FMO DATABASE

FMODB ID: YZVV2

Calculation Name: 1B4F-A-Xray372

Preferred Name: Ephrin type-B receptor 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1B4F

Chain ID: A

ChEMBL ID: CHEMBL3290

UniProt ID: P29323

Base Structure: X-ray

Registration Date: 2023-06-22

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-463257.39401
FMO2-HF: Nuclear repulsion	432652.329299
FMO2-HF: Total energy	-30605.064711
FMO2-MP2: Total energy	-30690.619726

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:6:PRO)

Summations of interaction energy for fragment #1(A:6:PRO)

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.
0.807	3.656	1.465	-1.498	-2.816	-0.003

Interaction energy analysis for fragmet #1(A:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.047

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	8	TYR	0	-0.005	-0.014	2.787	-0.427	2.422	1.465	-1.498	-2.816	-0.003
4	A	9	THR	0	-0.027	-0.022	5.985	0.145	0.145	0.000	0.000	0.000	0.000
5	A	10	SER	0	0.015	0.035	9.173	0.080	0.080	0.000	0.000	0.000	0.000
6	A	11	PHE	0	-0.011	-0.038	11.850	-0.077	-0.077	0.000	0.000	0.000	0.000
7	A	12	ASN	0	-0.018	0.000	15.362	0.041	0.041	0.000	0.000	0.000	0.000
8	A	13	THR	0	0.021	0.017	18.722	0.002	0.002	0.000	0.000	0.000	0.000
9	A	14	VAL	0	0.024	0.014	19.453	-0.028	-0.028	0.000	0.000	0.000	0.000
10	A	15	ASP	-1	-0.874	-0.947	20.458	-0.175	-0.175	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.832	-0.937	17.050	-0.160	-0.160	0.000	0.000	0.000	0.000
12	A	17	TRP	0	0.000	0.009	14.943	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.003	0.000	16.198	-0.067	-0.067	0.000	0.000	0.000	0.000
14	A	19	GLU	-1	-0.924	-0.970	17.673	-0.267	-0.267	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.026	0.033	12.361	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	21	ILE	0	-0.115	-0.041	13.101	-0.147	-0.147	0.000	0.000	0.000	0.000
17	A	22	LYS	1	0.872	0.903	12.352	0.816	0.816	0.000	0.000	0.000	0.000
18	A	23	MET	0	-0.013	0.004	17.431	0.039	0.039	0.000	0.000	0.000	0.000
19	A	24	GLY	0	0.063	0.028	20.225	0.031	0.031	0.000	0.000	0.000	0.000
20	A	25	GLN	0	-0.020	-0.009	21.805	0.003	0.003	0.000	0.000	0.000	0.000
21	A	26	TYR	0	-0.015	-0.088	23.354	0.021	0.021	0.000	0.000	0.000	0.000
22	A	27	LYS	1	0.906	0.970	22.036	0.200	0.200	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.876	-0.943	25.387	-0.104	-0.104	0.000	0.000	0.000	0.000
24	A	29	SER	0	-0.058	-0.012	28.493	0.011	0.011	0.000	0.000	0.000	0.000
25	A	30	PHE	0	0.015	-0.008	23.543	0.002	0.002	0.000	0.000	0.000	0.000
26	A	31	ALA	0	0.030	0.031	27.831	0.009	0.009	0.000	0.000	0.000	0.000
27	A	32	ASN	0	-0.001	-0.017	29.444	0.013	0.013	0.000	0.000	0.000	0.000
28	A	33	ALA	0	-0.113	-0.045	31.012	0.007	0.007	0.000	0.000	0.000	0.000
29	A	34	GLY	0	0.039	0.024	31.718	0.004	0.004	0.000	0.000	0.000	0.000
30	A	35	PHE	0	-0.039	-0.029	26.456	0.001	0.001	0.000	0.000	0.000	0.000
31	A	36	THR	0	-0.007	-0.018	26.423	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	37	SER	0	0.043	0.029	24.596	0.002	0.002	0.000	0.000	0.000	0.000
33	A	38	PHE	0	0.065	0.006	18.230	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.889	-0.935	22.331	-0.076	-0.076	0.000	0.000	0.000	0.000
35	A	40	VAL	0	0.015	0.010	25.077	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	41	VAL	0	0.005	-0.008	21.368	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	42	SER	0	-0.051	-0.026	21.701	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	43	GLN	0	-0.110	-0.069	22.826	0.003	0.003	0.000	0.000	0.000	0.000
39	A	44	MET	0	-0.061	0.002	25.025	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	45	MET	0	0.016	0.010	25.961	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	46	MET	0	-0.032	-0.032	27.581	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	47	GLU	-1	-0.922	-0.956	29.190	-0.102	-0.102	0.000	0.000	0.000	0.000
43	A	48	ASP	-1	-0.779	-0.895	28.721	-0.115	-0.115	0.000	0.000	0.000	0.000
44	A	49	ILE	0	-0.022	-0.011	24.471	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.027	-0.029	28.073	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	51	ARG	1	0.949	1.001	31.352	0.104	0.104	0.000	0.000	0.000	0.000
47	A	52	VAL	0	-0.076	-0.035	27.274	0.006	0.006	0.000	0.000	0.000	0.000
48	A	53	GLY	0	0.006	0.000	29.607	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	54	VAL	0	-0.033	-0.003	25.064	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	55	THR	0	0.051	0.015	28.300	0.005	0.005	0.000	0.000	0.000	0.000
51	A	56	LEU	0	0.005	0.005	26.679	0.002	0.002	0.000	0.000	0.000	0.000
52	A	57	ALA	0	0.071	0.034	26.430	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	58	GLY	0	-0.020	-0.017	23.370	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	59	HIS	0	0.034	0.078	21.763	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	60	GLN	0	0.039	0.012	22.222	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	61	LYS	1	0.938	0.975	21.338	0.236	0.236	0.000	0.000	0.000	0.000
57	A	62	LYS	1	0.904	0.965	14.942	0.569	0.569	0.000	0.000	0.000	0.000
58	A	63	ILE	0	0.024	0.005	18.047	-0.034	-0.034	0.000	0.000	0.000	0.000
59	A	64	LEU	0	0.062	0.025	19.867	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	65	ASN	0	-0.032	-0.019	17.257	0.036	0.036	0.000	0.000	0.000	0.000
61	A	66	SER	0	-0.010	0.000	15.405	-0.017	-0.017	0.000	0.000	0.000	0.000
62	A	67	ILE	0	0.065	0.046	16.406	0.000	0.000	0.000	0.000	0.000	0.000
63	A	68	GLN	0	-0.014	0.001	18.102	0.038	0.038	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.032	-0.031	12.048	0.019	0.019	0.000	0.000	0.000	0.000
65	A	70	MET	0	-0.004	0.018	15.178	0.037	0.037	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.972	0.969	16.550	0.181	0.181	0.000	0.000	0.000	0.000
67	A	72	ALA	0	-0.044	-0.013	16.030	0.031	0.031	0.000	0.000	0.000	0.000
68	A	73	GLN	0	0.020	0.017	11.584	0.077	0.077	0.000	0.000	0.000	0.000
69	A	74	MET	0	-0.027	-0.021	15.780	0.043	0.043	0.000	0.000	0.000	0.000
70	A	75	ASN	0	0.017	-0.008	19.188	0.035	0.035	0.000	0.000	0.000	0.000
71	A	76	GLN	0	-0.050	-0.009	13.196	-0.034	-0.034	0.000	0.000	0.000	0.000
72	A	77	ILE	0	-0.011	0.001	16.094	0.022	0.022	0.000	0.000	0.000	0.000
73	A	78	GLN	0	-0.033	0.001	19.349	0.014	0.014	0.000	0.000	0.000	0.000
74	A	79	SER	0	-0.095	-0.040	20.712	0.012	0.012	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:PRO)