FMO DATABASE

FMODB ID: 17KMZ

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-578509.118556
FMO2-HF: Nuclear repulsion	542279.780864
FMO2-HF: Total energy	-36229.337692
FMO2-MP2: Total energy	-36336.677706

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.
-0.706	2.215	0.651	-1.446	-2.126	0.003

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 : 0.057 / q_NPA : 0.029

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	0.005	0.002	3.883	0.872	2.027	-0.008	-0.532	-0.614	0.002
4	A	646	ALA	0	0.001	0.002	6.517	0.188	0.188	0.000	0.000	0.000	0.000
5	A	647	PRO	0	-0.003	0.011	9.771	-0.050	-0.050	0.000	0.000	0.000	0.000
6	A	648	ARG	1	0.815	0.866	12.623	0.730	0.730	0.000	0.000	0.000	0.000
7	A	649	HIS	0	-0.023	-0.034	15.364	0.025	0.025	0.000	0.000	0.000	0.000
8	A	650	LEU	0	0.042	0.032	16.889	0.007	0.007	0.000	0.000	0.000	0.000
9	A	651	HIS	0	-0.011	-0.010	19.401	0.024	0.024	0.000	0.000	0.000	0.000
10	A	652	ALA	0	0.018	0.011	22.987	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	653	GLN	0	-0.015	-0.005	25.066	0.009	0.009	0.000	0.000	0.000	0.000
12	A	654	ALA	0	-0.005	-0.003	28.757	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	655	LEU	0	-0.057	-0.014	30.234	0.000	0.000	0.000	0.000	0.000	0.000
14	A	656	SER	0	-0.006	-0.014	33.213	0.011	0.011	0.000	0.000	0.000	0.000
15	A	657	ASP	-1	-0.911	-0.949	34.060	-0.100	-0.100	0.000	0.000	0.000	0.000
16	A	658	SER	0	-0.001	-0.016	33.791	0.002	0.002	0.000	0.000	0.000	0.000
17	A	659	GLU	-1	-0.857	-0.897	30.246	-0.144	-0.144	0.000	0.000	0.000	0.000
18	A	660	ILE	0	-0.007	-0.004	26.079	0.004	0.004	0.000	0.000	0.000	0.000
19	A	661	GLN	0	0.004	0.021	26.081	0.000	0.000	0.000	0.000	0.000	0.000
20	A	662	LEU	0	0.011	0.003	19.216	0.005	0.005	0.000	0.000	0.000	0.000
21	A	663	THR	0	-0.026	-0.011	21.734	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	664	TRP	0	0.004	0.006	15.795	0.030	0.030	0.000	0.000	0.000	0.000
23	A	665	LYS	1	0.865	0.929	16.987	0.431	0.431	0.000	0.000	0.000	0.000
24	A	666	HIS	0	0.057	0.047	13.530	-0.149	-0.149	0.000	0.000	0.000	0.000
25	A	667	PRO	0	-0.020	0.000	9.353	0.134	0.134	0.000	0.000	0.000	0.000
26	A	668	GLU	-1	-0.808	-0.879	11.944	-0.788	-0.788	0.000	0.000	0.000	0.000
27	A	669	ALA	0	-0.025	-0.005	10.460	0.097	0.097	0.000	0.000	0.000	0.000
28	A	670	LEU	0	0.026	0.005	5.249	-0.379	-0.379	0.000	0.000	0.000	0.000
29	A	671	PRO	0	-0.044	0.002	2.415	-0.039	0.729	0.378	-0.370	-0.776	0.001
30	A	672	GLY	0	0.028	0.009	3.658	-1.118	-0.760	0.004	-0.208	-0.155	-0.001
31	A	673	PRO	0	-0.025	-0.012	6.383	-0.306	-0.306	0.000	0.000	0.000	0.000
32	A	674	ILE	0	-0.002	-0.002	6.792	-0.137	-0.137	0.000	0.000	0.000	0.000
33	A	675	SER	0	-0.021	-0.029	8.443	0.318	0.318	0.000	0.000	0.000	0.000
34	A	676	LYS	1	0.816	0.906	10.625	0.523	0.523	0.000	0.000	0.000	0.000
35	A	677	TYR	0	-0.056	-0.041	10.872	-0.307	-0.307	0.000	0.000	0.000	0.000
36	A	678	VAL	0	-0.014	-0.001	12.613	0.104	0.104	0.000	0.000	0.000	0.000
37	A	679	VAL	0	0.013	0.002	14.235	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	680	GLU	-1	-0.831	-0.876	15.967	-0.188	-0.188	0.000	0.000	0.000	0.000
39	A	681	VAL	0	0.023	0.004	18.900	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	682	GLN	0	0.014	-0.006	20.238	0.007	0.007	0.000	0.000	0.000	0.000
41	A	683	VAL	0	0.024	0.028	24.174	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	684	ALA	0	0.007	-0.010	25.185	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	685	GLY	0	-0.017	-0.002	27.272	0.005	0.005	0.000	0.000	0.000	0.000
44	A	686	GLY	0	0.010	-0.002	28.162	0.009	0.009	0.000	0.000	0.000	0.000
45	A	687	ALA	0	-0.029	-0.022	23.760	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	688	GLY	0	0.030	0.012	24.170	0.010	0.010	0.000	0.000	0.000	0.000
47	A	689	ASP	-1	-0.965	-0.973	23.776	-0.051	-0.051	0.000	0.000	0.000	0.000
48	A	690	PRO	0	-0.048	-0.025	20.874	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	691	LEU	0	0.039	0.039	21.993	0.005	0.005	0.000	0.000	0.000	0.000
50	A	692	TRP	0	-0.031	-0.042	13.085	-0.036	-0.036	0.000	0.000	0.000	0.000
51	A	693	ILE	0	-0.006	-0.008	18.661	0.023	0.023	0.000	0.000	0.000	0.000
52	A	694	ASP	-1	-0.825	-0.907	15.508	-0.413	-0.413	0.000	0.000	0.000	0.000
53	A	695	VAL	0	-0.005	-0.006	16.141	0.034	0.034	0.000	0.000	0.000	0.000
54	A	696	ASP	-1	-0.836	-0.927	15.753	-0.370	-0.370	0.000	0.000	0.000	0.000
55	A	697	ARG	1	0.792	0.894	16.267	0.337	0.337	0.000	0.000	0.000	0.000
56	A	698	PRO	0	-0.006	0.005	12.133	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	699	GLU	-1	-0.799	-0.899	14.012	-0.533	-0.533	0.000	0.000	0.000	0.000
58	A	700	GLU	-1	-0.910	-0.943	16.618	-0.315	-0.315	0.000	0.000	0.000	0.000
59	A	701	THR	0	-0.008	-0.021	17.249	-0.056	-0.056	0.000	0.000	0.000	0.000
60	A	702	SER	0	-0.027	-0.040	19.530	0.024	0.024	0.000	0.000	0.000	0.000
61	A	703	THR	0	0.037	0.030	20.983	0.018	0.018	0.000	0.000	0.000	0.000
62	A	704	ILE	0	-0.005	-0.016	23.348	0.006	0.006	0.000	0.000	0.000	0.000
63	A	705	ILE	0	-0.006	0.010	21.913	0.007	0.007	0.000	0.000	0.000	0.000
64	A	706	ARG	1	0.893	0.918	25.978	0.175	0.175	0.000	0.000	0.000	0.000
65	A	707	GLY	0	0.008	0.013	28.513	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	708	LEU	0	-0.037	-0.011	26.983	0.002	0.002	0.000	0.000	0.000	0.000
67	A	709	ASN	0	-0.015	-0.018	31.074	0.011	0.011	0.000	0.000	0.000	0.000
68	A	710	ALA	0	0.118	0.071	34.199	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	711	SER	0	-0.030	-0.021	36.746	0.005	0.005	0.000	0.000	0.000	0.000
70	A	712	THR	0	-0.044	-0.001	33.002	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	713	ARG	1	0.849	0.909	30.706	0.109	0.109	0.000	0.000	0.000	0.000
72	A	714	TYR	0	0.066	0.016	26.041	0.007	0.007	0.000	0.000	0.000	0.000
73	A	715	LEU	0	-0.043	-0.007	21.691	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	716	PHE	0	0.047	0.010	20.533	0.007	0.007	0.000	0.000	0.000	0.000
75	A	717	ARG	1	0.796	0.879	15.715	0.196	0.196	0.000	0.000	0.000	0.000
76	A	718	MET	0	0.020	0.009	14.237	0.030	0.030	0.000	0.000	0.000	0.000
77	A	719	ARG	1	0.913	0.969	8.412	0.372	0.372	0.000	0.000	0.000	0.000
78	A	720	ALA	0	0.064	0.040	7.843	0.167	0.167	0.000	0.000	0.000	0.000
79	A	721	SER	0	-0.022	-0.009	6.933	-0.098	-0.098	0.000	0.000	0.000	0.000
80	A	722	ILE	0	0.051	0.015	2.550	-0.918	-0.278	0.277	-0.336	-0.581	0.001
81	A	723	GLN	0	-0.038	-0.017	6.019	0.488	0.488	0.000	0.000	0.000	0.000
82	A	724	GLY	0	0.010	0.001	8.256	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	725	LEU	0	-0.028	-0.015	8.750	0.027	0.027	0.000	0.000	0.000	0.000
84	A	726	GLY	0	0.017	0.009	12.192	0.096	0.096	0.000	0.000	0.000	0.000
85	A	727	ASP	-1	-0.956	-0.974	14.701	0.262	0.262	0.000	0.000	0.000	0.000
86	A	728	TRP	0	-0.021	-0.009	18.148	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	729	SER	0	-0.024	-0.012	21.105	0.013	0.013	0.000	0.000	0.000	0.000
88	A	730	ASN	0	-0.038	-0.022	24.176	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	731	THR	0	0.004	0.002	27.548	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	732	VAL	0	-0.013	-0.009	29.466	0.002	0.002	0.000	0.000	0.000	0.000
91	A	733	GLU	-1	-0.847	-0.916	32.312	0.008	0.008	0.000	0.000	0.000	0.000
92	A	734	GLU	-1	-0.977	-0.980	35.097	0.031	0.031	0.000	0.000	0.000	0.000
93	A	735	SER	0	-0.040	-0.032	37.223	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	736	THR	0	-0.031	-0.013	38.225	0.000	0.000	0.000	0.000	0.000	0.000
95	A	737	LEU	0	-0.023	-0.009	40.511	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	738	GLY	0	-0.021	-0.006	44.343	-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)