FMO DATABASE

FMODB ID: J4M39

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

Total energy (hartree)

FMO2-HF: Electronic energy	-488509.555797
FMO2-HF: Nuclear repulsion	456708.423125
FMO2-HF: Total energy	-31801.132672
FMO2-MP2: Total energy	-31889.753303

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.
4.891	7.081	-0.014	-1.15	-1.026	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 : 0.149 / q_NPA : 0.085

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	0.884	1.045	3.660	2.778	3.315	0.001	-0.211	-0.326	0.001
5	B	6	PRO	0	0.040	-0.087	3.886	0.663	2.316	-0.015	-0.939	-0.700	0.002
6	B	7	ASP	0	0.098	0.011	6.546	0.230	0.230	0.000	0.000	0.000	0.000
7	B	7	ASP	-1	-0.951	-0.841	8.245	1.252	1.252	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.034	-0.125	8.631	-0.238	-0.238	0.000	0.000	0.000	0.000
9	B	8	TYR	0	-0.077	0.115	11.025	-0.019	-0.019	0.000	0.000	0.000	0.000
10	B	9	THR	0	-0.086	-0.117	11.756	0.061	0.061	0.000	0.000	0.000	0.000
11	B	9	THR	0	0.014	0.083	12.876	-0.029	-0.029	0.000	0.000	0.000	0.000
12	B	10	SER	0	0.063	-0.069	14.972	-0.021	-0.021	0.000	0.000	0.000	0.000
13	B	10	SER	0	-0.035	0.053	18.045	0.009	0.009	0.000	0.000	0.000	0.000
14	B	11	PHE	0	0.014	-0.103	17.098	0.006	0.006	0.000	0.000	0.000	0.000
15	B	11	PHE	0	-0.076	0.092	19.775	0.000	0.000	0.000	0.000	0.000	0.000
16	B	12	ASN	0	0.079	-0.061	19.547	-0.024	-0.024	0.000	0.000	0.000	0.000
17	B	12	ASN	0	-0.125	0.036	21.311	0.003	0.003	0.000	0.000	0.000	0.000
18	B	13	THR	0	0.047	-0.076	17.474	0.035	0.035	0.000	0.000	0.000	0.000
19	B	13	THR	0	-0.047	0.047	15.586	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	14	VAL	0	0.112	-0.092	18.030	-0.023	-0.023	0.000	0.000	0.000	0.000
21	B	14	VAL	0	-0.084	0.126	18.517	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	15	ASP	0	0.117	-0.118	18.911	-0.011	-0.011	0.000	0.000	0.000	0.000
23	B	15	ASP	-1	-0.921	-0.827	18.037	0.108	0.108	0.000	0.000	0.000	0.000
24	B	16	GLU	0	0.075	-0.124	20.416	-0.013	-0.013	0.000	0.000	0.000	0.000
25	B	16	GLU	-1	-0.821	-0.737	19.306	0.059	0.059	0.000	0.000	0.000	0.000
26	B	17	TRP	0	0.091	-0.048	22.438	-0.014	-0.014	0.000	0.000	0.000	0.000
27	B	17	TRP	0	-0.087	0.073	22.978	0.003	0.003	0.000	0.000	0.000	0.000
28	B	18	LEU	0	0.039	-0.133	23.693	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	18	LEU	0	-0.077	0.118	22.334	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	19	GLU	0	0.111	-0.106	24.587	-0.004	-0.004	0.000	0.000	0.000	0.000
31	B	19	GLU	-1	-0.895	-0.779	24.350	0.031	0.031	0.000	0.000	0.000	0.000
32	B	20	ALA	0	0.068	-0.116	26.295	-0.010	-0.010	0.000	0.000	0.000	0.000
33	B	20	ALA	0	-0.090	0.112	27.207	0.000	0.000	0.000	0.000	0.000	0.000
34	B	21	ILE	0	-0.009	-0.124	28.251	-0.007	-0.007	0.000	0.000	0.000	0.000
35	B	21	ILE	0	-0.131	0.070	27.900	0.000	0.000	0.000	0.000	0.000	0.000
36	B	22	LYS	0	0.004	-0.125	29.806	0.001	0.001	0.000	0.000	0.000	0.000
37	B	22	LYS	1	0.826	1.052	29.994	-0.027	-0.027	0.000	0.000	0.000	0.000
38	B	23	MET	0	0.060	-0.105	28.826	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	23	MET	0	-0.098	0.118	28.045	0.002	0.002	0.000	0.000	0.000	0.000
40	B	24	GLY	0	0.121	-0.069	25.783	0.006	0.006	0.000	0.000	0.000	0.000
41	B	25	GLN	0	0.089	0.029	25.603	0.001	0.001	0.000	0.000	0.000	0.000
42	B	25	GLN	0	-0.085	0.083	29.302	-0.005	-0.005	0.000	0.000	0.000	0.000
43	B	26	TYR	0	-0.009	-0.103	25.710	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	26	TYR	0	-0.073	0.055	25.881	0.000	0.000	0.000	0.000	0.000	0.000
45	B	27	LYS	0	0.131	-0.077	21.996	0.015	0.015	0.000	0.000	0.000	0.000
46	B	27	LYS	1	0.687	0.977	20.932	-0.045	-0.045	0.000	0.000	0.000	0.000
47	B	28	GLU	0	0.141	-0.098	19.798	0.020	0.020	0.000	0.000	0.000	0.000
48	B	28	GLU	-1	-0.952	-0.808	19.850	0.065	0.065	0.000	0.000	0.000	0.000
49	B	29	SER	0	-0.014	-0.089	20.371	0.017	0.017	0.000	0.000	0.000	0.000
50	B	29	SER	0	0.007	0.069	24.441	-0.005	-0.005	0.000	0.000	0.000	0.000
51	B	30	PHE	0	0.060	-0.067	21.274	0.008	0.008	0.000	0.000	0.000	0.000
52	B	30	PHE	0	-0.126	0.047	20.546	-0.004	-0.004	0.000	0.000	0.000	0.000
53	B	31	ALA	0	0.135	-0.082	17.115	0.026	0.026	0.000	0.000	0.000	0.000
54	B	31	ALA	0	-0.076	0.110	16.182	-0.004	-0.004	0.000	0.000	0.000	0.000
55	B	32	ASN	0	0.081	-0.085	16.939	0.036	0.036	0.000	0.000	0.000	0.000
56	B	32	ASN	0	-0.162	0.024	18.761	0.005	0.005	0.000	0.000	0.000	0.000
57	B	33	ALA	0	0.053	-0.099	18.868	0.011	0.011	0.000	0.000	0.000	0.000
58	B	33	ALA	0	-0.075	0.104	21.636	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	34	GLY	0	-0.035	-0.110	16.494	0.005	0.005	0.000	0.000	0.000	0.000
60	B	35	PHE	0	0.025	0.014	17.179	0.044	0.044	0.000	0.000	0.000	0.000
61	B	35	PHE	0	-0.107	0.076	20.720	-0.006	-0.006	0.000	0.000	0.000	0.000
62	B	36	THR	0	0.126	-0.099	14.843	-0.049	-0.049	0.000	0.000	0.000	0.000
63	B	36	THR	0	-0.031	0.087	13.492	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	37	SER	0	0.033	-0.082	15.905	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	37	SER	0	0.004	0.089	15.373	-0.007	-0.007	0.000	0.000	0.000	0.000
66	B	38	PHE	0	0.088	-0.090	17.313	-0.011	-0.011	0.000	0.000	0.000	0.000
67	B	38	PHE	0	-0.059	0.093	20.640	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	39	ASP	0	0.112	-0.075	19.438	-0.036	-0.036	0.000	0.000	0.000	0.000
69	B	39	ASP	-1	-0.947	-0.842	18.740	0.293	0.293	0.000	0.000	0.000	0.000
70	B	40	VAL	0	0.113	-0.092	19.453	-0.028	-0.028	0.000	0.000	0.000	0.000
71	B	40	VAL	0	-0.077	0.140	18.239	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	41	VAL	0	0.113	-0.090	20.921	-0.017	-0.017	0.000	0.000	0.000	0.000
73	B	41	VAL	0	-0.103	0.088	20.917	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	42	SER	0	-0.007	-0.117	23.109	-0.018	-0.018	0.000	0.000	0.000	0.000
75	B	42	SER	0	-0.028	0.068	23.853	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	43	GLN	0	-0.010	-0.128	24.491	-0.020	-0.020	0.000	0.000	0.000	0.000
77	B	43	GLN	0	-0.088	0.085	21.812	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	44	MET	0	0.097	-0.081	25.734	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	44	MET	0	-0.142	0.080	24.375	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	45	MET	0	0.081	-0.096	26.841	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	45	MET	0	-0.081	0.116	30.009	-0.002	-0.002	0.000	0.000	0.000	0.000
82	B	46	MET	0	0.123	-0.096	30.043	0.003	0.003	0.000	0.000	0.000	0.000
83	B	46	MET	0	-0.091	0.091	34.259	0.000	0.000	0.000	0.000	0.000	0.000
84	B	47	GLU	0	0.011	-0.156	31.724	-0.004	-0.004	0.000	0.000	0.000	0.000
85	B	47	GLU	-1	-0.898	-0.797	30.591	0.098	0.098	0.000	0.000	0.000	0.000
86	B	48	ASP	0	0.044	-0.119	27.136	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	48	ASP	-1	-0.823	-0.771	26.138	0.147	0.147	0.000	0.000	0.000	0.000
88	B	49	ILE	0	0.178	-0.044	27.329	0.005	0.005	0.000	0.000	0.000	0.000
89	B	49	ILE	0	-0.146	0.074	28.702	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	50	LEU	0	0.058	-0.127	29.182	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	50	LEU	0	-0.117	0.088	32.156	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	51	ARG	0	0.064	-0.081	27.931	-0.007	-0.007	0.000	0.000	0.000	0.000
93	B	51	ARG	1	0.763	1.006	22.923	-0.158	-0.158	0.000	0.000	0.000	0.000
94	B	52	VAL	0	0.016	-0.115	25.463	0.002	0.002	0.000	0.000	0.000	0.000
95	B	52	VAL	0	-0.111	0.105	23.841	0.000	0.000	0.000	0.000	0.000	0.000
96	B	53	GLY	0	0.036	-0.101	26.330	-0.004	-0.004	0.000	0.000	0.000	0.000
97	B	54	VAL	0	0.049	-0.013	29.509	-0.008	-0.008	0.000	0.000	0.000	0.000
98	B	54	VAL	0	-0.103	0.094	28.494	0.000	0.000	0.000	0.000	0.000	0.000
99	B	55	THR	0	0.079	-0.073	31.105	0.002	0.002	0.000	0.000	0.000	0.000
100	B	55	THR	0	-0.020	0.075	33.453	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	56	LEU	0	0.075	-0.096	34.606	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	56	LEU	0	-0.081	0.121	35.101	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	57	ALA	0	0.164	-0.077	35.693	0.003	0.003	0.000	0.000	0.000	0.000
104	B	57	ALA	0	-0.047	0.123	39.543	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	58	GLY	0	-0.045	-0.132	37.398	0.001	0.001	0.000	0.000	0.000	0.000
106	B	59	HIS	0	0.122	-0.002	33.329	0.000	0.000	0.000	0.000	0.000	0.000
107	B	59	HIS	0	-0.026	0.126	32.243	0.003	0.003	0.000	0.000	0.000	0.000
108	B	60	GLN	0	0.101	-0.094	32.660	0.005	0.005	0.000	0.000	0.000	0.000
109	B	60	GLN	0	-0.099	0.085	33.442	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	61	LYS	0	0.115	-0.053	33.336	0.006	0.006	0.000	0.000	0.000	0.000
111	B	61	LYS	1	0.862	1.060	37.325	-0.047	-0.047	0.000	0.000	0.000	0.000
112	B	62	LYS	0	0.065	-0.113	33.882	0.002	0.002	0.000	0.000	0.000	0.000
113	B	62	LYS	1	0.810	1.047	32.146	-0.061	-0.061	0.000	0.000	0.000	0.000
114	B	63	ILE	0	0.106	-0.088	29.896	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	63	ILE	0	-0.061	0.126	28.011	0.000	0.000	0.000	0.000	0.000	0.000
116	B	64	LEU	0	0.113	-0.099	30.189	0.007	0.007	0.000	0.000	0.000	0.000
117	B	64	LEU	0	-0.070	0.102	31.744	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	65	ASN	0	0.148	-0.045	32.319	0.004	0.004	0.000	0.000	0.000	0.000
119	B	65	ASN	0	-0.127	0.061	34.249	-0.002	-0.002	0.000	0.000	0.000	0.000
120	B	66	SER	0	0.006	-0.101	29.380	-0.003	-0.003	0.000	0.000	0.000	0.000
121	B	66	SER	0	-0.053	0.044	28.612	-0.002	-0.002	0.000	0.000	0.000	0.000
122	B	67	ILE	0	0.122	-0.071	27.984	0.003	0.003	0.000	0.000	0.000	0.000
123	B	67	ILE	0	-0.086	0.121	27.045	-0.002	-0.002	0.000	0.000	0.000	0.000
124	B	68	GLN	0	0.122	-0.082	29.005	0.007	0.007	0.000	0.000	0.000	0.000
125	B	68	GLN	0	-0.131	0.079	33.612	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	69	VAL	0	0.054	-0.105	31.555	0.001	0.001	0.000	0.000	0.000	0.000
127	B	69	VAL	0	-0.097	0.090	30.221	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	70	MET	0	0.080	-0.109	26.837	-0.005	-0.005	0.000	0.000	0.000	0.000
129	B	70	MET	0	-0.089	0.102	24.801	0.006	0.006	0.000	0.000	0.000	0.000
130	B	71	ARG	0	0.157	-0.071	27.958	0.007	0.007	0.000	0.000	0.000	0.000
131	B	71	ARG	1	0.769	1.027	28.582	-0.125	-0.125	0.000	0.000	0.000	0.000
132	B	72	ALA	0	0.085	-0.075	29.703	0.003	0.003	0.000	0.000	0.000	0.000
133	B	72	ALA	0	-0.102	0.093	32.831	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	73	GLN	0	0.105	-0.087	29.124	-0.003	-0.003	0.000	0.000	0.000	0.000
135	B	73	GLN	0	-0.087	0.081	28.007	0.006	0.006	0.000	0.000	0.000	0.000
136	B	74	MET	0	0.103	-0.101	27.310	-0.004	-0.004	0.000	0.000	0.000	0.000
137	B	74	MET	0	-0.105	0.100	23.182	0.000	0.000	0.000	0.000	0.000	0.000
138	B	75	ASN	0	0.089	-0.053	28.029	0.005	0.005	0.000	0.000	0.000	0.000
139	B	75	ASN	0	-0.119	0.052	31.245	0.006	0.006	0.000	0.000	0.000	0.000
140	B	76	GLN	0	0.127	-0.072	31.462	-0.002	-0.002	0.000	0.000	0.000	0.000
141	B	76	GLN	0	-0.122	0.063	31.893	0.000	0.000	0.000	0.000	0.000	0.000
142	B	77	ILE	0	0.091	-0.072	28.321	-0.009	-0.009	0.000	0.000	0.000	0.000
143	B	77	ILE	0	-0.096	0.094	26.064	0.001	0.001	0.000	0.000	0.000	0.000
144	B	78	GLN	0	0.063	-0.107	29.800	-0.001	-0.001	0.000	0.000	0.000	0.000
145	B	78	GLN	0	-0.118	0.063	28.315	0.003	0.003	0.000	0.000	0.000	0.000
146	B	79	SER	0	-0.047	-0.077	30.518	0.001	0.001	0.000	0.000	0.000	0.000
147	B	79	SER	0	-0.079	0.033	34.078	-0.003	-0.003	0.000	0.000	0.000	0.000
148	B	80	VAL	0	-0.100	-0.157	31.980	-0.010	-0.010	0.000	0.000	0.000	0.000
149	B	80	VAL	0	0.028	0.039	30.454	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)