FMO DATABASE

FMODB ID: 5JGKZ

Calculation Name: 1B0X-A-Xray372

Preferred Name: Ephrin type-A receptor 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1B0X

Chain ID: A

ChEMBL ID: CHEMBL1293259

UniProt ID: Q03137

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-430030.249345
FMO2-HF: Nuclear repulsion	401045.141045
FMO2-HF: Total energy	-28985.108301
FMO2-MP2: Total energy	-29066.757755

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:910:PHE)

Summations of interaction energy for fragment #1(A:910:PHE)

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.
-2.817	1.904	1.293	-1.894	-4.119	0.008

Interaction energy analysis for fragmet #1(A:910:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.005

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

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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	912	ALA	0	-0.002	0.003	2.972	-1.719	2.866	1.260	-2.042	-3.803	0.007
4	A	913	VAL	0	-0.031	-0.003	3.670	-0.245	-0.109	0.033	0.148	-0.316	0.001
5	A	914	VAL	0	-0.001	0.001	6.898	0.175	0.175	0.000	0.000	0.000	0.000
6	A	915	SER	0	0.000	-0.028	8.654	0.002	0.002	0.000	0.000	0.000	0.000
7	A	916	VAL	0	0.045	0.009	11.095	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	917	GLY	0	0.020	0.007	14.464	0.009	0.009	0.000	0.000	0.000	0.000
9	A	918	ASP	-1	-0.808	-0.884	11.003	-0.187	-0.187	0.000	0.000	0.000	0.000
10	A	919	TRP	0	0.000	-0.016	14.381	0.001	0.001	0.000	0.000	0.000	0.000
11	A	920	LEU	0	-0.007	-0.004	15.750	0.016	0.016	0.000	0.000	0.000	0.000
12	A	921	GLN	0	0.013	0.007	17.881	0.022	0.022	0.000	0.000	0.000	0.000
13	A	922	ALA	0	-0.010	0.012	16.782	0.012	0.012	0.000	0.000	0.000	0.000
14	A	923	ILE	0	-0.059	-0.017	18.897	0.010	0.010	0.000	0.000	0.000	0.000
15	A	924	LYS	1	0.944	0.970	21.527	0.116	0.116	0.000	0.000	0.000	0.000
16	A	925	MET	0	-0.039	-0.016	22.591	0.014	0.014	0.000	0.000	0.000	0.000
17	A	926	ASP	-1	-0.815	-0.900	20.728	-0.083	-0.083	0.000	0.000	0.000	0.000
18	A	927	ARG	1	0.933	0.977	22.452	0.090	0.090	0.000	0.000	0.000	0.000
19	A	928	TYR	0	-0.007	-0.041	24.077	0.009	0.009	0.000	0.000	0.000	0.000
20	A	929	LYS	1	0.847	0.920	18.169	0.061	0.061	0.000	0.000	0.000	0.000
21	A	930	ASP	-1	-0.857	-0.930	20.422	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	931	ASN	0	-0.062	-0.033	22.578	0.005	0.005	0.000	0.000	0.000	0.000
23	A	932	PHE	0	-0.002	-0.008	18.582	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	933	THR	0	-0.004	-0.007	17.325	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	934	ALA	0	-0.013	0.001	18.989	0.004	0.004	0.000	0.000	0.000	0.000
26	A	935	ALA	0	-0.029	-0.008	21.328	0.005	0.005	0.000	0.000	0.000	0.000
27	A	936	GLY	0	0.010	0.008	17.476	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	937	TYR	0	-0.026	-0.012	15.954	-0.028	-0.028	0.000	0.000	0.000	0.000
29	A	938	THR	0	0.011	-0.011	12.648	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	939	THR	0	-0.008	-0.025	9.060	0.070	0.070	0.000	0.000	0.000	0.000
31	A	940	LEU	0	0.039	-0.003	11.317	0.037	0.037	0.000	0.000	0.000	0.000
32	A	941	GLU	-1	-0.865	-0.911	8.401	-1.243	-1.243	0.000	0.000	0.000	0.000
33	A	942	ALA	0	0.000	0.006	12.961	0.051	0.051	0.000	0.000	0.000	0.000
34	A	943	VAL	0	0.005	-0.010	15.318	0.045	0.045	0.000	0.000	0.000	0.000
35	A	944	VAL	0	-0.052	-0.022	15.442	0.042	0.042	0.000	0.000	0.000	0.000
36	A	945	HIS	0	-0.005	-0.004	16.073	0.050	0.050	0.000	0.000	0.000	0.000
37	A	946	MET	0	-0.055	0.009	19.837	0.025	0.025	0.000	0.000	0.000	0.000
38	A	947	SER	0	-0.014	-0.028	22.193	0.002	0.002	0.000	0.000	0.000	0.000
39	A	948	GLN	0	-0.008	-0.032	25.952	0.009	0.009	0.000	0.000	0.000	0.000
40	A	949	ASP	-1	-0.900	-0.951	28.791	-0.110	-0.110	0.000	0.000	0.000	0.000
41	A	950	ASP	-1	-0.781	-0.842	23.838	-0.175	-0.175	0.000	0.000	0.000	0.000
42	A	951	LEU	0	-0.005	-0.011	23.546	0.008	0.008	0.000	0.000	0.000	0.000
43	A	952	ALA	0	-0.012	-0.004	26.544	0.011	0.011	0.000	0.000	0.000	0.000
44	A	953	ARG	1	0.873	0.929	23.073	0.148	0.148	0.000	0.000	0.000	0.000
45	A	954	ILE	0	-0.038	-0.011	23.011	0.009	0.009	0.000	0.000	0.000	0.000
46	A	955	GLY	0	0.028	0.023	26.388	0.009	0.009	0.000	0.000	0.000	0.000
47	A	956	ILE	0	-0.062	-0.023	24.599	0.005	0.005	0.000	0.000	0.000	0.000
48	A	957	THR	0	0.045	0.013	29.115	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	958	ALA	0	-0.003	0.012	32.231	0.001	0.001	0.000	0.000	0.000	0.000
50	A	959	ILE	0	0.124	0.046	31.825	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	960	THR	0	-0.008	-0.002	31.550	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	961	HIS	0	0.027	0.014	28.309	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	962	GLN	0	0.026	0.017	27.243	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	963	ASN	0	0.003	-0.011	27.218	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	964	LYS	1	0.837	0.935	24.383	0.141	0.141	0.000	0.000	0.000	0.000
56	A	965	ILE	0	0.017	0.004	22.224	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	966	LEU	0	0.038	0.009	22.550	-0.023	-0.023	0.000	0.000	0.000	0.000
58	A	967	SER	0	-0.004	-0.012	23.744	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	968	SER	0	-0.038	-0.002	19.404	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	969	VAL	0	0.052	0.022	19.059	-0.031	-0.031	0.000	0.000	0.000	0.000
61	A	970	GLN	0	0.004	-0.004	19.203	-0.029	-0.029	0.000	0.000	0.000	0.000
62	A	971	ALA	0	-0.003	0.003	20.013	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	972	MET	0	-0.011	-0.004	15.142	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	973	ARG	1	0.900	0.955	15.214	0.317	0.317	0.000	0.000	0.000	0.000
65	A	974	THR	0	-0.012	-0.013	16.713	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	975	GLN	0	-0.038	-0.017	12.768	-0.055	-0.055	0.000	0.000	0.000	0.000
67	A	976	MET	0	-0.002	-0.011	10.795	-0.084	-0.084	0.000	0.000	0.000	0.000
68	A	977	GLN	0	-0.026	-0.002	13.399	-0.024	-0.024	0.000	0.000	0.000	0.000
69	A	978	GLN	0	-0.045	-0.023	15.663	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	979	MET	0	-0.042	-0.004	9.091	0.004	0.004	0.000	0.000	0.000	0.000
71	A	980	HIS	0	-0.044	-0.031	11.305	-0.105	-0.105	0.000	0.000	0.000	0.000
72	A	981	GLY	0	0.012	0.028	13.917	0.056	0.056	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:910:PHE)