FMO DATABASE

FMODB ID: V5QQ1

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	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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-463758.72362
FMO2-HF: Nuclear repulsion	433152.934872
FMO2-HF: Total energy	-30605.788748
FMO2-MP2: Total energy	-30691.268365

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.
-4.418	-0.432	2.952	-2.804	-4.135	0

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 : -0.033 / q_NPA : -0.044

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].
3	A	8	TYR	0	-0.015	-0.019	2.476	-5.865	-1.879	2.952	-2.804	-4.135
4	A	9	THR	0	-0.034	-0.025	5.966	0.193	0.193	0.000	0.000	0.000
5	A	10	SER	0	0.016	0.038	9.061	0.113	0.113	0.000	0.000	0.000
6	A	11	PHE	0	-0.010	-0.033	11.656	-0.086	-0.086	0.000	0.000	0.000
7	A	12	ASN	0	-0.062	-0.026	15.250	0.056	0.056	0.000	0.000	0.000
8	A	13	THR	0	-0.016	-0.030	18.610	0.004	0.004	0.000	0.000	0.000
9	A	14	VAL	0	0.014	0.006	19.354	-0.033	-0.033	0.000	0.000	0.000
10	A	15	ASP	-1	-0.809	-0.912	20.370	-0.206	-0.206	0.000	0.000	0.000
11	A	16	GLU	-1	-0.747	-0.860	16.836	-0.167	-0.167	0.000	0.000	0.000
12	A	17	TRP	0	-0.011	0.006	14.819	-0.041	-0.041	0.000	0.000	0.000
13	A	18	LEU	0	0.002	0.001	16.121	-0.077	-0.077	0.000	0.000	0.000
14	A	19	GLU	-1	-0.843	-0.914	17.558	-0.299	-0.299	0.000	0.000	0.000
15	A	20	ALA	0	-0.006	0.020	12.360	-0.069	-0.069	0.000	0.000	0.000
16	A	21	ILE	0	-0.087	-0.036	13.035	-0.173	-0.173	0.000	0.000	0.000
17	A	22	LYS	1	0.913	0.944	12.359	0.907	0.907	0.000	0.000	0.000
18	A	23	MET	0	-0.008	0.007	17.376	0.044	0.044	0.000	0.000	0.000
19	A	24	GLY	0	0.072	0.029	20.164	0.036	0.036	0.000	0.000	0.000
20	A	25	GLN	0	-0.026	-0.006	21.732	0.010	0.010	0.000	0.000	0.000
21	A	26	TYR	0	-0.028	-0.042	23.447	0.023	0.023	0.000	0.000	0.000
22	A	27	LYS	1	0.788	0.888	21.584	0.220	0.220	0.000	0.000	0.000
23	A	28	GLU	-1	-0.875	-0.939	25.307	-0.117	-0.117	0.000	0.000	0.000
24	A	29	SER	0	-0.056	-0.016	28.432	0.013	0.013	0.000	0.000	0.000
25	A	30	PHE	0	0.019	-0.008	23.617	0.004	0.004	0.000	0.000	0.000
26	A	31	ALA	0	0.029	0.025	27.757	0.012	0.012	0.000	0.000	0.000
27	A	32	ASN	0	-0.029	-0.023	29.359	0.016	0.016	0.000	0.000	0.000
28	A	33	ALA	0	-0.108	-0.043	30.852	0.008	0.008	0.000	0.000	0.000
29	A	34	GLY	0	0.041	0.025	31.635	0.005	0.005	0.000	0.000	0.000
30	A	35	PHE	0	-0.046	-0.032	26.420	0.002	0.002	0.000	0.000	0.000
31	A	36	THR	0	-0.007	-0.021	26.342	-0.013	-0.013	0.000	0.000	0.000
32	A	37	SER	0	-0.011	-0.025	24.474	0.003	0.003	0.000	0.000	0.000
33	A	38	PHE	0	0.067	0.008	18.163	-0.013	-0.013	0.000	0.000	0.000
34	A	39	ASP	-1	-0.834	-0.872	22.253	-0.074	-0.074	0.000	0.000	0.000
35	A	40	VAL	0	0.010	0.005	25.006	-0.003	-0.003	0.000	0.000	0.000
36	A	41	VAL	0	0.005	-0.004	21.350	-0.008	-0.008	0.000	0.000	0.000
37	A	42	SER	0	-0.048	-0.036	21.511	-0.010	-0.010	0.000	0.000	0.000
38	A	43	GLN	0	-0.053	-0.029	22.775	-0.003	-0.003	0.000	0.000	0.000
39	A	44	MET	0	-0.056	0.006	24.963	-0.001	-0.001	0.000	0.000	0.000
40	A	45	MET	0	0.015	0.013	25.929	-0.015	-0.015	0.000	0.000	0.000
41	A	46	MET	0	-0.016	-0.019	27.337	-0.010	-0.010	0.000	0.000	0.000
42	A	47	GLU	-1	-0.883	-0.948	29.169	-0.125	-0.125	0.000	0.000	0.000
43	A	48	ASP	-1	-0.798	-0.898	28.618	-0.126	-0.126	0.000	0.000	0.000
44	A	49	ILE	0	-0.023	-0.021	24.275	-0.006	-0.006	0.000	0.000	0.000
45	A	50	LEU	0	-0.028	-0.023	28.035	-0.002	-0.002	0.000	0.000	0.000
46	A	51	ARG	1	0.945	0.991	31.317	0.116	0.116	0.000	0.000	0.000
47	A	52	VAL	0	-0.072	-0.028	27.142	0.007	0.007	0.000	0.000	0.000
48	A	53	GLY	0	0.007	0.000	29.553	-0.009	-0.009	0.000	0.000	0.000
49	A	54	VAL	0	-0.031	0.000	25.035	-0.009	-0.009	0.000	0.000	0.000
50	A	55	THR	0	0.044	0.011	28.264	0.006	0.006	0.000	0.000	0.000
51	A	56	LEU	0	0.001	0.006	26.640	0.002	0.002	0.000	0.000	0.000
52	A	57	ALA	0	0.074	0.031	26.417	-0.016	-0.016	0.000	0.000	0.000
53	A	58	GLY	0	-0.019	-0.013	23.376	-0.014	-0.014	0.000	0.000	0.000
54	A	59	HIS	0	0.030	0.025	21.758	-0.024	-0.024	0.000	0.000	0.000
55	A	60	GLN	0	0.034	0.013	22.201	-0.022	-0.022	0.000	0.000	0.000
56	A	61	LYS	1	0.937	0.973	21.449	0.261	0.261	0.000	0.000	0.000
57	A	62	LYS	1	0.870	0.926	14.473	0.672	0.672	0.000	0.000	0.000
58	A	63	ILE	0	0.031	0.008	18.027	-0.036	-0.036	0.000	0.000	0.000
59	A	64	LEU	0	0.062	0.023	19.837	-0.002	-0.002	0.000	0.000	0.000
60	A	65	ASN	0	-0.032	-0.016	17.086	0.043	0.043	0.000	0.000	0.000
61	A	66	SER	0	-0.006	0.004	15.386	-0.034	-0.034	0.000	0.000	0.000
62	A	67	ILE	0	0.038	0.034	16.379	0.000	0.000	0.000	0.000	0.000
63	A	68	GLN	0	-0.014	0.000	18.394	0.039	0.039	0.000	0.000	0.000
64	A	69	VAL	0	-0.026	-0.029	12.086	0.023	0.023	0.000	0.000	0.000
65	A	70	MET	0	-0.004	0.016	15.153	0.043	0.043	0.000	0.000	0.000
66	A	71	ARG	1	0.915	0.931	16.508	0.189	0.189	0.000	0.000	0.000
67	A	72	ALA	0	-0.030	-0.006	16.032	0.036	0.036	0.000	0.000	0.000
68	A	73	GLN	0	0.027	0.018	11.544	0.074	0.074	0.000	0.000	0.000
69	A	74	MET	0	-0.006	-0.010	15.749	0.048	0.048	0.000	0.000	0.000
70	A	75	ASN	0	-0.007	-0.008	19.145	0.033	0.033	0.000	0.000	0.000
71	A	76	GLN	0	-0.031	0.001	13.359	-0.027	-0.027	0.000	0.000	0.000
72	A	77	ILE	0	0.002	0.013	15.826	0.025	0.025	0.000	0.000	0.000
73	A	78	GLN	0	-0.045	-0.013	19.310	0.015	0.015	0.000	0.000	0.000
74	A	79	SER	0	-0.132	-0.066	20.539	0.016	0.016	0.000	0.000	0.000

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