FMO DATABASE

FMODB ID: 4JG4N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-429902.287689
FMO2-HF: Nuclear repulsion	400917.585107
FMO2-HF: Total energy	-28984.702583
FMO2-MP2: Total energy	-29066.378743

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.
-2.735	1.425	1.504	-1.636	-4.029	0.003

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 : -0.014 / q_NPA : -0.023

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	912	ALA	0	0.011	0.005	3.007	-1.897	2.048	1.485	-1.706	-3.724	0.002
4	A	913	VAL	0	-0.020	0.004	4.053	-0.773	-0.558	0.019	0.070	-0.305	0.001
5	A	914	VAL	0	0.013	0.006	6.589	0.191	0.191	0.000	0.000	0.000	0.000
6	A	915	SER	0	0.004	-0.014	8.347	0.135	0.135	0.000	0.000	0.000	0.000
7	A	916	VAL	0	0.046	0.014	10.690	-0.093	-0.093	0.000	0.000	0.000	0.000
8	A	917	GLY	0	-0.003	-0.013	14.117	-0.050	-0.050	0.000	0.000	0.000	0.000
9	A	918	ASP	-1	-0.794	-0.890	10.763	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	919	TRP	0	-0.012	-0.020	14.024	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	920	LEU	0	-0.008	-0.011	15.519	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	921	GLN	0	-0.007	-0.001	17.551	0.006	0.006	0.000	0.000	0.000	0.000
13	A	922	ALA	0	-0.014	0.007	16.727	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	923	ILE	0	-0.079	-0.029	18.784	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	924	LYS	1	0.926	0.951	21.508	0.025	0.025	0.000	0.000	0.000	0.000
16	A	925	MET	0	-0.041	-0.019	22.219	0.004	0.004	0.000	0.000	0.000	0.000
17	A	926	ASP	-1	-0.889	-0.950	20.527	0.065	0.065	0.000	0.000	0.000	0.000
18	A	927	ARG	1	0.952	0.983	22.094	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	928	TYR	0	-0.018	-0.047	23.714	0.002	0.002	0.000	0.000	0.000	0.000
20	A	929	LYS	1	0.916	0.971	17.466	-0.110	-0.110	0.000	0.000	0.000	0.000
21	A	930	ASP	-1	-0.862	-0.933	20.421	0.208	0.208	0.000	0.000	0.000	0.000
22	A	931	ASN	0	-0.058	-0.023	22.579	0.014	0.014	0.000	0.000	0.000	0.000
23	A	932	PHE	0	-0.005	-0.012	18.550	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	933	THR	0	0.004	0.000	17.563	0.034	0.034	0.000	0.000	0.000	0.000
25	A	934	ALA	0	-0.011	0.000	19.042	0.024	0.024	0.000	0.000	0.000	0.000
26	A	935	ALA	0	-0.034	-0.009	21.640	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	936	GLY	0	0.011	0.008	18.158	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	937	TYR	0	-0.028	-0.010	16.642	0.045	0.045	0.000	0.000	0.000	0.000
29	A	938	THR	0	0.017	-0.008	12.849	0.018	0.018	0.000	0.000	0.000	0.000
30	A	939	THR	0	0.022	0.011	9.502	0.029	0.029	0.000	0.000	0.000	0.000
31	A	940	LEU	0	0.035	-0.010	11.197	-0.080	-0.080	0.000	0.000	0.000	0.000
32	A	941	GLU	-1	-0.952	-0.965	9.085	0.044	0.044	0.000	0.000	0.000	0.000
33	A	942	ALA	0	0.005	0.009	13.240	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	943	VAL	0	-0.008	-0.015	15.632	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	944	VAL	0	-0.055	-0.029	15.793	-0.027	-0.027	0.000	0.000	0.000	0.000
36	A	945	HIS	0	-0.022	-0.014	16.431	-0.029	-0.029	0.000	0.000	0.000	0.000
37	A	946	MET	0	-0.054	0.010	20.185	0.009	0.009	0.000	0.000	0.000	0.000
38	A	947	SER	0	-0.003	0.004	22.529	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	948	GLN	0	-0.011	-0.035	26.267	0.010	0.010	0.000	0.000	0.000	0.000
40	A	949	ASP	-1	-0.904	-0.954	28.933	0.059	0.059	0.000	0.000	0.000	0.000
41	A	950	ASP	-1	-0.808	-0.899	24.254	0.086	0.086	0.000	0.000	0.000	0.000
42	A	951	LEU	0	-0.020	-0.020	23.573	0.011	0.011	0.000	0.000	0.000	0.000
43	A	952	ALA	0	-0.004	0.002	26.622	0.005	0.005	0.000	0.000	0.000	0.000
44	A	953	ARG	1	0.910	0.969	23.703	-0.118	-0.118	0.000	0.000	0.000	0.000
45	A	954	ILE	0	-0.036	-0.009	23.297	0.009	0.009	0.000	0.000	0.000	0.000
46	A	955	GLY	0	0.027	0.016	26.589	0.008	0.008	0.000	0.000	0.000	0.000
47	A	956	ILE	0	-0.062	-0.027	24.573	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	957	THR	0	0.041	0.010	29.111	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	958	ALA	0	-0.001	0.014	31.868	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	959	ILE	0	0.117	0.041	31.630	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	960	THR	0	-0.019	-0.011	31.287	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	961	HIS	0	0.019	0.016	28.038	0.000	0.000	0.000	0.000	0.000	0.000
53	A	962	GLN	0	0.021	0.015	27.170	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	963	ASN	0	0.040	0.012	27.205	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	964	LYS	1	0.872	0.962	24.506	0.014	0.014	0.000	0.000	0.000	0.000
56	A	965	ILE	0	0.012	0.001	22.084	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	966	LEU	0	0.042	0.008	22.523	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	967	SER	0	0.006	0.007	23.733	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	968	SER	0	-0.040	0.000	19.511	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	969	VAL	0	0.047	0.023	19.047	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	970	GLN	0	0.005	-0.007	19.376	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	971	ALA	0	0.002	0.004	19.891	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	972	MET	0	-0.017	-0.011	15.126	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	973	ARG	1	0.960	0.991	15.481	0.052	0.052	0.000	0.000	0.000	0.000
65	A	974	THR	0	-0.009	-0.007	17.006	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	975	GLN	0	-0.047	-0.023	12.679	-0.070	-0.070	0.000	0.000	0.000	0.000
67	A	976	MET	0	-0.001	-0.009	11.120	-0.065	-0.065	0.000	0.000	0.000	0.000
68	A	977	GLN	0	-0.035	-0.007	13.593	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	978	GLN	0	-0.031	-0.019	15.778	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	979	MET	0	-0.042	-0.003	9.207	-0.044	-0.044	0.000	0.000	0.000	0.000
71	A	980	HIS	0	-0.047	-0.034	11.331	-0.074	-0.074	0.000	0.000	0.000	0.000
72	A	981	GLY	0	0.011	0.029	13.922	0.055	0.055	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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