FMO DATABASE

FMODB ID: YY542

Calculation Name: 3VIR-A-Xray372

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: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, 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	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-302159.737049
FMO2-HF: Nuclear repulsion	274079.956144
FMO2-HF: Total energy	-28079.780905
FMO2-MP2: Total energy	-28161.815414

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:11:HIS)

Summations of interaction energy for fragment #1(A:11:HIS)

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.
-12.444	-8.784	11.152	-6.471	-8.343	0.027

Interaction energy analysis for fragmet #1(A:11:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.016

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	13	LEU	0	-0.043	-0.012	3.469	-1.791	2.541	-0.021	-2.226	-2.085	0.001
4	A	14	GLU	-1	-0.752	-0.883	3.337	-3.752	-3.005	0.018	-0.140	-0.626	0.000
5	A	15	GLN	0	-0.008	-0.006	1.957	-9.567	-10.986	11.155	-4.105	-5.632	0.026
6	A	16	GLN	0	-0.031	-0.024	5.928	0.956	0.956	0.000	0.000	0.000	0.000
7	A	17	LYS	1	0.824	0.925	7.958	3.703	3.703	0.000	0.000	0.000	0.000
8	A	18	GLU	-1	-0.781	-0.918	6.742	-2.289	-2.289	0.000	0.000	0.000	0.000
9	A	19	GLN	0	-0.030	-0.001	9.978	0.385	0.385	0.000	0.000	0.000	0.000
10	A	20	LEU	0	-0.002	0.018	11.918	0.117	0.117	0.000	0.000	0.000	0.000
11	A	21	GLU	-1	-0.920	-0.962	13.144	-0.712	-0.712	0.000	0.000	0.000	0.000
12	A	22	SER	0	0.002	-0.001	13.768	0.102	0.102	0.000	0.000	0.000	0.000
13	A	23	SER	0	-0.042	-0.044	15.512	0.065	0.065	0.000	0.000	0.000	0.000
14	A	24	LEU	0	-0.049	-0.014	17.521	0.032	0.032	0.000	0.000	0.000	0.000
15	A	25	GLN	0	0.048	0.009	18.477	0.076	0.076	0.000	0.000	0.000	0.000
16	A	26	ASP	-1	-0.810	-0.875	19.759	0.071	0.071	0.000	0.000	0.000	0.000
17	A	27	ALA	0	0.013	0.009	21.542	0.016	0.016	0.000	0.000	0.000	0.000
18	A	28	LEU	0	-0.021	-0.011	23.295	0.013	0.013	0.000	0.000	0.000	0.000
19	A	29	ALA	0	0.039	0.022	24.028	0.012	0.012	0.000	0.000	0.000	0.000
20	A	30	LYS	1	0.791	0.864	23.332	-0.042	-0.042	0.000	0.000	0.000	0.000
21	A	31	LEU	0	-0.067	-0.035	27.479	0.011	0.011	0.000	0.000	0.000	0.000
22	A	32	LYS	1	1.026	1.015	27.888	0.153	0.153	0.000	0.000	0.000	0.000
23	A	33	ASN	0	-0.063	-0.020	30.006	0.011	0.011	0.000	0.000	0.000	0.000
24	A	34	ARG	1	0.981	0.969	28.598	0.024	0.024	0.000	0.000	0.000	0.000
25	A	35	ASP	-1	-0.858	-0.918	33.633	-0.064	-0.064	0.000	0.000	0.000	0.000
26	A	36	ALA	0	0.005	0.013	34.693	0.002	0.002	0.000	0.000	0.000	0.000
27	A	37	LYS	1	0.930	0.956	34.938	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	38	GLN	0	-0.002	0.004	36.956	0.003	0.003	0.000	0.000	0.000	0.000
29	A	39	THR	0	-0.033	-0.027	38.932	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	40	VAL	0	-0.012	-0.004	40.005	0.001	0.001	0.000	0.000	0.000	0.000
31	A	41	GLN	0	-0.034	-0.022	42.114	0.005	0.005	0.000	0.000	0.000	0.000
32	A	42	LYS	1	0.998	1.012	41.872	0.045	0.045	0.000	0.000	0.000	0.000
33	A	43	HIS	0	-0.070	-0.042	43.832	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	44	ILE	0	0.008	-0.004	46.006	0.001	0.001	0.000	0.000	0.000	0.000
35	A	45	ASP	-1	-0.810	-0.891	47.985	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	46	LEU	0	-0.041	-0.027	49.424	0.000	0.000	0.000	0.000	0.000	0.000
37	A	47	LEU	0	-0.022	-0.008	51.128	0.000	0.000	0.000	0.000	0.000	0.000
38	A	48	HIS	0	0.041	0.027	50.875	0.001	0.001	0.000	0.000	0.000	0.000
39	A	49	THR	0	0.016	0.002	53.943	0.000	0.000	0.000	0.000	0.000	0.000
40	A	50	TYR	0	-0.037	-0.012	55.784	0.000	0.000	0.000	0.000	0.000	0.000
41	A	51	ASN	0	-0.035	-0.030	55.850	0.001	0.001	0.000	0.000	0.000	0.000
42	A	52	GLU	-1	-0.878	-0.923	58.405	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	53	ILE	0	-0.014	-0.013	59.336	0.000	0.000	0.000	0.000	0.000	0.000
44	A	54	ARG	1	0.753	0.862	60.340	0.005	0.005	0.000	0.000	0.000	0.000
45	A	55	ASP	-1	-0.783	-0.874	62.619	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	56	ILE	0	-0.022	-0.010	64.112	0.000	0.000	0.000	0.000	0.000	0.000
47	A	57	ALA	0	-0.042	-0.008	66.126	0.000	0.000	0.000	0.000	0.000	0.000
48	A	58	LEU	0	0.015	-0.022	66.037	0.000	0.000	0.000	0.000	0.000	0.000
49	A	59	GLY	0	0.028	0.024	69.124	0.001	0.001	0.000	0.000	0.000	0.000
50	A	60	MET	0	-0.063	-0.040	68.862	0.000	0.000	0.000	0.000	0.000	0.000
51	A	61	ILE	0	0.003	0.003	71.285	0.000	0.000	0.000	0.000	0.000	0.000
52	A	62	GLY	0	0.057	0.043	73.372	0.000	0.000	0.000	0.000	0.000	0.000
53	A	63	LYS	1	0.905	0.961	75.031	0.001	0.001	0.000	0.000	0.000	0.000
54	A	64	VAL	0	0.039	0.012	76.854	0.000	0.000	0.000	0.000	0.000	0.000
55	A	65	ALA	0	0.044	0.032	77.291	0.000	0.000	0.000	0.000	0.000	0.000
56	A	66	GLU	-1	-0.832	-0.920	79.169	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	67	HIS	0	-0.030	-0.005	81.233	0.001	0.001	0.000	0.000	0.000	0.000
58	A	68	GLU	-1	-0.912	-0.967	80.883	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	69	LYS	1	0.794	0.895	81.508	0.002	0.002	0.000	0.000	0.000	0.000
60	A	70	CYS	0	-0.053	-0.015	85.260	0.000	0.000	0.000	0.000	0.000	0.000
61	A	71	THR	0	0.053	0.015	86.715	0.000	0.000	0.000	0.000	0.000	0.000
62	A	72	SER	0	-0.045	-0.024	86.782	0.000	0.000	0.000	0.000	0.000	0.000
63	A	73	VAL	0	-0.013	-0.027	89.015	0.000	0.000	0.000	0.000	0.000	0.000
64	A	74	GLU	-1	-0.846	-0.886	91.324	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	75	LEU	0	-0.077	-0.057	91.043	0.000	0.000	0.000	0.000	0.000	0.000
66	A	76	PHE	0	-0.017	-0.006	89.939	0.000	0.000	0.000	0.000	0.000	0.000
67	A	77	ASP	-1	-0.868	-0.886	95.412	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	78	ARG	1	0.736	0.871	95.515	0.005	0.005	0.000	0.000	0.000	0.000
69	A	79	PHE	0	-0.114	-0.096	96.595	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:11:HIS)