FMO DATABASE

FMODB ID: NZ31Q

Calculation Name: 1B4F-B-Xray540

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: 2025-07-11

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	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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-486775.739479
FMO2-HF: Nuclear repulsion	454974.72429
FMO2-HF: Total energy	-31801.015188
FMO2-MP2: Total energy	-31889.655843

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.
3.941	5.987	-0.018	-1.183	-0.846	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 : 0.062 / q_NPA : 0.070

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].
4	B	5	ARG	1	0.902	1.056	3.704	2.653	2.924	-0.001	-0.080	-0.190	0.000
5	B	6	PRO	0	0.042	-0.100	3.931	-0.066	1.709	-0.017	-1.103	-0.656	0.003
6	B	7	ASP	0	0.102	0.029	6.975	0.124	0.124	0.000	0.000	0.000	0.000
7	B	7	ASP	-1	-0.964	-0.857	8.139	1.263	1.263	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.067	-0.116	8.585	-0.221	-0.221	0.000	0.000	0.000	0.000
9	B	8	TYR	0	-0.086	0.115	10.872	-0.023	-0.023	0.000	0.000	0.000	0.000
10	B	9	THR	0	-0.119	-0.142	11.719	0.063	0.063	0.000	0.000	0.000	0.000
11	B	9	THR	0	0.001	0.088	12.511	-0.021	-0.021	0.000	0.000	0.000	0.000
12	B	10	SER	0	0.109	-0.069	14.710	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	10	SER	0	-0.027	0.062	17.893	0.011	0.011	0.000	0.000	0.000	0.000
14	B	11	PHE	0	0.010	-0.097	17.143	-0.009	-0.009	0.000	0.000	0.000	0.000
15	B	11	PHE	0	-0.088	0.086	19.380	0.002	0.002	0.000	0.000	0.000	0.000
16	B	12	ASN	0	0.104	-0.027	19.382	-0.025	-0.025	0.000	0.000	0.000	0.000
17	B	12	ASN	0	-0.116	0.039	21.808	-0.009	-0.009	0.000	0.000	0.000	0.000
18	B	13	THR	0	0.069	-0.081	17.688	0.031	0.031	0.000	0.000	0.000	0.000
19	B	13	THR	0	-0.058	0.044	15.928	0.001	0.001	0.000	0.000	0.000	0.000
20	B	14	VAL	0	0.133	-0.095	17.982	-0.017	-0.017	0.000	0.000	0.000	0.000
21	B	14	VAL	0	-0.067	0.138	18.236	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	15	ASP	0	0.126	-0.126	18.852	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	15	ASP	-1	-0.938	-0.820	18.804	0.059	0.059	0.000	0.000	0.000	0.000
24	B	16	GLU	0	0.069	-0.131	20.525	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	16	GLU	-1	-0.883	-0.743	19.853	-0.013	-0.013	0.000	0.000	0.000	0.000
26	B	17	TRP	0	0.056	-0.078	22.376	-0.011	-0.011	0.000	0.000	0.000	0.000
27	B	17	TRP	0	-0.083	0.059	22.971	0.004	0.004	0.000	0.000	0.000	0.000
28	B	18	LEU	0	0.077	-0.124	23.625	-0.005	-0.005	0.000	0.000	0.000	0.000
29	B	18	LEU	0	-0.084	0.116	22.400	0.000	0.000	0.000	0.000	0.000	0.000
30	B	19	GLU	0	0.064	-0.114	24.718	0.000	0.000	0.000	0.000	0.000	0.000
31	B	19	GLU	-1	-0.896	-0.787	24.669	0.006	0.006	0.000	0.000	0.000	0.000
32	B	20	ALA	0	0.064	-0.121	26.434	-0.006	-0.006	0.000	0.000	0.000	0.000
33	B	20	ALA	0	-0.082	0.121	27.183	0.000	0.000	0.000	0.000	0.000	0.000
34	B	21	ILE	0	-0.002	-0.120	28.449	-0.006	-0.006	0.000	0.000	0.000	0.000
35	B	21	ILE	0	-0.145	0.073	28.283	0.000	0.000	0.000	0.000	0.000	0.000
36	B	22	LYS	0	-0.013	-0.124	29.958	0.002	0.002	0.000	0.000	0.000	0.000
37	B	22	LYS	1	0.875	1.064	30.898	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	23	MET	0	0.057	-0.113	28.956	-0.004	-0.004	0.000	0.000	0.000	0.000
39	B	23	MET	0	-0.083	0.108	28.194	0.003	0.003	0.000	0.000	0.000	0.000
40	B	24	GLY	0	0.123	-0.065	25.828	0.007	0.007	0.000	0.000	0.000	0.000
41	B	25	GLN	0	0.103	0.019	25.595	0.000	0.000	0.000	0.000	0.000	0.000
42	B	25	GLN	0	-0.085	0.088	29.395	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	26	TYR	0	-0.023	-0.103	25.864	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	26	TYR	0	-0.088	0.057	26.013	0.000	0.000	0.000	0.000	0.000	0.000
45	B	27	LYS	0	0.145	-0.082	22.087	0.016	0.016	0.000	0.000	0.000	0.000
46	B	27	LYS	1	0.694	0.986	21.008	-0.020	-0.020	0.000	0.000	0.000	0.000
47	B	28	GLU	0	0.141	-0.117	20.303	0.016	0.016	0.000	0.000	0.000	0.000
48	B	28	GLU	-1	-0.957	-0.798	20.340	0.055	0.055	0.000	0.000	0.000	0.000
49	B	29	SER	0	-0.005	-0.093	20.805	0.015	0.015	0.000	0.000	0.000	0.000
50	B	29	SER	0	-0.016	0.054	24.675	-0.005	-0.005	0.000	0.000	0.000	0.000
51	B	30	PHE	0	0.088	-0.070	21.477	0.013	0.013	0.000	0.000	0.000	0.000
52	B	30	PHE	0	-0.112	0.053	20.731	-0.004	-0.004	0.000	0.000	0.000	0.000
53	B	31	ALA	0	0.112	-0.068	17.309	0.029	0.029	0.000	0.000	0.000	0.000
54	B	31	ALA	0	-0.066	0.107	16.383	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	32	ASN	0	0.095	-0.047	17.057	0.038	0.038	0.000	0.000	0.000	0.000
56	B	32	ASN	0	-0.162	0.025	18.740	0.004	0.004	0.000	0.000	0.000	0.000
57	B	33	ALA	0	0.050	-0.113	18.664	0.018	0.018	0.000	0.000	0.000	0.000
58	B	33	ALA	0	-0.092	0.094	21.398	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	34	GLY	0	-0.028	-0.118	16.155	0.011	0.011	0.000	0.000	0.000	0.000
60	B	35	PHE	0	0.064	0.013	17.186	0.040	0.040	0.000	0.000	0.000	0.000
61	B	35	PHE	0	-0.115	0.076	20.571	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	36	THR	0	0.059	-0.115	14.841	-0.052	-0.052	0.000	0.000	0.000	0.000
63	B	36	THR	0	-0.042	0.085	13.430	0.001	0.001	0.000	0.000	0.000	0.000
64	B	37	SER	0	0.078	-0.061	15.706	-0.012	-0.012	0.000	0.000	0.000	0.000
65	B	37	SER	0	0.013	0.093	15.319	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	38	PHE	0	0.118	-0.087	17.171	-0.007	-0.007	0.000	0.000	0.000	0.000
67	B	38	PHE	0	-0.071	0.091	20.606	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	39	ASP	0	0.069	-0.094	19.209	-0.033	-0.033	0.000	0.000	0.000	0.000
69	B	39	ASP	-1	-0.959	-0.848	18.446	0.290	0.290	0.000	0.000	0.000	0.000
70	B	40	VAL	0	0.112	-0.102	19.216	-0.020	-0.020	0.000	0.000	0.000	0.000
71	B	40	VAL	0	-0.084	0.139	18.094	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	41	VAL	0	0.114	-0.092	20.634	-0.013	-0.013	0.000	0.000	0.000	0.000
73	B	41	VAL	0	-0.097	0.085	20.738	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	42	SER	0	-0.013	-0.117	22.890	-0.018	-0.018	0.000	0.000	0.000	0.000
75	B	42	SER	0	-0.022	0.078	23.508	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	43	GLN	0	-0.041	-0.127	24.364	-0.019	-0.019	0.000	0.000	0.000	0.000
77	B	43	GLN	0	-0.078	0.080	22.016	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	44	MET	0	0.084	-0.075	25.886	0.000	0.000	0.000	0.000	0.000	0.000
79	B	44	MET	0	-0.145	0.069	24.396	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	45	MET	0	0.079	-0.107	26.945	-0.009	-0.009	0.000	0.000	0.000	0.000
81	B	45	MET	0	-0.061	0.124	30.102	-0.003	-0.003	0.000	0.000	0.000	0.000
82	B	46	MET	0	0.122	-0.101	29.946	0.003	0.003	0.000	0.000	0.000	0.000
83	B	46	MET	0	-0.088	0.098	34.131	0.000	0.000	0.000	0.000	0.000	0.000
84	B	47	GLU	0	0.038	-0.142	31.698	-0.004	-0.004	0.000	0.000	0.000	0.000
85	B	47	GLU	-1	-0.968	-0.826	30.361	0.106	0.106	0.000	0.000	0.000	0.000
86	B	48	ASP	0	0.066	-0.120	27.046	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	48	ASP	-1	-0.824	-0.771	26.014	0.147	0.147	0.000	0.000	0.000	0.000
88	B	49	ILE	0	0.160	-0.046	27.196	0.005	0.005	0.000	0.000	0.000	0.000
89	B	49	ILE	0	-0.146	0.069	28.302	-0.002	-0.002	0.000	0.000	0.000	0.000
90	B	50	LEU	0	0.065	-0.117	28.872	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	50	LEU	0	-0.115	0.085	32.052	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	51	ARG	0	0.070	-0.077	28.035	-0.007	-0.007	0.000	0.000	0.000	0.000
93	B	51	ARG	1	0.765	1.011	23.282	-0.159	-0.159	0.000	0.000	0.000	0.000
94	B	52	VAL	0	0.043	-0.116	25.512	0.001	0.001	0.000	0.000	0.000	0.000
95	B	52	VAL	0	-0.122	0.110	23.773	0.000	0.000	0.000	0.000	0.000	0.000
96	B	53	GLY	0	0.028	-0.096	26.317	-0.004	-0.004	0.000	0.000	0.000	0.000
97	B	54	VAL	0	0.063	-0.011	29.419	-0.008	-0.008	0.000	0.000	0.000	0.000
98	B	54	VAL	0	-0.107	0.097	28.495	-0.001	-0.001	0.000	0.000	0.000	0.000
99	B	55	THR	0	0.039	-0.099	31.122	0.003	0.003	0.000	0.000	0.000	0.000
100	B	55	THR	0	-0.014	0.083	33.343	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	56	LEU	0	0.128	-0.081	34.761	-0.001	-0.001	0.000	0.000	0.000	0.000
102	B	56	LEU	0	-0.090	0.117	35.577	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	57	ALA	0	0.157	-0.073	35.992	0.003	0.003	0.000	0.000	0.000	0.000
104	B	57	ALA	0	-0.053	0.116	39.874	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	58	GLY	0	-0.048	-0.127	37.498	0.001	0.001	0.000	0.000	0.000	0.000
106	B	59	HIS	0	0.133	-0.011	33.640	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	59	HIS	0	-0.026	0.137	32.559	0.003	0.003	0.000	0.000	0.000	0.000
108	B	60	GLN	0	0.100	-0.104	32.800	0.003	0.003	0.000	0.000	0.000	0.000
109	B	60	GLN	0	-0.093	0.098	33.387	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	61	LYS	0	0.098	-0.055	33.617	0.005	0.005	0.000	0.000	0.000	0.000
111	B	61	LYS	1	0.846	1.059	37.429	-0.040	-0.040	0.000	0.000	0.000	0.000
112	B	62	LYS	0	0.069	-0.106	33.898	0.002	0.002	0.000	0.000	0.000	0.000
113	B	62	LYS	1	0.860	1.081	32.570	-0.045	-0.045	0.000	0.000	0.000	0.000
114	B	63	ILE	0	0.122	-0.103	29.857	-0.002	-0.002	0.000	0.000	0.000	0.000
115	B	63	ILE	0	-0.058	0.126	27.930	0.000	0.000	0.000	0.000	0.000	0.000
116	B	64	LEU	0	0.092	-0.111	30.108	0.007	0.007	0.000	0.000	0.000	0.000
117	B	64	LEU	0	-0.057	0.107	31.403	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	65	ASN	0	0.094	-0.054	32.205	0.004	0.004	0.000	0.000	0.000	0.000
119	B	65	ASN	0	-0.139	0.044	34.363	-0.003	-0.003	0.000	0.000	0.000	0.000
120	B	66	SER	0	0.015	-0.091	29.515	-0.002	-0.002	0.000	0.000	0.000	0.000
121	B	66	SER	0	-0.045	0.055	28.802	-0.003	-0.003	0.000	0.000	0.000	0.000
122	B	67	ILE	0	0.134	-0.077	27.995	0.001	0.001	0.000	0.000	0.000	0.000
123	B	67	ILE	0	-0.081	0.132	26.898	-0.002	-0.002	0.000	0.000	0.000	0.000
124	B	68	GLN	0	0.113	-0.095	28.994	0.007	0.007	0.000	0.000	0.000	0.000
125	B	68	GLN	0	-0.131	0.079	33.512	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	69	VAL	0	0.047	-0.108	31.612	0.001	0.001	0.000	0.000	0.000	0.000
127	B	69	VAL	0	-0.105	0.091	30.627	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	70	MET	0	0.061	-0.124	26.922	-0.005	-0.005	0.000	0.000	0.000	0.000
129	B	70	MET	0	-0.074	0.108	24.794	0.006	0.006	0.000	0.000	0.000	0.000
130	B	71	ARG	0	0.148	-0.055	28.068	0.005	0.005	0.000	0.000	0.000	0.000
131	B	71	ARG	1	0.816	1.055	28.501	-0.118	-0.118	0.000	0.000	0.000	0.000
132	B	72	ALA	0	0.081	-0.081	29.486	0.004	0.004	0.000	0.000	0.000	0.000
133	B	72	ALA	0	-0.076	0.094	33.081	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	73	GLN	0	0.080	-0.089	29.407	-0.003	-0.003	0.000	0.000	0.000	0.000
135	B	73	GLN	0	-0.074	0.084	28.278	0.003	0.003	0.000	0.000	0.000	0.000
136	B	74	MET	0	0.069	-0.107	27.251	-0.006	-0.006	0.000	0.000	0.000	0.000
137	B	74	MET	0	-0.115	0.087	23.201	0.002	0.002	0.000	0.000	0.000	0.000
138	B	75	ASN	0	0.084	-0.072	28.100	0.004	0.004	0.000	0.000	0.000	0.000
139	B	75	ASN	0	-0.118	0.049	31.157	0.006	0.006	0.000	0.000	0.000	0.000
140	B	76	GLN	0	0.103	-0.054	31.414	-0.001	-0.001	0.000	0.000	0.000	0.000
141	B	76	GLN	0	-0.122	0.050	31.950	0.000	0.000	0.000	0.000	0.000	0.000
142	B	77	ILE	0	0.120	-0.054	28.605	-0.007	-0.007	0.000	0.000	0.000	0.000
143	B	77	ILE	0	-0.083	0.090	26.403	0.000	0.000	0.000	0.000	0.000	0.000
144	B	78	GLN	0	0.079	-0.066	29.733	-0.003	-0.003	0.000	0.000	0.000	0.000
145	B	78	GLN	0	-0.069	0.093	26.942	-0.001	-0.001	0.000	0.000	0.000	0.000
146	B	79	SER	0	-0.063	-0.082	30.388	0.002	0.002	0.000	0.000	0.000	0.000
147	B	79	SER	0	-0.064	0.038	34.208	-0.003	-0.003	0.000	0.000	0.000	0.000
148	B	80	VAL	0	-0.120	-0.178	31.656	-0.010	-0.010	0.000	0.000	0.000	0.000
149	B	80	VAL	0	0.007	0.014	30.058	0.000	0.000	0.000	0.000	0.000	0.000

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