FMO DATABASE

FMODB ID: GNLK1

Calculation Name: 3VIR-A-Xray320

Preferred Name:

Target Type:

Ligand Name: octyl beta-d-glucopyranoside

ligand 3-letter code: BOG

PDB ID: 3VIR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UUB7

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	71
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-304123.907472
FMO2-HF: Nuclear repulsion	275874.005948
FMO2-HF: Total energy	-28249.901523
FMO2-MP2: Total energy	-28332.499848

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:10:ACE )

Summations of interaction energy for fragment #1(A:10:ACE )

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.
0.541	1.825	-0.005	-0.627	-0.653	-0.001

Interaction energy analysis for fragmet #1(A:10:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.006

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	12	LEU	0	0.003	0.001	3.852	0.313	1.597	-0.005	-0.627	-0.653	-0.001
4	A	13	LEU	0	-0.065	-0.021	5.750	0.418	0.418	0.000	0.000	0.000	0.000
5	A	14	GLU	-1	-0.856	-0.951	7.481	-0.343	-0.343	0.000	0.000	0.000	0.000
6	A	15	GLN	0	0.029	0.021	7.479	-0.059	-0.059	0.000	0.000	0.000	0.000
7	A	16	GLN	0	-0.012	-0.018	9.458	0.134	0.134	0.000	0.000	0.000	0.000
8	A	17	LYS	1	0.944	0.989	11.394	0.349	0.349	0.000	0.000	0.000	0.000
9	A	18	GLU	-1	-0.807	-0.918	13.373	-0.338	-0.338	0.000	0.000	0.000	0.000
10	A	19	GLN	0	-0.029	-0.001	14.820	0.018	0.018	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.015	0.019	15.973	0.029	0.029	0.000	0.000	0.000	0.000
12	A	21	GLU	-1	-0.919	-0.961	17.479	-0.121	-0.121	0.000	0.000	0.000	0.000
13	A	22	SER	0	-0.022	-0.010	19.267	0.016	0.016	0.000	0.000	0.000	0.000
14	A	23	SER	0	-0.012	-0.039	19.996	0.015	0.015	0.000	0.000	0.000	0.000
15	A	24	LEU	0	-0.059	-0.021	21.060	0.013	0.013	0.000	0.000	0.000	0.000
16	A	25	GLN	0	0.030	-0.001	23.541	0.011	0.011	0.000	0.000	0.000	0.000
17	A	26	ASP	-1	-0.874	-0.924	25.117	-0.047	-0.047	0.000	0.000	0.000	0.000
18	A	27	ALA	0	0.005	-0.002	26.420	0.007	0.007	0.000	0.000	0.000	0.000
19	A	28	LEU	0	-0.016	-0.016	27.932	0.006	0.006	0.000	0.000	0.000	0.000
20	A	29	ALA	0	0.031	0.026	29.444	0.003	0.003	0.000	0.000	0.000	0.000
21	A	30	LYS	1	0.888	0.942	29.087	0.039	0.039	0.000	0.000	0.000	0.000
22	A	31	LEU	0	-0.050	-0.030	31.836	0.003	0.003	0.000	0.000	0.000	0.000
23	A	32	LYS	1	1.009	1.005	32.899	0.039	0.039	0.000	0.000	0.000	0.000
24	A	33	ASN	0	-0.053	-0.018	35.451	0.003	0.003	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.961	0.965	32.690	0.022	0.022	0.000	0.000	0.000	0.000
26	A	35	ASP	-1	-0.852	-0.919	38.540	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	36	ALA	0	0.009	0.004	40.059	0.001	0.001	0.000	0.000	0.000	0.000
28	A	37	LYS	1	0.922	0.953	40.985	0.023	0.023	0.000	0.000	0.000	0.000
29	A	38	GLN	0	0.008	0.009	41.808	0.002	0.002	0.000	0.000	0.000	0.000
30	A	39	THR	0	-0.002	0.001	44.269	0.002	0.002	0.000	0.000	0.000	0.000
31	A	40	VAL	0	-0.021	-0.013	45.696	0.001	0.001	0.000	0.000	0.000	0.000
32	A	41	GLN	0	-0.017	-0.008	47.619	0.000	0.000	0.000	0.000	0.000	0.000
33	A	42	LYS	1	0.994	1.013	46.977	0.013	0.013	0.000	0.000	0.000	0.000
34	A	43	HIS	0	-0.070	-0.035	49.319	0.001	0.001	0.000	0.000	0.000	0.000
35	A	44	ILE	0	-0.003	-0.008	51.715	0.000	0.000	0.000	0.000	0.000	0.000
36	A	45	ASP	-1	-0.844	-0.915	53.159	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	46	LEU	0	-0.037	-0.032	54.165	0.001	0.001	0.000	0.000	0.000	0.000
38	A	47	LEU	0	-0.017	-0.006	56.677	0.000	0.000	0.000	0.000	0.000	0.000
39	A	48	HIS	0	0.040	0.030	56.620	0.001	0.001	0.000	0.000	0.000	0.000
40	A	49	THR	0	0.032	0.023	59.092	0.001	0.001	0.000	0.000	0.000	0.000
41	A	50	TYR	0	-0.023	-0.015	61.124	0.000	0.000	0.000	0.000	0.000	0.000
42	A	51	ASN	0	-0.058	-0.063	61.947	0.000	0.000	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.871	-0.923	63.202	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	53	ILE	0	-0.011	-0.006	64.098	0.000	0.000	0.000	0.000	0.000	0.000
45	A	54	ARG	1	0.816	0.933	65.915	0.010	0.010	0.000	0.000	0.000	0.000
46	A	55	ASP	-1	-0.846	-0.924	68.647	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	56	ILE	0	-0.027	-0.015	69.090	0.000	0.000	0.000	0.000	0.000	0.000
48	A	57	ALA	0	-0.046	-0.021	71.385	0.000	0.000	0.000	0.000	0.000	0.000
49	A	58	LEU	0	0.014	-0.016	72.369	0.000	0.000	0.000	0.000	0.000	0.000
50	A	59	GLY	0	0.027	0.024	74.608	0.000	0.000	0.000	0.000	0.000	0.000
51	A	60	MET	0	-0.056	-0.036	73.695	0.000	0.000	0.000	0.000	0.000	0.000
52	A	61	ILE	0	-0.005	0.001	76.696	0.000	0.000	0.000	0.000	0.000	0.000
53	A	62	GLY	0	0.053	0.038	78.970	0.000	0.000	0.000	0.000	0.000	0.000
54	A	63	LYS	1	0.911	0.962	80.296	0.005	0.005	0.000	0.000	0.000	0.000
55	A	64	VAL	0	0.036	0.015	81.904	0.000	0.000	0.000	0.000	0.000	0.000
56	A	65	ALA	0	0.016	0.017	82.886	0.000	0.000	0.000	0.000	0.000	0.000
57	A	66	GLU	-1	-0.942	-0.990	84.802	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	67	HIS	0	-0.051	-0.022	86.672	0.000	0.000	0.000	0.000	0.000	0.000
59	A	68	GLU	-1	-0.900	-0.960	85.876	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	69	LYS	1	0.924	0.982	88.036	0.006	0.006	0.000	0.000	0.000	0.000
61	A	70	CYS	0	-0.030	0.004	91.024	0.000	0.000	0.000	0.000	0.000	0.000
62	A	71	THR	0	0.068	0.026	92.053	0.000	0.000	0.000	0.000	0.000	0.000
63	A	72	SER	0	-0.059	-0.049	92.363	0.000	0.000	0.000	0.000	0.000	0.000
64	A	73	VAL	0	-0.022	-0.024	94.848	0.000	0.000	0.000	0.000	0.000	0.000
65	A	74	GLU	-1	-0.955	-0.962	97.007	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	75	LEU	0	-0.087	-0.060	96.305	0.000	0.000	0.000	0.000	0.000	0.000
67	A	76	PHE	0	-0.044	-0.029	96.087	0.000	0.000	0.000	0.000	0.000	0.000
68	A	77	ASP	-1	-0.865	-0.928	101.186	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	78	ARG	1	0.863	0.946	101.247	0.003	0.003	0.000	0.000	0.000	0.000
70	A	79	PHE	0	-0.091	-0.040	101.543	0.000	0.000	0.000	0.000	0.000	0.000
71	A	80	NME	0	-0.012	0.008	103.401	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ACE )