FMO DATABASE

FMODB ID: 9YV22

Calculation Name: 6W37-A-Xray116

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6W37

Chain ID: A

ChEMBL ID:

UniProt ID: P0DTC7

Base Structure: X-ray

Registration Date: 2020-05-11

Reference: A. Yamamoto, 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	OptHSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Selected crystal waters in PDB.
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	67
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-380937.256683
FMO2-HF: Nuclear repulsion	354075.989896
FMO2-HF: Total energy	-26861.266786
FMO2-MP2: Total energy	-26937.516092

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:GLU )

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

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.
-72.686	-58.961	11.986	-11.681	-14.03	-0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.084 / q_NPA : -0.052

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

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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	A	3	TYR	0	0.040	0.017	2.119	-10.191	-6.058	3.073	-3.005	-4.201	0.028
4	A	4	HIS	1	0.839	0.927	5.949	6.147	6.147	0.000	0.000	0.000	0.000
5	A	5	TYR	0	-0.038	-0.045	9.580	1.120	1.120	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.030	0.016	12.702	-0.543	-0.543	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.863	-0.910	16.308	0.342	0.342	0.000	0.000	0.000	0.000
8	A	43	CYS	0	-0.111	-0.013	19.608	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.057	0.022	22.081	0.111	0.111	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.983	0.973	24.323	-0.571	-0.571	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.020	0.024	25.893	-0.040	-0.040	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.036	-0.010	25.837	-0.049	-0.049	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.023	-0.006	24.016	0.054	0.054	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.006	0.007	19.120	-0.068	-0.068	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.009	-0.001	20.559	0.042	0.042	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.018	-0.005	14.609	-0.137	-0.137	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.857	0.935	15.461	2.269	2.269	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.828	-0.916	13.791	-1.735	-1.735	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.023	0.002	8.881	-0.199	-0.199	0.000	0.000	0.000	0.000
20	A	52	CYS	0	-0.059	-0.027	7.417	0.055	0.055	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.007	-0.002	12.571	0.354	0.354	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.036	0.020	15.388	0.140	0.140	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.018	0.006	12.128	-0.085	-0.085	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.022	-0.008	11.431	0.364	0.364	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.032	-0.032	11.313	0.188	0.188	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.933	-0.958	10.181	6.402	6.402	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.039	-0.006	12.151	0.313	0.313	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.060	-0.016	14.711	0.092	0.092	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.031	0.011	17.664	-0.137	-0.137	0.000	0.000	0.000	0.000
30	A	30	PRO	0	-0.009	0.011	19.099	0.053	0.053	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.003	0.008	15.808	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.004	-0.007	19.497	0.035	0.035	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.016	0.018	20.196	-0.122	-0.122	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.039	-0.029	21.467	0.090	0.090	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.037	0.016	22.857	-0.082	-0.082	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.906	-0.958	23.491	-1.101	-1.101	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.047	-0.025	18.375	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.934	0.968	18.536	1.090	1.090	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.052	0.029	13.477	0.185	0.185	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.005	-0.003	18.825	-0.089	-0.089	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.001	0.001	16.523	0.120	0.120	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.021	0.004	21.153	-0.079	-0.079	0.000	0.000	0.000	0.000
43	A	44	PHE	0	0.024	-0.027	19.438	0.064	0.064	0.000	0.000	0.000	0.000
44	A	45	SER	0	-0.031	-0.024	18.466	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.016	0.016	15.587	0.335	0.335	0.000	0.000	0.000	0.000
46	A	47	GLN	0	-0.019	-0.028	10.748	0.367	0.367	0.000	0.000	0.000	0.000
47	A	48	PHE	0	-0.004	0.016	11.233	0.152	0.152	0.000	0.000	0.000	0.000
48	A	49	ALA	0	-0.007	-0.010	7.340	0.291	0.291	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.023	0.017	7.470	-0.210	-0.210	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.008	-0.002	6.605	-1.129	-1.129	0.000	0.000	0.000	0.000
51	A	53	PRO	0	0.059	0.005	9.309	-0.123	-0.123	0.000	0.000	0.000	0.000
52	A	54	ASP	-1	-0.905	-0.953	7.745	-10.015	-10.015	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.034	0.035	7.107	-0.481	-0.481	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.051	-0.009	2.516	-8.485	-7.553	0.185	-0.360	-0.757	-0.004
55	A	57	LYS	1	0.940	0.969	2.128	-30.118	-25.942	3.769	-3.454	-4.491	0.029
56	A	58	HIS	0	0.036	0.006	2.279	-12.540	-10.762	3.430	-2.918	-2.291	-0.033
57	A	59	VAL	0	0.027	0.015	3.623	3.719	4.100	0.003	-0.038	-0.346	0.000
58	A	60	TYR	0	-0.006	-0.019	6.225	-2.526	-2.526	0.000	0.000	0.000	0.000
59	A	61	GLN	0	0.056	0.032	9.764	1.473	1.473	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.008	0.010	12.068	-0.526	-0.526	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.945	0.977	15.788	-0.375	-0.375	0.000	0.000	0.000	0.000
62	A	64	ALA	0	0.006	-0.005	18.444	-0.189	-0.189	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.902	0.958	21.967	0.252	0.252	0.000	0.000	0.000	0.000
64	A	66	SER	-1	-0.875	-0.932	25.075	0.102	0.102	0.000	0.000	0.000	0.000
65	A	101	HOH	0	-0.021	-0.018	27.060	0.024	0.024	0.000	0.000	0.000	0.000
66	A	102	HOH	0	-0.004	-0.018	2.336	-17.030	-14.705	1.526	-1.906	-1.944	-0.026
67	A	103	HOH	0	-0.037	-0.031	12.789	0.067	0.067	0.000	0.000	0.000	0.000

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