FMO DATABASE

FMODB ID: 49JLN

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	OptHSide
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	-486791.452479
FMO2-HF: Nuclear repulsion	454974.72429
FMO2-HF: Total energy	-31816.728189
FMO2-MP2: Total energy	-31905.77876

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.
-1.36	1.09	-0.016	-1.354	-1.08	0.003

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 : -0.005 / q_NPA : -0.014

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	B	6	PRO	0	0.038	0.011	3.771	-1.943	0.507	-0.016	-1.354	-1.080	0.003
4	B	7	ASP	-1	-0.883	-0.917	6.960	0.762	0.762	0.000	0.000	0.000	0.000
5	B	8	TYR	0	-0.029	-0.028	8.585	-0.098	-0.098	0.000	0.000	0.000	0.000
6	B	9	THR	0	-0.017	-0.024	10.752	0.020	0.020	0.000	0.000	0.000	0.000
7	B	10	SER	0	-0.015	-0.017	14.051	-0.038	-0.038	0.000	0.000	0.000	0.000
8	B	11	PHE	0	-0.052	-0.016	15.973	0.013	0.013	0.000	0.000	0.000	0.000
9	B	12	ASN	0	0.005	0.020	18.101	0.008	0.008	0.000	0.000	0.000	0.000
10	B	13	THR	0	0.014	-0.024	15.849	-0.002	-0.002	0.000	0.000	0.000	0.000
11	B	14	VAL	0	0.037	0.015	17.982	-0.007	-0.007	0.000	0.000	0.000	0.000
12	B	15	ASP	-1	-0.844	-0.934	18.804	-0.054	-0.054	0.000	0.000	0.000	0.000
13	B	16	GLU	-1	-0.841	-0.891	19.480	0.124	0.124	0.000	0.000	0.000	0.000
14	B	17	TRP	0	-0.017	-0.013	22.376	-0.002	-0.002	0.000	0.000	0.000	0.000
15	B	18	LEU	0	0.010	0.007	22.400	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	19	GLU	-1	-0.849	-0.917	24.669	-0.019	-0.019	0.000	0.000	0.000	0.000
17	B	20	ALA	0	-0.039	-0.013	26.434	-0.002	-0.002	0.000	0.000	0.000	0.000
18	B	21	ILE	0	-0.105	-0.043	28.283	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	22	LYS	1	0.888	0.937	29.958	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	23	MET	0	-0.006	0.007	28.194	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	24	GLY	0	0.081	0.040	25.828	-0.005	-0.005	0.000	0.000	0.000	0.000
22	B	25	GLN	0	-0.035	-0.015	25.595	-0.006	-0.006	0.000	0.000	0.000	0.000
23	B	26	TYR	0	-0.017	-0.038	25.864	-0.008	-0.008	0.000	0.000	0.000	0.000
24	B	27	LYS	1	0.795	0.896	21.008	0.033	0.033	0.000	0.000	0.000	0.000
25	B	28	GLU	-1	-0.841	-0.908	20.303	-0.164	-0.164	0.000	0.000	0.000	0.000
26	B	29	SER	0	-0.013	-0.008	20.805	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	30	PHE	0	0.012	-0.018	20.731	0.000	0.000	0.000	0.000	0.000	0.000
28	B	31	ALA	0	0.001	0.012	16.383	0.005	0.005	0.000	0.000	0.000	0.000
29	B	32	ASN	0	-0.048	-0.020	17.057	-0.034	-0.034	0.000	0.000	0.000	0.000
30	B	33	ALA	0	-0.058	-0.029	18.664	-0.011	-0.011	0.000	0.000	0.000	0.000
31	B	34	GLY	0	0.019	0.010	16.155	0.009	0.009	0.000	0.000	0.000	0.000
32	B	35	PHE	0	-0.025	-0.024	17.186	0.030	0.030	0.000	0.000	0.000	0.000
33	B	36	THR	0	0.019	-0.011	13.430	0.012	0.012	0.000	0.000	0.000	0.000
34	B	37	SER	0	0.052	0.037	15.319	0.016	0.016	0.000	0.000	0.000	0.000
35	B	38	PHE	0	0.045	-0.013	17.171	-0.024	-0.024	0.000	0.000	0.000	0.000
36	B	39	ASP	-1	-0.930	-0.947	18.446	0.142	0.142	0.000	0.000	0.000	0.000
37	B	40	VAL	0	0.053	0.046	18.094	-0.016	-0.016	0.000	0.000	0.000	0.000
38	B	41	VAL	0	-0.005	-0.014	20.634	-0.016	-0.016	0.000	0.000	0.000	0.000
39	B	42	SER	0	-0.074	-0.037	22.890	-0.009	-0.009	0.000	0.000	0.000	0.000
40	B	43	GLN	0	-0.067	-0.051	22.016	-0.012	-0.012	0.000	0.000	0.000	0.000
41	B	44	MET	0	-0.067	-0.003	24.396	-0.007	-0.007	0.000	0.000	0.000	0.000
42	B	45	MET	0	0.022	0.010	26.945	0.007	0.007	0.000	0.000	0.000	0.000
43	B	46	MET	0	-0.005	-0.018	29.946	-0.005	-0.005	0.000	0.000	0.000	0.000
44	B	47	GLU	-1	-0.922	-0.963	30.361	-0.012	-0.012	0.000	0.000	0.000	0.000
45	B	48	ASP	-1	-0.774	-0.869	26.014	-0.017	-0.017	0.000	0.000	0.000	0.000
46	B	49	ILE	0	0.006	-0.008	27.196	-0.007	-0.007	0.000	0.000	0.000	0.000
47	B	50	LEU	0	-0.028	-0.017	28.872	-0.006	-0.006	0.000	0.000	0.000	0.000
48	B	51	ARG	1	0.851	0.921	23.282	0.041	0.041	0.000	0.000	0.000	0.000
49	B	52	VAL	0	-0.039	-0.009	23.773	-0.010	-0.010	0.000	0.000	0.000	0.000
50	B	53	GLY	0	0.036	0.024	26.317	-0.008	-0.008	0.000	0.000	0.000	0.000
51	B	54	VAL	0	-0.046	-0.015	28.495	0.002	0.002	0.000	0.000	0.000	0.000
52	B	55	THR	0	0.018	-0.003	31.122	0.005	0.005	0.000	0.000	0.000	0.000
53	B	56	LEU	0	0.016	0.022	34.761	0.003	0.003	0.000	0.000	0.000	0.000
54	B	57	ALA	0	0.073	0.026	35.992	0.003	0.003	0.000	0.000	0.000	0.000
55	B	58	GLY	0	-0.019	-0.010	37.498	0.004	0.004	0.000	0.000	0.000	0.000
56	B	59	HIS	0	0.054	0.030	32.559	0.002	0.002	0.000	0.000	0.000	0.000
57	B	60	GLN	0	0.023	0.008	32.800	0.007	0.007	0.000	0.000	0.000	0.000
58	B	61	LYS	1	0.959	0.989	33.617	-0.011	-0.011	0.000	0.000	0.000	0.000
59	B	62	LYS	1	0.912	0.963	32.570	-0.028	-0.028	0.000	0.000	0.000	0.000
60	B	63	ILE	0	0.050	0.017	27.930	0.007	0.007	0.000	0.000	0.000	0.000
61	B	64	LEU	0	0.065	0.019	30.108	0.007	0.007	0.000	0.000	0.000	0.000
62	B	65	ASN	0	-0.037	-0.018	32.205	0.006	0.006	0.000	0.000	0.000	0.000
63	B	66	SER	0	-0.030	-0.019	28.802	0.006	0.006	0.000	0.000	0.000	0.000
64	B	67	ILE	0	0.041	0.039	26.898	0.009	0.009	0.000	0.000	0.000	0.000
65	B	68	GLN	0	-0.027	-0.013	28.994	0.004	0.004	0.000	0.000	0.000	0.000
66	B	69	VAL	0	-0.036	-0.018	30.326	0.005	0.005	0.000	0.000	0.000	0.000
67	B	70	MET	0	-0.009	0.008	24.794	0.008	0.008	0.000	0.000	0.000	0.000
68	B	71	ARG	1	0.958	0.978	27.770	-0.051	-0.051	0.000	0.000	0.000	0.000
69	B	72	ALA	0	-0.007	0.007	29.332	0.005	0.005	0.000	0.000	0.000	0.000
70	B	73	GLN	0	0.017	0.006	27.507	0.011	0.011	0.000	0.000	0.000	0.000
71	B	74	MET	0	-0.036	-0.023	22.816	0.006	0.006	0.000	0.000	0.000	0.000
72	B	75	ASN	0	-0.012	-0.014	27.337	0.008	0.008	0.000	0.000	0.000	0.000
73	B	76	GLN	0	-0.044	-0.016	30.575	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	77	ILE	0	0.029	0.030	24.895	0.001	0.001	0.000	0.000	0.000	0.000
75	B	78	GLN	0	0.022	0.015	26.026	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	79	SER	0	-0.128	-0.047	29.000	-0.004	-0.004	0.000	0.000	0.000	0.000
77	B	80	VAL	0	-0.056	-0.036	28.181	-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)