FMO DATABASE

FMODB ID: 7GGJK

Calculation Name: 7RBS-F-Xray89

Preferred Name:

Target Type:

Ligand Name: zinc ion

ligand 3-letter code: ZN

PDB ID: 7RBS

Chain ID: F

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	-1356918.057351
FMO2-HF: Nuclear repulsion	1297250.909331
FMO2-HF: Total energy	-59667.148021
FMO2-MP2: Total energy	-59842.228763

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(F:1:ALA )

Summations of interaction energy for fragment #1(F: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.
1.737	3.523	0.015	-0.641	-1.161	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.014

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	F	3	TRP	0	-0.051	-0.021	3.849	1.363	2.553	-0.017	-0.494	-0.679	0.001
4	F	4	ASP	-1	-0.774	-0.867	6.196	0.120	0.120	0.000	0.000	0.000	0.000
5	F	5	LEU	0	-0.028	-0.010	10.054	0.001	0.001	0.000	0.000	0.000	0.000
6	F	6	THR	0	-0.004	-0.010	12.836	0.002	0.002	0.000	0.000	0.000	0.000
7	F	7	VAL	0	-0.005	-0.015	16.548	-0.027	-0.027	0.000	0.000	0.000	0.000
8	F	8	LYS	1	0.878	0.938	19.277	-0.046	-0.046	0.000	0.000	0.000	0.000
9	F	9	MET	0	0.021	0.028	22.735	-0.013	-0.013	0.000	0.000	0.000	0.000
10	F	10	LEU	0	0.045	0.002	25.794	0.005	0.005	0.000	0.000	0.000	0.000
11	F	11	ALA	0	-0.040	-0.006	29.243	0.001	0.001	0.000	0.000	0.000	0.000
12	F	12	GLY	0	-0.006	0.007	28.438	0.003	0.003	0.000	0.000	0.000	0.000
13	F	13	ASN	0	-0.036	-0.026	25.908	0.002	0.002	0.000	0.000	0.000	0.000
14	F	14	GLU	-1	-0.846	-0.914	21.424	0.072	0.072	0.000	0.000	0.000	0.000
15	F	15	PHE	0	-0.034	-0.022	18.834	0.005	0.005	0.000	0.000	0.000	0.000
16	F	16	GLN	0	0.020	0.017	13.717	-0.044	-0.044	0.000	0.000	0.000	0.000
17	F	17	VAL	0	-0.015	-0.013	13.556	-0.015	-0.015	0.000	0.000	0.000	0.000
18	F	18	SER	0	0.022	0.005	9.680	0.024	0.024	0.000	0.000	0.000	0.000
19	F	19	LEU	0	-0.013	-0.005	8.686	-0.066	-0.066	0.000	0.000	0.000	0.000
20	F	20	SER	0	0.052	-0.007	5.196	-0.106	-0.053	-0.001	-0.020	-0.032	0.000
21	F	21	SER	0	0.017	0.008	3.140	-0.044	0.423	0.034	-0.122	-0.380	0.000
22	F	22	SER	0	-0.017	-0.019	4.908	0.322	0.398	-0.001	-0.005	-0.070	0.000
23	F	23	MET	0	-0.052	0.017	7.930	0.137	0.137	0.000	0.000	0.000	0.000
24	F	24	SER	0	0.039	0.024	10.046	0.028	0.028	0.000	0.000	0.000	0.000
25	F	25	VAL	0	0.020	0.000	13.304	0.005	0.005	0.000	0.000	0.000	0.000
26	F	26	SER	0	-0.038	-0.033	16.282	0.036	0.036	0.000	0.000	0.000	0.000
27	F	27	GLU	-1	-0.782	-0.894	13.348	-0.307	-0.307	0.000	0.000	0.000	0.000
28	F	28	LEU	0	0.003	0.009	14.431	0.021	0.021	0.000	0.000	0.000	0.000
29	F	29	LYS	1	0.965	0.991	15.605	0.144	0.144	0.000	0.000	0.000	0.000
30	F	30	ALA	0	0.015	0.022	17.421	0.024	0.024	0.000	0.000	0.000	0.000
31	F	31	GLN	0	-0.015	-0.014	12.169	0.073	0.073	0.000	0.000	0.000	0.000
32	F	32	ILE	0	-0.027	-0.006	17.555	0.032	0.032	0.000	0.000	0.000	0.000
33	F	33	THR	0	-0.081	-0.052	20.348	0.017	0.017	0.000	0.000	0.000	0.000
34	F	34	GLN	0	-0.034	-0.006	19.223	-0.004	-0.004	0.000	0.000	0.000	0.000
35	F	35	LYS	1	0.852	0.936	17.820	-0.064	-0.064	0.000	0.000	0.000	0.000
36	F	36	ILE	0	0.004	-0.013	22.140	0.009	0.009	0.000	0.000	0.000	0.000
37	F	37	GLY	0	0.003	0.029	24.797	0.000	0.000	0.000	0.000	0.000	0.000
38	F	38	VAL	0	-0.082	-0.055	25.608	0.004	0.004	0.000	0.000	0.000	0.000
39	F	39	HIS	0	0.084	0.038	25.338	-0.010	-0.010	0.000	0.000	0.000	0.000
40	F	40	ALA	0	0.072	0.028	22.400	0.006	0.006	0.000	0.000	0.000	0.000
41	F	41	PHE	0	0.003	0.006	24.133	0.002	0.002	0.000	0.000	0.000	0.000
42	F	42	GLN	0	-0.033	-0.007	26.876	0.006	0.006	0.000	0.000	0.000	0.000
43	F	43	GLN	0	-0.018	-0.010	22.154	0.005	0.005	0.000	0.000	0.000	0.000
44	F	44	ARG	1	0.798	0.877	25.037	0.038	0.038	0.000	0.000	0.000	0.000
45	F	45	LEU	0	0.019	0.004	19.046	0.006	0.006	0.000	0.000	0.000	0.000
46	F	46	ALA	0	0.012	0.013	22.263	-0.008	-0.008	0.000	0.000	0.000	0.000
47	F	47	VAL	0	0.040	0.027	18.252	0.006	0.006	0.000	0.000	0.000	0.000
48	F	48	HIS	0	-0.011	0.033	20.319	0.011	0.011	0.000	0.000	0.000	0.000
49	F	49	PRO	0	0.025	-0.022	20.472	0.004	0.004	0.000	0.000	0.000	0.000
50	F	50	SER	0	0.000	-0.010	21.721	-0.004	-0.004	0.000	0.000	0.000	0.000
51	F	51	GLY	0	0.014	0.009	23.859	-0.003	-0.003	0.000	0.000	0.000	0.000
52	F	52	VAL	0	-0.039	-0.007	21.055	-0.004	-0.004	0.000	0.000	0.000	0.000
53	F	53	ALA	0	0.019	0.002	22.307	-0.001	-0.001	0.000	0.000	0.000	0.000
54	F	54	LEU	0	0.007	0.001	17.086	-0.003	-0.003	0.000	0.000	0.000	0.000
55	F	55	GLN	0	-0.057	-0.035	18.142	-0.006	-0.006	0.000	0.000	0.000	0.000
56	F	56	ASP	-1	-0.898	-0.960	17.791	-0.158	-0.158	0.000	0.000	0.000	0.000
57	F	57	ARG	1	0.957	0.967	17.470	0.181	0.181	0.000	0.000	0.000	0.000
58	F	58	VAL	0	-0.018	0.009	14.036	-0.032	-0.032	0.000	0.000	0.000	0.000
59	F	59	PRO	0	0.053	0.021	9.558	0.020	0.020	0.000	0.000	0.000	0.000
60	F	60	LEU	0	-0.011	-0.020	10.908	0.051	0.051	0.000	0.000	0.000	0.000
61	F	61	ALA	0	0.006	0.004	7.129	0.045	0.045	0.000	0.000	0.000	0.000
62	F	62	SER	0	-0.051	-0.016	9.054	0.031	0.031	0.000	0.000	0.000	0.000
63	F	63	GLN	0	-0.022	0.002	11.760	0.068	0.068	0.000	0.000	0.000	0.000
64	F	64	GLY	0	0.008	0.001	13.427	0.001	0.001	0.000	0.000	0.000	0.000
65	F	65	LEU	0	-0.042	-0.009	12.811	0.026	0.026	0.000	0.000	0.000	0.000
66	F	66	GLY	0	0.094	0.046	9.314	-0.063	-0.063	0.000	0.000	0.000	0.000
67	F	67	PRO	0	-0.019	-0.009	7.119	-0.002	-0.002	0.000	0.000	0.000	0.000
68	F	68	GLY	0	-0.010	0.009	9.757	0.003	0.003	0.000	0.000	0.000	0.000
69	F	69	SER	0	-0.052	-0.028	12.902	-0.040	-0.040	0.000	0.000	0.000	0.000
70	F	70	THR	0	0.029	-0.001	14.886	0.010	0.010	0.000	0.000	0.000	0.000
71	F	71	VAL	0	-0.012	-0.010	16.780	-0.017	-0.017	0.000	0.000	0.000	0.000
72	F	72	LEU	0	-0.061	-0.026	19.130	0.012	0.012	0.000	0.000	0.000	0.000
73	F	73	LEU	0	0.005	-0.007	22.242	-0.012	-0.012	0.000	0.000	0.000	0.000
74	F	74	VAL	0	-0.014	-0.018	23.945	0.009	0.009	0.000	0.000	0.000	0.000
75	F	75	VAL	0	-0.009	-0.008	27.426	-0.007	-0.007	0.000	0.000	0.000	0.000
76	F	76	ASP	-1	-0.830	-0.902	29.232	-0.027	-0.027	0.000	0.000	0.000	0.000
77	F	77	LYS	1	0.926	0.955	30.978	0.014	0.014	0.000	0.000	0.000	0.000
78	F	78	CYS	0	-0.031	0.005	33.717	0.001	0.001	0.000	0.000	0.000	0.000
79	F	79	ASP	-1	-0.798	-0.903	35.205	-0.038	-0.038	0.000	0.000	0.000	0.000
80	F	80	GLU	-1	-0.903	-0.950	37.445	-0.021	-0.021	0.000	0.000	0.000	0.000
81	F	81	PRO	0	-0.052	-0.017	39.548	-0.003	-0.003	0.000	0.000	0.000	0.000
82	F	82	LEU	0	-0.015	-0.015	36.879	0.000	0.000	0.000	0.000	0.000	0.000
83	F	83	SER	0	0.017	0.010	41.588	0.000	0.000	0.000	0.000	0.000	0.000
84	F	84	ILE	0	-0.011	0.003	37.640	-0.001	-0.001	0.000	0.000	0.000	0.000
85	F	85	LEU	0	0.001	-0.003	40.993	0.002	0.002	0.000	0.000	0.000	0.000
86	F	86	VAL	0	0.025	0.003	39.993	-0.003	-0.003	0.000	0.000	0.000	0.000
87	F	87	ARG	1	0.856	0.944	41.367	0.048	0.048	0.000	0.000	0.000	0.000
88	F	88	ASN	0	0.030	0.006	42.125	-0.003	-0.003	0.000	0.000	0.000	0.000
89	F	89	ASN	0	0.045	0.001	44.486	0.002	0.002	0.000	0.000	0.000	0.000
90	F	90	LYS	1	0.944	0.979	45.333	0.036	0.036	0.000	0.000	0.000	0.000
91	F	91	GLY	0	0.018	0.027	45.884	0.001	0.001	0.000	0.000	0.000	0.000
92	F	92	ARG	1	0.811	0.869	46.969	0.035	0.035	0.000	0.000	0.000	0.000
93	F	93	SER	0	-0.007	-0.016	44.536	-0.002	-0.002	0.000	0.000	0.000	0.000
94	F	94	SER	0	-0.002	0.015	46.006	0.002	0.002	0.000	0.000	0.000	0.000
95	F	95	THR	0	-0.005	-0.018	45.282	-0.002	-0.002	0.000	0.000	0.000	0.000
96	F	96	TYR	0	-0.007	0.004	42.772	0.002	0.002	0.000	0.000	0.000	0.000
97	F	97	GLU	-1	-0.932	-0.963	43.425	-0.028	-0.028	0.000	0.000	0.000	0.000
98	F	98	VAL	0	-0.029	-0.014	38.601	0.000	0.000	0.000	0.000	0.000	0.000
99	F	99	ARG	1	0.946	0.974	38.342	0.028	0.028	0.000	0.000	0.000	0.000
100	F	100	LEU	0	0.017	0.002	32.893	-0.003	-0.003	0.000	0.000	0.000	0.000
101	F	101	THR	0	-0.015	-0.028	33.056	-0.005	-0.005	0.000	0.000	0.000	0.000
102	F	102	GLN	0	-0.032	0.012	34.370	0.002	0.002	0.000	0.000	0.000	0.000
103	F	103	THR	0	0.007	-0.008	33.033	-0.002	-0.002	0.000	0.000	0.000	0.000
104	F	104	VAL	0	0.022	0.012	31.738	0.004	0.004	0.000	0.000	0.000	0.000
105	F	105	ALA	0	0.001	0.002	34.808	0.002	0.002	0.000	0.000	0.000	0.000
106	F	106	HIS	0	-0.016	-0.002	36.967	0.001	0.001	0.000	0.000	0.000	0.000
107	F	107	LEU	0	0.047	0.032	37.076	0.002	0.002	0.000	0.000	0.000	0.000
108	F	108	LYS	1	0.828	0.910	36.475	0.059	0.059	0.000	0.000	0.000	0.000
109	F	109	GLN	0	-0.040	-0.016	40.204	0.003	0.003	0.000	0.000	0.000	0.000
110	F	110	GLN	0	-0.003	-0.004	42.177	0.000	0.000	0.000	0.000	0.000	0.000
111	F	111	VAL	0	-0.020	-0.018	41.303	0.001	0.001	0.000	0.000	0.000	0.000
112	F	112	SER	0	-0.076	-0.054	43.820	0.001	0.001	0.000	0.000	0.000	0.000
113	F	113	GLY	0	0.012	0.006	45.438	0.001	0.001	0.000	0.000	0.000	0.000
114	F	114	LEU	0	-0.064	-0.021	47.791	0.001	0.001	0.000	0.000	0.000	0.000
115	F	115	GLU	-1	-0.767	-0.865	45.833	-0.036	-0.036	0.000	0.000	0.000	0.000
116	F	116	GLY	0	-0.012	0.018	48.854	0.000	0.000	0.000	0.000	0.000	0.000
117	F	117	VAL	0	-0.080	-0.036	45.158	0.000	0.000	0.000	0.000	0.000	0.000
118	F	118	GLN	0	0.033	0.011	43.970	0.001	0.001	0.000	0.000	0.000	0.000
119	F	119	ASP	-1	-0.800	-0.909	40.191	-0.049	-0.049	0.000	0.000	0.000	0.000
120	F	120	ASP	-1	-0.775	-0.880	39.065	-0.052	-0.052	0.000	0.000	0.000	0.000
121	F	121	LEU	0	-0.032	-0.017	40.321	-0.002	-0.002	0.000	0.000	0.000	0.000
122	F	122	PHE	0	-0.032	-0.022	39.717	-0.001	-0.001	0.000	0.000	0.000	0.000
123	F	123	TRP	0	-0.016	-0.006	32.153	-0.002	-0.002	0.000	0.000	0.000	0.000
124	F	124	LEU	0	0.038	0.025	35.164	0.002	0.002	0.000	0.000	0.000	0.000
125	F	125	THR	0	0.005	-0.004	32.015	-0.005	-0.005	0.000	0.000	0.000	0.000
126	F	126	PHE	0	0.029	0.009	30.639	0.008	0.008	0.000	0.000	0.000	0.000
127	F	127	GLU	-1	-0.920	-0.960	30.094	-0.088	-0.088	0.000	0.000	0.000	0.000
128	F	128	GLY	0	-0.020	-0.005	29.446	-0.006	-0.006	0.000	0.000	0.000	0.000
129	F	129	LYS	1	0.844	0.927	24.186	0.124	0.124	0.000	0.000	0.000	0.000
130	F	130	PRO	0	-0.019	-0.018	27.365	0.007	0.007	0.000	0.000	0.000	0.000
131	F	131	LEU	0	-0.015	-0.009	28.672	-0.006	-0.006	0.000	0.000	0.000	0.000
132	F	132	GLU	-1	-0.806	-0.870	25.777	-0.119	-0.119	0.000	0.000	0.000	0.000
133	F	133	ASP	-1	-0.811	-0.915	29.918	-0.060	-0.060	0.000	0.000	0.000	0.000
134	F	134	GLN	0	0.028	0.002	27.010	0.008	0.008	0.000	0.000	0.000	0.000
135	F	135	LEU	0	-0.017	0.002	25.346	0.002	0.002	0.000	0.000	0.000	0.000
136	F	136	PRO	0	-0.009	-0.003	28.374	0.004	0.004	0.000	0.000	0.000	0.000
137	F	137	LEU	0	0.045	0.017	30.178	-0.006	-0.006	0.000	0.000	0.000	0.000
138	F	138	GLY	0	0.022	-0.003	30.931	-0.004	-0.004	0.000	0.000	0.000	0.000
139	F	139	GLU	-1	-0.938	-0.972	23.820	-0.103	-0.103	0.000	0.000	0.000	0.000
140	F	140	TYR	0	-0.060	-0.068	26.101	-0.009	-0.009	0.000	0.000	0.000	0.000
141	F	141	GLY	0	-0.007	0.008	28.482	0.001	0.001	0.000	0.000	0.000	0.000
142	F	142	LEU	0	0.004	0.015	29.531	0.002	0.002	0.000	0.000	0.000	0.000
143	F	143	LYS	1	0.906	0.936	30.050	0.072	0.072	0.000	0.000	0.000	0.000
144	F	144	PRO	0	0.032	0.011	35.730	0.000	0.000	0.000	0.000	0.000	0.000
145	F	145	LEU	0	-0.014	-0.001	39.551	0.000	0.000	0.000	0.000	0.000	0.000
146	F	146	SER	0	-0.030	-0.006	36.161	-0.002	-0.002	0.000	0.000	0.000	0.000
147	F	147	THR	0	-0.044	-0.029	37.835	0.003	0.003	0.000	0.000	0.000	0.000
148	F	148	VAL	0	-0.001	0.013	35.489	-0.004	-0.004	0.000	0.000	0.000	0.000
149	F	149	PHE	0	-0.019	-0.012	36.751	0.005	0.005	0.000	0.000	0.000	0.000
150	F	150	MET	0	0.032	0.018	37.539	-0.002	-0.002	0.000	0.000	0.000	0.000
151	F	151	ASN	0	-0.049	-0.021	36.559	0.000	0.000	0.000	0.000	0.000	0.000
152	F	152	LEU	0	0.030	0.006	39.473	0.000	0.000	0.000	0.000	0.000	0.000
153	F	153	ARG	1	0.846	0.934	34.946	0.063	0.063	0.000	0.000	0.000	0.000
154	F	154	LEU	0	0.020	0.009	39.818	0.003	0.003	0.000	0.000	0.000	0.000
155	F	155	ARG	1	0.771	0.869	39.330	0.049	0.049	0.000	0.000	0.000	0.000
156	F	156	GLY	0	-0.020	0.000	39.617	0.003	0.003	0.000	0.000	0.000	0.000
157	F	157	GLY	-1	-0.910	-0.943	38.931	-0.058	-0.058	0.000	0.000	0.000	0.000
158	F	201	HOH	0	0.040	0.025	43.847	-0.001	-0.001	0.000	0.000	0.000	0.000

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