FMO DATABASE

FMODB ID: 17NNZ

Calculation Name: 1B4F-A-Xray372

Preferred Name: Ephrin type-B receptor 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

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	-464389.196209
FMO2-HF: Nuclear repulsion	433783.23489
FMO2-HF: Total energy	-30605.961319
FMO2-MP2: Total energy	-30691.403523

3D Structure Molmil

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.
-15.19	-15.452	13.377	-5.94	-7.176	0.013

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 : -0.035

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	0.011	0.002	1.915	-16.644	-16.906	13.377	-5.940	-7.176	0.013
4	A	9	THR	0	-0.055	-0.044	5.865	0.280	0.280	0.000	0.000	0.000	0.000
5	A	10	SER	0	-0.012	0.002	8.797	0.049	0.049	0.000	0.000	0.000	0.000
6	A	11	PHE	0	-0.019	-0.020	11.515	-0.048	-0.048	0.000	0.000	0.000	0.000
7	A	12	ASN	0	-0.062	-0.040	15.037	0.052	0.052	0.000	0.000	0.000	0.000
8	A	13	THR	0	-0.029	-0.037	18.446	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	14	VAL	0	0.018	0.005	19.126	-0.034	-0.034	0.000	0.000	0.000	0.000
10	A	15	ASP	-1	-0.811	-0.908	20.478	-0.175	-0.175	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.721	-0.832	16.812	-0.115	-0.115	0.000	0.000	0.000	0.000
12	A	17	TRP	0	-0.024	-0.004	14.874	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	18	LEU	0	0.005	0.006	16.242	-0.076	-0.076	0.000	0.000	0.000	0.000
14	A	19	GLU	-1	-0.865	-0.930	17.645	-0.247	-0.247	0.000	0.000	0.000	0.000
15	A	20	ALA	0	-0.009	0.014	12.402	-0.060	-0.060	0.000	0.000	0.000	0.000
16	A	21	ILE	0	-0.069	-0.032	13.127	-0.157	-0.157	0.000	0.000	0.000	0.000
17	A	22	LYS	1	0.917	0.954	12.013	0.800	0.800	0.000	0.000	0.000	0.000
18	A	23	MET	0	-0.032	0.000	17.023	0.037	0.037	0.000	0.000	0.000	0.000
19	A	24	GLY	0	0.070	0.025	20.127	0.033	0.033	0.000	0.000	0.000	0.000
20	A	25	GLN	0	-0.024	-0.009	21.757	0.012	0.012	0.000	0.000	0.000	0.000
21	A	26	TYR	0	-0.020	-0.024	23.588	0.021	0.021	0.000	0.000	0.000	0.000
22	A	27	LYS	1	0.793	0.900	21.669	0.184	0.184	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.876	-0.942	25.398	-0.100	-0.100	0.000	0.000	0.000	0.000
24	A	29	SER	0	-0.040	-0.014	28.432	0.012	0.012	0.000	0.000	0.000	0.000
25	A	30	PHE	0	0.009	-0.007	23.672	0.001	0.001	0.000	0.000	0.000	0.000
26	A	31	ALA	0	0.039	0.028	27.925	0.010	0.010	0.000	0.000	0.000	0.000
27	A	32	ASN	0	-0.060	-0.036	29.633	0.016	0.016	0.000	0.000	0.000	0.000
28	A	33	ALA	0	-0.062	-0.042	30.751	0.004	0.004	0.000	0.000	0.000	0.000
29	A	34	GLY	0	0.015	0.022	31.647	0.003	0.003	0.000	0.000	0.000	0.000
30	A	35	PHE	0	-0.023	-0.010	26.555	0.002	0.002	0.000	0.000	0.000	0.000
31	A	36	THR	0	0.010	-0.017	26.016	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	37	SER	0	-0.025	-0.041	24.214	0.000	0.000	0.000	0.000	0.000	0.000
33	A	38	PHE	0	0.073	0.013	18.002	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.839	-0.875	22.270	-0.076	-0.076	0.000	0.000	0.000	0.000
35	A	40	VAL	0	0.000	0.008	25.244	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	41	VAL	0	0.030	0.004	21.298	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	42	SER	0	-0.045	-0.036	21.519	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	43	GLN	0	-0.047	-0.023	22.754	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	44	MET	0	-0.059	0.013	25.276	0.002	0.002	0.000	0.000	0.000	0.000
40	A	45	MET	0	0.001	0.002	26.144	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	46	MET	0	-0.010	-0.013	27.541	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	47	GLU	-1	-0.868	-0.944	29.555	-0.130	-0.130	0.000	0.000	0.000	0.000
43	A	48	ASP	-1	-0.809	-0.900	28.934	-0.124	-0.124	0.000	0.000	0.000	0.000
44	A	49	ILE	0	-0.004	-0.017	24.389	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.034	-0.021	28.230	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	51	ARG	1	0.892	0.964	31.515	0.109	0.109	0.000	0.000	0.000	0.000
47	A	52	VAL	0	-0.048	-0.012	27.223	0.007	0.007	0.000	0.000	0.000	0.000
48	A	53	GLY	0	0.033	0.008	29.506	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	54	VAL	0	-0.016	0.000	25.243	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	55	THR	0	0.007	-0.001	28.328	0.003	0.003	0.000	0.000	0.000	0.000
51	A	56	LEU	0	-0.006	0.003	26.281	0.001	0.001	0.000	0.000	0.000	0.000
52	A	57	ALA	0	0.067	0.024	26.060	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	58	GLY	0	-0.032	-0.015	23.096	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	59	HIS	0	0.049	0.028	21.687	-0.024	-0.024	0.000	0.000	0.000	0.000
55	A	60	GLN	0	0.016	0.004	22.359	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	61	LYS	1	0.957	0.981	21.786	0.253	0.253	0.000	0.000	0.000	0.000
57	A	62	LYS	1	0.855	0.921	14.176	0.640	0.640	0.000	0.000	0.000	0.000
58	A	63	ILE	0	0.022	0.010	18.073	-0.044	-0.044	0.000	0.000	0.000	0.000
59	A	64	LEU	0	0.051	0.020	19.811	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	65	ASN	0	-0.003	-0.007	17.395	0.033	0.033	0.000	0.000	0.000	0.000
61	A	66	SER	0	-0.012	0.000	15.596	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	67	ILE	0	0.020	0.024	16.561	0.000	0.000	0.000	0.000	0.000	0.000
63	A	68	GLN	0	0.016	0.009	18.775	0.038	0.038	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.021	-0.017	12.248	0.015	0.015	0.000	0.000	0.000	0.000
65	A	70	MET	0	-0.017	0.009	15.412	0.039	0.039	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.897	0.924	16.829	0.203	0.203	0.000	0.000	0.000	0.000
67	A	72	ALA	0	-0.041	-0.007	15.979	0.032	0.032	0.000	0.000	0.000	0.000
68	A	73	GLN	0	0.036	0.016	11.703	0.079	0.079	0.000	0.000	0.000	0.000
69	A	74	MET	0	0.008	-0.003	15.797	0.049	0.049	0.000	0.000	0.000	0.000
70	A	75	ASN	0	-0.025	-0.005	19.312	0.036	0.036	0.000	0.000	0.000	0.000
71	A	76	GLN	0	-0.030	-0.016	13.500	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	77	ILE	0	-0.008	0.015	16.129	0.031	0.031	0.000	0.000	0.000	0.000
73	A	78	GLN	0	-0.051	-0.039	19.360	0.021	0.021	0.000	0.000	0.000	0.000
74	A	79	SER	0	-0.122	-0.051	20.530	0.019	0.019	0.000	0.000	0.000	0.000

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