FMO DATABASE

FMODB ID: 9LYG2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-464374.00124
FMO2-HF: Nuclear repulsion	433783.23489
FMO2-HF: Total energy	-30590.766351
FMO2-MP2: Total energy	-30675.819478

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.
-34.26	-32.587	20.393	-10.79	-11.277	-0.052

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 : -0.054 / q_NPA : -0.047

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	-0.887	-0.822	1.935	-18.495	-16.570	7.059	-4.857	-4.127	-0.069
4	A	8	TYR	0	0.051	-0.067	3.586	-0.640	1.639	-0.027	-1.066	-1.186	-0.002
5	A	8	TYR	0	-0.068	0.068	1.915	-16.705	-19.236	13.361	-4.867	-5.964	0.019
6	A	9	THR	0	-0.054	-0.122	5.865	0.436	0.436	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.031	0.067	7.159	-0.018	-0.018	0.000	0.000	0.000	0.000
8	A	10	SER	0	0.106	-0.078	8.797	-0.043	-0.043	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.055	0.075	10.071	0.080	0.080	0.000	0.000	0.000	0.000
10	A	11	PHE	0	0.048	-0.090	11.515	-0.032	-0.032	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.069	0.085	11.802	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.068	-0.081	15.037	0.014	0.014	0.000	0.000	0.000	0.000
13	A	12	ASN	0	-0.147	0.035	17.412	0.035	0.035	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.002	-0.098	18.446	0.016	0.016	0.000	0.000	0.000	0.000
15	A	13	THR	0	-0.069	0.030	20.692	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	14	VAL	0	0.141	-0.089	19.126	-0.038	-0.038	0.000	0.000	0.000	0.000
17	A	14	VAL	0	-0.080	0.126	21.855	0.000	0.000	0.000	0.000	0.000	0.000
18	A	15	ASP	0	0.105	-0.081	20.478	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	15	ASP	-1	-0.930	-0.823	22.230	-0.168	-0.168	0.000	0.000	0.000	0.000
20	A	16	GLU	0	0.136	-0.117	17.842	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	16	GLU	-1	-0.817	-0.736	16.812	-0.131	-0.131	0.000	0.000	0.000	0.000
22	A	17	TRP	0	0.104	-0.054	15.634	-0.072	-0.072	0.000	0.000	0.000	0.000
23	A	17	TRP	0	-0.106	0.070	14.874	0.031	0.031	0.000	0.000	0.000	0.000
24	A	18	LEU	0	0.030	-0.126	16.242	-0.090	-0.090	0.000	0.000	0.000	0.000
25	A	18	LEU	0	-0.077	0.114	20.195	0.003	0.003	0.000	0.000	0.000	0.000
26	A	19	GLU	0	0.112	-0.110	17.809	-0.039	-0.039	0.000	0.000	0.000	0.000
27	A	19	GLU	-1	-0.927	-0.796	17.645	-0.245	-0.245	0.000	0.000	0.000	0.000
28	A	20	ALA	0	0.073	-0.111	13.455	-0.046	-0.046	0.000	0.000	0.000	0.000
29	A	20	ALA	0	-0.079	0.114	12.402	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	21	ILE	0	-0.006	-0.124	13.127	-0.179	-0.179	0.000	0.000	0.000	0.000
31	A	21	ILE	0	-0.101	0.100	13.520	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	22	LYS	0	0.051	-0.068	14.899	0.010	0.010	0.000	0.000	0.000	0.000
33	A	22	LYS	1	0.858	1.045	12.013	0.868	0.868	0.000	0.000	0.000	0.000
34	A	23	MET	0	0.033	-0.124	17.023	0.023	0.023	0.000	0.000	0.000	0.000
35	A	23	MET	0	-0.081	0.112	18.652	0.012	0.012	0.000	0.000	0.000	0.000
36	A	24	GLY	0	0.103	-0.086	20.127	0.036	0.036	0.000	0.000	0.000	0.000
37	A	25	GLN	0	0.102	0.033	21.757	0.025	0.025	0.000	0.000	0.000	0.000
38	A	25	GLN	0	-0.095	0.080	23.826	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	26	TYR	0	-0.002	-0.098	24.253	0.021	0.021	0.000	0.000	0.000	0.000
40	A	26	TYR	0	-0.086	0.056	23.588	0.003	0.003	0.000	0.000	0.000	0.000
41	A	27	LYS	0	0.150	-0.086	24.821	0.009	0.009	0.000	0.000	0.000	0.000
42	A	27	LYS	1	0.702	0.993	21.669	0.208	0.208	0.000	0.000	0.000	0.000
43	A	28	GLU	0	0.116	-0.126	25.398	0.008	0.008	0.000	0.000	0.000	0.000
44	A	28	GLU	-1	-0.983	-0.830	29.025	-0.127	-0.127	0.000	0.000	0.000	0.000
45	A	29	SER	0	-0.048	-0.091	28.755	0.016	0.016	0.000	0.000	0.000	0.000
46	A	29	SER	0	-0.004	0.067	28.432	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	30	PHE	0	0.080	-0.065	26.409	0.011	0.011	0.000	0.000	0.000	0.000
48	A	30	PHE	0	-0.092	0.070	23.672	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	31	ALA	0	0.155	-0.066	27.925	0.008	0.008	0.000	0.000	0.000	0.000
50	A	31	ALA	0	-0.075	0.113	28.465	0.001	0.001	0.000	0.000	0.000	0.000
51	A	32	ASN	0	0.017	-0.088	29.633	0.010	0.010	0.000	0.000	0.000	0.000
52	A	32	ASN	0	-0.139	0.046	32.227	0.008	0.008	0.000	0.000	0.000	0.000
53	A	33	ALA	0	0.043	-0.150	31.521	0.009	0.009	0.000	0.000	0.000	0.000
54	A	33	ALA	0	-0.040	0.104	30.751	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	34	GLY	0	-0.035	-0.102	31.647	0.003	0.003	0.000	0.000	0.000	0.000
56	A	35	PHE	0	0.018	0.015	27.536	0.010	0.010	0.000	0.000	0.000	0.000
57	A	35	PHE	0	-0.086	0.090	26.555	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	36	THR	0	0.106	-0.104	26.016	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	36	THR	0	-0.049	0.073	27.847	0.001	0.001	0.000	0.000	0.000	0.000
60	A	37	SER	0	0.014	-0.101	24.214	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	37	SER	0	-0.042	0.055	25.226	0.001	0.001	0.000	0.000	0.000	0.000
62	A	38	PHE	0	0.120	-0.086	21.028	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	38	PHE	0	-0.044	0.109	18.002	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	39	ASP	0	0.067	-0.093	22.270	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	39	ASP	-1	-0.863	-0.781	25.585	-0.074	-0.074	0.000	0.000	0.000	0.000
66	A	40	VAL	0	0.067	-0.090	25.244	0.002	0.002	0.000	0.000	0.000	0.000
67	A	40	VAL	0	-0.079	0.114	27.090	0.000	0.000	0.000	0.000	0.000	0.000
68	A	41	VAL	0	0.140	-0.095	23.025	0.000	0.000	0.000	0.000	0.000	0.000
69	A	41	VAL	0	-0.107	0.096	21.298	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	42	SER	0	0.013	-0.114	21.909	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	42	SER	0	-0.032	0.061	21.519	0.008	0.008	0.000	0.000	0.000	0.000
72	A	43	GLN	0	-0.061	-0.129	22.754	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	43	GLN	0	-0.021	0.116	24.869	0.003	0.003	0.000	0.000	0.000	0.000
74	A	44	MET	0	0.122	-0.066	25.596	0.014	0.014	0.000	0.000	0.000	0.000
75	A	44	MET	0	-0.147	0.082	25.276	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	45	MET	0	0.084	-0.101	26.144	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	45	MET	0	-0.095	0.109	29.019	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	46	MET	0	0.134	-0.090	28.552	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	46	MET	0	-0.096	0.087	27.541	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	47	GLU	0	0.002	-0.154	29.555	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	47	GLU	-1	-0.903	-0.798	32.239	-0.132	-0.132	0.000	0.000	0.000	0.000
82	A	48	ASP	0	0.084	-0.110	29.817	0.006	0.006	0.000	0.000	0.000	0.000
83	A	48	ASP	-1	-0.881	-0.809	28.934	-0.137	-0.137	0.000	0.000	0.000	0.000
84	A	49	ILE	0	0.119	-0.077	27.332	0.003	0.003	0.000	0.000	0.000	0.000
85	A	49	ILE	0	-0.129	0.085	24.389	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	50	LEU	0	0.081	-0.128	28.230	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	50	LEU	0	-0.106	0.097	31.134	0.001	0.001	0.000	0.000	0.000	0.000
88	A	51	ARG	0	0.063	-0.073	31.515	0.002	0.002	0.000	0.000	0.000	0.000
89	A	51	ARG	1	0.811	1.051	32.603	0.117	0.117	0.000	0.000	0.000	0.000
90	A	52	VAL	0	-0.020	-0.118	29.099	0.013	0.013	0.000	0.000	0.000	0.000
91	A	52	VAL	0	-0.092	0.114	27.223	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	53	GLY	0	0.065	-0.107	29.506	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	54	VAL	0	0.076	-0.008	27.100	0.001	0.001	0.000	0.000	0.000	0.000
94	A	54	VAL	0	-0.095	0.113	25.243	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	55	THR	0	0.091	-0.080	28.328	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	55	THR	0	-0.051	0.077	31.299	0.005	0.005	0.000	0.000	0.000	0.000
97	A	56	LEU	0	0.062	-0.111	26.952	0.010	0.010	0.000	0.000	0.000	0.000
98	A	56	LEU	0	-0.092	0.117	26.281	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	57	ALA	0	0.166	-0.078	26.060	-0.021	-0.021	0.000	0.000	0.000	0.000
100	A	57	ALA	0	-0.055	0.117	27.615	0.002	0.002	0.000	0.000	0.000	0.000
101	A	58	GLY	0	-0.061	-0.135	23.096	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	59	HIS	0	0.127	0.001	21.687	-0.044	-0.044	0.000	0.000	0.000	0.000
103	A	59	HIS	0	-0.035	0.122	22.068	0.014	0.014	0.000	0.000	0.000	0.000
104	A	60	GLN	0	0.105	-0.087	22.359	-0.024	-0.024	0.000	0.000	0.000	0.000
105	A	60	GLN	0	-0.107	0.080	26.012	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	61	LYS	0	0.081	-0.058	22.523	0.000	0.000	0.000	0.000	0.000	0.000
107	A	61	LYS	1	0.871	1.053	21.786	0.264	0.264	0.000	0.000	0.000	0.000
108	A	62	LYS	0	0.080	-0.076	18.530	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	62	LYS	1	0.776	1.001	14.176	0.700	0.700	0.000	0.000	0.000	0.000
110	A	63	ILE	0	0.075	-0.110	18.073	-0.064	-0.064	0.000	0.000	0.000	0.000
111	A	63	ILE	0	-0.087	0.106	20.596	0.002	0.002	0.000	0.000	0.000	0.000
112	A	64	LEU	0	0.103	-0.100	19.811	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	64	LEU	0	-0.065	0.111	22.901	0.001	0.001	0.000	0.000	0.000	0.000
114	A	65	ASN	0	0.112	-0.059	18.309	0.022	0.022	0.000	0.000	0.000	0.000
115	A	65	ASN	0	-0.123	0.049	17.395	0.027	0.027	0.000	0.000	0.000	0.000
116	A	66	SER	0	0.032	-0.073	15.596	-0.023	-0.023	0.000	0.000	0.000	0.000
117	A	66	SER	0	0.009	0.068	15.600	-0.024	-0.024	0.000	0.000	0.000	0.000
118	A	67	ILE	0	0.055	-0.090	16.561	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	67	ILE	0	-0.064	0.128	20.346	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	68	GLN	0	0.123	-0.068	19.327	0.029	0.029	0.000	0.000	0.000	0.000
121	A	68	GLN	0	-0.098	0.083	18.775	0.017	0.017	0.000	0.000	0.000	0.000
122	A	69	VAL	0	0.054	-0.121	14.383	0.056	0.056	0.000	0.000	0.000	0.000
123	A	69	VAL	0	-0.094	0.094	12.248	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	70	MET	0	0.125	-0.095	15.412	0.011	0.011	0.000	0.000	0.000	0.000
125	A	70	MET	0	-0.109	0.113	16.957	0.016	0.016	0.000	0.000	0.000	0.000
126	A	71	ARG	0	0.103	-0.105	16.829	0.040	0.040	0.000	0.000	0.000	0.000
127	A	71	ARG	1	0.769	1.015	20.344	0.168	0.168	0.000	0.000	0.000	0.000
128	A	72	ALA	0	0.070	-0.085	16.862	0.051	0.051	0.000	0.000	0.000	0.000
129	A	72	ALA	0	-0.100	0.093	15.979	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	73	GLN	0	0.148	-0.069	14.845	0.046	0.046	0.000	0.000	0.000	0.000
131	A	73	GLN	0	-0.103	0.086	11.703	0.031	0.031	0.000	0.000	0.000	0.000
132	A	74	MET	0	0.087	-0.110	15.797	0.050	0.050	0.000	0.000	0.000	0.000
133	A	74	MET	0	-0.100	0.099	18.860	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	75	ASN	0	0.069	-0.061	19.312	0.032	0.032	0.000	0.000	0.000	0.000
135	A	75	ASN	0	-0.109	0.053	20.265	0.006	0.006	0.000	0.000	0.000	0.000
136	A	76	GLN	0	0.112	-0.078	17.001	0.021	0.021	0.000	0.000	0.000	0.000
137	A	76	GLN	0	-0.116	0.070	13.500	-0.040	-0.040	0.000	0.000	0.000	0.000
138	A	77	ILE	0	0.097	-0.063	18.295	0.030	0.030	0.000	0.000	0.000	0.000
139	A	77	ILE	0	-0.097	0.094	16.129	0.002	0.002	0.000	0.000	0.000	0.000
140	A	78	GLN	0	0.045	-0.120	19.360	0.023	0.023	0.000	0.000	0.000	0.000
141	A	78	GLN	0	-0.118	0.062	22.427	0.002	0.002	0.000	0.000	0.000	0.000
142	A	79	SER	0	-0.178	-0.181	21.710	0.022	0.022	0.000	0.000	0.000	0.000
143	A	79	SER	0	0.003	0.024	20.530	0.000	0.000	0.000	0.000	0.000	0.000

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