FMO DATABASE

FMODB ID: N113Q

Calculation Name: 7RBS-D-Xray89

Preferred Name:

Target Type:

Ligand Name: zinc ion

ligand 3-letter code: ZN

PDB ID: 7RBS

Chain ID: D

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	160
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-1364622.3501
FMO2-HF: Nuclear repulsion	1304802.760809
FMO2-HF: Total energy	-59819.589291
FMO2-MP2: Total energy	-59995.05142

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(D:1:ALA )

Summations of interaction energy for fragment #1(D: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.
-11.244	-9.781	0.005	-0.779	-0.689	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.914

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	D	3	TRP	0	-0.023	-0.013	3.652	-4.312	-2.849	0.005	-0.779	-0.689	-0.002
4	D	4	ASP	-1	-0.756	-0.850	6.363	-25.858	-25.858	0.000	0.000	0.000	0.000
5	D	5	LEU	0	-0.029	-0.006	9.686	0.020	0.020	0.000	0.000	0.000	0.000
6	D	6	THR	0	0.025	0.008	13.244	-0.002	-0.002	0.000	0.000	0.000	0.000
7	D	7	VAL	0	0.018	0.004	16.660	0.154	0.154	0.000	0.000	0.000	0.000
8	D	8	LYS	1	0.865	0.923	19.610	12.341	12.341	0.000	0.000	0.000	0.000
9	D	9	MET	0	0.010	0.018	23.099	0.015	0.015	0.000	0.000	0.000	0.000
10	D	10	LEU	0	0.040	0.010	26.015	0.084	0.084	0.000	0.000	0.000	0.000
11	D	11	ALA	0	-0.033	-0.012	29.070	0.296	0.296	0.000	0.000	0.000	0.000
12	D	12	GLY	0	0.017	0.023	28.882	0.286	0.286	0.000	0.000	0.000	0.000
13	D	13	ASN	0	-0.037	-0.025	25.875	-0.091	-0.091	0.000	0.000	0.000	0.000
14	D	14	GLU	-1	-0.829	-0.907	21.121	-13.429	-13.429	0.000	0.000	0.000	0.000
15	D	15	PHE	0	-0.014	-0.018	18.322	0.237	0.237	0.000	0.000	0.000	0.000
16	D	16	GLN	0	-0.020	-0.015	12.269	0.804	0.804	0.000	0.000	0.000	0.000
17	D	17	VAL	0	-0.025	-0.007	13.610	0.766	0.766	0.000	0.000	0.000	0.000
18	D	18	SER	0	0.013	0.001	8.730	-0.332	-0.332	0.000	0.000	0.000	0.000
19	D	19	LEU	0	-0.018	-0.008	8.743	1.962	1.962	0.000	0.000	0.000	0.000
20	D	20	SER	0	0.033	-0.023	6.293	-5.489	-5.489	0.000	0.000	0.000	0.000
21	D	21	SER	0	0.008	0.005	6.006	3.258	3.258	0.000	0.000	0.000	0.000
22	D	22	SER	0	0.008	-0.011	7.676	2.669	2.669	0.000	0.000	0.000	0.000
23	D	23	MET	0	-0.045	0.022	10.182	1.992	1.992	0.000	0.000	0.000	0.000
24	D	24	SER	0	0.032	0.006	12.247	0.034	0.034	0.000	0.000	0.000	0.000
25	D	25	VAL	0	0.022	0.004	15.802	-0.334	-0.334	0.000	0.000	0.000	0.000
26	D	26	SER	0	0.011	0.007	18.846	0.465	0.465	0.000	0.000	0.000	0.000
27	D	27	GLU	-1	-0.818	-0.918	14.335	-18.848	-18.848	0.000	0.000	0.000	0.000
28	D	28	LEU	0	-0.003	0.016	15.786	-0.243	-0.243	0.000	0.000	0.000	0.000
29	D	29	LYS	1	0.949	0.974	16.800	14.020	14.020	0.000	0.000	0.000	0.000
30	D	30	ALA	0	0.010	0.014	17.905	0.526	0.526	0.000	0.000	0.000	0.000
31	D	31	GLN	0	-0.029	-0.038	12.480	1.692	1.692	0.000	0.000	0.000	0.000
32	D	32	ILE	0	-0.053	-0.021	17.349	0.401	0.401	0.000	0.000	0.000	0.000
33	D	33	THR	0	-0.066	-0.050	20.146	0.442	0.442	0.000	0.000	0.000	0.000
34	D	34	GLN	0	-0.012	0.015	18.392	0.236	0.236	0.000	0.000	0.000	0.000
35	D	35	LYS	1	0.878	0.954	16.395	17.619	17.619	0.000	0.000	0.000	0.000
36	D	36	ILE	0	-0.015	-0.018	21.452	0.517	0.517	0.000	0.000	0.000	0.000
37	D	37	GLY	0	0.034	0.038	24.416	0.530	0.530	0.000	0.000	0.000	0.000
38	D	38	VAL	0	-0.079	-0.051	25.690	0.628	0.628	0.000	0.000	0.000	0.000
39	D	39	HIS	0	0.081	0.044	25.871	-0.836	-0.836	0.000	0.000	0.000	0.000
40	D	40	ALA	0	0.069	0.028	23.806	0.042	0.042	0.000	0.000	0.000	0.000
41	D	41	PHE	0	-0.004	0.003	25.449	-0.059	-0.059	0.000	0.000	0.000	0.000
42	D	42	GLN	0	-0.013	-0.008	28.472	0.246	0.246	0.000	0.000	0.000	0.000
43	D	43	GLN	0	-0.023	-0.011	23.090	-0.282	-0.282	0.000	0.000	0.000	0.000
44	D	44	ARG	1	0.805	0.889	26.671	10.251	10.251	0.000	0.000	0.000	0.000
45	D	45	LEU	0	0.019	0.005	20.807	-0.090	-0.090	0.000	0.000	0.000	0.000
46	D	46	ALA	0	0.030	0.017	24.176	0.133	0.133	0.000	0.000	0.000	0.000
47	D	47	VAL	0	0.023	0.021	20.092	-0.322	-0.322	0.000	0.000	0.000	0.000
48	D	48	HIS	0	0.012	0.048	21.403	0.903	0.903	0.000	0.000	0.000	0.000
49	D	49	PRO	0	-0.003	-0.037	21.594	-0.620	-0.620	0.000	0.000	0.000	0.000
50	D	50	SER	0	-0.021	-0.017	23.486	0.374	0.374	0.000	0.000	0.000	0.000
51	D	51	GLY	0	0.069	0.032	25.232	0.481	0.481	0.000	0.000	0.000	0.000
52	D	52	VAL	0	-0.069	-0.026	23.893	0.362	0.362	0.000	0.000	0.000	0.000
53	D	53	ALA	0	0.007	-0.007	24.421	-0.535	-0.535	0.000	0.000	0.000	0.000
54	D	54	LEU	0	0.000	0.001	19.515	-0.208	-0.208	0.000	0.000	0.000	0.000
55	D	55	GLN	0	-0.024	-0.021	21.287	0.479	0.479	0.000	0.000	0.000	0.000
56	D	56	ASP	-1	-0.878	-0.954	20.635	-14.018	-14.018	0.000	0.000	0.000	0.000
57	D	57	ARG	1	0.928	0.965	20.260	14.207	14.207	0.000	0.000	0.000	0.000
58	D	58	VAL	0	0.002	0.010	17.211	-0.866	-0.866	0.000	0.000	0.000	0.000
59	D	59	PRO	0	0.038	0.025	12.587	0.443	0.443	0.000	0.000	0.000	0.000
60	D	60	LEU	0	-0.018	-0.022	13.510	0.719	0.719	0.000	0.000	0.000	0.000
61	D	61	ALA	0	0.015	0.006	9.933	0.417	0.417	0.000	0.000	0.000	0.000
62	D	62	SER	0	-0.059	-0.016	11.830	0.161	0.161	0.000	0.000	0.000	0.000
63	D	63	GLN	0	-0.018	0.006	14.696	1.786	1.786	0.000	0.000	0.000	0.000
64	D	64	GLY	0	0.020	0.007	15.897	-0.623	-0.623	0.000	0.000	0.000	0.000
65	D	65	LEU	0	-0.043	-0.011	14.637	-0.169	-0.169	0.000	0.000	0.000	0.000
66	D	66	GLY	0	0.098	0.051	11.101	-1.270	-1.270	0.000	0.000	0.000	0.000
67	D	67	PRO	0	-0.036	-0.026	7.854	0.818	0.818	0.000	0.000	0.000	0.000
68	D	68	GLY	0	0.002	0.013	10.272	1.016	1.016	0.000	0.000	0.000	0.000
69	D	69	SER	0	-0.047	-0.020	13.626	1.513	1.513	0.000	0.000	0.000	0.000
70	D	70	THR	0	0.014	-0.008	15.711	-0.229	-0.229	0.000	0.000	0.000	0.000
71	D	71	VAL	0	-0.021	-0.004	18.425	0.217	0.217	0.000	0.000	0.000	0.000
72	D	72	LEU	0	-0.011	-0.004	20.286	0.128	0.128	0.000	0.000	0.000	0.000
73	D	73	LEU	0	0.000	-0.008	22.830	-0.054	-0.054	0.000	0.000	0.000	0.000
74	D	74	VAL	0	-0.005	-0.016	24.867	0.374	0.374	0.000	0.000	0.000	0.000
75	D	75	VAL	0	-0.022	-0.007	27.962	-0.130	-0.130	0.000	0.000	0.000	0.000
76	D	76	ASP	-1	-0.824	-0.896	29.940	-9.006	-9.006	0.000	0.000	0.000	0.000
77	D	77	LYS	1	0.902	0.944	31.113	9.866	9.866	0.000	0.000	0.000	0.000
78	D	78	CYS	0	-0.013	0.012	34.640	0.300	0.300	0.000	0.000	0.000	0.000
79	D	79	ASP	-1	-0.789	-0.893	36.843	-8.730	-8.730	0.000	0.000	0.000	0.000
80	D	80	GLU	-1	-0.892	-0.940	38.834	-7.175	-7.175	0.000	0.000	0.000	0.000
81	D	81	PRO	0	-0.054	-0.011	41.206	-0.172	-0.172	0.000	0.000	0.000	0.000
82	D	82	LEU	0	-0.004	-0.008	39.152	0.043	0.043	0.000	0.000	0.000	0.000
83	D	83	SER	0	0.011	0.008	43.475	0.080	0.080	0.000	0.000	0.000	0.000
84	D	84	ILE	0	-0.003	0.009	39.735	-0.108	-0.108	0.000	0.000	0.000	0.000
85	D	85	LEU	0	-0.006	-0.011	42.831	0.218	0.218	0.000	0.000	0.000	0.000
86	D	86	VAL	0	0.023	0.009	41.703	-0.230	-0.230	0.000	0.000	0.000	0.000
87	D	87	ARG	1	0.861	0.948	43.315	7.185	7.185	0.000	0.000	0.000	0.000
88	D	88	ASN	0	0.046	0.003	43.894	-0.146	-0.146	0.000	0.000	0.000	0.000
89	D	89	ASN	0	0.057	0.002	46.025	-0.010	-0.010	0.000	0.000	0.000	0.000
90	D	90	LYS	1	0.852	0.936	46.846	6.433	6.433	0.000	0.000	0.000	0.000
91	D	91	GLY	0	0.036	0.035	47.882	0.093	0.093	0.000	0.000	0.000	0.000
92	D	92	ARG	1	0.845	0.919	48.957	6.277	6.277	0.000	0.000	0.000	0.000
93	D	93	SER	0	0.010	-0.015	46.745	-0.084	-0.084	0.000	0.000	0.000	0.000
94	D	94	SER	0	-0.007	0.009	47.379	0.229	0.229	0.000	0.000	0.000	0.000
95	D	95	THR	0	0.017	-0.004	46.925	-0.195	-0.195	0.000	0.000	0.000	0.000
96	D	96	TYR	0	0.004	0.002	44.391	0.135	0.135	0.000	0.000	0.000	0.000
97	D	97	GLU	-1	-0.936	-0.957	44.943	-6.932	-6.932	0.000	0.000	0.000	0.000
98	D	98	VAL	0	-0.014	-0.005	40.234	-0.017	-0.017	0.000	0.000	0.000	0.000
99	D	99	ARG	1	0.912	0.946	39.519	7.705	7.705	0.000	0.000	0.000	0.000
100	D	100	LEU	0	0.009	0.007	34.506	-0.104	-0.104	0.000	0.000	0.000	0.000
101	D	101	THR	0	-0.054	-0.059	34.349	-0.288	-0.288	0.000	0.000	0.000	0.000
102	D	102	GLN	0	-0.007	0.009	34.921	-0.085	-0.085	0.000	0.000	0.000	0.000
103	D	103	THR	0	0.036	0.007	33.587	-0.023	-0.023	0.000	0.000	0.000	0.000
104	D	104	VAL	0	0.017	0.015	32.786	0.312	0.312	0.000	0.000	0.000	0.000
105	D	105	ALA	0	-0.006	0.002	35.699	0.256	0.256	0.000	0.000	0.000	0.000
106	D	106	HIS	0	0.020	0.024	37.706	0.157	0.157	0.000	0.000	0.000	0.000
107	D	107	LEU	0	0.035	0.022	38.557	0.233	0.233	0.000	0.000	0.000	0.000
108	D	108	LYS	1	0.835	0.894	36.763	8.852	8.852	0.000	0.000	0.000	0.000
109	D	109	GLN	0	0.015	0.007	41.018	0.102	0.102	0.000	0.000	0.000	0.000
110	D	110	GLN	0	-0.011	-0.012	43.063	0.325	0.325	0.000	0.000	0.000	0.000
111	D	111	VAL	0	-0.031	-0.023	42.618	0.172	0.172	0.000	0.000	0.000	0.000
112	D	112	SER	0	-0.085	-0.054	44.885	0.166	0.166	0.000	0.000	0.000	0.000
113	D	113	GLY	0	0.008	0.003	46.574	0.140	0.140	0.000	0.000	0.000	0.000
114	D	114	LEU	0	-0.056	-0.017	49.078	0.165	0.165	0.000	0.000	0.000	0.000
115	D	115	GLU	-1	-0.820	-0.899	47.115	-6.436	-6.436	0.000	0.000	0.000	0.000
116	D	116	GLY	0	-0.020	0.015	49.947	0.084	0.084	0.000	0.000	0.000	0.000
117	D	117	VAL	0	-0.051	-0.027	46.309	0.058	0.058	0.000	0.000	0.000	0.000
118	D	118	GLN	0	0.049	0.037	45.791	-0.001	-0.001	0.000	0.000	0.000	0.000
119	D	119	ASP	-1	-0.848	-0.931	41.772	-7.728	-7.728	0.000	0.000	0.000	0.000
120	D	120	ASP	-1	-0.826	-0.906	40.218	-7.876	-7.876	0.000	0.000	0.000	0.000
121	D	121	LEU	0	-0.009	-0.009	41.191	-0.110	-0.110	0.000	0.000	0.000	0.000
122	D	122	PHE	0	-0.046	-0.020	40.854	0.047	0.047	0.000	0.000	0.000	0.000
123	D	123	TRP	0	-0.045	-0.020	33.576	-0.241	-0.241	0.000	0.000	0.000	0.000
124	D	124	LEU	0	0.048	0.023	36.296	0.209	0.209	0.000	0.000	0.000	0.000
125	D	125	THR	0	-0.002	-0.011	33.624	-0.299	-0.299	0.000	0.000	0.000	0.000
126	D	126	PHE	0	0.012	0.001	32.803	0.415	0.415	0.000	0.000	0.000	0.000
127	D	127	GLU	-1	-0.833	-0.890	32.164	-10.144	-10.144	0.000	0.000	0.000	0.000
128	D	128	GLY	0	-0.011	-0.002	31.654	-0.286	-0.286	0.000	0.000	0.000	0.000
129	D	129	LYS	1	0.838	0.927	25.484	11.951	11.951	0.000	0.000	0.000	0.000
130	D	130	PRO	0	-0.027	-0.014	28.956	0.305	0.305	0.000	0.000	0.000	0.000
131	D	131	LEU	0	-0.008	-0.011	29.952	-0.368	-0.368	0.000	0.000	0.000	0.000
132	D	132	GLU	-1	-0.813	-0.889	26.415	-11.845	-11.845	0.000	0.000	0.000	0.000
133	D	133	ASP	-1	-0.799	-0.889	30.918	-9.064	-9.064	0.000	0.000	0.000	0.000
134	D	134	GLN	0	0.035	0.003	27.271	0.527	0.527	0.000	0.000	0.000	0.000
135	D	135	LEU	0	-0.017	0.004	26.057	-0.082	-0.082	0.000	0.000	0.000	0.000
136	D	136	PRO	0	-0.011	0.003	29.139	0.381	0.381	0.000	0.000	0.000	0.000
137	D	137	LEU	0	0.043	0.015	31.452	-0.283	-0.283	0.000	0.000	0.000	0.000
138	D	138	GLY	0	0.012	-0.003	32.483	-0.063	-0.063	0.000	0.000	0.000	0.000
139	D	139	GLU	-1	-0.939	-0.974	25.115	-12.658	-12.658	0.000	0.000	0.000	0.000
140	D	140	TYR	0	-0.064	-0.055	27.985	-0.372	-0.372	0.000	0.000	0.000	0.000
141	D	141	GLY	0	0.011	0.016	30.438	0.189	0.189	0.000	0.000	0.000	0.000
142	D	142	LEU	0	-0.029	-0.005	31.663	0.249	0.249	0.000	0.000	0.000	0.000
143	D	143	LYS	1	0.884	0.933	33.648	9.455	9.455	0.000	0.000	0.000	0.000
144	D	144	PRO	0	0.056	0.017	38.042	0.080	0.080	0.000	0.000	0.000	0.000
145	D	145	LEU	0	-0.020	-0.015	41.824	-0.029	-0.029	0.000	0.000	0.000	0.000
146	D	146	SER	0	-0.032	-0.006	38.243	-0.047	-0.047	0.000	0.000	0.000	0.000
147	D	147	THR	0	-0.048	-0.025	40.265	0.202	0.202	0.000	0.000	0.000	0.000
148	D	148	VAL	0	0.003	0.005	37.216	-0.215	-0.215	0.000	0.000	0.000	0.000
149	D	149	PHE	0	-0.027	-0.019	38.476	0.352	0.352	0.000	0.000	0.000	0.000
150	D	150	MET	0	0.030	0.023	39.096	-0.188	-0.188	0.000	0.000	0.000	0.000
151	D	151	ASN	0	-0.035	-0.010	38.100	-0.002	-0.002	0.000	0.000	0.000	0.000
152	D	152	LEU	0	0.044	0.010	40.948	-0.049	-0.049	0.000	0.000	0.000	0.000
153	D	153	ARG	1	0.859	0.932	35.871	8.435	8.435	0.000	0.000	0.000	0.000
154	D	154	LEU	0	0.026	0.015	40.783	0.188	0.188	0.000	0.000	0.000	0.000
155	D	155	ARG	1	0.794	0.870	39.853	7.534	7.534	0.000	0.000	0.000	0.000
156	D	156	GLY	0	-0.014	0.003	40.506	0.186	0.186	0.000	0.000	0.000	0.000
157	D	157	GLY	-1	-0.915	-0.944	39.803	-7.907	-7.907	0.000	0.000	0.000	0.000
158	D	201	HOH	0	-0.043	-0.028	24.228	0.200	0.200	0.000	0.000	0.000	0.000
159	D	202	HOH	0	-0.055	-0.051	32.059	0.038	0.038	0.000	0.000	0.000	0.000
160	D	203	HOH	0	-0.018	-0.011	25.181	0.010	0.010	0.000	0.000	0.000	0.000

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