FMO DATABASE

FMODB ID: 531VZ

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	OptH
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	-301519.36594
FMO2-HF: Nuclear repulsion	273440.387436
FMO2-HF: Total energy	-28078.978504
FMO2-MP2: Total energy	-28161.035375

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.
-8.315	-6.153	10.727	-4.981	-7.909	0.004

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 : 0.032 / q_NPA : 0.005

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	A	13	LEU	0	-0.072	-0.029	3.467	-2.879	1.440	-0.022	-2.236	-2.061	0.003
4	A	14	GLU	-1	-0.859	-0.953	3.607	-2.939	-2.277	0.010	-0.114	-0.559	0.000
5	A	15	GLN	0	0.028	0.020	2.178	-3.279	-6.237	10.740	-2.627	-5.155	0.001
6	A	16	GLN	0	-0.010	-0.017	5.988	-0.046	0.093	-0.001	-0.004	-0.134	0.000
7	A	17	LYS	1	0.943	0.988	8.900	1.924	1.924	0.000	0.000	0.000	0.000
8	A	18	GLU	-1	-0.808	-0.918	6.819	-0.738	-0.738	0.000	0.000	0.000	0.000
9	A	19	GLN	0	-0.029	-0.001	10.324	0.227	0.227	0.000	0.000	0.000	0.000
10	A	20	LEU	0	-0.016	0.019	12.223	-0.045	-0.045	0.000	0.000	0.000	0.000
11	A	21	GLU	-1	-0.920	-0.961	13.371	-0.338	-0.338	0.000	0.000	0.000	0.000
12	A	22	SER	0	-0.022	-0.011	14.125	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	23	SER	0	-0.013	-0.039	15.863	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	24	LEU	0	-0.058	-0.020	17.889	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	25	GLN	0	0.030	-0.001	18.734	0.024	0.024	0.000	0.000	0.000	0.000
16	A	26	ASP	-1	-0.874	-0.924	20.096	0.218	0.218	0.000	0.000	0.000	0.000
17	A	27	ALA	0	0.004	-0.002	21.898	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	28	LEU	0	-0.019	-0.016	23.644	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	29	ALA	0	0.033	0.027	24.270	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	30	LYS	1	0.889	0.942	24.677	-0.215	-0.215	0.000	0.000	0.000	0.000
21	A	31	LEU	0	-0.049	-0.030	27.973	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	32	LYS	1	1.009	1.005	28.053	0.020	0.020	0.000	0.000	0.000	0.000
23	A	33	ASN	0	-0.052	-0.017	30.331	0.002	0.002	0.000	0.000	0.000	0.000
24	A	34	ARG	1	0.961	0.964	28.949	-0.105	-0.105	0.000	0.000	0.000	0.000
25	A	35	ASP	-1	-0.852	-0.919	34.000	0.026	0.026	0.000	0.000	0.000	0.000
26	A	36	ALA	0	0.009	0.004	35.022	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	37	LYS	1	0.923	0.953	35.436	-0.088	-0.088	0.000	0.000	0.000	0.000
28	A	38	GLN	0	0.008	0.010	37.955	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	39	THR	0	-0.004	0.001	39.531	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	40	VAL	0	-0.018	-0.013	40.002	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	41	GLN	0	-0.017	-0.009	42.443	0.003	0.003	0.000	0.000	0.000	0.000
32	A	42	LYS	1	0.993	1.013	42.967	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	43	HIS	0	-0.069	-0.035	44.204	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	44	ILE	0	-0.003	-0.007	46.074	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	45	ASP	-1	-0.843	-0.915	48.557	0.036	0.036	0.000	0.000	0.000	0.000
36	A	46	LEU	0	-0.038	-0.033	49.508	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	47	LEU	0	-0.016	-0.006	51.279	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	48	HIS	0	0.039	0.029	51.430	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	49	THR	0	0.033	0.024	54.476	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	50	TYR	0	-0.023	-0.014	56.101	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	51	ASN	0	-0.058	-0.062	56.404	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	52	GLU	-1	-0.870	-0.923	58.291	0.026	0.026	0.000	0.000	0.000	0.000
43	A	53	ILE	0	-0.011	-0.006	59.477	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	54	ARG	1	0.818	0.933	60.158	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	55	ASP	-1	-0.847	-0.925	63.359	0.018	0.018	0.000	0.000	0.000	0.000
46	A	56	ILE	0	-0.027	-0.015	64.444	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	57	ALA	0	-0.046	-0.021	66.445	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	58	LEU	0	0.013	-0.017	66.727	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	59	GLY	0	0.026	0.023	69.441	0.000	0.000	0.000	0.000	0.000	0.000
50	A	60	MET	0	-0.054	-0.035	69.152	0.000	0.000	0.000	0.000	0.000	0.000
51	A	61	ILE	0	-0.006	0.000	71.648	0.000	0.000	0.000	0.000	0.000	0.000
52	A	62	GLY	0	0.052	0.038	73.680	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	63	LYS	1	0.913	0.962	75.101	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	64	VAL	0	0.034	0.014	77.117	0.000	0.000	0.000	0.000	0.000	0.000
55	A	65	ALA	0	0.017	0.017	77.463	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	66	GLU	-1	-0.942	-0.990	79.469	0.011	0.011	0.000	0.000	0.000	0.000
57	A	67	HIS	0	-0.050	-0.022	81.545	0.000	0.000	0.000	0.000	0.000	0.000
58	A	68	GLU	-1	-0.900	-0.960	80.871	0.004	0.004	0.000	0.000	0.000	0.000
59	A	69	LYS	1	0.924	0.982	82.198	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	70	CYS	0	-0.030	0.004	85.576	0.000	0.000	0.000	0.000	0.000	0.000
61	A	71	THR	0	0.068	0.026	87.098	0.000	0.000	0.000	0.000	0.000	0.000
62	A	72	SER	0	-0.059	-0.048	87.039	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	73	VAL	0	-0.021	-0.023	89.266	0.000	0.000	0.000	0.000	0.000	0.000
64	A	74	GLU	-1	-0.956	-0.963	91.618	0.006	0.006	0.000	0.000	0.000	0.000
65	A	75	LEU	0	-0.088	-0.061	91.176	0.000	0.000	0.000	0.000	0.000	0.000
66	A	76	PHE	0	-0.022	-0.009	90.466	0.000	0.000	0.000	0.000	0.000	0.000
67	A	77	ASP	-1	-0.867	-0.894	95.696	0.006	0.006	0.000	0.000	0.000	0.000
68	A	78	ARG	1	0.860	0.951	96.532	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	79	PHE	0	-0.113	-0.088	96.591	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:11:HIS)