FMO DATABASE

FMODB ID: YZ842

Calculation Name: 5N06-A-Xray372

Preferred Name: Tyrosine-protein kinase receptor Tie-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5N06

Chain ID: A

ChEMBL ID: CHEMBL5274

UniProt ID: P35590

Base Structure: X-ray

Registration Date: 2023-09-19

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-576469.439269
FMO2-HF: Nuclear repulsion	540240.607187
FMO2-HF: Total energy	-36228.832082
FMO2-MP2: Total energy	-36336.146092

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:643:GLY)

Summations of interaction energy for fragment #1(A:643:GLY)

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.
0.05	1.868	0.206	-0.725	-1.299	0

Interaction energy analysis for fragmet #1(A:643:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / 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

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	645	PRO	0	0.006	0.005	3.828	0.440	1.456	-0.013	-0.401	-0.601	0.001
4	A	646	ALA	0	0.000	-0.001	6.605	0.085	0.085	0.000	0.000	0.000	0.000
5	A	647	PRO	0	0.013	0.016	9.697	0.041	0.041	0.000	0.000	0.000	0.000
6	A	648	ARG	1	0.840	0.892	12.753	0.268	0.268	0.000	0.000	0.000	0.000
7	A	649	HIS	0	-0.027	-0.034	15.376	0.023	0.023	0.000	0.000	0.000	0.000
8	A	650	LEU	0	0.065	0.040	17.179	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	651	HIS	0	0.005	-0.002	19.643	0.013	0.013	0.000	0.000	0.000	0.000
10	A	652	ALA	0	0.038	0.028	23.201	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	653	GLN	0	-0.034	-0.015	25.212	0.006	0.006	0.000	0.000	0.000	0.000
12	A	654	ALA	0	-0.014	-0.013	28.882	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	655	LEU	0	-0.045	-0.004	30.294	0.005	0.005	0.000	0.000	0.000	0.000
14	A	656	SER	0	0.003	0.002	33.090	0.008	0.008	0.000	0.000	0.000	0.000
15	A	657	ASP	-1	-0.916	-0.964	33.870	-0.073	-0.073	0.000	0.000	0.000	0.000
16	A	658	SER	0	0.001	-0.002	33.672	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	659	GLU	-1	-0.840	-0.908	30.109	-0.096	-0.096	0.000	0.000	0.000	0.000
18	A	660	ILE	0	-0.019	-0.014	26.705	0.005	0.005	0.000	0.000	0.000	0.000
19	A	661	GLN	0	0.009	0.029	25.951	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	662	LEU	0	0.001	-0.015	19.218	0.003	0.003	0.000	0.000	0.000	0.000
21	A	663	THR	0	-0.008	-0.009	22.121	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	664	TRP	0	-0.010	-0.001	15.925	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	665	LYS	1	0.853	0.921	17.210	0.192	0.192	0.000	0.000	0.000	0.000
24	A	666	HIS	0	0.030	0.012	14.100	-0.082	-0.082	0.000	0.000	0.000	0.000
25	A	667	PRO	0	-0.019	-0.003	9.943	0.060	0.060	0.000	0.000	0.000	0.000
26	A	668	GLU	-1	-0.823	-0.886	12.569	-0.202	-0.202	0.000	0.000	0.000	0.000
27	A	669	ALA	0	-0.010	0.009	11.392	0.041	0.041	0.000	0.000	0.000	0.000
28	A	670	LEU	0	0.001	-0.007	5.585	-0.238	-0.238	0.000	0.000	0.000	0.000
29	A	671	PRO	0	-0.035	-0.004	4.001	-0.357	-0.063	0.004	-0.095	-0.204	0.000
30	A	672	GLY	0	0.025	0.018	5.031	0.625	0.612	-0.001	-0.003	0.017	0.000
31	A	673	PRO	0	-0.002	-0.005	7.504	-0.234	-0.234	0.000	0.000	0.000	0.000
32	A	674	ILE	0	0.008	-0.008	6.372	-0.114	-0.114	0.000	0.000	0.000	0.000
33	A	675	SER	0	-0.051	-0.020	8.270	0.160	0.160	0.000	0.000	0.000	0.000
34	A	676	LYS	1	0.866	0.940	10.155	0.395	0.395	0.000	0.000	0.000	0.000
35	A	677	TYR	0	-0.019	-0.012	10.671	-0.202	-0.202	0.000	0.000	0.000	0.000
36	A	678	VAL	0	-0.010	0.006	11.914	0.053	0.053	0.000	0.000	0.000	0.000
37	A	679	VAL	0	-0.001	-0.005	14.316	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	680	GLU	-1	-0.817	-0.869	16.682	-0.239	-0.239	0.000	0.000	0.000	0.000
39	A	681	VAL	0	0.011	0.005	19.142	0.004	0.004	0.000	0.000	0.000	0.000
40	A	682	GLN	0	0.024	0.000	20.141	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	683	VAL	0	0.027	0.037	24.349	0.001	0.001	0.000	0.000	0.000	0.000
42	A	684	ALA	0	0.013	-0.018	25.225	0.001	0.001	0.000	0.000	0.000	0.000
43	A	685	GLY	0	-0.021	0.010	27.209	0.001	0.001	0.000	0.000	0.000	0.000
44	A	686	GLY	0	-0.002	-0.018	27.858	0.007	0.007	0.000	0.000	0.000	0.000
45	A	687	ALA	0	-0.013	-0.019	23.659	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	688	GLY	0	0.016	0.008	23.976	0.009	0.009	0.000	0.000	0.000	0.000
47	A	689	ASP	-1	-0.958	-0.979	23.788	-0.103	-0.103	0.000	0.000	0.000	0.000
48	A	690	PRO	0	-0.051	-0.014	21.040	0.000	0.000	0.000	0.000	0.000	0.000
49	A	691	LEU	0	0.043	0.038	22.074	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	692	TRP	0	-0.042	-0.041	13.668	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	693	ILE	0	-0.007	-0.018	18.935	0.017	0.017	0.000	0.000	0.000	0.000
52	A	694	ASP	-1	-0.863	-0.924	15.300	-0.373	-0.373	0.000	0.000	0.000	0.000
53	A	695	VAL	0	-0.013	-0.003	16.233	0.033	0.033	0.000	0.000	0.000	0.000
54	A	696	ASP	-1	-0.866	-0.954	15.596	-0.249	-0.249	0.000	0.000	0.000	0.000
55	A	697	ARG	1	0.839	0.901	15.894	0.128	0.128	0.000	0.000	0.000	0.000
56	A	698	PRO	0	0.022	0.024	12.505	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	699	GLU	-1	-0.867	-0.924	14.341	-0.189	-0.189	0.000	0.000	0.000	0.000
58	A	700	GLU	-1	-0.933	-0.971	16.699	-0.155	-0.155	0.000	0.000	0.000	0.000
59	A	701	THR	0	-0.044	-0.030	17.493	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	702	SER	0	-0.033	-0.035	19.718	0.007	0.007	0.000	0.000	0.000	0.000
61	A	703	THR	0	0.055	0.036	20.275	0.005	0.005	0.000	0.000	0.000	0.000
62	A	704	ILE	0	0.009	-0.010	22.999	0.002	0.002	0.000	0.000	0.000	0.000
63	A	705	ILE	0	-0.019	0.004	22.066	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	706	ARG	1	0.872	0.903	26.029	0.110	0.110	0.000	0.000	0.000	0.000
65	A	707	GLY	0	0.008	0.017	28.513	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	708	LEU	0	-0.039	-0.010	27.132	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	709	ASN	0	-0.002	-0.005	31.210	0.009	0.009	0.000	0.000	0.000	0.000
68	A	710	ALA	0	0.085	0.048	33.679	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	711	SER	0	-0.052	-0.036	36.391	0.002	0.002	0.000	0.000	0.000	0.000
70	A	712	THR	0	0.005	0.011	32.535	0.000	0.000	0.000	0.000	0.000	0.000
71	A	713	ARG	1	0.844	0.915	30.342	0.085	0.085	0.000	0.000	0.000	0.000
72	A	714	TYR	0	0.076	0.032	26.010	0.000	0.000	0.000	0.000	0.000	0.000
73	A	715	LEU	0	-0.064	-0.019	21.761	0.001	0.001	0.000	0.000	0.000	0.000
74	A	716	PHE	0	0.053	0.019	20.432	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	717	ARG	1	0.810	0.883	15.499	0.254	0.254	0.000	0.000	0.000	0.000
76	A	718	MET	0	0.026	0.017	14.173	0.017	0.017	0.000	0.000	0.000	0.000
77	A	719	ARG	1	0.921	0.964	8.253	0.562	0.562	0.000	0.000	0.000	0.000
78	A	720	ALA	0	0.062	0.040	7.588	0.126	0.126	0.000	0.000	0.000	0.000
79	A	721	SER	0	-0.016	-0.003	6.783	-0.333	-0.333	0.000	0.000	0.000	0.000
80	A	722	ILE	0	0.053	0.017	2.536	-0.532	-0.011	0.216	-0.226	-0.511	-0.001
81	A	723	GLN	0	-0.046	-0.023	5.713	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	724	GLY	0	0.009	0.000	8.323	0.089	0.089	0.000	0.000	0.000	0.000
83	A	725	LEU	0	-0.025	-0.014	8.859	0.002	0.002	0.000	0.000	0.000	0.000
84	A	726	GLY	0	0.020	0.016	12.550	0.037	0.037	0.000	0.000	0.000	0.000
85	A	727	ASP	-1	-0.940	-0.965	14.929	0.096	0.096	0.000	0.000	0.000	0.000
86	A	728	TRP	0	-0.020	-0.012	17.995	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	729	SER	0	-0.006	0.000	21.120	0.004	0.004	0.000	0.000	0.000	0.000
88	A	730	ASN	0	-0.060	-0.036	24.078	0.000	0.000	0.000	0.000	0.000	0.000
89	A	731	THR	0	0.013	-0.002	27.706	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	732	VAL	0	-0.018	-0.007	29.410	0.002	0.002	0.000	0.000	0.000	0.000
91	A	733	GLU	-1	-0.890	-0.945	32.299	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	734	GLU	-1	-0.973	-0.979	35.120	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	735	SER	0	-0.007	-0.004	36.889	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	736	THR	0	-0.054	-0.020	38.467	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	737	LEU	0	-0.011	-0.007	40.767	0.001	0.001	0.000	0.000	0.000	0.000
96	A	738	GLY	0	-0.015	-0.006	44.469	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:643:GLY)