FMO DATABASE

FMODB ID: KR443

Calculation Name: 7LGO-B-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7LGO

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-02-22

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	168
LigandCharge
Software	MIZUHO/ABINIT-MP 4.0(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1047205.918028
FMO2-HF: Nuclear repulsion	999039.286076
FMO2-HF: Total energy	-48166.631952
FMO2-MP2: Total energy	-48306.88716

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(B:2:THR )

Summations of interaction energy for fragment #1(B:2:THR )

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.
-1.399	1.49	0.165	-1.13	-1.923	0.002

Interaction energy analysis for fragmet #1(B:2:THR )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.029

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	B	4	GLN	0	-0.028	-0.018	2.740	-3.833	-1.040	0.166	-1.119	-1.839	0.002
4	B	5	PRO	0	-0.009	0.000	5.030	0.817	0.913	-0.001	-0.011	-0.084	0.000
5	B	6	ILE	0	-0.006	-0.017	5.711	0.024	0.024	0.000	0.000	0.000	0.000
6	B	7	ASP	-1	-0.899	-0.931	8.769	0.828	0.828	0.000	0.000	0.000	0.000
7	B	8	LEU	0	-0.060	-0.023	11.787	-0.121	-0.121	0.000	0.000	0.000	0.000
8	B	9	VAL	0	0.031	0.016	14.159	0.049	0.049	0.000	0.000	0.000	0.000
9	B	10	PRO	0	-0.038	-0.030	17.671	-0.041	-0.041	0.000	0.000	0.000	0.000
10	B	11	ASN	0	-0.013	0.005	20.683	0.018	0.018	0.000	0.000	0.000	0.000
11	B	12	GLN	0	0.005	-0.004	23.493	0.004	0.004	0.000	0.000	0.000	0.000
12	B	13	PRO	0	-0.018	0.008	27.065	0.000	0.000	0.000	0.000	0.000	0.000
13	B	14	TYR	0	0.051	0.020	29.475	0.011	0.011	0.000	0.000	0.000	0.000
14	B	15	PRO	0	0.002	-0.020	32.801	-0.005	-0.005	0.000	0.000	0.000	0.000
15	B	16	ASN	0	-0.030	0.002	35.944	0.001	0.001	0.000	0.000	0.000	0.000
16	B	17	ALA	0	0.015	0.024	33.808	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	18	SER	0	0.028	0.021	35.826	0.000	0.000	0.000	0.000	0.000	0.000
18	B	19	PHE	0	-0.007	-0.019	33.406	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	20	ASP	-1	-0.746	-0.823	34.653	-0.057	-0.057	0.000	0.000	0.000	0.000
20	B	21	ASN	0	0.035	0.026	34.586	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	22	PHE	0	-0.043	-0.009	28.933	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	23	LYS	1	0.856	0.924	31.490	0.114	0.114	0.000	0.000	0.000	0.000
23	B	24	PHE	0	0.006	0.004	24.743	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	25	VAL	0	-0.017	-0.010	27.174	0.002	0.002	0.000	0.000	0.000	0.000
25	B	26	CYS	0	-0.080	-0.032	21.866	-0.020	-0.020	0.000	0.000	0.000	0.000
26	B	27	ASP	-1	-0.763	-0.866	21.000	-0.325	-0.325	0.000	0.000	0.000	0.000
27	B	28	ASN	0	0.028	0.011	20.909	0.035	0.035	0.000	0.000	0.000	0.000
28	B	29	ILE	0	0.032	0.000	23.695	0.009	0.009	0.000	0.000	0.000	0.000
29	B	30	LYS	1	0.859	0.919	25.803	0.157	0.157	0.000	0.000	0.000	0.000
30	B	31	PHE	0	-0.029	-0.017	20.349	0.008	0.008	0.000	0.000	0.000	0.000
31	B	32	ALA	0	-0.001	0.008	24.435	0.007	0.007	0.000	0.000	0.000	0.000
32	B	33	ASP	-1	-0.837	-0.935	26.617	-0.116	-0.116	0.000	0.000	0.000	0.000
33	B	34	ASP	-1	-0.842	-0.887	26.747	-0.134	-0.134	0.000	0.000	0.000	0.000
34	B	35	LEU	0	0.024	0.009	23.046	0.011	0.011	0.000	0.000	0.000	0.000
35	B	36	ASN	0	-0.018	-0.005	27.555	0.015	0.015	0.000	0.000	0.000	0.000
36	B	37	GLN	0	-0.076	-0.021	29.332	0.015	0.015	0.000	0.000	0.000	0.000
37	B	38	LEU	0	-0.066	-0.034	27.034	0.008	0.008	0.000	0.000	0.000	0.000
38	B	39	THR	0	-0.061	-0.037	29.746	0.008	0.008	0.000	0.000	0.000	0.000
39	B	40	GLY	0	0.026	0.031	32.180	0.006	0.006	0.000	0.000	0.000	0.000
40	B	41	TYR	0	-0.019	0.001	33.879	0.002	0.002	0.000	0.000	0.000	0.000
41	B	42	LYS	1	0.974	0.986	35.801	0.060	0.060	0.000	0.000	0.000	0.000
42	B	43	LYS	1	0.943	1.013	38.941	0.079	0.079	0.000	0.000	0.000	0.000
43	B	44	PRO	0	0.016	-0.018	39.116	0.003	0.003	0.000	0.000	0.000	0.000
44	B	45	ALA	0	0.030	0.004	34.639	0.002	0.002	0.000	0.000	0.000	0.000
45	B	46	SER	0	-0.050	-0.051	36.108	0.003	0.003	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.865	0.930	30.147	0.069	0.069	0.000	0.000	0.000	0.000
47	B	48	GLU	-1	-0.750	-0.827	30.617	-0.109	-0.109	0.000	0.000	0.000	0.000
48	B	49	LEU	0	-0.001	0.013	26.465	0.001	0.001	0.000	0.000	0.000	0.000
49	B	50	LYS	1	0.914	0.945	22.239	0.257	0.257	0.000	0.000	0.000	0.000
50	B	51	VAL	0	-0.033	-0.016	20.171	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	52	THR	0	-0.013	-0.006	17.506	0.021	0.021	0.000	0.000	0.000	0.000
52	B	53	PHE	0	-0.002	-0.002	14.716	0.009	0.009	0.000	0.000	0.000	0.000
53	B	54	PHE	0	0.047	0.062	6.992	0.110	0.110	0.000	0.000	0.000	0.000
54	B	55	PRO	0	0.012	0.011	8.718	0.021	0.021	0.000	0.000	0.000	0.000
55	B	56	ASP	-1	-0.704	-0.843	10.958	-0.342	-0.342	0.000	0.000	0.000	0.000
56	B	57	LEU	0	-0.017	-0.008	12.959	0.054	0.054	0.000	0.000	0.000	0.000
57	B	58	ASN	0	0.010	-0.018	16.606	0.097	0.097	0.000	0.000	0.000	0.000
58	B	59	GLY	0	0.015	0.023	19.618	0.039	0.039	0.000	0.000	0.000	0.000
59	B	60	ASP	-1	-0.778	-0.848	21.081	-0.133	-0.133	0.000	0.000	0.000	0.000
60	B	61	VAL	0	-0.025	-0.003	20.788	0.020	0.020	0.000	0.000	0.000	0.000
61	B	62	VAL	0	0.031	0.016	14.706	-0.030	-0.030	0.000	0.000	0.000	0.000
62	B	63	ALA	0	-0.005	0.001	17.017	0.030	0.030	0.000	0.000	0.000	0.000
63	B	64	ILE	0	-0.020	-0.019	12.168	-0.112	-0.112	0.000	0.000	0.000	0.000
64	B	65	ASP	-1	-0.738	-0.834	11.562	-0.436	-0.436	0.000	0.000	0.000	0.000
65	B	66	TYR	0	0.043	-0.005	13.580	0.056	0.056	0.000	0.000	0.000	0.000
66	B	67	LYS	1	0.840	0.925	8.656	0.926	0.926	0.000	0.000	0.000	0.000
67	B	68	HIS	0	0.047	0.036	7.815	-0.163	-0.163	0.000	0.000	0.000	0.000
68	B	69	TYR	0	-0.006	0.011	13.020	0.067	0.067	0.000	0.000	0.000	0.000
69	B	70	THR	0	0.023	0.014	15.638	0.022	0.022	0.000	0.000	0.000	0.000
70	B	71	PRO	0	0.029	-0.005	18.446	-0.011	-0.011	0.000	0.000	0.000	0.000
71	B	72	SER	0	0.008	0.006	19.062	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	73	PHE	0	0.011	0.012	14.849	-0.010	-0.010	0.000	0.000	0.000	0.000
73	B	74	LYS	1	0.881	0.963	20.591	-0.074	-0.074	0.000	0.000	0.000	0.000
74	B	75	LYS	1	0.882	0.927	23.798	-0.029	-0.029	0.000	0.000	0.000	0.000
75	B	76	GLY	0	0.097	0.032	23.150	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	77	ALA	0	0.005	-0.013	18.059	0.019	0.019	0.000	0.000	0.000	0.000
77	B	78	LYS	1	0.870	0.952	18.686	-0.049	-0.049	0.000	0.000	0.000	0.000
78	B	79	LEU	0	0.027	0.020	11.809	0.024	0.024	0.000	0.000	0.000	0.000
79	B	80	LEU	0	0.045	0.021	12.706	-0.036	-0.036	0.000	0.000	0.000	0.000
80	B	81	HIS	0	0.023	0.025	16.909	-0.036	-0.036	0.000	0.000	0.000	0.000
81	B	82	LYS	1	0.888	0.958	17.629	0.164	0.164	0.000	0.000	0.000	0.000
82	B	83	PRO	0	-0.001	0.003	19.463	0.001	0.001	0.000	0.000	0.000	0.000
83	B	84	ILE	0	-0.008	0.000	16.662	-0.025	-0.025	0.000	0.000	0.000	0.000
84	B	85	VAL	0	-0.015	-0.009	18.800	0.027	0.027	0.000	0.000	0.000	0.000
85	B	86	TRP	0	0.002	-0.011	14.709	-0.039	-0.039	0.000	0.000	0.000	0.000
86	B	87	HIS	0	-0.022	0.012	13.818	0.085	0.085	0.000	0.000	0.000	0.000
87	B	88	VAL	0	-0.022	-0.016	16.616	-0.024	-0.024	0.000	0.000	0.000	0.000
88	B	89	ASN	0	-0.039	-0.025	16.579	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	90	ASN	0	0.012	0.013	15.498	0.009	0.009	0.000	0.000	0.000	0.000
90	B	91	ALA	0	0.055	0.024	18.565	0.027	0.027	0.000	0.000	0.000	0.000
91	B	92	THR	0	0.016	0.002	21.246	0.002	0.002	0.000	0.000	0.000	0.000
92	B	93	ASN	0	0.009	0.027	21.698	0.017	0.017	0.000	0.000	0.000	0.000
93	B	94	LYS	1	0.897	0.917	25.005	0.109	0.109	0.000	0.000	0.000	0.000
94	B	95	ALA	0	0.010	0.014	22.437	0.010	0.010	0.000	0.000	0.000	0.000
95	B	96	THR	0	0.023	-0.003	19.898	0.006	0.006	0.000	0.000	0.000	0.000
96	B	97	TYR	0	0.009	0.009	23.008	-0.001	-0.001	0.000	0.000	0.000	0.000
97	B	98	LYS	1	0.990	0.976	26.634	0.033	0.033	0.000	0.000	0.000	0.000
98	B	99	PRO	0	0.005	0.014	21.878	0.005	0.005	0.000	0.000	0.000	0.000
99	B	100	ASN	0	0.078	0.031	21.757	0.000	0.000	0.000	0.000	0.000	0.000
100	B	101	THR	0	-0.044	-0.005	24.421	0.005	0.005	0.000	0.000	0.000	0.000
101	B	102	TRP	0	0.011	0.012	25.642	0.014	0.014	0.000	0.000	0.000	0.000
102	B	103	CYS	0	-0.019	0.010	22.237	0.007	0.007	0.000	0.000	0.000	0.000
103	B	104	ILE	0	0.055	0.018	24.675	0.001	0.001	0.000	0.000	0.000	0.000
104	B	105	ARG	1	0.850	0.915	27.541	0.040	0.040	0.000	0.000	0.000	0.000
105	B	106	CYS	0	-0.108	-0.029	25.624	0.009	0.009	0.000	0.000	0.000	0.000
106	B	107	LEU	0	0.026	0.025	24.755	0.001	0.001	0.000	0.000	0.000	0.000
107	B	108	TRP	0	-0.048	-0.027	28.526	0.002	0.002	0.000	0.000	0.000	0.000
108	B	109	SER	0	0.025	0.013	32.098	0.001	0.001	0.000	0.000	0.000	0.000
109	B	110	THR	-1	-0.908	-0.915	32.620	-0.013	-0.013	0.000	0.000	0.000	0.000
110	B	201	HOH	0	0.013	-0.003	13.700	0.007	0.007	0.000	0.000	0.000	0.000
111	B	202	HOH	0	-0.007	-0.019	23.227	-0.007	-0.007	0.000	0.000	0.000	0.000
112	B	203	HOH	0	-0.063	-0.037	34.875	0.001	0.001	0.000	0.000	0.000	0.000
113	B	204	HOH	0	0.034	0.024	35.273	-0.001	-0.001	0.000	0.000	0.000	0.000
114	B	205	HOH	0	-0.040	-0.030	24.630	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	206	HOH	0	0.003	-0.005	19.006	-0.007	-0.007	0.000	0.000	0.000	0.000
116	B	207	HOH	0	-0.010	-0.020	19.641	0.021	0.021	0.000	0.000	0.000	0.000
117	B	208	HOH	0	-0.012	-0.016	22.436	-0.003	-0.003	0.000	0.000	0.000	0.000
118	B	209	HOH	0	-0.002	-0.004	27.759	0.003	0.003	0.000	0.000	0.000	0.000
119	B	210	HOH	0	-0.021	-0.015	18.610	0.021	0.021	0.000	0.000	0.000	0.000
120	B	211	HOH	0	0.003	-0.001	26.860	0.002	0.002	0.000	0.000	0.000	0.000
121	B	212	HOH	0	-0.012	-0.008	26.085	0.001	0.001	0.000	0.000	0.000	0.000
122	B	213	HOH	0	-0.005	-0.019	22.190	0.006	0.006	0.000	0.000	0.000	0.000
123	B	214	HOH	0	-0.009	-0.032	25.064	-0.007	-0.007	0.000	0.000	0.000	0.000
124	B	215	HOH	0	0.001	-0.005	35.116	0.002	0.002	0.000	0.000	0.000	0.000
125	B	216	HOH	0	0.028	0.019	11.876	0.038	0.038	0.000	0.000	0.000	0.000
126	B	217	HOH	0	-0.013	-0.012	38.792	0.001	0.001	0.000	0.000	0.000	0.000
127	B	218	HOH	0	-0.037	-0.039	14.734	0.027	0.027	0.000	0.000	0.000	0.000
128	B	219	HOH	0	-0.015	-0.009	40.563	0.001	0.001	0.000	0.000	0.000	0.000
129	B	220	HOH	0	-0.028	-0.036	8.754	-0.137	-0.137	0.000	0.000	0.000	0.000
130	B	221	HOH	0	0.031	0.014	10.602	0.010	0.010	0.000	0.000	0.000	0.000
131	B	222	HOH	0	-0.033	-0.027	35.052	0.000	0.000	0.000	0.000	0.000	0.000
132	B	223	HOH	0	-0.012	-0.021	22.214	-0.006	-0.006	0.000	0.000	0.000	0.000
133	B	224	HOH	0	-0.035	-0.029	13.828	-0.048	-0.048	0.000	0.000	0.000	0.000
134	B	225	HOH	0	0.016	0.004	25.476	-0.003	-0.003	0.000	0.000	0.000	0.000
135	B	226	HOH	0	0.017	0.012	19.856	-0.009	-0.009	0.000	0.000	0.000	0.000
136	B	227	HOH	0	-0.007	-0.013	22.729	-0.004	-0.004	0.000	0.000	0.000	0.000
137	B	228	HOH	0	-0.018	-0.020	36.282	-0.001	-0.001	0.000	0.000	0.000	0.000
138	B	229	HOH	0	-0.044	-0.027	22.931	0.002	0.002	0.000	0.000	0.000	0.000
139	B	230	HOH	0	-0.013	-0.013	5.809	0.318	0.318	0.000	0.000	0.000	0.000
140	B	231	HOH	0	-0.011	-0.007	27.458	0.004	0.004	0.000	0.000	0.000	0.000
141	B	232	HOH	0	-0.020	-0.019	31.075	0.003	0.003	0.000	0.000	0.000	0.000
142	B	233	HOH	0	-0.042	-0.035	36.344	0.000	0.000	0.000	0.000	0.000	0.000
143	B	234	HOH	0	-0.038	-0.032	11.899	-0.012	-0.012	0.000	0.000	0.000	0.000
144	B	235	HOH	0	0.026	0.010	27.282	-0.001	-0.001	0.000	0.000	0.000	0.000
145	B	236	HOH	0	-0.054	-0.031	12.713	0.003	0.003	0.000	0.000	0.000	0.000
146	B	237	HOH	0	0.056	0.037	27.774	0.002	0.002	0.000	0.000	0.000	0.000
147	B	238	HOH	0	-0.011	-0.020	38.496	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	239	HOH	0	0.016	0.001	39.157	0.001	0.001	0.000	0.000	0.000	0.000
149	B	240	HOH	0	-0.024	-0.025	23.349	-0.005	-0.005	0.000	0.000	0.000	0.000
150	B	241	HOH	0	-0.028	-0.022	23.784	0.005	0.005	0.000	0.000	0.000	0.000
151	B	242	HOH	0	-0.050	-0.053	20.888	0.017	0.017	0.000	0.000	0.000	0.000
152	B	243	HOH	0	0.017	0.015	18.965	0.003	0.003	0.000	0.000	0.000	0.000
153	B	244	HOH	0	-0.053	-0.033	26.423	0.002	0.002	0.000	0.000	0.000	0.000
154	B	245	HOH	0	-0.014	-0.020	34.093	0.003	0.003	0.000	0.000	0.000	0.000
155	B	246	HOH	0	-0.002	0.003	21.890	-0.009	-0.009	0.000	0.000	0.000	0.000
156	B	247	HOH	0	0.033	0.028	25.912	-0.001	-0.001	0.000	0.000	0.000	0.000
157	B	248	HOH	0	-0.026	-0.019	21.134	0.002	0.002	0.000	0.000	0.000	0.000
158	B	249	HOH	0	0.002	-0.001	22.249	0.002	0.002	0.000	0.000	0.000	0.000
159	B	250	HOH	0	-0.030	-0.018	36.686	0.003	0.003	0.000	0.000	0.000	0.000
160	B	251	HOH	0	-0.020	-0.019	22.261	0.000	0.000	0.000	0.000	0.000	0.000
161	B	252	HOH	0	-0.035	-0.024	42.638	0.001	0.001	0.000	0.000	0.000	0.000
162	B	253	HOH	0	-0.034	-0.023	36.216	0.001	0.001	0.000	0.000	0.000	0.000
163	B	254	HOH	0	-0.004	-0.004	30.016	0.002	0.002	0.000	0.000	0.000	0.000
164	B	255	HOH	0	-0.027	-0.017	36.373	0.001	0.001	0.000	0.000	0.000	0.000
165	B	256	HOH	0	0.056	0.032	20.744	-0.010	-0.010	0.000	0.000	0.000	0.000
166	B	257	HOH	0	0.026	0.022	29.509	-0.002	-0.002	0.000	0.000	0.000	0.000
167	B	258	HOH	0	-0.026	-0.018	37.279	0.000	0.000	0.000	0.000	0.000	0.000
168	B	259	HOH	0	-0.025	-0.022	29.840	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:THR )