FMO DATABASE

FMODB ID: VR391

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	OptAll
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	-302225.247705
FMO2-HF: Nuclear repulsion	274145.065814
FMO2-HF: Total energy	-28080.181891
FMO2-MP2: Total energy	-28162.162591

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.
-10.603	-8.53	12.047	-5.529	-8.593	0.013

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 : 0.029 / q_NPA : 0.007

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	-0.030	0.006	3.524	-0.615	2.575	-0.013	-1.558	-1.619	0.000
4	A	14	GLU	-1	-0.802	-0.878	3.076	-4.760	-3.637	0.052	-0.265	-0.911	-0.001
5	A	15	GLN	0	0.041	-0.002	2.074	-8.914	-11.154	12.008	-3.706	-6.063	0.014
6	A	16	GLN	0	-0.024	-0.026	5.840	1.414	1.414	0.000	0.000	0.000	0.000
7	A	17	LYS	1	0.818	0.923	7.534	4.470	4.470	0.000	0.000	0.000	0.000
8	A	18	GLU	-1	-0.799	-0.924	6.452	-2.923	-2.923	0.000	0.000	0.000	0.000
9	A	19	GLN	0	-0.022	-0.001	9.939	0.400	0.400	0.000	0.000	0.000	0.000
10	A	20	LEU	0	-0.003	0.012	11.896	0.203	0.203	0.000	0.000	0.000	0.000
11	A	21	GLU	-1	-0.922	-0.969	13.185	-0.844	-0.844	0.000	0.000	0.000	0.000
12	A	22	SER	0	0.010	-0.003	13.801	0.156	0.156	0.000	0.000	0.000	0.000
13	A	23	SER	0	-0.052	-0.039	15.582	0.130	0.130	0.000	0.000	0.000	0.000
14	A	24	LEU	0	-0.028	-0.009	17.175	0.066	0.066	0.000	0.000	0.000	0.000
15	A	25	GLN	0	0.038	0.010	18.305	0.104	0.104	0.000	0.000	0.000	0.000
16	A	26	ASP	-1	-0.798	-0.863	19.721	-0.054	-0.054	0.000	0.000	0.000	0.000
17	A	27	ALA	0	-0.005	0.000	21.523	0.036	0.036	0.000	0.000	0.000	0.000
18	A	28	LEU	0	-0.016	-0.011	23.321	0.031	0.031	0.000	0.000	0.000	0.000
19	A	29	ALA	0	0.029	0.012	24.051	0.021	0.021	0.000	0.000	0.000	0.000
20	A	30	LYS	1	0.850	0.882	23.463	0.097	0.097	0.000	0.000	0.000	0.000
21	A	31	LEU	0	-0.083	-0.010	27.361	0.018	0.018	0.000	0.000	0.000	0.000
22	A	32	LYS	1	1.030	1.014	27.029	0.240	0.240	0.000	0.000	0.000	0.000
23	A	33	ASN	0	-0.041	-0.014	29.812	0.018	0.018	0.000	0.000	0.000	0.000
24	A	34	ARG	1	0.903	0.929	28.730	0.110	0.110	0.000	0.000	0.000	0.000
25	A	35	ASP	-1	-0.811	-0.902	33.567	-0.113	-0.113	0.000	0.000	0.000	0.000
26	A	36	ALA	0	-0.005	0.009	34.467	0.005	0.005	0.000	0.000	0.000	0.000
27	A	37	LYS	1	0.935	0.968	34.467	0.042	0.042	0.000	0.000	0.000	0.000
28	A	38	GLN	0	0.017	0.005	37.030	0.010	0.010	0.000	0.000	0.000	0.000
29	A	39	THR	0	-0.036	-0.030	38.640	0.001	0.001	0.000	0.000	0.000	0.000
30	A	40	VAL	0	0.002	0.001	39.940	0.002	0.002	0.000	0.000	0.000	0.000
31	A	41	GLN	0	-0.047	-0.028	42.043	0.005	0.005	0.000	0.000	0.000	0.000
32	A	42	LYS	1	0.926	0.964	41.062	0.082	0.082	0.000	0.000	0.000	0.000
33	A	43	HIS	0	-0.041	-0.028	43.882	0.000	0.000	0.000	0.000	0.000	0.000
34	A	44	ILE	0	-0.021	0.000	45.989	0.003	0.003	0.000	0.000	0.000	0.000
35	A	45	ASP	-1	-0.795	-0.892	47.809	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	46	LEU	0	-0.027	-0.007	49.253	0.001	0.001	0.000	0.000	0.000	0.000
37	A	47	LEU	0	-0.010	0.005	51.074	0.001	0.001	0.000	0.000	0.000	0.000
38	A	48	HIS	0	0.016	0.011	50.611	0.002	0.002	0.000	0.000	0.000	0.000
39	A	49	THR	0	0.030	0.001	53.748	0.001	0.001	0.000	0.000	0.000	0.000
40	A	50	TYR	0	-0.046	-0.023	55.559	0.001	0.001	0.000	0.000	0.000	0.000
41	A	51	ASN	0	-0.017	-0.016	55.857	0.002	0.002	0.000	0.000	0.000	0.000
42	A	52	GLU	-1	-0.895	-0.935	58.225	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	53	ILE	0	-0.011	-0.009	59.108	0.001	0.001	0.000	0.000	0.000	0.000
44	A	54	ARG	1	0.745	0.845	60.238	0.023	0.023	0.000	0.000	0.000	0.000
45	A	55	ASP	-1	-0.789	-0.876	62.676	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	56	ILE	0	-0.020	-0.005	63.761	0.001	0.001	0.000	0.000	0.000	0.000
47	A	57	ALA	0	-0.005	-0.003	66.013	0.001	0.001	0.000	0.000	0.000	0.000
48	A	58	LEU	0	0.000	-0.011	65.891	0.001	0.001	0.000	0.000	0.000	0.000
49	A	59	GLY	0	0.018	0.018	68.878	0.001	0.001	0.000	0.000	0.000	0.000
50	A	60	MET	0	-0.062	-0.036	69.189	0.001	0.001	0.000	0.000	0.000	0.000
51	A	61	ILE	0	0.015	0.010	71.288	0.001	0.001	0.000	0.000	0.000	0.000
52	A	62	GLY	0	0.028	0.020	73.095	0.001	0.001	0.000	0.000	0.000	0.000
53	A	63	LYS	1	0.912	0.946	74.899	0.013	0.013	0.000	0.000	0.000	0.000
54	A	64	VAL	0	0.016	0.018	76.497	0.001	0.001	0.000	0.000	0.000	0.000
55	A	65	ALA	0	0.063	0.035	77.439	0.000	0.000	0.000	0.000	0.000	0.000
56	A	66	GLU	-1	-0.846	-0.909	78.953	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	67	HIS	0	0.028	0.028	81.132	0.001	0.001	0.000	0.000	0.000	0.000
58	A	68	GLU	-1	-0.920	-0.958	80.607	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	69	LYS	1	0.792	0.888	81.156	0.012	0.012	0.000	0.000	0.000	0.000
60	A	70	CYS	0	-0.038	-0.024	84.915	0.001	0.001	0.000	0.000	0.000	0.000
61	A	71	THR	0	-0.009	-0.012	86.372	0.000	0.000	0.000	0.000	0.000	0.000
62	A	72	SER	0	-0.047	-0.041	86.560	0.000	0.000	0.000	0.000	0.000	0.000
63	A	73	VAL	0	-0.002	-0.001	88.988	0.000	0.000	0.000	0.000	0.000	0.000
64	A	74	GLU	-1	-0.803	-0.865	91.270	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	75	LEU	0	-0.053	-0.036	91.134	0.000	0.000	0.000	0.000	0.000	0.000
66	A	76	PHE	0	-0.037	-0.019	89.502	0.000	0.000	0.000	0.000	0.000	0.000
67	A	77	ASP	-1	-0.891	-0.936	94.955	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	78	ARG	1	0.699	0.852	95.082	0.013	0.013	0.000	0.000	0.000	0.000
69	A	79	PHE	0	-0.090	-0.062	96.527	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)