR	0	0.017	0.009	11.687	-1.410	-1.410	0.000	0.000	0.000	0.000
69	A	794	VAL	0	0.007	0.004	7.160	-1.079	-1.079	0.000	0.000	0.000	0.000
70	A	795	GLU	-1	-0.905	-0.953	5.038	-49.027	-49.027	0.000	0.000	0.000	0.000
71	A	796	SER	0	-0.014	-0.005	6.430	-0.058	-0.058	0.000	0.000	0.000	0.000
72	A	797	ILE	0	-0.010	0.014	9.097	0.492	0.492	0.000	0.000	0.000	0.000
73	A	798	CYS	0	-0.035	-0.018	5.738	1.171	1.171	0.000	0.000	0.000	0.000
74	A	799	SER	0	-0.033	-0.013	4.573	0.467	0.545	-0.001	-0.011	-0.067	0.000
75	A	800	ASN	0	-0.016	-0.024	6.369	2.057	2.057	0.000	0.000	0.000	0.000
76	A	801	ASN	0	0.016	0.000	9.704	2.027	2.027	0.000	0.000	0.000	0.000
77	A	802	PHE	0	0.015	0.009	12.398	-0.442	-0.442	0.000	0.000	0.000	0.000
78	A	803	ASP	-1	-0.807	-0.927	15.258	-15.248	-15.248	0.000	0.000	0.000	0.000
79	A	804	SER	0	0.014	0.003	17.221	0.124	0.124	0.000	0.000	0.000	0.000
80	A	805	PHE	0	-0.048	-0.028	20.329	0.382	0.382	0.000	0.000	0.000	0.000
81	A	806	LEU	0	-0.039	-0.013	14.086	0.096	0.096	0.000	0.000	0.000	0.000
82	A	807	HIS	0	0.037	0.014	13.449	0.205	0.205	0.000	0.000	0.000	0.000
83	A	808	GLU	-1	-0.780	-0.850	18.200	-13.777	-13.777	0.000	0.000	0.000	0.000
84	A	809	THR	0	-0.031	-0.021	21.188	0.429	0.429	0.000	0.000	0.000	0.000
85	A	810	HIS	0	-0.043	0.008	23.692	0.635	0.635	0.000	0.000	0.000	0.000
86	A	811	GLU	-1	-0.910	-0.951	26.316	-9.367	-9.367	0.000	0.000	0.000	0.000
87	A	812	ASN	0	-0.088	-0.046	29.631	-0.197	-0.197	0.000	0.000	0.000	0.000
88	A	813	LYS	1	1.005	1.005	30.743	9.456	9.456	0.000	0.000	0.000	0.000
89	A	814	TYR	0	0.005	-0.008	30.347	0.414	0.414	0.000	0.000	0.000	0.000
90	A	815	GLY	0	0.078	0.051	30.707	0.000	0.000	0.000	0.000	0.000	0.000
91	A	816	LYS	1	0.903	0.953	27.208	10.689	10.689	0.000	0.000	0.000	0.000
92	A	817	GLY	0	0.015	0.004	24.470	-0.093	-0.093	0.000	0.000	0.000	0.000
93	A	818	ILE	0	-0.041	-0.018	18.584	-0.103	-0.103	0.000	0.000	0.000	0.000
94	A	819	TYR	0	-0.030	-0.036	22.405	0.551	0.551	0.000	0.000	0.000	0.000
95	A	820	PHE	0	-0.006	0.002	18.014	-0.492	-0.492	0.000	0.000	0.000	0.000
96	A	821	ALA	0	-0.008	-0.004	23.114	0.662	0.662	0.000	0.000	0.000	0.000
97	A	822	LYS	1	0.954	0.978	24.468	9.806	9.806	0.000	0.000	0.000	0.000
98	A	823	ASP	-1	-0.894	-0.942	26.601	-10.708	-10.708	0.000	0.000	0.000	0.000
99	A	824	ALA	0	0.031	0.003	23.282	-0.087	-0.087	0.000	0.000	0.000	0.000
100	A	825	ILE	0	0.009	-0.017	24.621	-0.160	-0.160	0.000	0.000	0.000	0.000
101	A	826	TYR	0	-0.065	-0.067	26.595	0.248	0.248	0.000	0.000	0.000	0.000
102	A	827	SER	0	0.068	0.020	22.267	-0.217	-0.217	0.000	0.000	0.000	0.000
103	A	828	HIS	0	0.054	0.049	23.600	-0.563	-0.563	0.000	0.000	0.000	0.000
104	A	829	LYS	1	0.907	0.954	24.547	10.134	10.134	0.000	0.000	0.000	0.000
105	A	830	ASN	0	-0.023	-0.006	26.725	0.541	0.541	0.000	0.000	0.000	0.000
106	A	831	CYS	0	-0.051	0.014	21.049	-0.265	-0.265	0.000	0.000	0.000	0.000
107	A	832	PRO	0	0.029	0.014	22.755	0.207	0.207	0.000	0.000	0.000	0.000
108	A	833	TYR	0	-0.028	-0.025	19.621	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	834	ASP	-1	-0.820	-0.917	22.419	-12.855	-12.855	0.000	0.000	0.000	0.000
110	A	835	ALA	0	0.102	0.045	21.392	-0.798	-0.798	0.000	0.000	0.000	0.000
111	A	836	LYS	1	0.911	0.962	20.481	13.564	13.564	0.000	0.000	0.000	0.000
112	A	837	ASN	0	-0.071	-0.045	17.343	-1.403	-1.403	0.000	0.000	0.000	0.000
113	A	838	VAL	0	-0.027	0.003	16.715	-1.173	-1.173	0.000	0.000	0.000	0.000
114	A	839	VAL	0	-0.032	-0.003	12.953	-0.460	-0.460	0.000	0.000	0.000	0.000
115	A	840	MET	0	-0.020	-0.006	16.019	0.673	0.673	0.000	0.000	0.000	0.000
116	A	841	PHE	0	0.005	-0.002	10.218	-1.128	-1.128	0.000	0.000	0.000	0.000
117	A	842	VAL	0	-0.010	-0.007	15.362	1.445	1.445	0.000	0.000	0.000	0.000
118	A	843	ALA	0	-0.001	-0.004	15.561	-1.508	-1.508	0.000	0.000	0.000	0.000
119	A	844	GLN	0	-0.032	-0.018	17.120	1.760	1.760	0.000	0.000	0.000	0.000
120	A	845	VAL	0	-0.006	-0.010	18.916	-0.435	-0.435	0.000	0.000	0.000	0.000
121	A	846	LEU	0	0.003	0.012	21.610	0.473	0.473	0.000	0.000	0.000	0.000
122	A	847	VAL	0	-0.016	-0.018	24.356	0.010	0.010	0.000	0.000	0.000	0.000
123	A	848	GLY	0	0.041	0.039	27.184	0.224	0.224	0.000	0.000	0.000	0.000
124	A	849	LYS	1	0.833	0.918	29.937	8.749	8.749	0.000	0.000	0.000	0.000
125	A	850	PHE	0	0.005	0.004	31.355	-0.083	-0.083	0.000	0.000	0.000	0.000
126	A	851	ILE	0	-0.038	-0.027	33.195	0.341	0.341	0.000	0.000	0.000	0.000
127	A	852	GLU	-1	-0.783	-0.891	34.182	-8.475	-8.475	0.000	0.000	0.000	0.000
128	A	853	GLY	0	-0.016	-0.003	33.363	0.037	0.037	0.000	0.000	0.000	0.000
129	A	854	ASN	0	0.010	0.010	34.196	0.187	0.187	0.000	0.000	0.000	0.000
130	A	855	ILE	0	0.050	0.031	33.876	-0.220	-0.220	0.000	0.000	0.000	0.000
131	A	856	THR	0	-0.065	-0.045	33.821	-0.185	-0.185	0.000	0.000	0.000	0.000
132	A	857	TYR	0	0.006	0.011	32.326	0.078	0.078	0.000	0.000	0.000	0.000
133	A	858	THR	0	0.009	-0.014	28.764	-0.221	-0.221	0.000	0.000	0.000	0.000
134	A	859	SER	0	-0.007	0.001	28.026	-0.304	-0.304	0.000	0.000	0.000	0.000
135	A	860	PRO	0	0.003	0.014	28.621	0.236	0.236	0.000	0.000	0.000	0.000
136	A	861	PRO	0	0.013	0.012	31.850	0.071	0.071	0.000	0.000	0.000	0.000
137	A	862	PRO	0	0.062	0.014	34.233	-0.181	-0.181	0.000	0.000	0.000	0.000
138	A	863	GLN	0	-0.047	-0.028	34.528	0.176	0.176	0.000	0.000	0.000	0.000
139	A	864	PHE	0	-0.003	0.011	33.306	0.123	0.123	0.000	0.000	0.000	0.000
140	A	865	ASP	-1	-0.819	-0.907	28.165	-10.295	-10.295	0.000	0.000	0.000	0.000
141	A	866	SER	0	-0.052	-0.040	27.630	-0.442	-0.442	0.000	0.000	0.000	0.000
142	A	867	CYS	0	-0.071	-0.026	29.150	0.503	0.503	0.000	0.000	0.000	0.000
143	A	868	VAL	0	0.019	0.017	29.769	-0.392	-0.392	0.000	0.000	0.000	0.000
144	A	869	ASP	-1	-0.794	-0.902	32.004	-9.407	-9.407	0.000	0.000	0.000	0.000
145	A	870	THR	0	-0.039	-0.025	33.992	0.352	0.352	0.000	0.000	0.000	0.000
146	A	871	ARG	1	0.915	0.938	35.409	7.805	7.805	0.000	0.000	0.000	0.000
147	A	872	SER	0	-0.017	-0.054	37.241	0.018	0.018	0.000	0.000	0.000	0.000
148	A	873	ASN	0	-0.087	0.005	35.865	-0.013	-0.013	0.000	0.000	0.000	0.000
149	A	874	PRO	0	0.026	0.061	31.825	-0.110	-0.110	0.000	0.000	0.000	0.000
150	A	875	SER	0	-0.018	-0.047	30.414	-0.208	-0.208	0.000	0.000	0.000	0.000
151	A	876	VAL	0	-0.055	-0.011	27.395	-0.453	-0.453	0.000	0.000	0.000	0.000
152	A	877	PHE	0	0.002	-0.007	25.783	0.367	0.367	0.000	0.000	0.000	0.000
153	A	878	VAL	0	-0.010	0.002	25.376	-0.551	-0.551	0.000	0.000	0.000	0.000
154	A	879	ILE	0	-0.015	-0.013	21.998	0.372	0.372	0.000	0.000	0.000	0.000
155	A	880	PHE	0	0.042	0.007	23.506	-0.334	-0.334	0.000	0.000	0.000	0.000
156	A	881	GLN	0	0.010	0.009	21.570	-0.304	-0.304	0.000	0.000	0.000	0.000
157	A	882	LYS	1	0.873	0.926	14.627	16.874	16.874	0.000	0.000	0.000	0.000
158	A	883	ASP	-1	-0.870	-0.941	17.380	-16.067	-16.067	0.000	0.000	0.000	0.000
159	A	884	GLN	0	-0.090	-0.050	18.848	0.266	0.266	0.000	0.000	0.000	0.000
160	A	885	VAL	0	-0.002	-0.001	16.215	0.270	0.270	0.000	0.000	0.000	0.000
161	A	886	TYR	0	0.023	0.031	11.493	-1.253	-1.253	0.000	0.000	0.000	0.000
162	A	887	PRO	0	-0.007	-0.003	11.033	0.701	0.701	0.000	0.000	0.000	0.000
163	A	888	GLN	0	0.016	0.018	12.133	-0.164	-0.164	0.000	0.000	0.000	0.000
164	A	889	TYR	0	-0.053	-0.077	12.778	-0.910	-0.910	0.000	0.000	0.000	0.000
165	A	890	VAL	0	-0.004	0.002	9.823	0.228	0.228	0.000	0.000	0.000	0.000
166	A	891	ILE	0	-0.016	-0.006	12.717	-0.422	-0.422	0.000	0.000	0.000	0.000
167	A	892	GLU	-1	-0.790	-0.875	12.780	-22.234	-22.234	0.000	0.000	0.000	0.000
168	A	893	TYR	0	-0.059	-0.070	15.978	0.393	0.393	0.000	0.000	0.000	0.000
169	A	894	THR	0	0.001	-0.006	19.777	0.120	0.120	0.000	0.000	0.000	0.000
170	A	895	GLU	-1	-0.944	-0.966	22.745	-10.829	-10.829	0.000	0.000	0.000	0.000
171	A	896	ASP	-1	-0.968	-0.989	26.456	-11.098	-11.098	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:726:LYS)