FMO DATABASE

FMODB ID: 5911Z

Calculation Name: 7DE1-A-Xray89

Preferred Name:

Target Type:

Ligand Name: di(hydroxyethyl)ether

ligand 3-letter code: PEG

PDB ID: 7DE1

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-02-22

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHLSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Waters within average of the temperature factors of receptor.
Procedure	Auto-FMO protocol ver. 1.20200406

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	MIZUHO/ABINIT-MP 4.0(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-821866.481521
FMO2-HF: Nuclear repulsion	778093.418995
FMO2-HF: Total energy	-43773.062526
FMO2-MP2: Total energy	-43901.904957

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:257:LYS )

Summations of interaction energy for fragment #1(A:257: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.
66.37	72.908	2.161	-2.892	-5.805	-0.02

Interaction energy analysis for fragmet #1(A:257:LYS )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.000 / q_NPA : 0.996

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

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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	259	ARG	1	0.937	0.962	2.798	13.851	16.282	0.403	-1.232	-1.601	-0.006
4	A	260	GLN	0	0.075	0.027	4.989	-3.332	-3.199	-0.001	-0.006	-0.126	0.000
5	A	261	LYS	1	0.926	0.956	3.243	36.013	36.660	0.036	-0.110	-0.572	0.000
6	A	262	ARG	1	0.797	0.926	2.417	25.125	28.478	1.705	-1.845	-3.213	-0.013
7	A	263	THR	0	0.026	0.007	3.320	3.377	3.351	0.018	0.301	-0.293	-0.001
8	A	264	ALA	0	0.010	0.018	6.004	-1.301	-1.301	0.000	0.000	0.000	0.000
9	A	265	THR	0	0.002	0.001	8.408	1.217	1.217	0.000	0.000	0.000	0.000
10	A	266	LYS	1	0.937	0.961	10.959	18.430	18.430	0.000	0.000	0.000	0.000
11	A	267	ALA	0	-0.015	0.009	11.194	1.017	1.017	0.000	0.000	0.000	0.000
12	A	268	TYR	0	-0.026	-0.015	4.922	-2.376	-2.376	0.000	0.000	0.000	0.000
13	A	269	ASN	0	0.067	0.050	9.322	-2.218	-2.218	0.000	0.000	0.000	0.000
14	A	270	VAL	0	0.054	0.014	10.648	-1.719	-1.719	0.000	0.000	0.000	0.000
15	A	271	THR	0	-0.018	-0.004	11.884	-0.125	-0.125	0.000	0.000	0.000	0.000
16	A	272	GLN	0	-0.031	-0.001	10.065	0.370	0.370	0.000	0.000	0.000	0.000
17	A	273	ALA	0	-0.031	0.011	7.119	-1.302	-1.302	0.000	0.000	0.000	0.000
18	A	274	PHE	0	-0.041	-0.039	7.216	-1.001	-1.001	0.000	0.000	0.000	0.000
19	A	275	GLY	0	0.063	0.053	10.227	1.574	1.574	0.000	0.000	0.000	0.000
20	A	276	ARG	1	0.973	0.967	13.439	15.993	15.993	0.000	0.000	0.000	0.000
21	A	277	ARG	1	0.830	0.930	13.413	18.414	18.414	0.000	0.000	0.000	0.000
22	A	278	GLY	0	0.010	0.007	18.662	0.496	0.496	0.000	0.000	0.000	0.000
23	A	279	PRO	0	-0.019	-0.007	20.766	-0.319	-0.319	0.000	0.000	0.000	0.000
24	A	280	GLU	-1	-0.920	-0.953	21.049	-12.010	-12.010	0.000	0.000	0.000	0.000
25	A	281	GLN	0	0.022	0.014	18.933	-1.092	-1.092	0.000	0.000	0.000	0.000
26	A	282	THR	0	-0.007	0.003	15.203	-0.440	-0.440	0.000	0.000	0.000	0.000
27	A	283	GLN	0	-0.013	-0.014	15.085	-0.993	-0.993	0.000	0.000	0.000	0.000
28	A	284	GLY	0	0.012	0.015	15.538	0.133	0.133	0.000	0.000	0.000	0.000
29	A	285	ASN	0	0.026	-0.009	16.370	-0.349	-0.349	0.000	0.000	0.000	0.000
30	A	286	PHE	0	-0.002	0.007	17.000	0.433	0.433	0.000	0.000	0.000	0.000
31	A	287	GLY	0	-0.012	-0.021	17.503	-1.178	-1.178	0.000	0.000	0.000	0.000
32	A	288	ASP	-1	-0.692	-0.864	19.327	-13.668	-13.668	0.000	0.000	0.000	0.000
33	A	289	GLN	0	0.034	0.021	20.314	-0.910	-0.910	0.000	0.000	0.000	0.000
34	A	290	GLU	-1	-0.870	-0.908	20.173	-14.314	-14.314	0.000	0.000	0.000	0.000
35	A	291	LEU	0	0.019	0.012	15.607	-0.820	-0.820	0.000	0.000	0.000	0.000
36	A	292	ILE	0	-0.027	-0.002	15.991	-1.583	-1.583	0.000	0.000	0.000	0.000
37	A	293	ARG	1	0.942	0.965	15.168	13.428	13.428	0.000	0.000	0.000	0.000
38	A	294	GLN	0	-0.002	-0.005	15.741	-0.792	-0.792	0.000	0.000	0.000	0.000
39	A	295	GLY	0	0.029	0.022	12.427	-1.277	-1.277	0.000	0.000	0.000	0.000
40	A	296	THR	0	-0.048	-0.054	10.176	1.206	1.206	0.000	0.000	0.000	0.000
41	A	297	ASP	-1	-0.844	-0.915	12.906	-22.651	-22.651	0.000	0.000	0.000	0.000
42	A	298	TYR	0	-0.074	-0.039	15.127	1.625	1.625	0.000	0.000	0.000	0.000
43	A	299	LYS	1	0.901	0.934	17.910	12.799	12.799	0.000	0.000	0.000	0.000
44	A	300	HIS	0	0.017	0.002	20.725	0.022	0.022	0.000	0.000	0.000	0.000
45	A	301	TRP	0	0.032	0.022	12.287	0.003	0.003	0.000	0.000	0.000	0.000
46	A	302	PRO	0	0.014	0.000	17.079	-0.332	-0.332	0.000	0.000	0.000	0.000
47	A	303	GLN	0	0.070	0.025	18.018	-0.429	-0.429	0.000	0.000	0.000	0.000
48	A	304	ILE	0	-0.019	0.001	17.113	0.362	0.362	0.000	0.000	0.000	0.000
49	A	305	ALA	0	-0.019	-0.021	14.651	-0.071	-0.071	0.000	0.000	0.000	0.000
50	A	306	GLN	0	-0.009	0.010	16.353	-0.286	-0.286	0.000	0.000	0.000	0.000
51	A	307	PHE	0	-0.003	-0.008	19.050	0.591	0.591	0.000	0.000	0.000	0.000
52	A	308	ALA	0	-0.052	-0.010	14.106	0.001	0.001	0.000	0.000	0.000	0.000
53	A	309	PRO	0	0.014	0.023	15.244	0.137	0.137	0.000	0.000	0.000	0.000
54	A	310	SER	0	0.091	0.038	14.692	-1.658	-1.658	0.000	0.000	0.000	0.000
55	A	311	ALA	0	0.034	0.009	12.918	0.225	0.225	0.000	0.000	0.000	0.000
56	A	312	SER	0	0.020	0.016	14.815	0.796	0.796	0.000	0.000	0.000	0.000
57	A	313	ALA	0	0.063	0.028	18.414	0.694	0.694	0.000	0.000	0.000	0.000
58	A	314	PHE	0	-0.032	0.005	14.674	0.470	0.470	0.000	0.000	0.000	0.000
59	A	315	PHE	0	0.062	0.022	13.986	0.290	0.290	0.000	0.000	0.000	0.000
60	A	316	GLY	0	-0.020	0.022	19.149	0.737	0.737	0.000	0.000	0.000	0.000
61	A	317	MET	0	-0.036	-0.020	20.474	0.697	0.697	0.000	0.000	0.000	0.000
62	A	318	SER	0	-0.045	-0.016	19.168	0.527	0.527	0.000	0.000	0.000	0.000
63	A	319	ARG	1	0.966	0.992	21.788	11.372	11.372	0.000	0.000	0.000	0.000
64	A	320	ILE	0	0.009	0.002	17.833	-0.520	-0.520	0.000	0.000	0.000	0.000
65	A	321	GLY	0	0.020	0.021	20.191	0.728	0.728	0.000	0.000	0.000	0.000
66	A	322	MET	0	-0.035	-0.022	18.557	-1.092	-1.092	0.000	0.000	0.000	0.000
67	A	323	GLU	-1	-0.877	-0.925	19.864	-12.151	-12.151	0.000	0.000	0.000	0.000
68	A	324	VAL	0	-0.001	0.000	19.833	-0.672	-0.672	0.000	0.000	0.000	0.000
69	A	325	THR	0	0.005	0.003	19.193	0.437	0.437	0.000	0.000	0.000	0.000
70	A	326	PRO	0	0.026	-0.008	21.011	-0.166	-0.166	0.000	0.000	0.000	0.000
71	A	327	SER	0	-0.018	0.005	16.503	-0.273	-0.273	0.000	0.000	0.000	0.000
72	A	328	GLY	0	0.028	0.018	16.210	-0.710	-0.710	0.000	0.000	0.000	0.000
73	A	329	THR	0	-0.014	-0.014	16.278	0.592	0.592	0.000	0.000	0.000	0.000
74	A	330	TRP	0	-0.048	-0.019	13.275	-1.860	-1.860	0.000	0.000	0.000	0.000
75	A	331	LEU	0	-0.010	-0.001	14.534	0.592	0.592	0.000	0.000	0.000	0.000
76	A	332	THR	0	-0.039	-0.030	15.644	-0.834	-0.834	0.000	0.000	0.000	0.000
77	A	333	TYR	0	-0.005	-0.021	13.769	-0.391	-0.391	0.000	0.000	0.000	0.000
78	A	334	THR	0	0.000	0.001	18.773	0.186	0.186	0.000	0.000	0.000	0.000
79	A	335	GLY	0	0.040	0.012	21.457	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	336	ALA	0	-0.024	-0.007	23.181	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	337	ILE	0	0.001	0.007	20.095	0.054	0.054	0.000	0.000	0.000	0.000
82	A	338	LYS	1	0.862	0.929	24.576	10.083	10.083	0.000	0.000	0.000	0.000
83	A	339	LEU	0	0.033	0.025	25.106	-0.240	-0.240	0.000	0.000	0.000	0.000
84	A	340	ASP	-1	-0.831	-0.916	27.960	-9.748	-9.748	0.000	0.000	0.000	0.000
85	A	341	ASP	-1	-0.839	-0.909	30.180	-9.246	-9.246	0.000	0.000	0.000	0.000
86	A	342	LYS	1	0.874	0.921	33.164	8.992	8.992	0.000	0.000	0.000	0.000
87	A	343	ASP	-1	-0.750	-0.846	27.774	-11.189	-11.189	0.000	0.000	0.000	0.000
88	A	344	PRO	0	0.045	0.028	31.451	0.074	0.074	0.000	0.000	0.000	0.000
89	A	345	ASN	0	-0.070	-0.034	28.074	0.162	0.162	0.000	0.000	0.000	0.000
90	A	346	PHE	0	0.001	0.010	29.311	-0.200	-0.200	0.000	0.000	0.000	0.000
91	A	347	LYS	1	0.925	0.946	30.083	8.978	8.978	0.000	0.000	0.000	0.000
92	A	348	ASP	-1	-0.876	-0.942	28.856	-10.383	-10.383	0.000	0.000	0.000	0.000
93	A	349	GLN	0	-0.053	-0.039	25.181	-0.178	-0.178	0.000	0.000	0.000	0.000
94	A	350	VAL	0	-0.011	0.001	26.070	-0.397	-0.397	0.000	0.000	0.000	0.000
95	A	351	ILE	0	0.004	0.007	27.974	-0.155	-0.155	0.000	0.000	0.000	0.000
96	A	352	LEU	0	-0.025	-0.014	22.095	-0.293	-0.293	0.000	0.000	0.000	0.000
97	A	353	LEU	0	-0.012	-0.020	21.464	-0.472	-0.472	0.000	0.000	0.000	0.000
98	A	354	ASN	0	-0.011	-0.010	24.055	-0.082	-0.082	0.000	0.000	0.000	0.000
99	A	355	LYS	1	0.805	0.919	23.310	13.286	13.286	0.000	0.000	0.000	0.000
100	A	356	HIS	0	0.014	0.004	20.586	-0.274	-0.274	0.000	0.000	0.000	0.000
101	A	357	ILE	0	0.016	0.010	22.121	-0.568	-0.568	0.000	0.000	0.000	0.000
102	A	358	ASP	-1	-0.733	-0.831	22.670	-11.751	-11.751	0.000	0.000	0.000	0.000
103	A	359	ALA	0	-0.006	0.007	23.044	0.388	0.388	0.000	0.000	0.000	0.000
104	A	360	TYR	0	0.030	-0.024	21.893	0.314	0.314	0.000	0.000	0.000	0.000
105	A	361	LYS	1	0.793	0.902	23.984	11.589	11.589	0.000	0.000	0.000	0.000
106	A	362	THR	0	-0.043	-0.019	27.237	0.397	0.397	0.000	0.000	0.000	0.000
107	A	363	PHE	0	-0.099	-0.035	21.558	-0.243	-0.243	0.000	0.000	0.000	0.000
108	A	364	PRO	-1	-0.907	-0.935	27.524	-10.042	-10.042	0.000	0.000	0.000	0.000
109	A	402	HOH	0	-0.042	-0.048	20.543	-0.038	-0.038	0.000	0.000	0.000	0.000
110	A	419	HOH	0	-0.032	-0.038	23.772	0.221	0.221	0.000	0.000	0.000	0.000
111	A	431	HOH	0	-0.040	-0.034	33.584	0.042	0.042	0.000	0.000	0.000	0.000
112	A	432	HOH	0	-0.055	-0.030	12.243	-0.373	-0.373	0.000	0.000	0.000	0.000
113	A	436	HOH	0	0.002	-0.001	22.102	-0.156	-0.156	0.000	0.000	0.000	0.000
114	A	439	HOH	0	-0.057	-0.035	22.697	0.179	0.179	0.000	0.000	0.000	0.000
115	A	440	HOH	0	-0.018	-0.015	20.992	0.138	0.138	0.000	0.000	0.000	0.000
116	A	442	HOH	0	-0.020	-0.018	33.756	0.070	0.070	0.000	0.000	0.000	0.000
117	A	443	HOH	0	-0.017	-0.020	12.443	-0.289	-0.289	0.000	0.000	0.000	0.000
118	A	444	HOH	0	-0.026	-0.021	20.814	-0.115	-0.115	0.000	0.000	0.000	0.000
119	A	445	HOH	0	-0.028	-0.022	14.078	0.039	0.039	0.000	0.000	0.000	0.000
120	A	449	HOH	0	-0.007	-0.004	25.915	-0.021	-0.021	0.000	0.000	0.000	0.000
121	A	456	HOH	0	-0.018	-0.016	21.750	0.119	0.119	0.000	0.000	0.000	0.000
122	A	468	HOH	0	-0.038	-0.031	25.002	0.055	0.055	0.000	0.000	0.000	0.000
123	A	469	HOH	0	-0.035	-0.036	20.548	-0.105	-0.105	0.000	0.000	0.000	0.000
124	A	472	HOH	0	0.003	-0.006	26.052	0.085	0.085	0.000	0.000	0.000	0.000
125	A	487	HOH	0	0.029	0.016	16.156	-0.059	-0.059	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:257:LYS )