FMO DATABASE

FMODB ID: 52JNZ

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:

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	-488525.442452
FMO2-HF: Nuclear repulsion	456708.423125
FMO2-HF: Total energy	-31817.019327
FMO2-MP2: Total energy	-31906.050858

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.
-0.689	1.615	-0.017	-1.195	-1.091	0.001

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 : 0.032 / 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

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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	0.045	0.019	3.800	-1.293	1.011	-0.017	-1.195	-1.091	0.001
4	B	7	ASP	-1	-0.879	-0.921	6.546	0.715	0.715	0.000	0.000	0.000	0.000
5	B	8	TYR	0	-0.039	-0.026	8.631	-0.097	-0.097	0.000	0.000	0.000	0.000
6	B	9	THR	0	-0.007	-0.014	10.974	-0.023	-0.023	0.000	0.000	0.000	0.000
7	B	10	SER	0	-0.027	-0.025	14.382	-0.038	-0.038	0.000	0.000	0.000	0.000
8	B	11	PHE	0	-0.043	-0.017	16.098	0.020	0.020	0.000	0.000	0.000	0.000
9	B	12	ASN	0	-0.043	-0.012	18.277	-0.001	-0.001	0.000	0.000	0.000	0.000
10	B	13	THR	0	0.012	-0.020	15.586	-0.004	-0.004	0.000	0.000	0.000	0.000
11	B	14	VAL	0	0.018	0.008	18.030	-0.013	-0.013	0.000	0.000	0.000	0.000
12	B	15	ASP	-1	-0.857	-0.941	18.037	0.070	0.070	0.000	0.000	0.000	0.000
13	B	16	GLU	-1	-0.767	-0.850	19.154	0.156	0.156	0.000	0.000	0.000	0.000
14	B	17	TRP	0	0.005	0.004	22.438	-0.009	-0.009	0.000	0.000	0.000	0.000
15	B	18	LEU	0	-0.009	0.000	22.334	-0.007	-0.007	0.000	0.000	0.000	0.000
16	B	19	GLU	-1	-0.811	-0.898	24.350	0.058	0.058	0.000	0.000	0.000	0.000
17	B	20	ALA	0	-0.049	-0.016	26.295	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	21	ILE	0	-0.101	-0.057	27.900	-0.006	-0.006	0.000	0.000	0.000	0.000
19	B	22	LYS	1	0.865	0.925	29.806	-0.062	-0.062	0.000	0.000	0.000	0.000
20	B	23	MET	0	-0.018	0.019	28.045	-0.006	-0.006	0.000	0.000	0.000	0.000
21	B	24	GLY	0	0.085	0.040	25.783	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	25	GLN	0	-0.032	-0.013	25.603	0.001	0.001	0.000	0.000	0.000	0.000
23	B	26	TYR	0	-0.006	-0.023	25.710	-0.005	-0.005	0.000	0.000	0.000	0.000
24	B	27	LYS	1	0.780	0.887	20.932	-0.062	-0.062	0.000	0.000	0.000	0.000
25	B	28	GLU	-1	-0.837	-0.908	19.798	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	29	SER	0	0.003	0.005	20.371	-0.006	-0.006	0.000	0.000	0.000	0.000
27	B	30	PHE	0	-0.013	-0.023	20.546	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	31	ALA	0	0.005	0.007	16.182	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	32	ASN	0	-0.050	-0.042	16.939	-0.017	-0.017	0.000	0.000	0.000	0.000
30	B	33	ALA	0	-0.056	-0.017	18.868	-0.010	-0.010	0.000	0.000	0.000	0.000
31	B	34	GLY	0	0.018	0.013	16.494	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	35	PHE	0	-0.033	-0.025	17.179	0.014	0.014	0.000	0.000	0.000	0.000
33	B	36	THR	0	0.036	0.000	13.492	0.007	0.007	0.000	0.000	0.000	0.000
34	B	37	SER	0	0.032	0.012	15.373	0.015	0.015	0.000	0.000	0.000	0.000
35	B	38	PHE	0	0.055	-0.010	17.313	-0.020	-0.020	0.000	0.000	0.000	0.000
36	B	39	ASP	-1	-0.887	-0.924	18.740	0.071	0.071	0.000	0.000	0.000	0.000
37	B	40	VAL	0	0.044	0.050	18.239	-0.014	-0.014	0.000	0.000	0.000	0.000
38	B	41	VAL	0	-0.004	-0.009	20.917	-0.011	-0.011	0.000	0.000	0.000	0.000
39	B	42	SER	0	-0.071	-0.045	23.109	-0.009	-0.009	0.000	0.000	0.000	0.000
40	B	43	GLN	0	-0.062	-0.048	21.812	-0.014	-0.014	0.000	0.000	0.000	0.000
41	B	44	MET	0	-0.065	0.008	24.375	-0.004	-0.004	0.000	0.000	0.000	0.000
42	B	45	MET	0	0.011	0.008	26.841	0.003	0.003	0.000	0.000	0.000	0.000
43	B	46	MET	0	-0.012	-0.013	30.043	0.001	0.001	0.000	0.000	0.000	0.000
44	B	47	GLU	-1	-0.859	-0.942	30.591	0.005	0.005	0.000	0.000	0.000	0.000
45	B	48	ASP	-1	-0.780	-0.876	26.138	0.005	0.005	0.000	0.000	0.000	0.000
46	B	49	ILE	0	0.001	-0.006	27.329	0.000	0.000	0.000	0.000	0.000	0.000
47	B	50	LEU	0	-0.032	-0.021	29.182	0.000	0.000	0.000	0.000	0.000	0.000
48	B	51	ARG	1	0.830	0.917	22.923	0.004	0.004	0.000	0.000	0.000	0.000
49	B	52	VAL	0	-0.031	-0.010	23.841	-0.003	-0.003	0.000	0.000	0.000	0.000
50	B	53	GLY	0	0.028	0.017	26.330	0.000	0.000	0.000	0.000	0.000	0.000
51	B	54	VAL	0	-0.040	-0.016	28.494	0.002	0.002	0.000	0.000	0.000	0.000
52	B	55	THR	0	0.017	0.003	31.105	0.000	0.000	0.000	0.000	0.000	0.000
53	B	56	LEU	0	0.004	0.013	34.606	0.000	0.000	0.000	0.000	0.000	0.000
54	B	57	ALA	0	0.074	0.029	35.693	0.002	0.002	0.000	0.000	0.000	0.000
55	B	58	GLY	0	-0.024	-0.013	37.398	0.001	0.001	0.000	0.000	0.000	0.000
56	B	59	HIS	0	0.052	0.029	32.243	0.002	0.002	0.000	0.000	0.000	0.000
57	B	60	GLN	0	0.032	0.006	32.660	0.003	0.003	0.000	0.000	0.000	0.000
58	B	61	LYS	1	0.970	0.992	33.336	-0.021	-0.021	0.000	0.000	0.000	0.000
59	B	62	LYS	1	0.867	0.932	32.146	-0.043	-0.043	0.000	0.000	0.000	0.000
60	B	63	ILE	0	0.044	0.029	28.011	0.005	0.005	0.000	0.000	0.000	0.000
61	B	64	LEU	0	0.057	0.021	30.189	0.003	0.003	0.000	0.000	0.000	0.000
62	B	65	ASN	0	0.001	0.003	32.319	0.004	0.004	0.000	0.000	0.000	0.000
63	B	66	SER	0	-0.033	-0.027	28.612	0.003	0.003	0.000	0.000	0.000	0.000
64	B	67	ILE	0	0.040	0.032	27.045	0.005	0.005	0.000	0.000	0.000	0.000
65	B	68	GLN	0	-0.030	-0.013	29.005	0.001	0.001	0.000	0.000	0.000	0.000
66	B	69	VAL	0	-0.009	-0.006	30.031	0.000	0.000	0.000	0.000	0.000	0.000
67	B	70	MET	0	-0.013	0.004	24.801	0.002	0.002	0.000	0.000	0.000	0.000
68	B	71	ARG	1	0.927	0.954	27.862	-0.034	-0.034	0.000	0.000	0.000	0.000
69	B	72	ALA	0	-0.031	0.000	29.676	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	73	GLN	0	0.028	0.006	27.426	0.004	0.004	0.000	0.000	0.000	0.000
71	B	74	MET	0	0.006	0.000	22.943	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	75	ASN	0	-0.010	0.001	27.422	0.000	0.000	0.000	0.000	0.000	0.000
73	B	76	GLN	0	-0.030	-0.017	30.755	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	77	ILE	0	-0.009	0.012	24.728	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	78	GLN	0	-0.040	-0.038	27.275	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	79	SER	0	-0.100	-0.042	29.327	-0.005	-0.005	0.000	0.000	0.000	0.000
77	B	80	VAL	0	-0.034	-0.004	28.741	-0.004	-0.004	0.000	0.000	0.000	0.000

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