FMO DATABASE

FMODB ID: V5L91

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	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	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-576845.235344
FMO2-HF: Nuclear repulsion	540616.1295
FMO2-HF: Total energy	-36229.105844
FMO2-MP2: Total energy	-36336.387276

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.
-0.258	2.139	0.515	-1.226	-1.686	0.004

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 : 0.053 / q_NPA : 0.028

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	0.015	0.003	3.828	0.724	2.164	-0.017	-0.703	-0.720	0.003
4	A	646	ALA	0	-0.002	-0.003	6.605	0.145	0.145	0.000	0.000	0.000	0.000
5	A	647	PRO	0	0.012	0.015	9.693	-0.044	-0.044	0.000	0.000	0.000	0.000
6	A	648	ARG	1	0.841	0.892	12.753	0.737	0.737	0.000	0.000	0.000	0.000
7	A	649	HIS	0	-0.031	-0.036	15.376	0.027	0.027	0.000	0.000	0.000	0.000
8	A	650	LEU	0	0.063	0.039	16.946	-0.007	-0.007	0.000	0.000	0.000	0.000
9	A	651	HIS	0	0.001	0.000	19.636	0.024	0.024	0.000	0.000	0.000	0.000
10	A	652	ALA	0	0.020	0.025	23.193	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	653	GLN	0	-0.014	-0.012	25.202	0.006	0.006	0.000	0.000	0.000	0.000
12	A	654	ALA	0	-0.011	-0.012	28.870	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	655	LEU	0	-0.037	0.002	30.237	0.004	0.004	0.000	0.000	0.000	0.000
14	A	656	SER	0	-0.010	-0.015	33.074	0.010	0.010	0.000	0.000	0.000	0.000
15	A	657	ASP	-1	-0.914	-0.950	33.855	-0.087	-0.087	0.000	0.000	0.000	0.000
16	A	658	SER	0	-0.005	-0.017	33.672	0.002	0.002	0.000	0.000	0.000	0.000
17	A	659	GLU	-1	-0.835	-0.901	30.089	-0.129	-0.129	0.000	0.000	0.000	0.000
18	A	660	ILE	0	-0.032	-0.015	26.533	0.002	0.002	0.000	0.000	0.000	0.000
19	A	661	GLN	0	0.022	0.030	25.930	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	662	LEU	0	0.009	-0.004	19.154	0.004	0.004	0.000	0.000	0.000	0.000
21	A	663	THR	0	-0.014	0.000	22.100	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	664	TRP	0	0.004	0.006	16.010	0.026	0.026	0.000	0.000	0.000	0.000
23	A	665	LYS	1	0.853	0.918	17.209	0.416	0.416	0.000	0.000	0.000	0.000
24	A	666	HIS	0	0.045	0.023	14.113	-0.124	-0.124	0.000	0.000	0.000	0.000
25	A	667	PRO	0	-0.022	-0.003	9.912	0.121	0.121	0.000	0.000	0.000	0.000
26	A	668	GLU	-1	-0.823	-0.892	12.528	-0.783	-0.783	0.000	0.000	0.000	0.000
27	A	669	ALA	0	-0.017	0.008	11.141	0.044	0.044	0.000	0.000	0.000	0.000
28	A	670	LEU	0	0.008	-0.004	5.482	-0.327	-0.327	0.000	0.000	0.000	0.000
29	A	671	PRO	0	-0.035	-0.007	3.164	0.376	0.743	0.015	-0.113	-0.269	0.000
30	A	672	GLY	0	0.026	0.021	4.427	-0.806	-0.814	-0.001	-0.015	0.024	0.000
31	A	673	PRO	0	-0.005	-0.004	7.054	-0.309	-0.309	0.000	0.000	0.000	0.000
32	A	674	ILE	0	0.001	-0.007	6.471	-0.255	-0.255	0.000	0.000	0.000	0.000
33	A	675	SER	0	-0.040	-0.027	8.356	0.311	0.311	0.000	0.000	0.000	0.000
34	A	676	LYS	1	0.831	0.908	10.183	0.438	0.438	0.000	0.000	0.000	0.000
35	A	677	TYR	0	-0.035	-0.016	10.694	-0.281	-0.281	0.000	0.000	0.000	0.000
36	A	678	VAL	0	-0.011	0.003	12.054	0.097	0.097	0.000	0.000	0.000	0.000
37	A	679	VAL	0	0.011	0.002	14.294	-0.034	-0.034	0.000	0.000	0.000	0.000
38	A	680	GLU	-1	-0.812	-0.857	16.115	-0.124	-0.124	0.000	0.000	0.000	0.000
39	A	681	VAL	0	0.009	0.003	19.127	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	682	GLN	0	0.010	-0.002	20.304	0.005	0.005	0.000	0.000	0.000	0.000
41	A	683	VAL	0	0.027	0.028	24.339	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	684	ALA	0	0.016	-0.006	25.177	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	685	GLY	0	-0.017	0.012	27.203	0.005	0.005	0.000	0.000	0.000	0.000
44	A	686	GLY	0	-0.001	-0.020	27.863	0.008	0.008	0.000	0.000	0.000	0.000
45	A	687	ALA	0	-0.022	-0.019	23.500	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	688	GLY	0	0.036	0.014	23.886	0.007	0.007	0.000	0.000	0.000	0.000
47	A	689	ASP	-1	-0.969	-0.980	23.519	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	690	PRO	0	-0.045	-0.015	21.016	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	691	LEU	0	0.033	0.033	22.060	0.008	0.008	0.000	0.000	0.000	0.000
50	A	692	TRP	0	-0.050	-0.058	13.251	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	693	ILE	0	-0.010	-0.017	18.927	0.017	0.017	0.000	0.000	0.000	0.000
52	A	694	ASP	-1	-0.847	-0.909	15.334	-0.339	-0.339	0.000	0.000	0.000	0.000
53	A	695	VAL	0	-0.018	-0.006	16.249	0.026	0.026	0.000	0.000	0.000	0.000
54	A	696	ASP	-1	-0.846	-0.941	15.614	-0.299	-0.299	0.000	0.000	0.000	0.000
55	A	697	ARG	1	0.806	0.887	15.930	0.293	0.293	0.000	0.000	0.000	0.000
56	A	698	PRO	0	0.007	0.014	12.526	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	699	GLU	-1	-0.861	-0.924	14.412	-0.496	-0.496	0.000	0.000	0.000	0.000
58	A	700	GLU	-1	-0.901	-0.948	16.782	-0.261	-0.261	0.000	0.000	0.000	0.000
59	A	701	THR	0	-0.022	-0.021	17.572	-0.044	-0.044	0.000	0.000	0.000	0.000
60	A	702	SER	0	-0.050	-0.056	19.799	0.024	0.024	0.000	0.000	0.000	0.000
61	A	703	THR	0	0.059	0.030	20.697	0.013	0.013	0.000	0.000	0.000	0.000
62	A	704	ILE	0	-0.010	-0.013	23.038	0.005	0.005	0.000	0.000	0.000	0.000
63	A	705	ILE	0	-0.015	0.007	21.957	0.005	0.005	0.000	0.000	0.000	0.000
64	A	706	ARG	1	0.882	0.912	26.010	0.154	0.154	0.000	0.000	0.000	0.000
65	A	707	GLY	0	0.009	0.016	28.493	0.001	0.001	0.000	0.000	0.000	0.000
66	A	708	LEU	0	-0.036	-0.010	27.042	0.000	0.000	0.000	0.000	0.000	0.000
67	A	709	ASN	0	-0.019	-0.017	31.193	0.009	0.009	0.000	0.000	0.000	0.000
68	A	710	ALA	0	0.079	0.049	33.665	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	711	SER	0	-0.047	-0.035	36.378	0.004	0.004	0.000	0.000	0.000	0.000
70	A	712	THR	0	0.029	0.032	32.520	0.003	0.003	0.000	0.000	0.000	0.000
71	A	713	ARG	1	0.835	0.912	30.390	0.094	0.094	0.000	0.000	0.000	0.000
72	A	714	TYR	0	0.081	0.027	26.005	0.007	0.007	0.000	0.000	0.000	0.000
73	A	715	LEU	0	-0.049	-0.014	21.730	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	716	PHE	0	0.044	0.011	20.460	0.005	0.005	0.000	0.000	0.000	0.000
75	A	717	ARG	1	0.814	0.885	15.561	0.144	0.144	0.000	0.000	0.000	0.000
76	A	718	MET	0	0.019	0.014	14.191	0.025	0.025	0.000	0.000	0.000	0.000
77	A	719	ARG	1	0.924	0.966	8.219	0.234	0.234	0.000	0.000	0.000	0.000
78	A	720	ALA	0	0.053	0.034	7.774	0.154	0.154	0.000	0.000	0.000	0.000
79	A	721	SER	0	-0.015	0.001	6.772	-0.175	-0.175	0.000	0.000	0.000	0.000
80	A	722	ILE	0	0.054	0.019	2.390	-0.891	-0.293	0.518	-0.395	-0.721	0.001
81	A	723	GLN	0	-0.040	-0.015	5.666	0.585	0.585	0.000	0.000	0.000	0.000
82	A	724	GLY	0	0.008	0.001	8.289	-0.078	-0.078	0.000	0.000	0.000	0.000
83	A	725	LEU	0	-0.029	-0.017	8.819	0.025	0.025	0.000	0.000	0.000	0.000
84	A	726	GLY	0	0.025	0.018	12.521	0.082	0.082	0.000	0.000	0.000	0.000
85	A	727	ASP	-1	-0.943	-0.967	14.887	0.286	0.286	0.000	0.000	0.000	0.000
86	A	728	TRP	0	-0.022	-0.013	18.057	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	729	SER	0	-0.003	0.003	21.086	0.012	0.012	0.000	0.000	0.000	0.000
88	A	730	ASN	0	-0.058	-0.037	24.039	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	731	THR	0	0.011	-0.003	27.680	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	732	VAL	0	-0.018	-0.009	29.377	0.001	0.001	0.000	0.000	0.000	0.000
91	A	733	GLU	-1	-0.882	-0.945	32.259	0.019	0.019	0.000	0.000	0.000	0.000
92	A	734	GLU	-1	-0.977	-0.977	35.088	0.040	0.040	0.000	0.000	0.000	0.000
93	A	735	SER	0	-0.023	-0.008	36.856	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	736	THR	0	-0.039	-0.015	38.413	0.001	0.001	0.000	0.000	0.000	0.000
95	A	737	LEU	0	-0.015	-0.012	40.736	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	738	GLY	0	-0.011	-0.002	44.438	-0.002	-0.002	0.000	0.000	0.000	0.000

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