FMO DATABASE

FMODB ID: MRM3Z

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	OptH
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	-463241.694201
FMO2-HF: Nuclear repulsion	432652.329299
FMO2-HF: Total energy	-30589.364902
FMO2-MP2: Total energy	-30674.538372

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.
-13.959	-9.72	6.508	-4.744	-6.002	-0.048

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 : -0.052 / q_NPA : -0.060

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	-0.912	-0.815	2.023	-14.549	-13.126	5.051	-3.273	-3.201	-0.046
4	A	8	TYR	0	0.073	-0.115	3.770	1.118	2.212	-0.015	-0.334	-0.745	0.002
5	A	8	TYR	0	-0.129	0.108	2.787	-1.835	-0.113	1.472	-1.137	-2.056	-0.004
6	A	9	THR	0	-0.041	-0.085	5.985	0.383	0.383	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.003	0.062	8.018	-0.138	-0.138	0.000	0.000	0.000	0.000
8	A	10	SER	0	0.069	-0.050	9.173	0.005	0.005	0.000	0.000	0.000	0.000
9	A	10	SER	0	0.024	0.069	10.729	0.055	0.055	0.000	0.000	0.000	0.000
10	A	11	PHE	0	0.070	-0.074	11.984	-0.063	-0.063	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.074	0.084	11.850	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.067	-0.087	15.362	0.012	0.012	0.000	0.000	0.000	0.000
13	A	12	ASN	0	-0.118	0.078	17.545	0.023	0.023	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.113	-0.141	18.722	0.019	0.019	0.000	0.000	0.000	0.000
15	A	13	THR	0	-0.045	0.131	20.713	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	14	VAL	0	0.081	-0.081	19.453	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	14	VAL	0	-0.065	0.128	22.029	0.000	0.000	0.000	0.000	0.000	0.000
18	A	15	ASP	0	0.150	-0.139	20.458	-0.035	-0.035	0.000	0.000	0.000	0.000
19	A	15	ASP	-1	-0.963	-0.836	22.446	-0.168	-0.168	0.000	0.000	0.000	0.000
20	A	16	GLU	0	0.043	-0.088	18.065	-0.032	-0.032	0.000	0.000	0.000	0.000
21	A	16	GLU	-1	-0.929	-0.831	17.050	-0.172	-0.172	0.000	0.000	0.000	0.000
22	A	17	TRP	0	0.135	-0.050	15.603	-0.072	-0.072	0.000	0.000	0.000	0.000
23	A	17	TRP	0	-0.088	0.048	14.943	0.021	0.021	0.000	0.000	0.000	0.000
24	A	18	LEU	0	0.046	-0.119	16.198	-0.081	-0.081	0.000	0.000	0.000	0.000
25	A	18	LEU	0	-0.072	0.112	20.074	0.003	0.003	0.000	0.000	0.000	0.000
26	A	19	GLU	0	0.049	-0.106	17.894	-0.041	-0.041	0.000	0.000	0.000	0.000
27	A	19	GLU	-1	-0.950	-0.848	17.673	-0.259	-0.259	0.000	0.000	0.000	0.000
28	A	20	ALA	0	0.070	-0.100	13.373	-0.036	-0.036	0.000	0.000	0.000	0.000
29	A	20	ALA	0	-0.051	0.114	12.361	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	21	ILE	0	-0.032	-0.144	13.101	-0.173	-0.173	0.000	0.000	0.000	0.000
31	A	21	ILE	0	-0.102	0.104	13.409	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	22	LYS	0	0.031	-0.097	14.815	0.026	0.026	0.000	0.000	0.000	0.000
33	A	22	LYS	1	0.825	1.034	12.352	0.853	0.853	0.000	0.000	0.000	0.000
34	A	23	MET	0	0.086	-0.107	17.431	0.024	0.024	0.000	0.000	0.000	0.000
35	A	23	MET	0	-0.107	0.102	18.741	0.013	0.013	0.000	0.000	0.000	0.000
36	A	24	GLY	0	0.068	-0.093	20.225	0.034	0.034	0.000	0.000	0.000	0.000
37	A	25	GLN	0	0.118	0.018	21.805	0.025	0.025	0.000	0.000	0.000	0.000
38	A	25	GLN	0	-0.089	0.094	24.127	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	26	TYR	0	0.003	-0.102	24.054	0.021	0.021	0.000	0.000	0.000	0.000
40	A	26	TYR	0	-0.071	0.001	23.354	0.003	0.003	0.000	0.000	0.000	0.000
41	A	27	LYS	0	0.132	-0.092	24.775	0.008	0.008	0.000	0.000	0.000	0.000
42	A	27	LYS	1	0.819	1.057	22.036	0.220	0.220	0.000	0.000	0.000	0.000
43	A	28	GLU	0	0.108	-0.093	25.387	0.006	0.006	0.000	0.000	0.000	0.000
44	A	28	GLU	-1	-1.017	-0.851	29.677	-0.128	-0.128	0.000	0.000	0.000	0.000
45	A	29	SER	0	0.018	-0.079	28.914	0.013	0.013	0.000	0.000	0.000	0.000
46	A	29	SER	0	-0.053	0.073	28.493	0.001	0.001	0.000	0.000	0.000	0.000
47	A	30	PHE	0	0.065	-0.081	26.309	0.012	0.012	0.000	0.000	0.000	0.000
48	A	30	PHE	0	-0.086	0.068	23.543	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	31	ALA	0	0.081	-0.076	27.831	0.007	0.007	0.000	0.000	0.000	0.000
50	A	31	ALA	0	-0.011	0.098	28.336	0.001	0.001	0.000	0.000	0.000	0.000
51	A	32	ASN	0	0.126	-0.072	29.444	0.009	0.009	0.000	0.000	0.000	0.000
52	A	32	ASN	0	-0.158	0.063	33.086	0.004	0.004	0.000	0.000	0.000	0.000
53	A	33	ALA	0	-0.015	-0.105	31.428	0.011	0.011	0.000	0.000	0.000	0.000
54	A	33	ALA	0	-0.073	0.071	31.012	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	34	GLY	0	-0.006	-0.098	31.718	0.005	0.005	0.000	0.000	0.000	0.000
56	A	35	PHE	0	0.062	0.007	27.467	0.009	0.009	0.000	0.000	0.000	0.000
57	A	35	PHE	0	-0.126	0.082	26.456	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	36	THR	0	0.024	-0.122	26.423	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	36	THR	0	-0.058	0.071	28.074	0.002	0.002	0.000	0.000	0.000	0.000
60	A	37	SER	0	0.110	-0.079	24.596	0.002	0.002	0.000	0.000	0.000	0.000
61	A	37	SER	0	0.006	0.119	25.694	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	38	PHE	0	0.099	-0.077	21.038	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	38	PHE	0	-0.043	0.104	18.230	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	39	ASP	0	0.107	-0.122	22.331	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	39	ASP	-1	-0.948	-0.807	24.945	-0.080	-0.080	0.000	0.000	0.000	0.000
66	A	40	VAL	0	0.069	-0.111	25.077	0.000	0.000	0.000	0.000	0.000	0.000
67	A	40	VAL	0	-0.063	0.106	27.005	0.000	0.000	0.000	0.000	0.000	0.000
68	A	41	VAL	0	0.105	-0.098	23.123	0.002	0.002	0.000	0.000	0.000	0.000
69	A	41	VAL	0	-0.107	0.092	21.368	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	42	SER	0	0.007	-0.111	21.982	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	42	SER	0	-0.028	0.091	21.701	0.006	0.006	0.000	0.000	0.000	0.000
72	A	43	GLN	0	-0.060	-0.165	22.826	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	43	GLN	0	-0.096	0.086	25.114	0.010	0.010	0.000	0.000	0.000	0.000
74	A	44	MET	0	0.087	-0.079	25.424	0.012	0.012	0.000	0.000	0.000	0.000
75	A	44	MET	0	-0.121	0.079	25.025	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	45	MET	0	0.071	-0.096	25.961	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	45	MET	0	-0.074	0.109	28.786	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	46	MET	0	0.106	-0.068	28.280	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	46	MET	0	-0.103	0.061	27.581	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	47	GLU	0	0.035	-0.137	29.190	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	47	GLU	-1	-0.943	-0.830	32.227	-0.105	-0.105	0.000	0.000	0.000	0.000
82	A	48	ASP	0	0.069	-0.095	29.668	0.004	0.004	0.000	0.000	0.000	0.000
83	A	48	ASP	-1	-0.886	-0.808	28.721	-0.128	-0.128	0.000	0.000	0.000	0.000
84	A	49	ILE	0	0.130	-0.095	27.344	0.001	0.001	0.000	0.000	0.000	0.000
85	A	49	ILE	0	-0.108	0.075	24.471	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	50	LEU	0	0.064	-0.131	28.073	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	50	LEU	0	-0.099	0.108	31.003	0.001	0.001	0.000	0.000	0.000	0.000
88	A	51	ARG	0	0.103	-0.095	31.352	0.003	0.003	0.000	0.000	0.000	0.000
89	A	51	ARG	1	0.835	1.101	32.373	0.112	0.112	0.000	0.000	0.000	0.000
90	A	52	VAL	0	-0.052	-0.136	29.235	0.011	0.011	0.000	0.000	0.000	0.000
91	A	52	VAL	0	-0.096	0.124	27.274	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	53	GLY	0	0.017	-0.118	29.607	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	54	VAL	0	0.077	-0.038	26.973	0.000	0.000	0.000	0.000	0.000	0.000
94	A	54	VAL	0	-0.095	0.142	25.064	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	55	THR	0	0.083	-0.077	28.300	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	55	THR	0	-0.018	0.088	31.256	0.005	0.005	0.000	0.000	0.000	0.000
97	A	56	LEU	0	0.126	-0.128	27.346	0.010	0.010	0.000	0.000	0.000	0.000
98	A	56	LEU	0	-0.109	0.137	26.679	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	57	ALA	0	0.108	-0.066	26.430	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	57	ALA	0	-0.010	0.106	27.331	0.002	0.002	0.000	0.000	0.000	0.000
101	A	58	GLY	0	-0.064	-0.128	23.370	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	59	HIS	0	0.120	0.010	21.763	-0.042	-0.042	0.000	0.000	0.000	0.000
103	A	59	HIS	0	-0.023	0.171	22.482	0.015	0.015	0.000	0.000	0.000	0.000
104	A	60	GLN	0	0.139	-0.122	22.222	-0.024	-0.024	0.000	0.000	0.000	0.000
105	A	60	GLN	0	-0.126	0.122	25.850	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	61	LYS	0	0.036	-0.103	22.127	0.001	0.001	0.000	0.000	0.000	0.000
107	A	61	LYS	1	0.891	1.066	21.338	0.250	0.250	0.000	0.000	0.000	0.000
108	A	62	LYS	0	0.096	-0.069	18.296	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	62	LYS	1	0.819	1.049	14.942	0.628	0.628	0.000	0.000	0.000	0.000
110	A	63	ILE	0	0.104	-0.113	18.047	-0.052	-0.052	0.000	0.000	0.000	0.000
111	A	63	ILE	0	-0.094	0.128	20.587	0.001	0.001	0.000	0.000	0.000	0.000
112	A	64	LEU	0	0.101	-0.124	19.867	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	64	LEU	0	-0.058	0.132	22.569	0.002	0.002	0.000	0.000	0.000	0.000
114	A	65	ASN	0	0.116	-0.070	17.967	0.025	0.025	0.000	0.000	0.000	0.000
115	A	65	ASN	0	-0.137	0.059	17.257	0.027	0.027	0.000	0.000	0.000	0.000
116	A	66	SER	0	0.064	-0.038	15.405	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	66	SER	0	-0.046	0.048	15.626	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	67	ILE	0	0.121	-0.102	16.406	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	67	ILE	0	-0.080	0.134	20.206	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	68	GLN	0	0.094	-0.085	19.038	0.027	0.027	0.000	0.000	0.000	0.000
121	A	68	GLN	0	-0.109	0.094	18.102	0.018	0.018	0.000	0.000	0.000	0.000
122	A	69	VAL	0	0.005	-0.140	14.192	0.059	0.059	0.000	0.000	0.000	0.000
123	A	69	VAL	0	-0.062	0.094	12.048	-0.018	-0.018	0.000	0.000	0.000	0.000
124	A	70	MET	0	0.145	-0.100	15.178	0.010	0.010	0.000	0.000	0.000	0.000
125	A	70	MET	0	-0.110	0.116	16.781	0.017	0.017	0.000	0.000	0.000	0.000
126	A	71	ARG	0	0.100	-0.124	16.550	0.036	0.036	0.000	0.000	0.000	0.000
127	A	71	ARG	1	0.853	1.080	20.245	0.154	0.154	0.000	0.000	0.000	0.000
128	A	72	ALA	0	0.060	-0.093	16.958	0.045	0.045	0.000	0.000	0.000	0.000
129	A	72	ALA	0	-0.089	0.118	16.030	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	73	GLN	0	0.093	-0.066	14.683	0.039	0.039	0.000	0.000	0.000	0.000
131	A	73	GLN	0	-0.080	0.079	11.584	0.039	0.039	0.000	0.000	0.000	0.000
132	A	74	MET	0	0.056	-0.103	15.780	0.045	0.045	0.000	0.000	0.000	0.000
133	A	74	MET	0	-0.101	0.083	18.528	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	75	ASN	0	0.105	-0.060	19.188	0.027	0.027	0.000	0.000	0.000	0.000
135	A	75	ASN	0	-0.131	0.043	20.077	0.011	0.011	0.000	0.000	0.000	0.000
136	A	76	GLN	0	0.092	-0.078	17.095	0.014	0.014	0.000	0.000	0.000	0.000
137	A	76	GLN	0	-0.121	0.052	13.196	-0.049	-0.049	0.000	0.000	0.000	0.000
138	A	77	ILE	0	0.071	-0.074	18.138	0.024	0.024	0.000	0.000	0.000	0.000
139	A	77	ILE	0	-0.066	0.111	16.094	0.001	0.001	0.000	0.000	0.000	0.000
140	A	78	GLN	0	0.044	-0.104	19.349	0.018	0.018	0.000	0.000	0.000	0.000
141	A	78	GLN	0	-0.075	0.095	22.667	0.000	0.000	0.000	0.000	0.000	0.000
142	A	79	SER	0	-0.173	-0.192	21.650	0.010	0.010	0.000	0.000	0.000	0.000
143	A	79	SER	0	0.030	0.043	20.712	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)