FMO DATABASE

FMODB ID: J33M9

Calculation Name: 7RBS-J-Xray89

Preferred Name:

Target Type:

Ligand Name: zinc ion

ligand 3-letter code: ZN

PDB ID: 7RBS

Chain ID: J

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-10-07

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:

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	158
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-1356102.275844
FMO2-HF: Nuclear repulsion	1296434.904075
FMO2-HF: Total energy	-59667.371768
FMO2-MP2: Total energy	-59842.442077

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(J:1:ALA )

Summations of interaction energy for fragment #1(J:1:ALA )

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.
-9.572	-7.858	0.001	-0.802	-0.913	-0.002

Interaction energy analysis for fragmet #1(J:1:ALA )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.913

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	J	3	TRP	0	-0.041	-0.015	3.581	-4.626	-3.099	0.002	-0.778	-0.750	-0.002
4	J	4	ASP	-1	-0.820	-0.891	6.472	-27.527	-27.527	0.000	0.000	0.000	0.000
5	J	5	LEU	0	-0.043	-0.017	10.219	-0.173	-0.173	0.000	0.000	0.000	0.000
6	J	6	THR	0	-0.011	-0.010	13.473	0.504	0.504	0.000	0.000	0.000	0.000
7	J	7	VAL	0	0.016	0.001	16.977	-0.005	-0.005	0.000	0.000	0.000	0.000
8	J	8	LYS	1	0.883	0.936	19.832	12.866	12.866	0.000	0.000	0.000	0.000
9	J	9	MET	0	0.019	0.016	23.270	0.026	0.026	0.000	0.000	0.000	0.000
10	J	10	LEU	0	0.022	0.001	26.314	0.087	0.087	0.000	0.000	0.000	0.000
11	J	11	ALA	0	-0.036	-0.015	29.771	0.257	0.257	0.000	0.000	0.000	0.000
12	J	12	GLY	0	0.008	0.016	29.016	0.282	0.282	0.000	0.000	0.000	0.000
13	J	13	ASN	0	-0.039	-0.022	26.366	-0.033	-0.033	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.836	-0.909	21.566	-13.605	-13.605	0.000	0.000	0.000	0.000
15	J	15	PHE	0	-0.039	-0.028	19.088	0.345	0.345	0.000	0.000	0.000	0.000
16	J	16	GLN	0	0.048	0.035	13.613	0.523	0.523	0.000	0.000	0.000	0.000
17	J	17	VAL	0	-0.007	-0.004	14.064	0.862	0.862	0.000	0.000	0.000	0.000
18	J	18	SER	0	0.012	-0.007	9.173	-0.246	-0.246	0.000	0.000	0.000	0.000
19	J	19	LEU	0	-0.030	-0.019	9.057	2.111	2.111	0.000	0.000	0.000	0.000
20	J	20	SER	0	0.032	-0.014	5.214	-4.874	-4.874	0.000	0.000	0.000	0.000
21	J	21	SER	0	0.014	0.006	4.066	4.656	4.843	-0.001	-0.024	-0.163	0.000
22	J	22	SER	0	-0.003	-0.013	5.750	5.528	5.528	0.000	0.000	0.000	0.000
23	J	23	MET	0	-0.054	0.013	8.726	3.398	3.398	0.000	0.000	0.000	0.000
24	J	24	SER	0	0.049	0.031	10.873	-0.457	-0.457	0.000	0.000	0.000	0.000
25	J	25	VAL	0	0.035	-0.002	14.297	-0.447	-0.447	0.000	0.000	0.000	0.000
26	J	26	SER	0	-0.001	0.000	17.260	0.472	0.472	0.000	0.000	0.000	0.000
27	J	27	GLU	-1	-0.832	-0.926	13.429	-19.896	-19.896	0.000	0.000	0.000	0.000
28	J	28	LEU	0	0.010	0.015	15.068	0.060	0.060	0.000	0.000	0.000	0.000
29	J	29	LYS	1	0.909	0.954	16.113	14.207	14.207	0.000	0.000	0.000	0.000
30	J	30	ALA	0	0.044	0.037	17.650	0.675	0.675	0.000	0.000	0.000	0.000
31	J	31	GLN	0	0.027	0.015	13.529	1.339	1.339	0.000	0.000	0.000	0.000
32	J	32	ILE	0	-0.013	0.000	17.374	0.456	0.456	0.000	0.000	0.000	0.000
33	J	33	THR	0	-0.086	-0.061	20.334	0.503	0.503	0.000	0.000	0.000	0.000
34	J	34	GLN	0	-0.057	-0.025	16.695	1.255	1.255	0.000	0.000	0.000	0.000
35	J	35	LYS	1	0.904	0.977	19.275	15.355	15.355	0.000	0.000	0.000	0.000
36	J	36	ILE	0	-0.047	-0.041	21.274	0.515	0.515	0.000	0.000	0.000	0.000
37	J	37	GLY	0	0.011	0.028	24.449	0.551	0.551	0.000	0.000	0.000	0.000
38	J	38	VAL	0	-0.048	-0.035	25.499	0.596	0.596	0.000	0.000	0.000	0.000
39	J	39	HIS	0	0.082	0.047	25.377	-0.946	-0.946	0.000	0.000	0.000	0.000
40	J	40	ALA	0	0.077	0.037	23.055	0.022	0.022	0.000	0.000	0.000	0.000
41	J	41	PHE	0	0.010	0.005	24.646	-0.106	-0.106	0.000	0.000	0.000	0.000
42	J	42	GLN	0	-0.040	-0.008	27.612	0.192	0.192	0.000	0.000	0.000	0.000
43	J	43	GLN	0	-0.002	-0.007	22.676	-0.354	-0.354	0.000	0.000	0.000	0.000
44	J	44	ARG	1	0.789	0.871	25.685	10.495	10.495	0.000	0.000	0.000	0.000
45	J	45	LEU	0	0.030	0.007	19.853	-0.079	-0.079	0.000	0.000	0.000	0.000
46	J	46	ALA	0	-0.002	0.007	23.187	0.182	0.182	0.000	0.000	0.000	0.000
47	J	47	VAL	0	0.024	0.024	18.960	-0.374	-0.374	0.000	0.000	0.000	0.000
48	J	48	HIS	0	-0.034	0.014	20.841	1.020	1.020	0.000	0.000	0.000	0.000
49	J	49	PRO	0	0.033	-0.012	21.430	-0.635	-0.635	0.000	0.000	0.000	0.000
50	J	50	SER	0	-0.008	-0.018	22.191	0.420	0.420	0.000	0.000	0.000	0.000
51	J	51	GLY	0	0.027	0.019	24.470	0.461	0.461	0.000	0.000	0.000	0.000
52	J	52	VAL	0	-0.035	-0.008	22.300	0.462	0.462	0.000	0.000	0.000	0.000
53	J	53	ALA	0	0.005	-0.007	23.078	-0.563	-0.563	0.000	0.000	0.000	0.000
54	J	54	LEU	0	0.012	0.004	18.067	-0.261	-0.261	0.000	0.000	0.000	0.000
55	J	55	GLN	0	-0.026	-0.026	19.096	-0.014	-0.014	0.000	0.000	0.000	0.000
56	J	56	ASP	-1	-0.898	-0.946	18.768	-15.089	-15.089	0.000	0.000	0.000	0.000
57	J	57	ARG	1	0.952	0.960	18.365	14.547	14.547	0.000	0.000	0.000	0.000
58	J	58	VAL	0	-0.039	0.003	15.226	-0.755	-0.755	0.000	0.000	0.000	0.000
59	J	59	PRO	0	0.057	0.016	10.710	0.288	0.288	0.000	0.000	0.000	0.000
60	J	60	LEU	0	0.014	0.014	11.958	0.858	0.858	0.000	0.000	0.000	0.000
61	J	61	ALA	0	0.004	0.005	8.489	0.583	0.583	0.000	0.000	0.000	0.000
62	J	62	SER	0	-0.043	-0.032	10.470	-0.118	-0.118	0.000	0.000	0.000	0.000
63	J	63	GLN	0	-0.067	-0.016	13.056	2.403	2.403	0.000	0.000	0.000	0.000
64	J	64	GLY	0	0.011	0.005	14.498	-0.613	-0.613	0.000	0.000	0.000	0.000
65	J	65	LEU	0	-0.045	-0.015	13.563	-0.352	-0.352	0.000	0.000	0.000	0.000
66	J	66	GLY	0	0.108	0.056	9.999	-1.710	-1.710	0.000	0.000	0.000	0.000
67	J	67	PRO	0	-0.042	-0.030	7.941	1.008	1.008	0.000	0.000	0.000	0.000
68	J	68	GLY	0	0.014	0.015	10.105	1.234	1.234	0.000	0.000	0.000	0.000
69	J	69	SER	0	-0.047	-0.009	13.412	1.885	1.885	0.000	0.000	0.000	0.000
70	J	70	THR	0	0.038	-0.002	15.515	-0.322	-0.322	0.000	0.000	0.000	0.000
71	J	71	VAL	0	-0.037	-0.011	18.193	0.326	0.326	0.000	0.000	0.000	0.000
72	J	72	LEU	0	-0.024	-0.015	19.973	0.218	0.218	0.000	0.000	0.000	0.000
73	J	73	LEU	0	0.016	0.001	22.918	-0.194	-0.194	0.000	0.000	0.000	0.000
74	J	74	VAL	0	-0.016	-0.013	24.947	0.428	0.428	0.000	0.000	0.000	0.000
75	J	75	VAL	0	-0.003	-0.010	27.675	-0.253	-0.253	0.000	0.000	0.000	0.000
76	J	76	ASP	-1	-0.848	-0.901	29.886	-9.191	-9.191	0.000	0.000	0.000	0.000
77	J	77	LYS	1	0.954	0.958	31.546	9.869	9.869	0.000	0.000	0.000	0.000
78	J	78	CYS	0	-0.029	0.005	34.341	0.244	0.244	0.000	0.000	0.000	0.000
79	J	79	ASP	-1	-0.790	-0.900	36.287	-8.884	-8.884	0.000	0.000	0.000	0.000
80	J	80	GLU	-1	-0.944	-0.966	38.186	-7.243	-7.243	0.000	0.000	0.000	0.000
81	J	81	PRO	0	-0.044	-0.016	40.596	-0.177	-0.177	0.000	0.000	0.000	0.000
82	J	82	LEU	0	0.003	0.005	38.268	0.033	0.033	0.000	0.000	0.000	0.000
83	J	83	SER	0	0.014	0.007	42.568	0.083	0.083	0.000	0.000	0.000	0.000
84	J	84	ILE	0	-0.014	0.001	38.765	-0.125	-0.125	0.000	0.000	0.000	0.000
85	J	85	LEU	0	-0.024	-0.020	41.917	0.235	0.235	0.000	0.000	0.000	0.000
86	J	86	VAL	0	0.040	0.017	40.623	-0.240	-0.240	0.000	0.000	0.000	0.000
87	J	87	ARG	1	0.902	0.971	42.312	7.300	7.300	0.000	0.000	0.000	0.000
88	J	88	ASN	0	0.028	-0.004	43.113	-0.129	-0.129	0.000	0.000	0.000	0.000
89	J	89	ASN	0	0.059	0.004	45.337	-0.010	-0.010	0.000	0.000	0.000	0.000
90	J	90	LYS	1	0.857	0.937	46.193	6.471	6.471	0.000	0.000	0.000	0.000
91	J	91	GLY	0	0.032	0.029	47.269	0.095	0.095	0.000	0.000	0.000	0.000
92	J	92	ARG	1	0.794	0.883	48.323	6.354	6.354	0.000	0.000	0.000	0.000
93	J	93	SER	0	-0.001	-0.017	45.394	-0.096	-0.096	0.000	0.000	0.000	0.000
94	J	94	SER	0	0.008	0.021	46.585	0.219	0.219	0.000	0.000	0.000	0.000
95	J	95	THR	0	0.008	-0.012	45.943	-0.136	-0.136	0.000	0.000	0.000	0.000
96	J	96	TYR	0	0.008	0.006	43.573	0.153	0.153	0.000	0.000	0.000	0.000
97	J	97	GLU	-1	-0.933	-0.958	44.034	-7.045	-7.045	0.000	0.000	0.000	0.000
98	J	98	VAL	0	-0.025	-0.017	39.505	-0.004	-0.004	0.000	0.000	0.000	0.000
99	J	99	ARG	1	0.938	0.970	38.846	7.905	7.905	0.000	0.000	0.000	0.000
100	J	100	LEU	0	0.006	0.005	33.653	-0.125	-0.125	0.000	0.000	0.000	0.000
101	J	101	THR	0	-0.024	-0.040	33.584	-0.328	-0.328	0.000	0.000	0.000	0.000
102	J	102	GLN	0	0.022	0.027	34.686	-0.153	-0.153	0.000	0.000	0.000	0.000
103	J	103	THR	0	0.023	0.008	33.097	-0.113	-0.113	0.000	0.000	0.000	0.000
104	J	104	VAL	0	0.010	0.005	32.166	0.339	0.339	0.000	0.000	0.000	0.000
105	J	105	ALA	0	0.006	-0.002	35.106	0.252	0.252	0.000	0.000	0.000	0.000
106	J	106	HIS	0	-0.030	-0.003	37.051	0.337	0.337	0.000	0.000	0.000	0.000
107	J	107	LEU	0	0.001	0.006	37.619	0.231	0.231	0.000	0.000	0.000	0.000
108	J	108	LYS	1	0.842	0.901	36.521	8.941	8.941	0.000	0.000	0.000	0.000
109	J	109	GLN	0	0.023	0.023	40.513	0.135	0.135	0.000	0.000	0.000	0.000
110	J	110	GLN	0	0.010	0.013	42.700	0.059	0.059	0.000	0.000	0.000	0.000
111	J	111	VAL	0	-0.015	-0.014	41.883	0.177	0.177	0.000	0.000	0.000	0.000
112	J	112	SER	0	-0.092	-0.069	44.238	0.182	0.182	0.000	0.000	0.000	0.000
113	J	113	GLY	0	0.010	-0.007	45.920	0.149	0.149	0.000	0.000	0.000	0.000
114	J	114	LEU	0	-0.059	-0.019	48.318	0.165	0.165	0.000	0.000	0.000	0.000
115	J	115	GLU	-1	-0.811	-0.892	46.845	-6.457	-6.457	0.000	0.000	0.000	0.000
116	J	116	GLY	0	-0.005	0.020	49.593	0.087	0.087	0.000	0.000	0.000	0.000
117	J	117	VAL	0	-0.044	-0.028	45.561	0.055	0.055	0.000	0.000	0.000	0.000
118	J	118	GLN	0	0.052	0.039	45.103	0.019	0.019	0.000	0.000	0.000	0.000
119	J	119	ASP	-1	-0.826	-0.925	40.981	-7.733	-7.733	0.000	0.000	0.000	0.000
120	J	120	ASP	-1	-0.859	-0.917	39.363	-8.000	-8.000	0.000	0.000	0.000	0.000
121	J	121	LEU	0	-0.003	0.003	40.557	-0.084	-0.084	0.000	0.000	0.000	0.000
122	J	122	PHE	0	-0.044	-0.028	40.329	0.043	0.043	0.000	0.000	0.000	0.000
123	J	123	TRP	0	-0.057	-0.026	33.106	-0.244	-0.244	0.000	0.000	0.000	0.000
124	J	124	LEU	0	0.046	0.024	35.733	0.198	0.198	0.000	0.000	0.000	0.000
125	J	125	THR	0	0.010	0.002	32.825	-0.302	-0.302	0.000	0.000	0.000	0.000
126	J	126	PHE	0	0.024	0.008	31.720	0.452	0.452	0.000	0.000	0.000	0.000
127	J	127	GLU	-1	-0.902	-0.949	31.248	-10.313	-10.313	0.000	0.000	0.000	0.000
128	J	128	GLY	0	-0.021	-0.007	30.624	-0.309	-0.309	0.000	0.000	0.000	0.000
129	J	129	LYS	1	0.934	0.977	24.337	12.569	12.569	0.000	0.000	0.000	0.000
130	J	130	PRO	0	-0.015	-0.013	28.175	0.323	0.323	0.000	0.000	0.000	0.000
131	J	131	LEU	0	-0.031	-0.026	29.442	-0.345	-0.345	0.000	0.000	0.000	0.000
132	J	132	GLU	-1	-0.867	-0.923	25.658	-12.170	-12.170	0.000	0.000	0.000	0.000
133	J	133	ASP	-1	-0.824	-0.905	30.347	-9.168	-9.168	0.000	0.000	0.000	0.000
134	J	134	GLN	0	0.041	0.004	26.766	0.636	0.636	0.000	0.000	0.000	0.000
135	J	135	LEU	0	-0.016	0.007	25.663	-0.087	-0.087	0.000	0.000	0.000	0.000
136	J	136	PRO	0	-0.002	-0.002	28.493	0.371	0.371	0.000	0.000	0.000	0.000
137	J	137	LEU	0	0.037	0.011	30.779	-0.290	-0.290	0.000	0.000	0.000	0.000
138	J	138	GLY	0	0.010	-0.007	31.635	-0.041	-0.041	0.000	0.000	0.000	0.000
139	J	139	GLU	-1	-0.956	-0.978	24.324	-13.065	-13.065	0.000	0.000	0.000	0.000
140	J	140	TYR	0	-0.026	-0.012	27.102	-0.441	-0.441	0.000	0.000	0.000	0.000
141	J	141	GLY	0	-0.010	0.009	29.520	0.126	0.126	0.000	0.000	0.000	0.000
142	J	142	LEU	0	-0.019	-0.002	30.844	0.202	0.202	0.000	0.000	0.000	0.000
143	J	143	LYS	1	0.902	0.941	31.605	9.856	9.856	0.000	0.000	0.000	0.000
144	J	144	PRO	0	0.046	0.006	37.132	0.080	0.080	0.000	0.000	0.000	0.000
145	J	145	LEU	0	-0.016	-0.002	40.945	0.020	0.020	0.000	0.000	0.000	0.000
146	J	146	SER	0	0.004	0.020	37.290	-0.092	-0.092	0.000	0.000	0.000	0.000
147	J	147	THR	0	-0.027	-0.019	39.144	0.236	0.236	0.000	0.000	0.000	0.000
148	J	148	VAL	0	-0.004	0.003	36.414	-0.208	-0.208	0.000	0.000	0.000	0.000
149	J	149	PHE	0	-0.024	-0.017	37.649	0.366	0.366	0.000	0.000	0.000	0.000
150	J	150	MET	0	0.021	0.015	38.389	-0.174	-0.174	0.000	0.000	0.000	0.000
151	J	151	ASN	0	-0.037	-0.005	37.486	0.007	0.007	0.000	0.000	0.000	0.000
152	J	152	LEU	0	0.047	0.013	40.315	-0.060	-0.060	0.000	0.000	0.000	0.000
153	J	153	ARG	1	0.876	0.943	35.515	8.495	8.495	0.000	0.000	0.000	0.000
154	J	154	LEU	0	0.010	0.004	40.533	0.192	0.192	0.000	0.000	0.000	0.000
155	J	155	ARG	1	0.809	0.880	39.310	7.603	7.603	0.000	0.000	0.000	0.000
156	J	156	GLY	0	-0.021	0.001	40.342	0.196	0.196	0.000	0.000	0.000	0.000
157	J	157	GLY	-1	-0.909	-0.942	39.798	-7.888	-7.888	0.000	0.000	0.000	0.000
158	J	201	HOH	0	-0.051	-0.038	24.644	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(J:1:ALA )