FMO DATABASE

FMODB ID: 8JV7Y

Calculation Name: 6YI3-A-NMR105-

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6YI3

Chain ID: A

ChEMBL ID:

UniProt ID: P0DTC9

Base Structure: NMR

Registration Date: 2020-04-16

Reference: K. Kato, Y. Handa, Y. Kawashima, K. Fukuzawa et. Al., FMO Calculation for SARS Cov-2 related proteins. To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1152154.336103
FMO2-HF: Nuclear repulsion	1099679.866246
FMO2-HF: Total energy	-52474.469857
FMO2-MP2: Total energy	-52629.552525

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(A:1:GLY )

Summations of interaction energy for fragment #1(A:1:GLY )

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.
1.186	2.902	-0.001	-0.992	-0.722	0.005

Interaction energy analysis for fragmet #1(A:1:GLY )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : ******

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].	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	A	3	MET	0	0.005	3.797	-0.867	0.849	-0.001	-0.992	-0.722	0.005
4	A	4	GLY	0	0.010	6.547	0.335	0.335	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.030	9.508	0.207	0.207	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.012	12.053	-0.006	-0.006	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.043	15.314	0.077	0.077	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.008	16.621	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.015	18.787	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.027	20.920	-0.026	-0.026	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.028	22.829	0.027	0.027	0.000	0.000	0.000	0.000
12	A	12	TRP	0	0.027	25.413	0.003	0.003	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.027	28.627	0.012	0.012	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.066	28.064	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.006	26.543	0.000	0.000	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.019	28.228	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.049	28.510	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.006	29.292	0.018	0.018	0.000	0.000	0.000	0.000
19	A	19	HIS	0	-0.032	30.725	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.016	32.699	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.896	32.518	0.114	0.114	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.860	31.812	-0.144	-0.144	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.812	26.027	-0.249	-0.249	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.016	29.138	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.929	30.752	0.152	0.152	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.037	32.632	0.006	0.006	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.020	35.721	0.000	0.000	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.978	38.136	0.100	0.100	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.013	38.625	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.069	38.619	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.083	35.616	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.059	34.355	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.024	32.376	0.010	0.010	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.008	35.679	0.003	0.003	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.033	33.538	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.005	36.297	0.003	0.003	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.026	33.085	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.000	34.159	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.060	36.510	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.009	38.240	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.782	37.158	-0.135	-0.135	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.771	34.352	-0.163	-0.163	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.051	33.707	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.026	32.217	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.021	29.617	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	46	TYR	0	-0.040	22.582	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	TYR	0	0.017	27.110	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.941	16.221	0.572	0.572	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.853	21.614	0.284	0.284	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.039	19.807	-0.054	-0.054	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.041	18.942	0.026	0.026	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.958	14.375	0.718	0.718	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.826	16.995	0.360	0.360	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.021	15.908	-0.077	-0.077	0.000	0.000	0.000	0.000
55	A	55	ARG	1	1.003	13.888	0.210	0.210	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.035	16.355	0.009	0.009	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.018	18.251	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.831	19.241	-0.068	-0.068	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.024	20.079	0.006	0.006	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.809	21.135	0.100	0.100	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.019	17.825	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.924	20.825	0.300	0.300	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.836	21.549	-0.248	-0.248	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.006	22.371	0.020	0.020	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.055	23.464	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	66	PRO	0	-0.035	24.162	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.846	24.163	0.293	0.293	0.000	0.000	0.000	0.000
68	A	68	TRP	0	0.015	24.456	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	69	TYR	0	0.007	23.119	0.003	0.003	0.000	0.000	0.000	0.000
70	A	70	PHE	0	0.021	26.033	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.041	21.050	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	72	TYR	0	0.085	26.357	0.004	0.004	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.016	26.525	-0.023	-0.023	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.003	24.842	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.006	23.215	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.007	19.731	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.004	18.106	0.025	0.025	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.915	16.003	-0.377	-0.377	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.034	17.827	-0.026	-0.026	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.011	19.399	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.070	21.281	0.013	0.013	0.000	0.000	0.000	0.000
82	A	82	PRO	0	0.047	23.760	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.041	27.460	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.013	29.493	0.012	0.012	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.045	25.010	0.006	0.006	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.009	25.950	-0.026	-0.026	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.963	18.317	0.373	0.373	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.880	19.791	-0.312	-0.312	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.008	21.135	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.043	21.251	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.052	24.864	0.024	0.024	0.000	0.000	0.000	0.000
92	A	92	TRP	0	-0.014	25.315	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.039	30.326	0.011	0.011	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.004	33.263	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	95	THR	0	0.010	36.000	0.005	0.005	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.919	39.571	-0.089	-0.089	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.013	42.386	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	ALA	0	-0.054	36.773	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.004	37.000	0.004	0.004	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.028	32.919	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.002	32.529	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.006	27.881	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.804	28.905	0.170	0.170	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.893	24.806	-0.251	-0.251	0.000	0.000	0.000	0.000
105	A	105	HIS	0	-0.056	26.607	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.020	29.059	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.027	25.492	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.015	24.314	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.821	25.550	0.289	0.289	0.000	0.000	0.000	0.000
110	A	110	ASN	0	0.048	22.726	-0.056	-0.056	0.000	0.000	0.000	0.000
111	A	111	PRO	0	-0.057	22.097	0.026	0.026	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.021	23.427	0.012	0.012	0.000	0.000	0.000	0.000
113	A	113	ASN	0	-0.007	25.404	0.014	0.014	0.000	0.000	0.000	0.000
114	A	114	ASN	0	0.037	28.326	0.006	0.006	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.008	28.695	-0.019	-0.019	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.016	28.257	0.004	0.004	0.000	0.000	0.000	0.000
117	A	117	ILE	0	0.004	30.315	0.012	0.012	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.007	32.607	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.007	30.697	0.009	0.009	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.026	34.115	0.014	0.014	0.000	0.000	0.000	0.000
121	A	121	LEU	0	0.018	36.563	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	122	PRO	0	0.033	39.162	0.004	0.004	0.000	0.000	0.000	0.000
123	A	123	GLN	0	0.057	42.321	0.002	0.002	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.002	45.870	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.054	40.209	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	THR	0	0.007	41.582	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.001	35.065	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	128	PRO	0	-0.002	35.379	0.008	0.008	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.988	37.889	0.091	0.091	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.012	36.496	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	131	PHE	0	-0.009	29.823	-0.009	-0.009	0.000	0.000	0.000	0.000
132	A	132	TYR	0	-0.021	32.434	0.007	0.007	0.000	0.000	0.000	0.000
133	A	133	ALA	0	0.041	33.088	-0.012	-0.012	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.790	28.415	-0.250	-0.250	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.015	32.468	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	136	SER	0	-0.019	35.108	0.011	0.011	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.920	37.817	0.126	0.126	0.000	0.000	0.000	0.000
138	A	138	GLY	0	0.037	40.895	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	139	GLY	0	-0.047	44.174	0.001	0.001	0.000	0.000	0.000	0.000
140	A	140	SER	-1	-0.923	46.745	-0.090	-0.090	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLY )