FMO DATABASE

FMODB ID: 9RLG2

Calculation Name: 2E7H-A-Other547

Preferred Name: Ephrin type-B receptor 4

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2E7H

Chain ID: A

ChEMBL ID: CHEMBL5147

UniProt ID: P54760

Base Structure: SolutionNMR

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-717504.616519
FMO2-HF: Nuclear repulsion	677936.107329
FMO2-HF: Total energy	-39568.50919
FMO2-MP2: Total energy	-39686.25673

3D Structure Molmil

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:1:GLY)

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

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.
29.178	30	-0.008	-0.311	-0.503	-0.001

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.869 / q_NPA : 0.920

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	3	SER	0	0.013	0.002	3.842	-1.250	-0.428	-0.008	-0.311	-0.503	-0.001
4	A	4	GLY	0	0.056	0.041	6.473	4.978	4.978	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.052	-0.030	6.972	-2.227	-2.227	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.027	0.005	8.964	2.086	2.086	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.002	0.010	11.730	1.906	1.906	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.027	-0.011	11.810	-1.863	-1.863	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.006	-0.007	10.525	-0.734	-0.734	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.007	0.010	11.364	1.574	1.574	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.022	-0.002	13.330	-0.030	-0.030	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.021	0.002	15.503	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.920	-0.972	17.699	-14.046	-14.046	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.029	-0.005	19.776	0.565	0.565	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.948	0.979	22.977	11.915	11.915	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.031	0.017	26.585	0.063	0.063	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.021	-0.017	29.677	0.266	0.266	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.945	0.961	32.994	8.032	8.032	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.045	0.038	34.767	0.043	0.043	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.026	0.001	36.312	0.333	0.333	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.019	-0.003	38.232	-0.155	-0.155	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.025	-0.004	39.426	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.014	-0.005	36.699	0.058	0.058	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.008	0.001	31.838	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.027	0.018	32.459	-0.193	-0.193	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.009	0.000	26.789	-0.121	-0.121	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.024	0.005	26.907	0.130	0.130	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.014	0.015	21.416	-0.061	-0.061	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.021	0.024	20.730	0.351	0.351	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.013	0.000	20.339	-0.554	-0.554	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.007	0.013	15.768	-0.272	-0.272	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.946	0.963	14.864	17.925	17.925	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.041	0.017	13.651	-1.436	-1.436	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.006	0.002	9.844	0.352	0.352	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.017	-0.027	11.918	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.019	0.027	15.167	0.203	0.203	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.019	0.011	18.921	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.032	-0.013	18.236	-0.508	-0.508	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.033	0.000	20.439	0.522	0.522	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.849	-0.934	22.954	-12.403	-12.403	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.020	0.003	20.504	-0.890	-0.890	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.849	-0.956	22.529	-11.719	-11.719	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.008	0.003	22.921	-0.556	-0.556	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.971	1.010	22.943	13.084	13.084	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.009	-0.012	25.332	-0.270	-0.270	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.001	-0.010	26.347	-0.101	-0.101	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.815	-0.893	29.591	-8.820	-8.820	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.928	0.968	27.950	10.582	10.582	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.003	-0.015	30.893	0.070	0.070	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.031	0.004	32.097	0.275	0.275	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.890	-0.940	30.975	-10.061	-10.061	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.049	0.040	31.393	0.313	0.313	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.027	-0.027	29.890	-0.149	-0.149	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.010	-0.019	30.888	-0.101	-0.101	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.033	-0.024	32.804	0.221	0.221	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.069	-0.019	27.083	-0.081	-0.081	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.952	0.985	30.487	8.928	8.928	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.003	-0.015	24.438	-0.475	-0.475	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.021	-0.001	27.820	0.469	0.469	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.956	0.979	27.017	10.626	10.626	0.000	0.000	0.000	0.000
61	A	61	THR	0	0.000	0.004	26.645	0.503	0.503	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.040	0.006	26.718	-0.393	-0.393	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.859	-0.905	27.247	-10.533	-10.533	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.029	-0.018	24.117	0.163	0.163	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.891	0.913	25.456	10.368	10.368	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.017	0.010	28.170	0.063	0.063	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.933	-0.971	30.182	-8.357	-8.357	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.000	0.016	29.426	0.120	0.120	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.953	0.956	33.514	8.100	8.100	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.020	0.007	36.771	-0.072	-0.072	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.020	-0.010	33.700	-0.193	-0.193	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.956	0.979	37.165	7.776	7.776	0.000	0.000	0.000	0.000
73	A	73	ARG	1	1.002	0.992	37.324	7.141	7.141	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.001	0.006	37.536	0.156	0.156	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.028	0.001	36.211	-0.119	-0.119	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.018	-0.009	30.656	-0.278	-0.278	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.030	-0.043	30.210	0.051	0.051	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.014	0.019	24.249	-0.114	-0.114	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.006	-0.001	25.359	0.151	0.151	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.029	-0.021	20.728	-0.481	-0.481	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.023	0.010	20.865	0.375	0.375	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.904	0.962	18.024	13.551	13.551	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.051	0.019	17.291	0.797	0.797	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.870	0.954	17.769	13.308	13.308	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.007	-0.014	16.505	0.137	0.137	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.909	-0.959	18.596	-14.018	-14.018	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.024	-0.010	14.958	0.314	0.314	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.050	0.024	17.009	0.099	0.099	0.000	0.000	0.000	0.000
89	A	89	TYR	0	-0.095	-0.062	17.359	0.114	0.114	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.018	0.026	13.929	-0.945	-0.945	0.000	0.000	0.000	0.000
91	A	91	PRO	0	-0.036	-0.021	10.920	1.175	1.175	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.052	-0.048	14.210	0.433	0.433	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.007	-0.002	15.281	-1.097	-1.097	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.035	-0.014	13.372	0.988	0.988	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.889	-0.924	17.222	-13.496	-13.496	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.023	-0.011	20.633	0.525	0.525	0.000	0.000	0.000	0.000
97	A	97	HIS	0	-0.039	-0.034	23.274	0.644	0.644	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.001	-0.001	26.988	0.145	0.145	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.026	0.002	29.969	-0.104	-0.104	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.096	-0.043	32.828	0.185	0.185	0.000	0.000	0.000	0.000
101	A	101	GLN	0	0.085	0.038	35.547	0.326	0.326	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.071	-0.040	38.189	0.102	0.102	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.880	-0.934	40.657	-7.513	-7.513	0.000	0.000	0.000	0.000
104	A	104	SER	0	-0.052	-0.034	43.360	0.006	0.006	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.024	0.016	45.179	0.007	0.007	0.000	0.000	0.000	0.000
106	A	106	PRO	0	-0.021	0.005	41.027	0.060	0.060	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.035	-0.022	42.999	0.072	0.072	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.070	-0.033	41.211	-0.242	-0.242	0.000	0.000	0.000	0.000
109	A	109	GLY	-1	-0.899	-0.941	41.615	-7.427	-7.427	0.000	0.000	0.000	0.000

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