FMO DATABASE

FMODB ID: K9G23

Calculation Name: 1B4F-B-Xray372

Preferred Name: Ephrin type-B receptor 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1B4F

Chain ID: B

ChEMBL ID: CHEMBL3290

UniProt ID: P29323

Base Structure: X-ray

Registration Date: 2023-06-22

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

Total energy (hartree)

FMO2-HF: Electronic energy	-486167.945325
FMO2-HF: Nuclear repulsion	454351.837263
FMO2-HF: Total energy	-31816.108062
FMO2-MP2: Total energy	-31905.256151

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(B:4:THR)

Summations of interaction energy for fragment #1(B:4:THR)

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.
-1.118	1.151	-0.002	-1.234	-1.033	0.002

Interaction energy analysis for fragmet #1(B:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / 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	B	6	PRO	0	0.016	0.000	3.748	-1.476	0.793	-0.002	-1.234	-1.033	0.002
4	B	7	ASP	-1	-0.865	-0.903	6.911	0.468	0.468	0.000	0.000	0.000	0.000
5	B	8	TYR	0	-0.041	-0.033	8.554	-0.092	-0.092	0.000	0.000	0.000	0.000
6	B	9	THR	0	-0.020	-0.022	10.713	0.025	0.025	0.000	0.000	0.000	0.000
7	B	10	SER	0	-0.041	-0.051	13.991	-0.007	-0.007	0.000	0.000	0.000	0.000
8	B	11	PHE	0	-0.044	-0.016	15.965	-0.001	-0.001	0.000	0.000	0.000	0.000
9	B	12	ASN	0	0.027	0.036	18.113	-0.002	-0.002	0.000	0.000	0.000	0.000
10	B	13	THR	0	0.050	0.041	15.859	0.002	0.002	0.000	0.000	0.000	0.000
11	B	14	VAL	0	0.052	0.020	17.956	0.001	0.001	0.000	0.000	0.000	0.000
12	B	15	ASP	-1	-0.840	-0.938	18.367	-0.035	-0.035	0.000	0.000	0.000	0.000
13	B	16	GLU	-1	-0.889	-0.945	19.962	0.012	0.012	0.000	0.000	0.000	0.000
14	B	17	TRP	0	-0.025	-0.021	22.348	0.002	0.002	0.000	0.000	0.000	0.000
15	B	18	LEU	0	0.007	0.004	22.443	0.001	0.001	0.000	0.000	0.000	0.000
16	B	19	GLU	-1	-0.897	-0.956	24.580	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	20	ALA	0	-0.024	0.000	26.405	0.001	0.001	0.000	0.000	0.000	0.000
18	B	21	ILE	0	-0.121	-0.051	28.286	0.001	0.001	0.000	0.000	0.000	0.000
19	B	22	LYS	1	0.899	0.938	29.946	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	23	MET	0	-0.008	0.010	28.175	-0.001	-0.001	0.000	0.000	0.000	0.000
21	B	24	GLY	0	0.068	0.035	25.810	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	25	GLN	0	-0.024	-0.016	25.577	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	26	TYR	0	-0.029	-0.056	25.847	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	27	LYS	1	0.850	0.940	20.931	0.017	0.017	0.000	0.000	0.000	0.000
25	B	28	GLU	-1	-0.872	-0.934	20.213	-0.045	-0.045	0.000	0.000	0.000	0.000
26	B	29	SER	0	-0.021	-0.012	20.793	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	30	PHE	0	0.014	-0.019	20.737	0.001	0.001	0.000	0.000	0.000	0.000
28	B	31	ALA	0	0.000	0.014	16.394	0.003	0.003	0.000	0.000	0.000	0.000
29	B	32	ASN	0	-0.010	0.008	17.045	-0.013	-0.013	0.000	0.000	0.000	0.000
30	B	33	ALA	0	-0.068	-0.032	18.658	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	34	GLY	0	0.027	0.011	16.141	0.005	0.005	0.000	0.000	0.000	0.000
32	B	35	PHE	0	-0.025	-0.028	17.169	0.013	0.013	0.000	0.000	0.000	0.000
33	B	36	THR	0	0.013	-0.012	13.401	0.002	0.002	0.000	0.000	0.000	0.000
34	B	37	SER	0	0.057	0.045	15.381	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	38	PHE	0	0.050	-0.010	17.145	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	39	ASP	-1	-0.933	-0.951	18.475	0.055	0.055	0.000	0.000	0.000	0.000
37	B	40	VAL	0	0.042	0.040	18.039	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	41	VAL	0	-0.002	-0.011	20.611	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	42	SER	0	-0.069	-0.043	22.866	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	43	GLN	0	-0.073	-0.049	22.089	-0.004	-0.004	0.000	0.000	0.000	0.000
41	B	44	MET	0	-0.077	-0.005	24.267	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	45	MET	0	0.010	-0.004	26.924	0.001	0.001	0.000	0.000	0.000	0.000
43	B	46	MET	0	-0.012	-0.024	29.928	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	47	GLU	-1	-0.924	-0.961	30.053	0.000	0.000	0.000	0.000	0.000	0.000
45	B	48	ASP	-1	-0.761	-0.868	25.982	0.001	0.001	0.000	0.000	0.000	0.000
46	B	49	ILE	0	0.021	0.004	27.181	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	50	LEU	0	-0.034	-0.015	28.855	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	51	ARG	1	0.849	0.921	24.930	0.004	0.004	0.000	0.000	0.000	0.000
49	B	52	VAL	0	-0.054	-0.009	23.845	-0.003	-0.003	0.000	0.000	0.000	0.000
50	B	53	GLY	0	0.038	0.018	26.304	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	54	VAL	0	-0.045	-0.009	28.532	0.000	0.000	0.000	0.000	0.000	0.000
52	B	55	THR	0	0.024	-0.013	31.106	0.001	0.001	0.000	0.000	0.000	0.000
53	B	56	LEU	0	0.017	0.024	34.746	0.001	0.001	0.000	0.000	0.000	0.000
54	B	57	ALA	0	0.069	0.025	35.974	0.000	0.000	0.000	0.000	0.000	0.000
55	B	58	GLY	0	-0.026	-0.012	37.478	0.001	0.001	0.000	0.000	0.000	0.000
56	B	59	HIS	0	0.066	0.045	32.525	0.000	0.000	0.000	0.000	0.000	0.000
57	B	60	GLN	0	0.034	0.020	32.773	0.001	0.001	0.000	0.000	0.000	0.000
58	B	61	LYS	1	0.957	0.987	33.595	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	62	LYS	1	0.925	0.967	32.822	-0.004	-0.004	0.000	0.000	0.000	0.000
60	B	63	ILE	0	0.045	0.017	27.757	0.001	0.001	0.000	0.000	0.000	0.000
61	B	64	LEU	0	0.063	0.021	30.083	0.001	0.001	0.000	0.000	0.000	0.000
62	B	65	ASN	0	-0.072	-0.033	32.181	0.002	0.002	0.000	0.000	0.000	0.000
63	B	66	SER	0	0.017	0.007	28.430	0.001	0.001	0.000	0.000	0.000	0.000
64	B	67	ILE	0	0.027	0.037	26.899	0.002	0.002	0.000	0.000	0.000	0.000
65	B	68	GLN	0	-0.021	-0.013	28.967	0.001	0.001	0.000	0.000	0.000	0.000
66	B	69	VAL	0	-0.038	-0.016	30.109	0.001	0.001	0.000	0.000	0.000	0.000
67	B	70	MET	0	-0.004	0.007	24.602	0.002	0.002	0.000	0.000	0.000	0.000
68	B	71	ARG	1	0.980	0.991	27.750	-0.014	-0.014	0.000	0.000	0.000	0.000
69	B	72	ALA	0	-0.014	0.004	29.433	0.001	0.001	0.000	0.000	0.000	0.000
70	B	73	GLN	0	0.013	0.006	27.071	0.003	0.003	0.000	0.000	0.000	0.000
71	B	74	MET	0	-0.035	-0.025	22.853	0.001	0.001	0.000	0.000	0.000	0.000
72	B	75	ASN	0	0.005	-0.011	27.364	0.002	0.002	0.000	0.000	0.000	0.000
73	B	76	GLN	0	-0.053	-0.019	30.591	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	77	ILE	0	0.024	0.027	24.734	0.000	0.000	0.000	0.000	0.000	0.000
75	B	78	GLN	0	0.017	0.009	25.806	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	79	SER	0	-0.125	-0.038	29.139	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	80	VAL	0	-0.056	-0.036	27.957	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:THR)