FMO DATABASE

FMODB ID: 4N11N

Calculation Name: 7DE1-B-Xray89

Preferred Name:

Target Type:

Ligand Name: di(hydroxyethyl)ether

ligand 3-letter code: PEG

PDB ID: 7DE1

Chain ID: B

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	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	MIZUHO/ABINIT-MP 4.0(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-902283.353726
FMO2-HF: Nuclear repulsion	855784.498684
FMO2-HF: Total energy	-46498.855043
FMO2-MP2: Total energy	-46635.578059

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(B:250:SER )

Summations of interaction energy for fragment #1(B:250:SER )

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.
-2.669	1.878	0.868	-1.926	-3.489	-0.001

Interaction energy analysis for fragmet #1(B:250:SER )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.084 / q_NPA : 0.028

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	B	252	ALA	0	0.048	0.025	3.813	-2.326	-1.060	-0.007	-0.476	-0.783	0.002
4	B	253	GLU	-1	-0.835	-0.908	3.092	-2.863	-2.306	0.062	-0.157	-0.463	0.000
5	B	254	ALA	0	-0.024	-0.014	2.566	-0.822	0.541	0.317	-0.789	-0.891	-0.001
6	B	255	SER	0	-0.081	-0.057	4.531	1.023	1.110	-0.001	-0.016	-0.070	0.000
7	B	256	LYS	1	0.859	0.925	7.387	2.045	2.045	0.000	0.000	0.000	0.000
8	B	257	LYS	1	0.921	0.986	7.624	1.667	1.667	0.000	0.000	0.000	0.000
9	B	258	PRO	0	0.063	0.020	10.563	0.075	0.075	0.000	0.000	0.000	0.000
10	B	259	ARG	1	0.930	0.950	12.427	0.114	0.114	0.000	0.000	0.000	0.000
11	B	260	GLN	0	0.049	0.016	12.903	-0.039	-0.039	0.000	0.000	0.000	0.000
12	B	261	LYS	1	0.906	0.942	12.418	0.451	0.451	0.000	0.000	0.000	0.000
13	B	262	ARG	1	0.809	0.931	8.603	0.529	0.529	0.000	0.000	0.000	0.000
14	B	263	THR	0	0.010	-0.006	6.667	0.088	0.088	0.000	0.000	0.000	0.000
15	B	264	ALA	0	0.016	0.020	6.021	-0.220	-0.220	0.000	0.000	0.000	0.000
16	B	265	THR	0	-0.005	0.000	3.620	-0.392	-0.179	0.002	-0.033	-0.182	0.000
17	B	266	LYS	1	0.920	0.936	6.592	-1.048	-1.048	0.000	0.000	0.000	0.000
18	B	267	ALA	0	-0.041	-0.006	2.579	-0.820	-0.211	0.471	-0.348	-0.732	-0.001
19	B	268	TYR	0	-0.023	-0.027	3.235	-0.246	0.143	0.025	-0.106	-0.308	-0.001
20	B	269	ASN	0	0.084	0.064	4.937	-0.579	-0.516	-0.001	-0.001	-0.060	0.000
21	B	270	VAL	0	0.051	0.011	8.482	-0.187	-0.187	0.000	0.000	0.000	0.000
22	B	271	THR	0	-0.007	0.003	11.581	-0.109	-0.109	0.000	0.000	0.000	0.000
23	B	272	GLN	0	-0.010	0.004	6.806	-0.063	-0.063	0.000	0.000	0.000	0.000
24	B	273	ALA	0	-0.042	-0.003	8.352	-0.136	-0.136	0.000	0.000	0.000	0.000
25	B	274	PHE	0	-0.056	-0.045	10.105	-0.071	-0.071	0.000	0.000	0.000	0.000
26	B	275	GLY	0	0.060	0.052	13.712	0.002	0.002	0.000	0.000	0.000	0.000
27	B	276	ARG	1	0.856	0.886	15.771	-0.172	-0.172	0.000	0.000	0.000	0.000
28	B	277	ARG	1	0.812	0.910	16.180	-0.079	-0.079	0.000	0.000	0.000	0.000
29	B	278	GLY	0	0.010	-0.003	19.955	0.013	0.013	0.000	0.000	0.000	0.000
30	B	279	PRO	0	-0.038	-0.012	23.509	-0.007	-0.007	0.000	0.000	0.000	0.000
31	B	280	GLU	-1	-0.852	-0.888	25.418	0.004	0.004	0.000	0.000	0.000	0.000
32	B	281	GLN	0	0.006	0.003	25.882	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	282	THR	0	0.008	0.000	23.302	-0.005	-0.005	0.000	0.000	0.000	0.000
34	B	283	GLN	0	-0.008	0.019	20.959	-0.018	-0.018	0.000	0.000	0.000	0.000
35	B	284	GLY	0	-0.018	0.002	19.289	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	285	ASN	0	0.035	-0.001	20.342	0.012	0.012	0.000	0.000	0.000	0.000
37	B	286	PHE	0	-0.007	0.005	18.355	0.016	0.016	0.000	0.000	0.000	0.000
38	B	287	GLY	0	0.001	-0.014	17.917	0.004	0.004	0.000	0.000	0.000	0.000
39	B	288	ASP	-1	-0.691	-0.824	18.919	0.219	0.219	0.000	0.000	0.000	0.000
40	B	289	GLN	0	0.015	0.003	17.871	0.028	0.028	0.000	0.000	0.000	0.000
41	B	290	GLU	-1	-0.815	-0.864	16.350	0.338	0.338	0.000	0.000	0.000	0.000
42	B	291	LEU	0	0.030	0.008	14.137	0.063	0.063	0.000	0.000	0.000	0.000
43	B	292	ILE	0	-0.015	0.009	13.378	0.034	0.034	0.000	0.000	0.000	0.000
44	B	293	ARG	1	0.915	0.957	11.818	-0.488	-0.488	0.000	0.000	0.000	0.000
45	B	294	GLN	0	-0.059	-0.048	10.242	0.225	0.225	0.000	0.000	0.000	0.000
46	B	295	GLY	0	0.021	0.015	9.775	0.070	0.070	0.000	0.000	0.000	0.000
47	B	296	THR	0	-0.053	-0.059	8.708	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	297	ASP	-1	-0.794	-0.877	8.050	1.322	1.322	0.000	0.000	0.000	0.000
49	B	298	TYR	0	-0.090	-0.047	11.262	-0.008	-0.008	0.000	0.000	0.000	0.000
50	B	299	LYS	1	0.903	0.940	14.482	-0.273	-0.273	0.000	0.000	0.000	0.000
51	B	300	HIS	0	0.024	0.021	17.488	-0.018	-0.018	0.000	0.000	0.000	0.000
52	B	301	TRP	0	0.036	0.026	13.885	-0.017	-0.017	0.000	0.000	0.000	0.000
53	B	302	PRO	0	0.026	0.012	16.638	-0.035	-0.035	0.000	0.000	0.000	0.000
54	B	303	GLN	0	0.080	0.030	18.672	-0.015	-0.015	0.000	0.000	0.000	0.000
55	B	304	ILE	0	-0.009	0.008	18.013	-0.006	-0.006	0.000	0.000	0.000	0.000
56	B	305	ALA	0	-0.020	-0.015	16.796	-0.020	-0.020	0.000	0.000	0.000	0.000
57	B	306	GLN	0	0.037	0.049	18.834	-0.012	-0.012	0.000	0.000	0.000	0.000
58	B	307	PHE	0	0.013	0.009	22.017	-0.006	-0.006	0.000	0.000	0.000	0.000
59	B	308	ALA	0	-0.058	-0.015	18.942	-0.006	-0.006	0.000	0.000	0.000	0.000
60	B	309	PRO	0	-0.003	0.006	20.795	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	310	SER	0	0.051	0.016	20.780	-0.023	-0.023	0.000	0.000	0.000	0.000
62	B	311	ALA	0	0.018	0.001	20.666	0.004	0.004	0.000	0.000	0.000	0.000
63	B	312	SER	0	0.040	0.026	22.335	0.011	0.011	0.000	0.000	0.000	0.000
64	B	313	ALA	0	0.064	0.030	25.370	0.010	0.010	0.000	0.000	0.000	0.000
65	B	314	PHE	0	-0.036	-0.004	22.537	0.008	0.008	0.000	0.000	0.000	0.000
66	B	315	PHE	0	0.047	0.012	22.996	0.005	0.005	0.000	0.000	0.000	0.000
67	B	316	GLY	0	-0.016	0.021	27.258	0.007	0.007	0.000	0.000	0.000	0.000
68	B	317	MET	0	-0.057	-0.026	26.706	0.010	0.010	0.000	0.000	0.000	0.000
69	B	318	SER	0	-0.066	-0.027	26.608	0.011	0.011	0.000	0.000	0.000	0.000
70	B	319	ARG	1	0.954	0.977	29.294	0.062	0.062	0.000	0.000	0.000	0.000
71	B	320	ILE	0	0.009	0.003	26.573	-0.002	-0.002	0.000	0.000	0.000	0.000
72	B	321	GLY	0	0.029	0.018	29.180	0.008	0.008	0.000	0.000	0.000	0.000
73	B	322	MET	0	-0.049	-0.030	28.084	-0.013	-0.013	0.000	0.000	0.000	0.000
74	B	323	GLU	-1	-0.900	-0.933	29.478	-0.072	-0.072	0.000	0.000	0.000	0.000
75	B	324	VAL	0	0.000	-0.004	29.732	-0.011	-0.011	0.000	0.000	0.000	0.000
76	B	325	THR	0	-0.001	-0.003	29.312	0.010	0.010	0.000	0.000	0.000	0.000
77	B	326	PRO	0	0.029	-0.006	31.151	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	327	SER	0	-0.022	0.007	26.156	-0.005	-0.005	0.000	0.000	0.000	0.000
79	B	328	GLY	0	0.012	0.010	26.293	-0.014	-0.014	0.000	0.000	0.000	0.000
80	B	329	THR	0	-0.028	-0.026	26.775	0.014	0.014	0.000	0.000	0.000	0.000
81	B	330	TRP	0	-0.059	-0.028	21.776	-0.025	-0.025	0.000	0.000	0.000	0.000
82	B	331	LEU	0	-0.011	-0.002	23.917	0.006	0.006	0.000	0.000	0.000	0.000
83	B	332	THR	0	-0.002	-0.002	24.687	-0.006	-0.006	0.000	0.000	0.000	0.000
84	B	333	TYR	0	-0.002	-0.016	20.744	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	334	THR	0	0.016	0.009	26.771	0.008	0.008	0.000	0.000	0.000	0.000
86	B	335	GLY	0	0.045	0.014	28.610	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	336	ALA	0	-0.012	0.000	29.207	0.006	0.006	0.000	0.000	0.000	0.000
88	B	337	ILE	0	0.008	0.008	24.996	-0.006	-0.006	0.000	0.000	0.000	0.000
89	B	338	LYS	1	0.804	0.915	29.166	0.023	0.023	0.000	0.000	0.000	0.000
90	B	339	LEU	0	0.031	0.015	28.155	-0.002	-0.002	0.000	0.000	0.000	0.000
91	B	340	ASP	-1	-0.846	-0.925	31.428	-0.014	-0.014	0.000	0.000	0.000	0.000
92	B	341	ASP	-1	-0.807	-0.893	33.617	-0.002	-0.002	0.000	0.000	0.000	0.000
93	B	342	LYS	1	0.931	0.960	36.105	0.014	0.014	0.000	0.000	0.000	0.000
94	B	343	ASP	-1	-0.758	-0.845	30.425	0.006	0.006	0.000	0.000	0.000	0.000
95	B	344	PRO	0	0.019	0.008	33.845	0.005	0.005	0.000	0.000	0.000	0.000
96	B	345	ASN	0	-0.090	-0.056	29.559	0.013	0.013	0.000	0.000	0.000	0.000
97	B	346	PHE	0	0.022	0.026	30.499	0.005	0.005	0.000	0.000	0.000	0.000
98	B	347	LYS	1	0.879	0.923	31.589	-0.034	-0.034	0.000	0.000	0.000	0.000
99	B	348	ASP	-1	-0.850	-0.935	28.903	0.056	0.056	0.000	0.000	0.000	0.000
100	B	349	GLN	0	-0.024	-0.016	26.789	0.004	0.004	0.000	0.000	0.000	0.000
101	B	350	VAL	0	0.020	0.015	27.381	0.002	0.002	0.000	0.000	0.000	0.000
102	B	351	ILE	0	-0.018	-0.001	27.970	0.005	0.005	0.000	0.000	0.000	0.000
103	B	352	LEU	0	-0.055	-0.025	21.472	0.012	0.012	0.000	0.000	0.000	0.000
104	B	353	LEU	0	-0.014	-0.016	23.469	0.009	0.009	0.000	0.000	0.000	0.000
105	B	354	ASN	0	0.010	-0.009	25.255	0.000	0.000	0.000	0.000	0.000	0.000
106	B	355	LYS	1	0.779	0.894	20.960	-0.183	-0.183	0.000	0.000	0.000	0.000
107	B	356	HIS	0	0.014	0.001	19.273	0.019	0.019	0.000	0.000	0.000	0.000
108	B	357	ILE	0	0.012	0.002	22.529	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	358	ASP	-1	-0.747	-0.840	24.124	0.041	0.041	0.000	0.000	0.000	0.000
110	B	359	ALA	0	0.025	0.019	22.373	0.006	0.006	0.000	0.000	0.000	0.000
111	B	360	TYR	0	0.023	-0.006	21.593	0.004	0.004	0.000	0.000	0.000	0.000
112	B	361	LYS	1	0.821	0.918	23.180	-0.044	-0.044	0.000	0.000	0.000	0.000
113	B	362	THR	0	-0.084	-0.044	25.716	0.002	0.002	0.000	0.000	0.000	0.000
114	B	363	PHE	0	-0.046	-0.010	20.000	0.016	0.016	0.000	0.000	0.000	0.000
115	B	364	PRO	-1	-0.778	-0.836	22.045	0.183	0.183	0.000	0.000	0.000	0.000
116	B	502	HOH	0	0.002	-0.007	19.707	-0.010	-0.010	0.000	0.000	0.000	0.000
117	B	504	HOH	0	-0.024	-0.037	29.580	-0.004	-0.004	0.000	0.000	0.000	0.000
118	B	517	HOH	0	0.014	-0.009	17.073	0.008	0.008	0.000	0.000	0.000	0.000
119	B	520	HOH	0	-0.005	-0.017	22.386	0.007	0.007	0.000	0.000	0.000	0.000
120	B	525	HOH	0	-0.036	-0.036	28.495	-0.003	-0.003	0.000	0.000	0.000	0.000
121	B	526	HOH	0	-0.042	-0.036	34.854	-0.001	-0.001	0.000	0.000	0.000	0.000
122	B	528	HOH	0	-0.023	-0.032	27.263	0.001	0.001	0.000	0.000	0.000	0.000
123	B	529	HOH	0	-0.036	-0.034	38.961	-0.002	-0.002	0.000	0.000	0.000	0.000
124	B	536	HOH	0	-0.058	-0.035	30.895	0.002	0.002	0.000	0.000	0.000	0.000
125	B	542	HOH	0	-0.037	-0.032	19.853	-0.003	-0.003	0.000	0.000	0.000	0.000
126	B	543	HOH	0	0.033	0.025	29.411	-0.003	-0.003	0.000	0.000	0.000	0.000
127	B	545	HOH	0	-0.043	-0.034	25.141	0.003	0.003	0.000	0.000	0.000	0.000
128	B	552	HOH	0	-0.018	-0.022	20.905	0.000	0.000	0.000	0.000	0.000	0.000
129	B	555	HOH	0	0.000	-0.003	30.538	-0.003	-0.003	0.000	0.000	0.000	0.000
130	B	559	HOH	0	-0.025	-0.021	28.660	-0.004	-0.004	0.000	0.000	0.000	0.000
131	B	560	HOH	0	-0.017	-0.020	25.897	0.002	0.002	0.000	0.000	0.000	0.000
132	B	563	HOH	0	-0.002	-0.014	29.902	-0.002	-0.002	0.000	0.000	0.000	0.000
133	B	569	HOH	0	-0.045	-0.030	29.872	0.003	0.003	0.000	0.000	0.000	0.000
134	B	575	HOH	0	-0.036	-0.040	23.076	-0.003	-0.003	0.000	0.000	0.000	0.000
135	B	576	HOH	0	0.029	0.016	23.634	0.002	0.002	0.000	0.000	0.000	0.000
136	B	577	HOH	0	-0.023	-0.023	15.922	0.002	0.002	0.000	0.000	0.000	0.000
137	B	604	HOH	0	0.002	0.001	20.199	-0.011	-0.011	0.000	0.000	0.000	0.000
138	B	612	HOH	0	0.038	0.027	25.011	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:250:SER )