FMO DATABASE

FMODB ID: 3M72L

Calculation Name: 2DJS-A-Other547

Preferred Name: Ephrin type-B receptor 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DJS

Chain ID: A

ChEMBL ID: CHEMBL5072

UniProt ID: P54762

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	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-772147.11602
FMO2-HF: Nuclear repulsion	729774.055809
FMO2-HF: Total energy	-42373.06021
FMO2-MP2: Total energy	-42493.226178

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.
58.155	59.163	-0.019	-0.351	-0.638	-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 : 0.846 / q_NPA : 0.911

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	0.021	0.005	3.828	1.114	2.021	-0.018	-0.338	-0.552	-0.001
90	A	90	LYS	1	0.919	0.948	4.085	35.524	35.625	-0.001	-0.013	-0.086	0.000
4	A	4	GLY	0	0.025	0.035	5.996	2.703	2.703	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.019	0.011	6.932	1.519	1.519	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.018	-0.011	8.179	-3.320	-3.320	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.034	0.016	9.471	1.173	1.173	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.062	-0.004	10.265	0.113	0.113	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.042	-0.020	10.050	-3.471	-3.471	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.063	-0.061	8.819	0.550	0.550	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.012	0.012	11.600	1.189	1.189	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.017	0.005	12.758	-1.571	-1.571	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.024	-0.005	14.114	-0.676	-0.676	0.000	0.000	0.000	0.000
14	A	14	MET	0	-0.049	-0.005	15.329	0.085	0.085	0.000	0.000	0.000	0.000
15	A	15	HIS	0	0.046	0.023	17.976	0.321	0.321	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.001	-0.007	21.787	-0.169	-0.169	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.016	0.003	23.756	0.337	0.337	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.022	0.004	26.744	0.457	0.457	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.005	0.014	26.498	-0.573	-0.573	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.028	0.008	28.316	0.350	0.350	0.000	0.000	0.000	0.000
21	A	21	MET	0	0.048	0.025	29.609	-0.250	-0.250	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.954	0.986	29.399	9.917	9.917	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.005	-0.017	26.407	-0.068	-0.068	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.016	0.019	22.389	0.255	0.255	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.041	-0.016	24.033	-0.299	-0.299	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.016	0.002	18.886	0.043	0.043	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.010	-0.008	21.786	0.369	0.369	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.039	0.006	17.667	-0.680	-0.680	0.000	0.000	0.000	0.000
29	A	29	PRO	0	0.033	0.031	18.406	0.495	0.495	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.006	-0.006	18.497	-1.089	-1.089	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.050	-0.018	15.201	0.269	0.269	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.872	-0.943	17.600	-15.201	-15.201	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.014	0.014	15.794	0.503	0.503	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.008	-0.007	15.032	-1.800	-1.800	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.061	-0.044	14.090	-0.474	-0.474	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.048	0.029	16.383	0.100	0.100	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.013	0.006	18.948	0.037	0.037	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.020	-0.015	16.718	-0.709	-0.709	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.053	-0.015	17.998	0.799	0.799	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.782	-0.863	17.918	-15.507	-15.507	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.044	0.022	15.630	-1.519	-1.519	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.809	-0.908	13.376	-20.851	-20.851	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.010	-0.019	14.106	-1.435	-1.435	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.923	0.973	8.158	29.454	29.454	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.045	0.000	14.237	-0.184	-0.184	0.000	0.000	0.000	0.000
46	A	46	TYR	0	0.005	-0.026	11.253	0.332	0.332	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.847	-0.923	17.373	-13.347	-13.347	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.898	0.944	17.882	14.401	14.401	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.944	-0.964	18.555	-13.309	-13.309	0.000	0.000	0.000	0.000
50	A	50	HIS	0	-0.045	-0.014	18.367	-0.346	-0.346	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.010	0.001	13.884	-1.034	-1.034	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.875	-0.943	9.228	-27.229	-27.229	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.040	-0.007	12.679	0.193	0.193	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.007	0.015	15.073	0.487	0.487	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.058	-0.037	14.083	0.030	0.030	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.029	0.025	16.406	0.269	0.269	0.000	0.000	0.000	0.000
57	A	57	MET	0	-0.070	-0.046	12.338	-1.482	-1.482	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.024	0.023	17.164	0.988	0.988	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.900	0.949	17.959	13.631	13.631	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.015	-0.008	19.437	0.988	0.988	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.008	-0.012	20.747	-0.628	-0.628	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.028	0.011	22.400	0.333	0.333	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.025	-0.016	19.343	-0.266	-0.266	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.004	0.001	21.659	-0.112	-0.112	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.037	0.016	21.082	0.082	0.082	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.898	0.953	23.204	10.828	10.828	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.007	0.023	19.278	-0.151	-0.151	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.939	-0.988	23.155	-11.138	-11.138	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.026	0.026	24.934	-0.326	-0.326	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.071	-0.022	22.535	-0.247	-0.247	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.975	0.975	26.356	10.769	10.769	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.038	0.036	28.038	-0.306	-0.306	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.007	-0.003	29.769	0.014	0.014	0.000	0.000	0.000	0.000
74	A	74	MET	0	-0.009	0.018	24.154	-0.122	-0.122	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.001	-0.010	20.503	-0.190	-0.190	0.000	0.000	0.000	0.000
76	A	76	TYR	0	0.053	0.018	19.543	-0.057	-0.057	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.003	0.012	13.153	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.031	-0.017	15.407	-0.175	-0.175	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.033	-0.017	9.668	-3.670	-3.670	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.046	0.023	12.916	0.291	0.291	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.853	0.925	8.473	26.020	26.020	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.042	0.026	11.850	1.874	1.874	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.835	0.889	12.054	15.173	15.173	0.000	0.000	0.000	0.000
84	A	84	THR	0	0.008	-0.001	13.892	1.380	1.380	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.018	-0.009	16.027	-0.310	-0.310	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.004	0.024	14.961	0.240	0.240	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.035	0.015	12.150	-0.621	-0.621	0.000	0.000	0.000	0.000
88	A	88	TYR	0	-0.057	-0.032	9.231	0.558	0.558	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.036	0.025	8.567	-2.094	-2.094	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.015	-0.004	6.443	3.659	3.659	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.035	0.029	8.225	-2.420	-2.420	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.015	0.023	10.114	-1.691	-1.691	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.853	0.916	7.514	35.525	35.525	0.000	0.000	0.000	0.000
95	A	95	MET	0	0.028	0.026	12.396	1.020	1.020	0.000	0.000	0.000	0.000
96	A	96	CYS	0	-0.025	-0.011	15.924	-0.598	-0.598	0.000	0.000	0.000	0.000
97	A	97	PHE	0	0.055	0.016	17.478	0.518	0.518	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.017	-0.012	21.484	-0.297	-0.297	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.045	-0.038	24.666	0.152	0.152	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.010	-0.011	27.626	0.068	0.068	0.000	0.000	0.000	0.000
101	A	101	THR	0	0.014	0.003	30.850	-0.099	-0.099	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.922	-0.957	33.201	-8.040	-8.040	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.041	-0.038	36.351	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.006	0.026	37.854	0.171	0.171	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.023	-0.010	34.572	0.074	0.074	0.000	0.000	0.000	0.000
106	A	106	SER	0	0.026	-0.001	36.698	0.060	0.060	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.077	-0.049	36.985	0.253	0.253	0.000	0.000	0.000	0.000
108	A	108	GLY	-1	-0.939	-0.939	33.058	-9.721	-9.721	0.000	0.000	0.000	0.000

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