FMO DATABASE

FMODB ID: YV7L2

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	-431414.793167
FMO2-HF: Nuclear repulsion	402429.576791
FMO2-HF: Total energy	-28985.216376
FMO2-MP2: Total energy	-29066.852936

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.
-2.232	2.079	1.038	-1.689	-3.66	0.006

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 : 0.018 / q_NPA : 0.006

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	-0.013	-0.001	3.084	-1.099	3.034	1.016	-1.764	-3.385	0.006
4	A	913	VAL	0	-0.031	-0.006	3.755	-0.332	-0.154	0.022	0.075	-0.275	0.000
5	A	914	VAL	0	-0.002	0.004	6.891	0.185	0.185	0.000	0.000	0.000	0.000
6	A	915	SER	0	0.004	-0.028	8.894	-0.031	-0.031	0.000	0.000	0.000	0.000
7	A	916	VAL	0	0.019	0.002	11.139	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	917	GLY	0	0.027	0.008	14.255	0.011	0.011	0.000	0.000	0.000	0.000
9	A	918	ASP	-1	-0.808	-0.881	11.125	-0.097	-0.097	0.000	0.000	0.000	0.000
10	A	919	TRP	0	0.007	-0.010	14.276	0.002	0.002	0.000	0.000	0.000	0.000
11	A	920	LEU	0	-0.004	0.003	15.695	0.014	0.014	0.000	0.000	0.000	0.000
12	A	921	GLN	0	0.025	0.024	17.779	0.021	0.021	0.000	0.000	0.000	0.000
13	A	922	ALA	0	-0.015	0.001	16.851	0.010	0.010	0.000	0.000	0.000	0.000
14	A	923	ILE	0	-0.056	-0.016	18.938	0.010	0.010	0.000	0.000	0.000	0.000
15	A	924	LYS	1	0.964	0.986	21.507	0.093	0.093	0.000	0.000	0.000	0.000
16	A	925	MET	0	-0.043	-0.016	22.719	0.012	0.012	0.000	0.000	0.000	0.000
17	A	926	ASP	-1	-0.795	-0.892	20.620	-0.066	-0.066	0.000	0.000	0.000	0.000
18	A	927	ARG	1	0.886	0.947	22.287	0.083	0.083	0.000	0.000	0.000	0.000
19	A	928	TYR	0	0.008	-0.011	23.613	0.008	0.008	0.000	0.000	0.000	0.000
20	A	929	LYS	1	0.836	0.892	18.302	0.031	0.031	0.000	0.000	0.000	0.000
21	A	930	ASP	-1	-0.864	-0.916	19.765	-0.024	-0.024	0.000	0.000	0.000	0.000
22	A	931	ASN	0	-0.053	-0.027	21.964	0.003	0.003	0.000	0.000	0.000	0.000
23	A	932	PHE	0	0.010	-0.008	18.311	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	933	THR	0	-0.039	-0.028	16.684	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	934	ALA	0	-0.016	-0.010	18.368	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	935	ALA	0	-0.026	-0.003	20.985	0.003	0.003	0.000	0.000	0.000	0.000
27	A	936	GLY	0	0.016	0.009	16.925	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	937	TYR	0	-0.013	-0.006	15.424	-0.038	-0.038	0.000	0.000	0.000	0.000
29	A	938	THR	0	0.015	-0.009	12.245	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	939	THR	0	-0.030	-0.039	8.750	0.076	0.076	0.000	0.000	0.000	0.000
31	A	940	LEU	0	0.050	0.005	10.903	0.033	0.033	0.000	0.000	0.000	0.000
32	A	941	GLU	-1	-0.813	-0.875	8.051	-1.245	-1.245	0.000	0.000	0.000	0.000
33	A	942	ALA	0	-0.008	0.008	12.547	0.051	0.051	0.000	0.000	0.000	0.000
34	A	943	VAL	0	0.007	-0.014	14.822	0.049	0.049	0.000	0.000	0.000	0.000
35	A	944	VAL	0	-0.050	-0.015	14.635	0.044	0.044	0.000	0.000	0.000	0.000
36	A	945	HIS	0	0.021	0.016	15.784	0.059	0.059	0.000	0.000	0.000	0.000
37	A	946	MET	0	-0.049	0.012	19.730	0.023	0.023	0.000	0.000	0.000	0.000
38	A	947	SER	0	-0.016	-0.036	22.038	0.006	0.006	0.000	0.000	0.000	0.000
39	A	948	GLN	0	-0.022	-0.039	25.868	0.003	0.003	0.000	0.000	0.000	0.000
40	A	949	ASP	-1	-0.902	-0.938	28.725	-0.118	-0.118	0.000	0.000	0.000	0.000
41	A	950	ASP	-1	-0.777	-0.843	23.508	-0.189	-0.189	0.000	0.000	0.000	0.000
42	A	951	LEU	0	0.006	-0.005	23.096	0.009	0.009	0.000	0.000	0.000	0.000
43	A	952	ALA	0	-0.023	-0.013	26.208	0.011	0.011	0.000	0.000	0.000	0.000
44	A	953	ARG	1	0.866	0.922	22.895	0.165	0.165	0.000	0.000	0.000	0.000
45	A	954	ILE	0	-0.035	-0.007	22.371	0.007	0.007	0.000	0.000	0.000	0.000
46	A	955	GLY	0	0.037	0.018	25.658	0.011	0.011	0.000	0.000	0.000	0.000
47	A	956	ILE	0	-0.053	-0.013	24.322	0.007	0.007	0.000	0.000	0.000	0.000
48	A	957	THR	0	0.036	0.006	28.772	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	958	ALA	0	0.006	0.011	31.446	0.001	0.001	0.000	0.000	0.000	0.000
50	A	959	ILE	0	0.089	0.039	31.405	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	960	THR	0	-0.004	-0.002	31.537	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	961	HIS	0	0.033	0.015	27.909	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	962	GLN	0	0.048	0.027	26.933	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	963	ASN	0	0.011	-0.001	26.877	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	964	LYS	1	0.846	0.930	24.371	0.123	0.123	0.000	0.000	0.000	0.000
56	A	965	ILE	0	0.013	0.005	21.918	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	966	LEU	0	0.034	0.008	22.283	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	967	SER	0	0.000	-0.009	23.399	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	968	SER	0	-0.036	0.000	19.187	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	969	VAL	0	0.041	0.017	18.742	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	970	GLN	0	0.008	0.002	18.944	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	971	ALA	0	-0.009	0.007	19.509	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	972	MET	0	-0.013	-0.003	14.931	-0.029	-0.029	0.000	0.000	0.000	0.000
64	A	973	ARG	1	0.867	0.919	15.056	0.324	0.324	0.000	0.000	0.000	0.000
65	A	974	THR	0	0.002	-0.003	16.558	-0.020	-0.020	0.000	0.000	0.000	0.000
66	A	975	GLN	0	-0.018	-0.010	12.343	-0.053	-0.053	0.000	0.000	0.000	0.000
67	A	976	MET	0	-0.017	-0.022	10.216	-0.081	-0.081	0.000	0.000	0.000	0.000
68	A	977	GLN	0	-0.016	-0.007	13.012	-0.024	-0.024	0.000	0.000	0.000	0.000
69	A	978	GLN	0	-0.045	-0.027	15.626	0.001	0.001	0.000	0.000	0.000	0.000
70	A	979	MET	0	-0.040	-0.008	8.962	0.020	0.020	0.000	0.000	0.000	0.000
71	A	980	HIS	0	-0.035	-0.009	11.190	-0.079	-0.079	0.000	0.000	0.000	0.000
72	A	981	GLY	0	-0.020	0.006	13.513	0.054	0.054	0.000	0.000	0.000	0.000

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