FMO DATABASE

FMODB ID: 3QNVL

Calculation Name: 7RQG-D-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7RQG

Chain ID: D

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-17

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	111
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-590217.370066
FMO2-HF: Nuclear repulsion	554769.359101
FMO2-HF: Total energy	-35448.010965
FMO2-MP2: Total energy	-35546.840208

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:1844:ASP )

Summations of interaction energy for fragment #1(D:1844:ASP )

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.
-125.365	-133.982	18.53	-6.746	-3.166	0.049

Interaction energy analysis for fragmet #1(D:1844:ASP )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.894 / q_NPA : -0.949

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	1846	GLU	-1	-0.836	-0.915	3.757	43.034	45.278	0.034	-1.118	-1.160	0.004
4	D	1847	VAL	0	-0.064	-0.039	6.494	-3.810	-3.810	0.000	0.000	0.000	0.000
5	D	1848	THR	0	-0.009	-0.043	9.082	-1.733	-1.733	0.000	0.000	0.000	0.000
6	D	1849	GLY	0	0.037	0.027	12.551	-0.203	-0.203	0.000	0.000	0.000	0.000
7	D	1850	ASP	-1	-0.799	-0.832	15.283	18.574	18.574	0.000	0.000	0.000	0.000
8	D	1851	SER	0	0.004	0.003	17.137	0.393	0.393	0.000	0.000	0.000	0.000
9	D	1852	CYS	0	-0.050	-0.007	17.112	0.458	0.458	0.000	0.000	0.000	0.000
10	D	1853	ASN	0	0.020	-0.021	16.915	-0.454	-0.454	0.000	0.000	0.000	0.000
11	D	1854	ASN	0	-0.025	-0.022	17.008	0.202	0.202	0.000	0.000	0.000	0.000
12	D	1855	TYR	0	0.041	0.039	17.103	-1.101	-1.101	0.000	0.000	0.000	0.000
13	D	1856	MET	0	-0.037	-0.006	16.394	1.126	1.126	0.000	0.000	0.000	0.000
14	D	1857	LEU	0	-0.016	-0.006	14.932	-0.978	-0.978	0.000	0.000	0.000	0.000
15	D	1858	THR	0	0.012	0.020	18.823	-0.081	-0.081	0.000	0.000	0.000	0.000
16	D	1859	TYR	0	0.030	-0.004	18.673	0.108	0.108	0.000	0.000	0.000	0.000
17	D	1860	ASN	0	-0.010	0.016	24.491	-0.718	-0.718	0.000	0.000	0.000	0.000
18	D	1861	LYS	1	0.910	0.932	27.295	-9.369	-9.369	0.000	0.000	0.000	0.000
19	D	1862	VAL	0	0.054	0.000	27.929	0.024	0.024	0.000	0.000	0.000	0.000
20	D	1863	GLU	-1	-0.807	-0.865	30.297	8.577	8.577	0.000	0.000	0.000	0.000
21	D	1864	ASN	0	-0.052	-0.003	32.125	-0.397	-0.397	0.000	0.000	0.000	0.000
22	D	1865	MET	0	-0.096	-0.029	25.648	0.195	0.195	0.000	0.000	0.000	0.000
23	D	1866	THR	0	0.074	0.037	30.971	-0.190	-0.190	0.000	0.000	0.000	0.000
24	D	1867	PRO	0	-0.030	-0.009	30.276	0.386	0.386	0.000	0.000	0.000	0.000
25	D	1868	NME	0	-0.014	-0.003	31.186	-0.066	-0.066	0.000	0.000	0.000	0.000
26	D	1875	ACE	0	0.005	-0.002	23.440	-0.124	-0.124	0.000	0.000	0.000	0.000
27	D	1876	CYS	0	-0.011	-0.014	19.777	0.294	0.294	0.000	0.000	0.000	0.000
28	D	1877	SER	0	-0.003	0.007	21.595	0.156	0.156	0.000	0.000	0.000	0.000
29	D	1878	ALA	0	0.037	0.019	20.210	0.353	0.353	0.000	0.000	0.000	0.000
30	D	1879	ARG	1	0.931	0.972	21.033	-12.766	-12.766	0.000	0.000	0.000	0.000
31	D	1880	HIS	0	0.025	0.006	21.194	0.450	0.450	0.000	0.000	0.000	0.000
32	D	1881	ILE	0	0.007	0.013	19.657	-0.554	-0.554	0.000	0.000	0.000	0.000
33	D	1882	ASN	0	0.024	-0.001	21.925	0.451	0.451	0.000	0.000	0.000	0.000
34	D	1883	ALA	0	0.031	0.012	19.992	0.279	0.279	0.000	0.000	0.000	0.000
35	D	1884	GLN	0	0.051	0.023	20.477	0.646	0.646	0.000	0.000	0.000	0.000
36	D	1885	VAL	0	0.015	0.019	22.859	-0.029	-0.029	0.000	0.000	0.000	0.000
37	D	1886	ALA	0	0.022	0.007	18.155	0.088	0.088	0.000	0.000	0.000	0.000
38	D	1887	LYS	1	0.886	0.929	17.488	-14.350	-14.350	0.000	0.000	0.000	0.000
39	D	1888	SER	0	-0.038	-0.019	19.020	0.021	0.021	0.000	0.000	0.000	0.000
40	D	1889	HIS	0	-0.054	-0.032	21.156	-0.533	-0.533	0.000	0.000	0.000	0.000
41	D	1890	ASN	0	-0.045	0.003	16.268	0.786	0.786	0.000	0.000	0.000	0.000
42	D	1891	ILE	0	0.006	0.025	16.257	0.546	0.546	0.000	0.000	0.000	0.000
43	D	1892	ALA	0	0.057	0.019	12.694	0.822	0.822	0.000	0.000	0.000	0.000
44	D	1893	LEU	0	-0.041	-0.030	12.488	-1.042	-1.042	0.000	0.000	0.000	0.000
45	D	1894	ILE	0	0.001	0.019	12.196	2.469	2.469	0.000	0.000	0.000	0.000
46	D	1895	TRP	0	-0.003	-0.018	12.466	-1.953	-1.953	0.000	0.000	0.000	0.000
47	D	1896	ASN	0	0.029	-0.005	13.228	1.496	1.496	0.000	0.000	0.000	0.000
48	D	1897	VAL	0	0.008	0.002	11.408	0.213	0.213	0.000	0.000	0.000	0.000
49	D	1898	LYS	1	0.943	0.962	13.828	-15.227	-15.227	0.000	0.000	0.000	0.000
50	D	1899	ASP	-1	-0.773	-0.861	17.123	15.780	15.780	0.000	0.000	0.000	0.000
51	D	1900	PHE	0	-0.020	-0.025	9.782	0.070	0.070	0.000	0.000	0.000	0.000
52	D	1901	MET	0	-0.041	-0.031	9.462	0.114	0.114	0.000	0.000	0.000	0.000
53	D	1902	SER	0	0.000	0.001	14.759	-0.865	-0.865	0.000	0.000	0.000	0.000
54	D	1903	LEU	0	-0.030	0.002	16.464	-0.945	-0.945	0.000	0.000	0.000	0.000
55	D	1904	SER	0	0.051	0.016	16.871	0.975	0.975	0.000	0.000	0.000	0.000
56	D	1905	GLU	-1	-0.821	-0.913	13.023	23.576	23.576	0.000	0.000	0.000	0.000
57	D	1906	GLN	0	0.050	0.015	15.187	1.048	1.048	0.000	0.000	0.000	0.000
58	D	1907	LEU	0	0.006	0.003	17.021	0.129	0.129	0.000	0.000	0.000	0.000
59	D	1908	ARG	1	0.888	0.957	12.160	-21.183	-21.183	0.000	0.000	0.000	0.000
60	D	1909	LYS	1	0.866	0.924	11.593	-20.939	-20.939	0.000	0.000	0.000	0.000
61	D	1910	GLN	0	-0.002	-0.001	12.560	0.460	0.460	0.000	0.000	0.000	0.000
62	D	1911	ILE	0	-0.002	0.010	12.683	0.002	0.002	0.000	0.000	0.000	0.000
63	D	1912	ARG	1	0.960	0.992	4.418	-45.299	-45.221	-0.001	-0.004	-0.072	0.000
64	D	1913	SER	0	-0.033	-0.020	10.027	0.556	0.556	0.000	0.000	0.000	0.000
65	D	1914	ALA	0	0.003	0.001	11.810	-0.510	-0.510	0.000	0.000	0.000	0.000
66	D	1915	ALA	0	0.043	0.029	10.271	-1.025	-1.025	0.000	0.000	0.000	0.000
67	D	1916	LYS	1	0.981	1.002	5.460	-35.116	-35.116	0.000	0.000	0.000	0.000
68	D	1917	LYS	1	0.896	0.953	10.279	-19.742	-19.742	0.000	0.000	0.000	0.000
69	D	1918	ASN	0	-0.038	-0.027	13.843	-2.024	-2.024	0.000	0.000	0.000	0.000
70	D	1919	ASN	0	0.014	0.021	11.367	0.635	0.635	0.000	0.000	0.000	0.000
71	D	1920	LEU	0	0.020	0.007	11.659	-0.902	-0.902	0.000	0.000	0.000	0.000
72	D	1921	PRO	0	-0.008	0.007	8.562	2.098	2.098	0.000	0.000	0.000	0.000
73	D	1922	PHE	0	-0.008	-0.019	7.248	-1.902	-1.902	0.000	0.000	0.000	0.000
74	D	1923	LYS	1	0.910	0.951	7.585	-19.448	-19.448	0.000	0.000	0.000	0.000
75	D	1924	LEU	0	-0.014	0.004	7.524	-2.073	-2.073	0.000	0.000	0.000	0.000
76	D	1925	THR	0	0.024	0.011	10.405	0.388	0.388	0.000	0.000	0.000	0.000
77	D	1926	CYS	0	0.010	-0.009	13.444	-0.347	-0.347	0.000	0.000	0.000	0.000
78	D	1927	ALA	0	-0.001	0.017	15.807	-1.272	-1.272	0.000	0.000	0.000	0.000
79	D	1928	THR	0	0.007	-0.010	18.509	0.477	0.477	0.000	0.000	0.000	0.000
80	D	1929	THR	0	0.023	0.028	21.040	-0.205	-0.205	0.000	0.000	0.000	0.000
81	D	1930	ARG	1	0.865	0.910	21.338	-13.292	-13.292	0.000	0.000	0.000	0.000
82	D	1931	GLN	-1	-0.813	-0.848	19.778	12.813	12.813	0.000	0.000	0.000	0.000
83	D	2001	HOH	0	-0.057	-0.048	36.595	-0.054	-0.054	0.000	0.000	0.000	0.000
84	D	2004	HOH	0	-0.007	-0.015	23.937	-0.057	-0.057	0.000	0.000	0.000	0.000
85	D	2005	HOH	0	-0.019	-0.019	16.010	0.250	0.250	0.000	0.000	0.000	0.000
86	D	2006	HOH	0	-0.029	-0.028	36.613	-0.106	-0.106	0.000	0.000	0.000	0.000
87	D	2008	HOH	0	-0.019	-0.025	14.280	-0.274	-0.274	0.000	0.000	0.000	0.000
88	D	2010	HOH	0	-0.052	-0.040	38.814	-0.093	-0.093	0.000	0.000	0.000	0.000
89	D	2014	HOH	0	0.040	0.029	34.493	0.097	0.097	0.000	0.000	0.000	0.000
90	D	2016	HOH	0	0.038	0.022	14.519	-0.433	-0.433	0.000	0.000	0.000	0.000
91	D	2018	HOH	0	-0.029	-0.021	15.347	-0.272	-0.272	0.000	0.000	0.000	0.000
92	D	2019	HOH	0	0.011	0.003	14.525	0.328	0.328	0.000	0.000	0.000	0.000
93	D	2020	HOH	0	0.038	0.021	25.402	0.162	0.162	0.000	0.000	0.000	0.000
94	D	2022	HOH	0	-0.040	-0.031	21.009	-0.280	-0.280	0.000	0.000	0.000	0.000
95	D	2025	HOH	0	0.040	0.029	21.073	-0.015	-0.015	0.000	0.000	0.000	0.000
96	D	2026	HOH	0	-0.027	-0.036	24.131	0.090	0.090	0.000	0.000	0.000	0.000
97	D	2027	HOH	0	0.030	0.013	9.414	1.085	1.085	0.000	0.000	0.000	0.000
98	D	2028	HOH	0	-0.041	-0.023	20.742	-0.283	-0.283	0.000	0.000	0.000	0.000
99	D	2029	HOH	0	0.039	0.026	34.343	0.106	0.106	0.000	0.000	0.000	0.000
100	D	2030	HOH	0	-0.012	-0.007	25.643	-0.040	-0.040	0.000	0.000	0.000	0.000
101	D	2035	HOH	0	-0.016	-0.014	15.864	0.436	0.436	0.000	0.000	0.000	0.000
102	D	2036	HOH	0	-0.006	-0.004	23.710	0.054	0.054	0.000	0.000	0.000	0.000
103	D	2041	HOH	0	-0.038	-0.029	26.058	-0.007	-0.007	0.000	0.000	0.000	0.000
104	D	2043	HOH	0	0.022	0.001	30.188	-0.091	-0.091	0.000	0.000	0.000	0.000
105	D	2044	HOH	0	-0.006	-0.018	21.706	-0.081	-0.081	0.000	0.000	0.000	0.000
106	D	2049	HOH	0	0.033	0.026	22.598	0.080	0.080	0.000	0.000	0.000	0.000
107	D	2052	HOH	0	-0.045	-0.035	1.622	-16.565	-27.504	18.497	-5.624	-1.934	0.045
108	D	2055	HOH	0	-0.044	-0.040	18.324	0.001	0.001	0.000	0.000	0.000	0.000
109	D	2056	HOH	0	-0.018	-0.018	9.138	1.031	1.031	0.000	0.000	0.000	0.000
110	D	2057	HOH	0	0.000	0.000	19.818	-0.124	-0.124	0.000	0.000	0.000	0.000
111	D	2063	HOH	0	0.000	0.000	6.702	1.189	1.189	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1844:ASP )