FMO DATABASE

FMODB ID: LQLJ9

Calculation Name: 1B4F-A-Xray540

Preferred Name: Ephrin type-B receptor 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1B4F

Chain ID: A

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-463743.673955
FMO2-HF: Nuclear repulsion	433152.934872
FMO2-HF: Total energy	-30590.739084
FMO2-MP2: Total energy	-30675.832584

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(A:6:PRO)

Summations of interaction energy for fragment #1(A:6:PRO)

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.
-20.744	-12.994	5.188	-5.876	-7.06	-0.043

Interaction energy analysis for fragmet #1(A:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.053

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	A	7	ASP	-1	-0.933	-0.838	2.222	-16.071	-12.233	2.200	-3.095	-2.942	-0.044
4	A	8	TYR	0	0.021	-0.092	3.673	1.283	2.359	-0.013	-0.335	-0.728	0.001
5	A	8	TYR	0	-0.107	0.086	2.476	-7.479	-4.643	3.001	-2.446	-3.390	0.000
6	A	9	THR	0	-0.033	-0.084	5.966	0.471	0.471	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.015	0.054	8.287	-0.176	-0.176	0.000	0.000	0.000	0.000
8	A	10	SER	0	0.131	-0.042	9.061	0.009	0.009	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.028	0.070	10.367	0.085	0.085	0.000	0.000	0.000	0.000
10	A	11	PHE	0	0.091	-0.110	11.866	-0.076	-0.076	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.085	0.087	11.656	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.042	-0.083	15.250	0.016	0.016	0.000	0.000	0.000	0.000
13	A	12	ASN	0	-0.140	0.048	17.323	0.036	0.036	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.010	-0.080	18.610	0.019	0.019	0.000	0.000	0.000	0.000
15	A	13	THR	0	-0.080	0.034	20.721	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	14	VAL	0	0.150	-0.091	19.354	-0.037	-0.037	0.000	0.000	0.000	0.000
17	A	14	VAL	0	-0.080	0.122	21.991	0.000	0.000	0.000	0.000	0.000	0.000
18	A	15	ASP	0	0.121	-0.116	20.370	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	15	ASP	-1	-0.904	-0.816	22.136	-0.196	-0.196	0.000	0.000	0.000	0.000
20	A	16	GLU	0	0.077	-0.103	17.893	-0.035	-0.035	0.000	0.000	0.000	0.000
21	A	16	GLU	-1	-0.820	-0.753	16.836	-0.178	-0.178	0.000	0.000	0.000	0.000
22	A	17	TRP	0	0.149	-0.045	15.514	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	17	TRP	0	-0.105	0.060	14.819	0.035	0.035	0.000	0.000	0.000	0.000
24	A	18	LEU	0	0.037	-0.115	16.121	-0.092	-0.092	0.000	0.000	0.000	0.000
25	A	18	LEU	0	-0.080	0.109	20.043	0.003	0.003	0.000	0.000	0.000	0.000
26	A	19	GLU	0	0.114	-0.103	17.812	-0.047	-0.047	0.000	0.000	0.000	0.000
27	A	19	GLU	-1	-0.907	-0.792	17.558	-0.288	-0.288	0.000	0.000	0.000	0.000
28	A	20	ALA	0	0.056	-0.103	13.387	-0.049	-0.049	0.000	0.000	0.000	0.000
29	A	20	ALA	0	-0.074	0.107	12.360	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	21	ILE	0	0.001	-0.122	13.035	-0.197	-0.197	0.000	0.000	0.000	0.000
31	A	21	ILE	0	-0.111	0.091	13.185	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	22	LYS	0	0.009	-0.054	14.760	0.029	0.029	0.000	0.000	0.000	0.000
33	A	22	LYS	1	0.855	1.031	12.359	0.951	0.951	0.000	0.000	0.000	0.000
34	A	23	MET	0	0.095	-0.122	17.376	0.026	0.026	0.000	0.000	0.000	0.000
35	A	23	MET	0	-0.083	0.113	18.752	0.015	0.015	0.000	0.000	0.000	0.000
36	A	24	GLY	0	0.099	-0.089	20.164	0.039	0.039	0.000	0.000	0.000	0.000
37	A	25	GLN	0	0.106	0.035	21.732	0.029	0.029	0.000	0.000	0.000	0.000
38	A	25	GLN	0	-0.086	0.076	23.872	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	26	TYR	0	-0.004	-0.090	23.986	0.023	0.023	0.000	0.000	0.000	0.000
40	A	26	TYR	0	-0.096	0.046	23.447	0.003	0.003	0.000	0.000	0.000	0.000
41	A	27	LYS	0	0.153	-0.104	24.734	0.012	0.012	0.000	0.000	0.000	0.000
42	A	27	LYS	1	0.682	0.998	21.584	0.242	0.242	0.000	0.000	0.000	0.000
43	A	28	GLU	0	0.110	-0.127	25.307	0.008	0.008	0.000	0.000	0.000	0.000
44	A	28	GLU	-1	-0.992	-0.834	29.199	-0.145	-0.145	0.000	0.000	0.000	0.000
45	A	29	SER	0	-0.061	-0.093	28.818	0.016	0.016	0.000	0.000	0.000	0.000
46	A	29	SER	0	-0.007	0.067	28.432	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	30	PHE	0	0.097	-0.067	26.240	0.014	0.014	0.000	0.000	0.000	0.000
48	A	30	PHE	0	-0.102	0.070	23.617	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	31	ALA	0	0.154	-0.079	27.757	0.010	0.010	0.000	0.000	0.000	0.000
50	A	31	ALA	0	-0.071	0.122	28.162	0.000	0.000	0.000	0.000	0.000	0.000
51	A	32	ASN	0	0.073	-0.074	29.359	0.010	0.010	0.000	0.000	0.000	0.000
52	A	32	ASN	0	-0.154	0.049	32.698	0.007	0.007	0.000	0.000	0.000	0.000
53	A	33	ALA	0	0.025	-0.133	31.352	0.012	0.012	0.000	0.000	0.000	0.000
54	A	33	ALA	0	-0.086	0.081	30.852	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	34	GLY	0	-0.013	-0.099	31.635	0.005	0.005	0.000	0.000	0.000	0.000
56	A	35	PHE	0	0.052	0.006	27.404	0.011	0.011	0.000	0.000	0.000	0.000
57	A	35	PHE	0	-0.125	0.081	26.420	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	36	THR	0	-0.004	-0.118	26.342	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	36	THR	0	-0.060	0.072	27.944	0.002	0.002	0.000	0.000	0.000	0.000
60	A	37	SER	0	0.096	-0.082	24.474	0.001	0.001	0.000	0.000	0.000	0.000
61	A	37	SER	0	-0.033	0.063	25.644	0.001	0.001	0.000	0.000	0.000	0.000
62	A	38	PHE	0	0.131	-0.087	20.963	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	38	PHE	0	-0.045	0.109	18.163	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	39	ASP	0	0.075	-0.102	22.253	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	39	ASP	-1	-0.871	-0.775	25.388	-0.076	-0.076	0.000	0.000	0.000	0.000
66	A	40	VAL	0	0.104	-0.090	25.006	0.000	0.000	0.000	0.000	0.000	0.000
67	A	40	VAL	0	-0.086	0.113	27.060	0.000	0.000	0.000	0.000	0.000	0.000
68	A	41	VAL	0	0.119	-0.107	23.074	0.002	0.002	0.000	0.000	0.000	0.000
69	A	41	VAL	0	-0.111	0.092	21.350	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	42	SER	0	0.005	-0.105	21.935	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	42	SER	0	-0.038	0.069	21.511	0.009	0.009	0.000	0.000	0.000	0.000
72	A	43	GLN	0	-0.065	-0.126	22.775	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	43	GLN	0	-0.042	0.106	25.069	0.004	0.004	0.000	0.000	0.000	0.000
74	A	44	MET	0	0.115	-0.064	25.385	0.013	0.013	0.000	0.000	0.000	0.000
75	A	44	MET	0	-0.148	0.069	24.963	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	45	MET	0	0.090	-0.106	25.929	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	45	MET	0	-0.074	0.120	28.741	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	46	MET	0	0.131	-0.088	28.253	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	46	MET	0	-0.099	0.080	27.337	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	47	GLU	0	0.009	-0.146	29.169	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	47	GLU	-1	-0.901	-0.808	32.157	-0.126	-0.126	0.000	0.000	0.000	0.000
82	A	48	ASP	0	0.067	-0.119	29.535	0.005	0.005	0.000	0.000	0.000	0.000
83	A	48	ASP	-1	-0.880	-0.806	28.618	-0.139	-0.139	0.000	0.000	0.000	0.000
84	A	49	ILE	0	0.121	-0.074	27.191	0.002	0.002	0.000	0.000	0.000	0.000
85	A	49	ILE	0	-0.135	0.077	24.275	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	50	LEU	0	0.070	-0.122	28.035	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	50	LEU	0	-0.102	0.091	30.861	0.001	0.001	0.000	0.000	0.000	0.000
88	A	51	ARG	0	0.112	-0.054	31.317	0.003	0.003	0.000	0.000	0.000	0.000
89	A	51	ARG	1	0.823	1.061	32.386	0.124	0.124	0.000	0.000	0.000	0.000
90	A	52	VAL	0	-0.049	-0.143	29.145	0.012	0.012	0.000	0.000	0.000	0.000
91	A	52	VAL	0	-0.096	0.119	27.142	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	53	GLY	0	0.029	-0.109	29.553	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	54	VAL	0	0.054	-0.016	26.943	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	54	VAL	0	-0.093	0.116	25.035	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	55	THR	0	0.102	-0.072	28.264	0.000	0.000	0.000	0.000	0.000	0.000
96	A	55	THR	0	-0.021	0.085	31.316	0.005	0.005	0.000	0.000	0.000	0.000
97	A	56	LEU	0	0.087	-0.107	27.359	0.011	0.011	0.000	0.000	0.000	0.000
98	A	56	LEU	0	-0.095	0.116	26.640	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	57	ALA	0	0.171	-0.073	26.417	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	57	ALA	0	-0.054	0.123	27.432	0.002	0.002	0.000	0.000	0.000	0.000
101	A	58	GLY	0	-0.058	-0.137	23.376	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	59	HIS	0	0.128	0.006	21.758	-0.047	-0.047	0.000	0.000	0.000	0.000
103	A	59	HIS	0	-0.044	0.128	22.674	0.016	0.016	0.000	0.000	0.000	0.000
104	A	60	GLN	0	0.130	-0.101	22.201	-0.027	-0.027	0.000	0.000	0.000	0.000
105	A	60	GLN	0	-0.112	0.095	25.856	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	61	LYS	0	0.039	-0.081	22.127	0.003	0.003	0.000	0.000	0.000	0.000
107	A	61	LYS	1	0.878	1.062	21.449	0.272	0.272	0.000	0.000	0.000	0.000
108	A	62	LYS	0	0.115	-0.066	18.294	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	62	LYS	1	0.757	0.997	14.473	0.735	0.735	0.000	0.000	0.000	0.000
110	A	63	ILE	0	0.078	-0.108	18.027	-0.056	-0.056	0.000	0.000	0.000	0.000
111	A	63	ILE	0	-0.075	0.115	20.497	0.002	0.002	0.000	0.000	0.000	0.000
112	A	64	LEU	0	0.100	-0.115	19.837	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	64	LEU	0	-0.057	0.119	22.613	0.002	0.002	0.000	0.000	0.000	0.000
114	A	65	ASN	0	0.101	-0.066	17.971	0.030	0.030	0.000	0.000	0.000	0.000
115	A	65	ASN	0	-0.128	0.048	17.086	0.031	0.031	0.000	0.000	0.000	0.000
116	A	66	SER	0	0.023	-0.071	15.386	-0.010	-0.010	0.000	0.000	0.000	0.000
117	A	66	SER	0	0.012	0.069	15.472	-0.028	-0.028	0.000	0.000	0.000	0.000
118	A	67	ILE	0	0.072	-0.088	16.379	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	67	ILE	0	-0.050	0.126	20.133	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	68	GLN	0	0.098	-0.070	19.008	0.031	0.031	0.000	0.000	0.000	0.000
121	A	68	GLN	0	-0.101	0.086	18.394	0.015	0.015	0.000	0.000	0.000	0.000
122	A	69	VAL	0	0.026	-0.135	14.240	0.064	0.064	0.000	0.000	0.000	0.000
123	A	69	VAL	0	-0.093	0.092	12.086	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	70	MET	0	0.156	-0.089	15.153	0.018	0.018	0.000	0.000	0.000	0.000
125	A	70	MET	0	-0.117	0.107	16.622	0.015	0.015	0.000	0.000	0.000	0.000
126	A	71	ARG	0	0.110	-0.104	16.508	0.042	0.042	0.000	0.000	0.000	0.000
127	A	71	ARG	1	0.784	1.027	20.262	0.153	0.153	0.000	0.000	0.000	0.000
128	A	72	ALA	0	0.056	-0.087	16.959	0.050	0.050	0.000	0.000	0.000	0.000
129	A	72	ALA	0	-0.078	0.100	16.032	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	73	GLN	0	0.127	-0.076	14.728	0.048	0.048	0.000	0.000	0.000	0.000
131	A	73	GLN	0	-0.098	0.091	11.544	0.027	0.027	0.000	0.000	0.000	0.000
132	A	74	MET	0	0.072	-0.114	15.749	0.054	0.054	0.000	0.000	0.000	0.000
133	A	74	MET	0	-0.091	0.098	18.569	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	75	ASN	0	0.077	-0.073	19.145	0.031	0.031	0.000	0.000	0.000	0.000
135	A	75	ASN	0	-0.110	0.060	20.055	0.004	0.004	0.000	0.000	0.000	0.000
136	A	76	GLN	0	0.105	-0.059	17.086	0.013	0.013	0.000	0.000	0.000	0.000
137	A	76	GLN	0	-0.105	0.065	13.359	-0.043	-0.043	0.000	0.000	0.000	0.000
138	A	77	ILE	0	0.073	-0.068	18.085	0.027	0.027	0.000	0.000	0.000	0.000
139	A	77	ILE	0	-0.067	0.104	15.826	0.002	0.002	0.000	0.000	0.000	0.000
140	A	78	GLN	0	0.068	-0.117	19.310	0.020	0.020	0.000	0.000	0.000	0.000
141	A	78	GLN	0	-0.110	0.071	22.317	0.000	0.000	0.000	0.000	0.000	0.000
142	A	79	SER	0	-0.218	-0.196	21.647	0.013	0.013	0.000	0.000	0.000	0.000
143	A	79	SER	0	0.016	0.031	20.539	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:PRO)