FMO DATABASE

FMODB ID: 822JY

Calculation Name: 7RBS-H-Xray89

Preferred Name:

Target Type:

Ligand Name: zinc ion

ligand 3-letter code: ZN

PDB ID: 7RBS

Chain ID: H

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	159
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-1359961.17859
FMO2-HF: Nuclear repulsion	1300217.599485
FMO2-HF: Total energy	-59743.579106
FMO2-MP2: Total energy	-59918.840914

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(H:1:ALA )

Summations of interaction energy for fragment #1(H: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.
-11.118	-9.506	-0.006	-0.835	-0.771	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.909

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	H	3	TRP	0	-0.033	-0.012	3.733	-3.983	-2.371	-0.006	-0.835	-0.771	-0.002
4	H	4	ASP	-1	-0.833	-0.896	6.604	-27.555	-27.555	0.000	0.000	0.000	0.000
5	H	5	LEU	0	-0.039	-0.016	9.952	0.029	0.029	0.000	0.000	0.000	0.000
6	H	6	THR	0	-0.008	-0.013	13.434	0.397	0.397	0.000	0.000	0.000	0.000
7	H	7	VAL	0	-0.003	0.000	16.948	0.251	0.251	0.000	0.000	0.000	0.000
8	H	8	LYS	1	0.886	0.940	19.402	12.657	12.657	0.000	0.000	0.000	0.000
9	H	9	MET	0	0.018	0.017	22.964	-0.049	-0.049	0.000	0.000	0.000	0.000
10	H	10	LEU	0	0.055	0.019	26.088	0.143	0.143	0.000	0.000	0.000	0.000
11	H	11	ALA	0	-0.061	-0.019	29.205	0.275	0.275	0.000	0.000	0.000	0.000
12	H	12	GLY	0	0.009	0.015	29.139	0.205	0.205	0.000	0.000	0.000	0.000
13	H	13	ASN	0	-0.035	-0.019	24.962	-0.034	-0.034	0.000	0.000	0.000	0.000
14	H	14	GLU	-1	-0.831	-0.922	21.259	-13.255	-13.255	0.000	0.000	0.000	0.000
15	H	15	PHE	0	-0.031	-0.023	18.001	0.250	0.250	0.000	0.000	0.000	0.000
16	H	16	GLN	0	0.062	0.043	13.092	0.641	0.641	0.000	0.000	0.000	0.000
17	H	17	VAL	0	-0.030	-0.020	13.403	0.791	0.791	0.000	0.000	0.000	0.000
18	H	18	SER	0	0.008	-0.008	8.212	-0.324	-0.324	0.000	0.000	0.000	0.000
19	H	19	LEU	0	-0.014	-0.007	8.628	1.756	1.756	0.000	0.000	0.000	0.000
20	H	20	SER	0	0.050	-0.011	5.468	-5.292	-5.292	0.000	0.000	0.000	0.000
21	H	21	SER	0	0.020	0.010	5.546	3.857	3.857	0.000	0.000	0.000	0.000
22	H	22	SER	0	-0.006	-0.013	7.199	2.553	2.553	0.000	0.000	0.000	0.000
23	H	23	MET	0	-0.048	0.018	9.195	2.726	2.726	0.000	0.000	0.000	0.000
24	H	24	SER	0	0.053	0.031	11.838	0.097	0.097	0.000	0.000	0.000	0.000
25	H	25	VAL	0	0.054	0.014	15.438	-0.482	-0.482	0.000	0.000	0.000	0.000
26	H	26	SER	0	-0.054	-0.040	18.293	0.757	0.757	0.000	0.000	0.000	0.000
27	H	27	GLU	-1	-0.785	-0.897	13.897	-19.130	-19.130	0.000	0.000	0.000	0.000
28	H	28	LEU	0	-0.012	0.006	15.367	-0.356	-0.356	0.000	0.000	0.000	0.000
29	H	29	LYS	1	0.896	0.952	16.293	13.941	13.941	0.000	0.000	0.000	0.000
30	H	30	ALA	0	0.032	0.034	17.200	0.587	0.587	0.000	0.000	0.000	0.000
31	H	31	GLN	0	0.000	-0.002	12.210	1.397	1.397	0.000	0.000	0.000	0.000
32	H	32	ILE	0	-0.042	-0.021	16.719	0.377	0.377	0.000	0.000	0.000	0.000
33	H	33	THR	0	-0.059	-0.045	19.629	0.468	0.468	0.000	0.000	0.000	0.000
34	H	34	GLN	0	-0.024	-0.005	17.255	0.861	0.861	0.000	0.000	0.000	0.000
35	H	35	LYS	1	0.890	0.962	16.379	17.295	17.295	0.000	0.000	0.000	0.000
36	H	36	ILE	0	-0.023	-0.015	20.693	0.482	0.482	0.000	0.000	0.000	0.000
37	H	37	GLY	0	0.014	0.023	23.762	0.548	0.548	0.000	0.000	0.000	0.000
38	H	38	VAL	0	-0.070	-0.035	25.071	0.587	0.587	0.000	0.000	0.000	0.000
39	H	39	HIS	0	0.106	0.053	25.167	-0.834	-0.834	0.000	0.000	0.000	0.000
40	H	40	ALA	0	0.088	0.046	22.955	0.072	0.072	0.000	0.000	0.000	0.000
41	H	41	PHE	0	-0.004	0.005	24.612	-0.062	-0.062	0.000	0.000	0.000	0.000
42	H	42	GLN	0	-0.037	0.000	27.852	0.201	0.201	0.000	0.000	0.000	0.000
43	H	43	GLN	0	-0.024	-0.009	22.478	-0.270	-0.270	0.000	0.000	0.000	0.000
44	H	44	ARG	1	0.780	0.842	26.206	10.481	10.481	0.000	0.000	0.000	0.000
45	H	45	LEU	0	0.010	0.004	20.306	-0.040	-0.040	0.000	0.000	0.000	0.000
46	H	46	ALA	0	0.016	0.023	23.993	0.108	0.108	0.000	0.000	0.000	0.000
47	H	47	VAL	0	0.038	0.024	20.199	-0.369	-0.369	0.000	0.000	0.000	0.000
48	H	48	HIS	0	-0.022	0.028	21.401	1.235	1.235	0.000	0.000	0.000	0.000
49	H	49	PRO	0	0.010	-0.018	21.778	-0.628	-0.628	0.000	0.000	0.000	0.000
50	H	50	SER	0	-0.002	-0.020	23.432	0.386	0.386	0.000	0.000	0.000	0.000
51	H	51	GLY	0	0.039	0.021	25.307	0.449	0.449	0.000	0.000	0.000	0.000
52	H	52	VAL	0	-0.050	-0.015	23.563	0.419	0.419	0.000	0.000	0.000	0.000
53	H	53	ALA	0	0.015	-0.007	24.500	-0.476	-0.476	0.000	0.000	0.000	0.000
54	H	54	LEU	0	-0.002	-0.002	18.991	-0.270	-0.270	0.000	0.000	0.000	0.000
55	H	55	GLN	0	-0.032	-0.021	20.814	0.251	0.251	0.000	0.000	0.000	0.000
56	H	56	ASP	-1	-0.854	-0.943	20.128	-14.256	-14.256	0.000	0.000	0.000	0.000
57	H	57	ARG	1	0.874	0.929	19.155	14.556	14.556	0.000	0.000	0.000	0.000
58	H	58	VAL	0	0.006	0.019	16.968	-0.932	-0.932	0.000	0.000	0.000	0.000
59	H	59	PRO	0	0.047	0.021	12.114	0.365	0.365	0.000	0.000	0.000	0.000
60	H	60	LEU	0	0.002	-0.012	13.029	0.664	0.664	0.000	0.000	0.000	0.000
61	H	61	ALA	0	-0.011	-0.002	9.784	0.440	0.440	0.000	0.000	0.000	0.000
62	H	62	SER	0	-0.056	-0.019	11.863	0.256	0.256	0.000	0.000	0.000	0.000
63	H	63	GLN	0	-0.046	-0.010	14.923	1.964	1.964	0.000	0.000	0.000	0.000
64	H	64	GLY	0	0.008	0.002	16.434	-0.416	-0.416	0.000	0.000	0.000	0.000
65	H	65	LEU	0	-0.041	-0.013	14.697	-0.125	-0.125	0.000	0.000	0.000	0.000
66	H	66	GLY	0	0.102	0.052	11.327	-1.152	-1.152	0.000	0.000	0.000	0.000
67	H	67	PRO	0	-0.031	-0.025	8.349	0.845	0.845	0.000	0.000	0.000	0.000
68	H	68	GLY	0	0.009	0.013	10.414	1.169	1.169	0.000	0.000	0.000	0.000
69	H	69	SER	0	-0.047	-0.012	13.647	1.693	1.693	0.000	0.000	0.000	0.000
70	H	70	THR	0	0.022	-0.002	15.792	-0.272	-0.272	0.000	0.000	0.000	0.000
71	H	71	VAL	0	-0.026	-0.018	18.334	0.083	0.083	0.000	0.000	0.000	0.000
72	H	72	LEU	0	-0.015	-0.012	20.267	0.141	0.141	0.000	0.000	0.000	0.000
73	H	73	LEU	0	-0.008	-0.012	22.450	-0.110	-0.110	0.000	0.000	0.000	0.000
74	H	74	VAL	0	-0.002	-0.010	24.705	0.393	0.393	0.000	0.000	0.000	0.000
75	H	75	VAL	0	-0.013	-0.007	27.278	-0.264	-0.264	0.000	0.000	0.000	0.000
76	H	76	ASP	-1	-0.839	-0.911	29.520	-9.136	-9.136	0.000	0.000	0.000	0.000
77	H	77	LYS	1	0.950	0.961	30.520	9.978	9.978	0.000	0.000	0.000	0.000
78	H	78	CYS	0	-0.027	0.007	34.056	0.278	0.278	0.000	0.000	0.000	0.000
79	H	79	ASP	-1	-0.760	-0.880	35.941	-8.864	-8.864	0.000	0.000	0.000	0.000
80	H	80	GLU	-1	-0.915	-0.944	38.219	-7.227	-7.227	0.000	0.000	0.000	0.000
81	H	81	PRO	0	-0.062	-0.014	40.682	-0.165	-0.165	0.000	0.000	0.000	0.000
82	H	82	LEU	0	-0.015	-0.011	38.218	0.045	0.045	0.000	0.000	0.000	0.000
83	H	83	SER	0	0.021	0.004	42.889	0.036	0.036	0.000	0.000	0.000	0.000
84	H	84	ILE	0	-0.022	-0.003	39.085	-0.125	-0.125	0.000	0.000	0.000	0.000
85	H	85	LEU	0	-0.016	-0.018	42.381	0.219	0.219	0.000	0.000	0.000	0.000
86	H	86	VAL	0	0.033	0.016	41.175	-0.224	-0.224	0.000	0.000	0.000	0.000
87	H	87	ARG	1	0.855	0.951	43.119	7.315	7.315	0.000	0.000	0.000	0.000
88	H	88	ASN	0	0.053	0.015	43.597	-0.170	-0.170	0.000	0.000	0.000	0.000
89	H	89	ASN	0	0.065	0.002	45.589	-0.010	-0.010	0.000	0.000	0.000	0.000
90	H	90	LYS	1	0.825	0.918	46.607	6.548	6.548	0.000	0.000	0.000	0.000
91	H	91	GLY	0	0.029	0.028	47.759	0.110	0.110	0.000	0.000	0.000	0.000
92	H	92	ARG	1	0.841	0.910	48.796	6.311	6.311	0.000	0.000	0.000	0.000
93	H	93	SER	0	0.024	-0.004	46.195	-0.094	-0.094	0.000	0.000	0.000	0.000
94	H	94	SER	0	-0.009	0.011	46.999	0.241	0.241	0.000	0.000	0.000	0.000
95	H	95	THR	0	0.025	-0.002	46.491	-0.175	-0.175	0.000	0.000	0.000	0.000
96	H	96	TYR	0	0.004	0.008	43.687	0.129	0.129	0.000	0.000	0.000	0.000
97	H	97	GLU	-1	-0.866	-0.908	44.373	-6.976	-6.976	0.000	0.000	0.000	0.000
98	H	98	VAL	0	-0.020	-0.010	39.446	-0.022	-0.022	0.000	0.000	0.000	0.000
99	H	99	ARG	1	0.927	0.953	38.895	7.707	7.707	0.000	0.000	0.000	0.000
100	H	100	LEU	0	0.024	0.007	33.943	-0.116	-0.116	0.000	0.000	0.000	0.000
101	H	101	THR	0	-0.049	-0.061	33.616	-0.294	-0.294	0.000	0.000	0.000	0.000
102	H	102	GLN	0	-0.018	0.010	34.164	-0.183	-0.183	0.000	0.000	0.000	0.000
103	H	103	THR	0	0.031	0.002	32.669	-0.008	-0.008	0.000	0.000	0.000	0.000
104	H	104	VAL	0	0.029	0.013	32.052	0.345	0.345	0.000	0.000	0.000	0.000
105	H	105	ALA	0	-0.003	0.000	34.938	0.263	0.263	0.000	0.000	0.000	0.000
106	H	106	HIS	0	-0.029	-0.004	36.824	0.328	0.328	0.000	0.000	0.000	0.000
107	H	107	LEU	0	0.021	0.012	37.818	0.236	0.236	0.000	0.000	0.000	0.000
108	H	108	LYS	1	0.827	0.886	36.061	8.916	8.916	0.000	0.000	0.000	0.000
109	H	109	GLN	0	-0.030	-0.028	40.238	0.295	0.295	0.000	0.000	0.000	0.000
110	H	110	GLN	0	-0.010	-0.004	42.897	0.074	0.074	0.000	0.000	0.000	0.000
111	H	111	VAL	0	-0.013	-0.010	42.001	0.172	0.172	0.000	0.000	0.000	0.000
112	H	112	SER	0	-0.086	-0.051	44.192	0.164	0.164	0.000	0.000	0.000	0.000
113	H	113	GLY	0	0.015	0.005	45.848	0.143	0.143	0.000	0.000	0.000	0.000
114	H	114	LEU	0	-0.054	-0.016	48.385	0.147	0.147	0.000	0.000	0.000	0.000
115	H	115	GLU	-1	-0.806	-0.892	46.823	-6.441	-6.441	0.000	0.000	0.000	0.000
116	H	116	GLY	0	0.004	0.024	49.519	0.101	0.101	0.000	0.000	0.000	0.000
117	H	117	VAL	0	-0.061	-0.038	45.561	0.052	0.052	0.000	0.000	0.000	0.000
118	H	118	GLN	0	0.053	0.039	45.218	0.017	0.017	0.000	0.000	0.000	0.000
119	H	119	ASP	-1	-0.778	-0.894	40.936	-7.729	-7.729	0.000	0.000	0.000	0.000
120	H	120	ASP	-1	-0.895	-0.933	39.392	-7.896	-7.896	0.000	0.000	0.000	0.000
121	H	121	LEU	0	-0.044	-0.027	40.518	-0.043	-0.043	0.000	0.000	0.000	0.000
122	H	122	PHE	0	-0.048	-0.030	40.290	0.039	0.039	0.000	0.000	0.000	0.000
123	H	123	TRP	0	-0.027	-0.013	33.399	-0.236	-0.236	0.000	0.000	0.000	0.000
124	H	124	LEU	0	0.040	0.020	35.971	0.195	0.195	0.000	0.000	0.000	0.000
125	H	125	THR	0	0.011	-0.003	33.379	-0.290	-0.290	0.000	0.000	0.000	0.000
126	H	126	PHE	0	0.030	0.014	32.511	0.383	0.383	0.000	0.000	0.000	0.000
127	H	127	GLU	-1	-0.876	-0.937	30.974	-10.677	-10.677	0.000	0.000	0.000	0.000
128	H	128	GLY	0	-0.021	-0.012	31.313	-0.313	-0.313	0.000	0.000	0.000	0.000
129	H	129	LYS	1	0.842	0.930	26.865	10.862	10.862	0.000	0.000	0.000	0.000
130	H	130	PRO	0	0.006	-0.010	28.705	0.304	0.304	0.000	0.000	0.000	0.000
131	H	131	LEU	0	-0.031	-0.008	29.558	-0.337	-0.337	0.000	0.000	0.000	0.000
132	H	132	GLU	-1	-0.914	-0.963	25.631	-12.002	-12.002	0.000	0.000	0.000	0.000
133	H	133	ASP	-1	-0.788	-0.858	30.261	-9.131	-9.131	0.000	0.000	0.000	0.000
134	H	134	GLN	0	0.025	0.000	26.941	0.578	0.578	0.000	0.000	0.000	0.000
135	H	135	LEU	0	0.006	0.014	25.396	-0.101	-0.101	0.000	0.000	0.000	0.000
136	H	136	PRO	0	0.013	0.006	28.414	0.395	0.395	0.000	0.000	0.000	0.000
137	H	137	LEU	0	0.035	0.012	30.735	-0.277	-0.277	0.000	0.000	0.000	0.000
138	H	138	GLY	0	0.024	-0.004	31.691	-0.063	-0.063	0.000	0.000	0.000	0.000
139	H	139	GLU	-1	-0.891	-0.954	25.604	-12.247	-12.247	0.000	0.000	0.000	0.000
140	H	140	TYR	0	-0.016	-0.003	27.345	-0.333	-0.333	0.000	0.000	0.000	0.000
141	H	141	GLY	0	-0.012	0.006	30.029	0.154	0.154	0.000	0.000	0.000	0.000
142	H	142	LEU	0	-0.019	-0.001	31.521	0.228	0.228	0.000	0.000	0.000	0.000
143	H	143	LYS	1	0.896	0.932	33.050	9.562	9.562	0.000	0.000	0.000	0.000
144	H	144	PRO	0	0.050	0.009	37.938	0.081	0.081	0.000	0.000	0.000	0.000
145	H	145	LEU	0	-0.026	-0.008	41.695	-0.011	-0.011	0.000	0.000	0.000	0.000
146	H	146	SER	0	0.000	0.023	37.939	-0.103	-0.103	0.000	0.000	0.000	0.000
147	H	147	THR	0	-0.037	-0.023	39.868	0.236	0.236	0.000	0.000	0.000	0.000
148	H	148	VAL	0	-0.008	-0.005	36.946	-0.215	-0.215	0.000	0.000	0.000	0.000
149	H	149	PHE	0	-0.040	-0.018	37.968	0.301	0.301	0.000	0.000	0.000	0.000
150	H	150	MET	0	0.043	0.033	38.729	-0.175	-0.175	0.000	0.000	0.000	0.000
151	H	151	ASN	0	-0.059	-0.027	37.898	-0.002	-0.002	0.000	0.000	0.000	0.000
152	H	152	LEU	0	0.059	0.024	40.461	-0.071	-0.071	0.000	0.000	0.000	0.000
153	H	153	ARG	1	0.859	0.951	35.432	8.423	8.423	0.000	0.000	0.000	0.000
154	H	154	LEU	0	0.028	0.013	40.556	0.179	0.179	0.000	0.000	0.000	0.000
155	H	155	ARG	1	0.842	0.899	39.271	7.591	7.591	0.000	0.000	0.000	0.000
156	H	156	GLY	0	-0.013	0.003	40.037	0.192	0.192	0.000	0.000	0.000	0.000
157	H	157	GLY	-1	-0.913	-0.945	39.530	-7.762	-7.762	0.000	0.000	0.000	0.000
158	H	201	HOH	0	-0.042	-0.041	33.585	0.115	0.115	0.000	0.000	0.000	0.000
159	H	202	HOH	0	-0.029	-0.028	46.575	-0.025	-0.025	0.000	0.000	0.000	0.000

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