FMO DATABASE

FMODB ID: YY192

Calculation Name: 2B8I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B8I

Chain ID: A

ChEMBL ID:

UniProt ID: Q56GA4

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-486221.208935
FMO2-HF: Nuclear repulsion	456558.820262
FMO2-HF: Total energy	-29662.388673
FMO2-MP2: Total energy	-29750.337898

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:ILE)

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

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.
-9.444	-4.912	12.579	-4.466	-12.645	-0.019

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.000

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	PRO	0	0.060	0.019	3.550	-2.494	-0.239	0.025	-1.014	-1.266	0.004
4	A	4	TYR	0	0.004	0.001	5.045	-0.231	-0.066	-0.001	-0.006	-0.158	0.000
5	A	5	MET	0	0.041	0.030	2.327	-1.128	-2.310	6.918	-1.389	-4.348	-0.007
6	A	6	LYS	1	0.854	0.917	4.440	0.593	0.798	-0.001	-0.017	-0.187	0.000
7	A	7	ALA	0	-0.013	-0.007	5.316	0.085	0.121	-0.001	-0.001	-0.034	0.000
8	A	8	LEU	0	0.009	0.013	7.632	0.029	0.029	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.031	0.025	4.136	-0.100	0.020	0.000	-0.013	-0.106	0.000
10	A	10	TYR	0	-0.006	-0.023	8.178	0.061	0.061	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.862	-0.934	10.430	-0.075	-0.075	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.020	-0.013	11.326	0.054	0.054	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.050	-0.027	10.618	0.015	0.015	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.010	0.011	13.794	0.020	0.020	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.037	-0.029	16.044	0.039	0.039	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.048	-0.032	14.671	0.012	0.012	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.019	0.001	18.004	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.088	-0.053	19.768	0.014	0.014	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.039	0.004	20.581	0.021	0.021	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.861	-0.931	22.984	-0.053	-0.053	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.008	-0.027	23.828	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.938	-0.943	24.304	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.026	-0.023	22.852	0.009	0.009	0.000	0.000	0.000	0.000
24	A	24	HIS	0	-0.015	-0.015	20.080	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.037	-0.014	19.164	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.020	0.000	19.249	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.006	0.005	16.035	0.020	0.020	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.895	0.940	14.730	0.111	0.111	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.026	-0.020	14.128	-0.032	-0.032	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.012	-0.011	14.402	0.064	0.064	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.007	0.006	8.665	0.051	0.051	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.064	-0.049	10.286	0.050	0.050	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.865	-0.926	11.859	0.305	0.305	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.054	-0.025	10.897	0.051	0.051	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.097	-0.052	5.799	0.183	0.183	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.941	-0.955	7.560	0.907	0.907	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.026	-0.007	4.980	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.017	0.020	8.013	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.053	0.009	10.594	-0.118	-0.118	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.874	-0.946	10.786	-0.435	-0.435	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.838	0.907	5.668	1.448	1.448	0.000	0.000	0.000	0.000
42	A	42	GLN	0	0.013	0.008	8.259	-0.092	-0.092	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.002	0.014	10.419	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.009	-0.005	8.599	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.029	0.011	6.812	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	46	TYR	0	0.000	-0.003	9.078	0.049	0.049	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.019	-0.020	12.888	0.012	0.012	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.004	0.005	11.558	0.023	0.023	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.006	-0.010	10.138	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.021	0.018	11.210	0.061	0.061	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.030	0.031	13.771	0.045	0.045	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.005	0.004	14.926	0.034	0.034	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.013	0.000	14.977	0.020	0.020	0.000	0.000	0.000	0.000
54	A	54	SER	0	0.004	-0.012	16.999	0.032	0.032	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.086	-0.050	19.450	0.018	0.018	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.062	0.048	21.311	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.793	0.889	19.489	0.180	0.180	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.000	0.003	13.853	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.881	-0.933	18.347	-0.141	-0.141	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.053	-0.030	19.721	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	HIS	0	0.077	0.031	15.819	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.871	-0.910	15.920	-0.388	-0.388	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.035	0.018	15.596	-0.045	-0.045	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.017	0.008	12.939	-0.047	-0.047	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.002	-0.003	11.508	-0.062	-0.062	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.081	-0.052	10.852	-0.076	-0.076	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.032	0.035	11.432	-0.084	-0.084	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.009	-0.002	6.769	-0.115	-0.115	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.812	-0.896	6.453	-1.263	-1.263	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.023	-0.022	7.320	-0.213	-0.213	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.008	-0.002	5.554	-0.099	-0.099	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.019	-0.020	2.476	-1.175	-0.562	1.259	-0.328	-1.544	0.001
73	A	73	GLN	0	-0.017	-0.009	3.168	-2.278	-1.219	0.095	-0.494	-0.659	-0.005
74	A	74	LEU	0	-0.004	0.010	5.879	0.122	0.122	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.021	-0.003	2.341	-0.345	-0.209	1.995	-0.499	-1.632	-0.003
76	A	76	GLU	-1	-0.918	-0.915	2.138	-4.588	-2.971	2.163	-1.377	-2.404	-0.008
77	A	77	ILE	0	-0.079	-0.064	3.053	1.645	1.153	0.127	0.672	-0.307	-0.001

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