FMO DATABASE

FMODB ID: 3KNQL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-486151.495972
FMO2-HF: Nuclear repulsion	454351.837263
FMO2-HF: Total energy	-31799.658709
FMO2-MP2: Total energy	-31888.408576

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.
3.836	6.083	-0.019	-1.344	-0.883	0.004

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 : 0.032 / q_NPA : 0.093

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	0.945	1.070	3.803	2.550	2.833	-0.001	-0.085	-0.197	0.000
5	B	6	PRO	0	-0.023	-0.080	3.931	-0.287	1.677	-0.018	-1.259	-0.686	0.004
6	B	7	ASP	0	0.145	0.024	6.946	0.209	0.209	0.000	0.000	0.000	0.000
7	B	7	ASP	-1	-0.966	-0.854	7.684	1.411	1.411	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.022	-0.126	8.554	-0.259	-0.259	0.000	0.000	0.000	0.000
9	B	8	TYR	0	-0.075	0.118	10.855	-0.030	-0.030	0.000	0.000	0.000	0.000
10	B	9	THR	0	-0.082	-0.148	11.685	0.080	0.080	0.000	0.000	0.000	0.000
11	B	9	THR	0	0.025	0.091	12.623	-0.028	-0.028	0.000	0.000	0.000	0.000
12	B	10	SER	0	0.051	-0.065	14.678	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	10	SER	0	-0.042	0.042	17.905	0.007	0.007	0.000	0.000	0.000	0.000
14	B	11	PHE	0	0.010	-0.073	17.110	-0.004	-0.004	0.000	0.000	0.000	0.000
15	B	11	PHE	0	-0.092	0.067	19.068	0.000	0.000	0.000	0.000	0.000	0.000
16	B	12	ASN	0	0.143	-0.005	19.382	-0.025	-0.025	0.000	0.000	0.000	0.000
17	B	12	ASN	0	-0.115	0.035	21.768	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	13	THR	0	0.072	-0.068	17.660	0.039	0.039	0.000	0.000	0.000	0.000
19	B	13	THR	0	-0.009	0.097	15.958	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	14	VAL	0	0.130	-0.094	17.956	-0.019	-0.019	0.000	0.000	0.000	0.000
21	B	14	VAL	0	-0.073	0.146	18.278	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	15	ASP	0	0.121	-0.138	18.832	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	15	ASP	-1	-0.938	-0.825	18.367	0.053	0.053	0.000	0.000	0.000	0.000
24	B	16	GLU	0	0.042	-0.116	20.498	-0.011	-0.011	0.000	0.000	0.000	0.000
25	B	16	GLU	-1	-0.918	-0.821	20.441	0.000	0.000	0.000	0.000	0.000	0.000
26	B	17	TRP	0	0.077	-0.087	22.348	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	17	TRP	0	-0.102	0.061	22.802	0.005	0.005	0.000	0.000	0.000	0.000
28	B	18	LEU	0	0.076	-0.134	23.600	-0.005	-0.005	0.000	0.000	0.000	0.000
29	B	18	LEU	0	-0.093	0.128	22.443	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	19	GLU	0	0.066	-0.141	24.695	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	19	GLU	-1	-0.931	-0.801	24.580	0.000	0.000	0.000	0.000	0.000	0.000
32	B	20	ALA	0	0.092	-0.144	26.405	-0.008	-0.008	0.000	0.000	0.000	0.000
33	B	20	ALA	0	-0.091	0.145	27.172	0.001	0.001	0.000	0.000	0.000	0.000
34	B	21	ILE	0	-0.016	-0.140	28.422	-0.006	-0.006	0.000	0.000	0.000	0.000
35	B	21	ILE	0	-0.161	0.095	28.286	0.000	0.000	0.000	0.000	0.000	0.000
36	B	22	LYS	0	0.020	-0.117	29.946	0.002	0.002	0.000	0.000	0.000	0.000
37	B	22	LYS	1	0.867	1.067	31.866	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	23	MET	0	0.065	-0.102	28.935	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	23	MET	0	-0.096	0.105	28.175	0.003	0.003	0.000	0.000	0.000	0.000
40	B	24	GLY	0	0.103	-0.071	25.810	0.007	0.007	0.000	0.000	0.000	0.000
41	B	25	GLN	0	0.103	0.001	25.577	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	25	GLN	0	-0.097	0.097	29.364	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	26	TYR	0	-0.002	-0.103	25.847	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	26	TYR	0	-0.092	0.038	25.982	0.001	0.001	0.000	0.000	0.000	0.000
45	B	27	LYS	0	0.150	-0.102	22.034	0.018	0.018	0.000	0.000	0.000	0.000
46	B	27	LYS	1	0.745	1.033	20.931	-0.015	-0.015	0.000	0.000	0.000	0.000
47	B	28	GLU	0	0.150	-0.113	20.290	0.018	0.018	0.000	0.000	0.000	0.000
48	B	28	GLU	-1	-0.987	-0.803	20.213	0.032	0.032	0.000	0.000	0.000	0.000
49	B	29	SER	0	-0.019	-0.106	20.793	0.014	0.014	0.000	0.000	0.000	0.000
50	B	29	SER	0	-0.012	0.053	24.628	-0.005	-0.005	0.000	0.000	0.000	0.000
51	B	30	PHE	0	0.083	-0.060	21.461	0.013	0.013	0.000	0.000	0.000	0.000
52	B	30	PHE	0	-0.117	0.056	20.737	-0.004	-0.004	0.000	0.000	0.000	0.000
53	B	31	ALA	0	0.095	-0.077	17.274	0.034	0.034	0.000	0.000	0.000	0.000
54	B	31	ALA	0	-0.046	0.097	16.394	-0.006	-0.006	0.000	0.000	0.000	0.000
55	B	32	ASN	0	0.134	-0.053	17.045	0.039	0.039	0.000	0.000	0.000	0.000
56	B	32	ASN	0	-0.150	0.063	18.604	0.005	0.005	0.000	0.000	0.000	0.000
57	B	33	ALA	0	0.010	-0.093	18.658	0.017	0.017	0.000	0.000	0.000	0.000
58	B	33	ALA	0	-0.080	0.075	21.480	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	34	GLY	0	-0.011	-0.108	16.141	0.013	0.013	0.000	0.000	0.000	0.000
60	B	35	PHE	0	0.045	0.001	17.169	0.047	0.047	0.000	0.000	0.000	0.000
61	B	35	PHE	0	-0.111	0.079	20.524	-0.006	-0.006	0.000	0.000	0.000	0.000
62	B	36	THR	0	0.094	-0.107	14.832	-0.057	-0.057	0.000	0.000	0.000	0.000
63	B	36	THR	0	-0.059	0.089	13.401	0.002	0.002	0.000	0.000	0.000	0.000
64	B	37	SER	0	0.057	-0.091	15.680	-0.009	-0.009	0.000	0.000	0.000	0.000
65	B	37	SER	0	0.029	0.111	15.381	-0.009	-0.009	0.000	0.000	0.000	0.000
66	B	38	PHE	0	0.098	-0.077	17.145	-0.012	-0.012	0.000	0.000	0.000	0.000
67	B	38	PHE	0	-0.042	0.090	20.816	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	39	ASP	0	0.100	-0.101	19.183	-0.039	-0.039	0.000	0.000	0.000	0.000
69	B	39	ASP	-1	-0.987	-0.840	18.475	0.338	0.338	0.000	0.000	0.000	0.000
70	B	40	VAL	0	0.041	-0.087	19.202	-0.022	-0.022	0.000	0.000	0.000	0.000
71	B	40	VAL	0	-0.046	0.114	18.039	0.000	0.000	0.000	0.000	0.000	0.000
72	B	41	VAL	0	0.104	-0.081	20.611	-0.017	-0.017	0.000	0.000	0.000	0.000
73	B	41	VAL	0	-0.070	0.072	20.690	-0.005	-0.005	0.000	0.000	0.000	0.000
74	B	42	SER	0	-0.014	-0.110	22.866	-0.021	-0.021	0.000	0.000	0.000	0.000
75	B	42	SER	0	-0.024	0.077	23.498	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	43	GLN	0	-0.056	-0.121	24.342	-0.020	-0.020	0.000	0.000	0.000	0.000
77	B	43	GLN	0	-0.068	0.071	22.089	-0.005	-0.005	0.000	0.000	0.000	0.000
78	B	44	MET	0	0.077	-0.063	25.884	0.000	0.000	0.000	0.000	0.000	0.000
79	B	44	MET	0	-0.132	0.051	24.267	-0.003	-0.003	0.000	0.000	0.000	0.000
80	B	45	MET	0	0.054	-0.100	26.924	-0.008	-0.008	0.000	0.000	0.000	0.000
81	B	45	MET	0	-0.059	0.101	29.968	-0.003	-0.003	0.000	0.000	0.000	0.000
82	B	46	MET	0	0.114	-0.125	29.928	0.003	0.003	0.000	0.000	0.000	0.000
83	B	46	MET	0	-0.081	0.107	34.102	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	47	GLU	0	0.034	-0.191	31.683	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	47	GLU	-1	-0.967	-0.774	30.053	0.120	0.120	0.000	0.000	0.000	0.000
86	B	48	ASP	0	0.071	-0.102	27.039	-0.005	-0.005	0.000	0.000	0.000	0.000
87	B	48	ASP	-1	-0.815	-0.763	25.982	0.155	0.155	0.000	0.000	0.000	0.000
88	B	49	ILE	0	0.205	-0.080	27.181	0.004	0.004	0.000	0.000	0.000	0.000
89	B	49	ILE	0	-0.173	0.125	28.209	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	50	LEU	0	0.064	-0.143	28.855	-0.005	-0.005	0.000	0.000	0.000	0.000
91	B	50	LEU	0	-0.103	0.085	32.008	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	51	ARG	0	0.040	-0.119	27.982	-0.008	-0.008	0.000	0.000	0.000	0.000
93	B	51	ARG	1	0.740	1.049	24.930	-0.158	-0.158	0.000	0.000	0.000	0.000
94	B	52	VAL	0	0.011	-0.106	25.485	0.000	0.000	0.000	0.000	0.000	0.000
95	B	52	VAL	0	-0.091	0.107	23.845	0.000	0.000	0.000	0.000	0.000	0.000
96	B	53	GLY	0	0.020	-0.090	26.304	-0.006	-0.006	0.000	0.000	0.000	0.000
97	B	54	VAL	0	0.043	-0.022	29.407	-0.009	-0.009	0.000	0.000	0.000	0.000
98	B	54	VAL	0	-0.068	0.090	28.532	0.000	0.000	0.000	0.000	0.000	0.000
99	B	55	THR	0	0.045	-0.101	31.106	0.004	0.004	0.000	0.000	0.000	0.000
100	B	55	THR	0	-0.024	0.091	33.305	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	56	LEU	0	0.126	-0.085	34.746	-0.001	-0.001	0.000	0.000	0.000	0.000
102	B	56	LEU	0	-0.090	0.126	35.503	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	57	ALA	0	0.144	-0.079	35.974	0.004	0.004	0.000	0.000	0.000	0.000
104	B	57	ALA	0	-0.041	0.115	39.851	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	58	GLY	0	-0.059	-0.125	37.478	0.002	0.002	0.000	0.000	0.000	0.000
106	B	59	HIS	0	0.172	-0.039	33.603	0.000	0.000	0.000	0.000	0.000	0.000
107	B	59	HIS	0	-0.029	0.184	32.525	0.003	0.003	0.000	0.000	0.000	0.000
108	B	60	GLN	0	0.062	-0.112	32.773	0.004	0.004	0.000	0.000	0.000	0.000
109	B	60	GLN	0	-0.061	0.113	33.355	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	61	LYS	0	0.119	-0.080	33.595	0.006	0.006	0.000	0.000	0.000	0.000
111	B	61	LYS	1	0.825	1.080	37.371	-0.046	-0.046	0.000	0.000	0.000	0.000
112	B	62	LYS	0	0.071	-0.115	33.789	0.003	0.003	0.000	0.000	0.000	0.000
113	B	62	LYS	1	0.877	1.088	32.822	-0.046	-0.046	0.000	0.000	0.000	0.000
114	B	63	ILE	0	0.100	-0.100	29.828	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	63	ILE	0	-0.064	0.122	27.757	0.000	0.000	0.000	0.000	0.000	0.000
116	B	64	LEU	0	0.090	-0.100	30.083	0.008	0.008	0.000	0.000	0.000	0.000
117	B	64	LEU	0	-0.059	0.105	31.106	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	65	ASN	0	0.086	-0.082	32.181	0.005	0.005	0.000	0.000	0.000	0.000
119	B	65	ASN	0	-0.148	0.050	34.205	-0.002	-0.002	0.000	0.000	0.000	0.000
120	B	66	SER	0	0.025	-0.094	29.401	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	66	SER	0	0.019	0.081	28.430	-0.001	-0.001	0.000	0.000	0.000	0.000
122	B	67	ILE	0	0.110	-0.084	27.970	0.002	0.002	0.000	0.000	0.000	0.000
123	B	67	ILE	0	-0.081	0.149	26.899	-0.002	-0.002	0.000	0.000	0.000	0.000
124	B	68	GLN	0	0.088	-0.096	28.967	0.009	0.009	0.000	0.000	0.000	0.000
125	B	68	GLN	0	-0.132	0.088	33.492	0.000	0.000	0.000	0.000	0.000	0.000
126	B	69	VAL	0	0.060	-0.122	31.596	0.002	0.002	0.000	0.000	0.000	0.000
127	B	69	VAL	0	-0.103	0.099	30.409	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	70	MET	0	-0.002	-0.140	26.863	-0.004	-0.004	0.000	0.000	0.000	0.000
129	B	70	MET	0	-0.035	0.114	24.602	0.007	0.007	0.000	0.000	0.000	0.000
130	B	71	ARG	0	0.145	-0.049	28.038	0.008	0.008	0.000	0.000	0.000	0.000
131	B	71	ARG	1	0.850	1.065	28.433	-0.135	-0.135	0.000	0.000	0.000	0.000
132	B	72	ALA	0	0.079	-0.094	29.457	0.006	0.006	0.000	0.000	0.000	0.000
133	B	72	ALA	0	-0.060	0.102	33.025	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	73	GLN	0	0.041	-0.091	29.320	-0.003	-0.003	0.000	0.000	0.000	0.000
135	B	73	GLN	0	-0.054	0.078	27.906	0.007	0.007	0.000	0.000	0.000	0.000
136	B	74	MET	0	0.057	-0.086	27.162	-0.006	-0.006	0.000	0.000	0.000	0.000
137	B	74	MET	0	-0.088	0.082	23.124	0.003	0.003	0.000	0.000	0.000	0.000
138	B	75	ASN	0	0.128	-0.053	28.069	0.005	0.005	0.000	0.000	0.000	0.000
139	B	75	ASN	0	-0.132	0.053	31.147	0.006	0.006	0.000	0.000	0.000	0.000
140	B	76	GLN	0	0.070	-0.082	31.384	-0.001	-0.001	0.000	0.000	0.000	0.000
141	B	76	GLN	0	-0.121	0.040	31.734	-0.001	-0.001	0.000	0.000	0.000	0.000
142	B	77	ILE	0	0.128	-0.063	28.547	-0.008	-0.008	0.000	0.000	0.000	0.000
143	B	77	ILE	0	-0.071	0.094	26.231	0.001	0.001	0.000	0.000	0.000	0.000
144	B	78	GLN	0	0.048	-0.060	29.712	-0.002	-0.002	0.000	0.000	0.000	0.000
145	B	78	GLN	0	-0.071	0.098	26.483	-0.006	-0.006	0.000	0.000	0.000	0.000
146	B	79	SER	0	-0.077	-0.103	30.359	0.003	0.003	0.000	0.000	0.000	0.000
147	B	79	SER	0	-0.047	0.052	34.255	-0.004	-0.004	0.000	0.000	0.000	0.000
148	B	80	VAL	0	-0.115	-0.159	31.683	-0.012	-0.012	0.000	0.000	0.000	0.000
149	B	80	VAL	0	0.009	0.017	29.732	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)