FMO DATABASE

FMODB ID: 7266K

Calculation Name: 1AVZ-A-Xray372

Preferred Name: Tyrosine-protein kinase FYN

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1AVZ

Chain ID: A

ChEMBL ID: CHEMBL1841

UniProt ID: P06241

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	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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-835199.718695
FMO2-HF: Nuclear repulsion	794025.210115
FMO2-HF: Total energy	-41174.508581
FMO2-MP2: Total energy	-41297.34602

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:74:VAL)

Summations of interaction energy for fragment #1(A:74:VAL)

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.
-8.549	-2.962	2.966	-2.819	-5.733	-0.027

Interaction energy analysis for fragmet #1(A:74:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.021

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	76	LEU	0	0.009	0.017	3.903	-1.841	-0.579	-0.011	-0.538	-0.713	0.002
4	A	77	ARG	1	0.848	0.921	4.456	1.458	1.623	-0.001	-0.011	-0.153	0.000
5	A	78	PRO	0	0.014	0.013	8.353	-0.153	-0.153	0.000	0.000	0.000	0.000
6	A	79	MET	0	0.016	0.021	11.012	0.057	0.057	0.000	0.000	0.000	0.000
7	A	80	THR	0	-0.038	-0.031	12.468	0.093	0.093	0.000	0.000	0.000	0.000
8	A	81	TYR	0	0.012	-0.011	15.438	-0.017	-0.017	0.000	0.000	0.000	0.000
9	A	82	LYS	1	0.981	0.989	14.120	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	83	ALA	0	0.032	0.031	11.583	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	84	ALA	0	0.057	0.023	12.897	-0.062	-0.062	0.000	0.000	0.000	0.000
12	A	85	VAL	0	0.016	0.033	15.059	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	86	ASP	-1	-0.937	-0.972	12.901	-0.082	-0.082	0.000	0.000	0.000	0.000
14	A	87	LEU	0	-0.040	-0.015	10.199	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	88	SER	0	-0.019	-0.033	12.958	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	89	HIS	0	0.007	0.005	16.386	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	90	PHE	0	0.095	0.055	9.650	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	91	LEU	0	-0.029	-0.028	12.028	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	92	LYS	1	0.801	0.917	15.443	0.172	0.172	0.000	0.000	0.000	0.000
20	A	93	GLU	-1	-0.932	-0.987	15.827	-0.109	-0.109	0.000	0.000	0.000	0.000
21	A	94	LYS	1	0.821	0.920	11.834	0.321	0.321	0.000	0.000	0.000	0.000
22	A	95	GLY	0	0.022	0.033	17.354	0.009	0.009	0.000	0.000	0.000	0.000
23	A	96	GLY	0	-0.011	-0.009	18.328	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	97	LEU	0	-0.007	-0.007	16.597	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	98	GLU	-1	-0.812	-0.913	19.591	-0.167	-0.167	0.000	0.000	0.000	0.000
26	A	99	GLY	0	0.024	0.018	22.903	0.008	0.008	0.000	0.000	0.000	0.000
27	A	100	LEU	0	-0.087	-0.018	19.539	0.005	0.005	0.000	0.000	0.000	0.000
28	A	101	ILE	0	0.035	0.004	23.593	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	102	HIS	0	0.002	-0.009	22.141	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	103	SER	0	0.000	-0.008	22.870	0.007	0.007	0.000	0.000	0.000	0.000
31	A	104	GLN	0	0.018	0.007	20.370	0.000	0.000	0.000	0.000	0.000	0.000
32	A	105	ARG	1	0.961	1.001	18.346	0.345	0.345	0.000	0.000	0.000	0.000
33	A	106	ARG	1	0.894	0.932	18.100	0.237	0.237	0.000	0.000	0.000	0.000
34	A	107	GLN	0	0.070	0.057	17.060	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	108	ASP	-1	-0.799	-0.921	15.757	-0.490	-0.490	0.000	0.000	0.000	0.000
36	A	109	ILE	0	-0.047	-0.026	13.699	-0.091	-0.091	0.000	0.000	0.000	0.000
37	A	110	LEU	0	-0.042	-0.004	12.304	-0.121	-0.121	0.000	0.000	0.000	0.000
38	A	111	ASP	-1	-0.757	-0.886	11.475	-0.852	-0.852	0.000	0.000	0.000	0.000
39	A	112	LEU	0	-0.009	-0.003	9.591	-0.219	-0.219	0.000	0.000	0.000	0.000
40	A	113	TRP	0	-0.018	-0.002	7.782	-0.321	-0.321	0.000	0.000	0.000	0.000
41	A	114	ILE	0	0.011	0.015	6.871	-0.378	-0.378	0.000	0.000	0.000	0.000
42	A	115	TYR	0	0.001	0.005	5.925	-0.537	-0.537	0.000	0.000	0.000	0.000
43	A	116	HIS	0	-0.004	-0.019	3.673	-1.584	-1.258	0.004	-0.068	-0.262	0.000
44	A	117	THR	0	-0.066	-0.045	2.405	-4.098	-2.059	1.582	-1.505	-2.116	-0.018
45	A	118	GLN	0	-0.052	-0.020	2.783	-0.213	0.973	1.323	-0.525	-1.984	-0.010
46	A	119	GLY	0	0.044	0.039	3.491	-0.412	0.096	0.069	-0.156	-0.420	-0.001
47	A	120	TYR	0	0.000	-0.011	4.211	0.798	0.899	0.000	-0.016	-0.085	0.000
48	A	121	PHE	0	0.019	0.005	7.750	-0.140	-0.140	0.000	0.000	0.000	0.000
49	A	122	PRO	0	0.000	0.003	10.262	0.085	0.085	0.000	0.000	0.000	0.000
50	A	123	ASP	-1	-0.910	-0.949	12.705	-0.443	-0.443	0.000	0.000	0.000	0.000
51	A	124	TRP	0	0.001	-0.011	12.017	0.097	0.097	0.000	0.000	0.000	0.000
52	A	125	GLN	0	-0.019	0.019	15.016	0.119	0.119	0.000	0.000	0.000	0.000
53	A	126	ASN	0	-0.010	-0.001	16.793	0.036	0.036	0.000	0.000	0.000	0.000
54	A	127	TYR	0	-0.018	-0.029	18.820	0.021	0.021	0.000	0.000	0.000	0.000
55	A	128	THR	0	0.020	0.022	23.553	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	129	PRO	0	-0.024	-0.001	27.294	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	130	GLY	0	-0.024	0.005	29.875	0.004	0.004	0.000	0.000	0.000	0.000
58	A	131	PRO	0	-0.025	-0.024	32.453	0.003	0.003	0.000	0.000	0.000	0.000
59	A	132	GLY	0	0.006	-0.001	33.826	0.004	0.004	0.000	0.000	0.000	0.000
60	A	133	VAL	0	-0.058	-0.032	28.851	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	134	ARG	1	0.813	0.896	25.763	0.175	0.175	0.000	0.000	0.000	0.000
62	A	135	TYR	0	0.042	0.006	25.715	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	136	PRO	0	0.011	0.014	20.976	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	137	LEU	0	0.011	-0.012	21.781	0.017	0.017	0.000	0.000	0.000	0.000
65	A	138	THR	0	-0.024	-0.033	16.527	0.029	0.029	0.000	0.000	0.000	0.000
66	A	139	PHE	0	0.021	0.011	19.992	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	140	GLY	0	0.031	0.000	19.523	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	141	TRP	0	0.009	0.007	15.571	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	142	CYS	0	-0.076	-0.040	18.665	0.026	0.026	0.000	0.000	0.000	0.000
70	A	143	TYR	0	-0.016	-0.019	18.046	0.016	0.016	0.000	0.000	0.000	0.000
71	A	144	LYS	1	0.890	0.943	21.626	0.140	0.140	0.000	0.000	0.000	0.000
72	A	145	LEU	0	0.005	0.008	22.355	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	146	VAL	0	-0.025	-0.020	26.033	0.013	0.013	0.000	0.000	0.000	0.000
74	A	147	PRO	0	0.010	0.006	29.655	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	148	VAL	0	-0.045	-0.010	31.396	0.008	0.008	0.000	0.000	0.000	0.000
76	A	179	GLU	-1	-0.782	-0.883	33.449	-0.144	-0.144	0.000	0.000	0.000	0.000
77	A	180	VAL	0	0.015	0.007	30.625	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	181	LEU	0	0.035	0.027	27.550	0.007	0.007	0.000	0.000	0.000	0.000
79	A	182	GLU	-1	-0.788	-0.876	26.091	-0.169	-0.169	0.000	0.000	0.000	0.000
80	A	183	TRP	0	-0.005	-0.002	19.356	0.007	0.007	0.000	0.000	0.000	0.000
81	A	184	ARG	1	0.777	0.868	23.813	0.165	0.165	0.000	0.000	0.000	0.000
82	A	185	PHE	0	0.050	0.011	20.263	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	186	ASP	-1	-0.816	-0.882	23.799	-0.104	-0.104	0.000	0.000	0.000	0.000
84	A	187	SER	0	0.046	0.022	23.862	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	188	ARG	1	0.861	0.897	24.913	0.106	0.106	0.000	0.000	0.000	0.000
86	A	189	LEU	0	0.026	0.017	23.799	0.008	0.008	0.000	0.000	0.000	0.000
87	A	190	ALA	0	0.002	0.012	22.265	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	191	PHE	0	-0.069	-0.034	23.902	0.013	0.013	0.000	0.000	0.000	0.000
89	A	192	HIS	0	0.007	0.018	27.581	0.008	0.008	0.000	0.000	0.000	0.000
90	A	193	HIS	0	-0.056	-0.031	24.303	0.001	0.001	0.000	0.000	0.000	0.000
91	A	194	VAL	0	0.084	0.035	27.827	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	195	ALA	0	-0.037	-0.029	25.784	0.003	0.003	0.000	0.000	0.000	0.000
93	A	196	ARG	1	0.883	0.971	27.420	0.109	0.109	0.000	0.000	0.000	0.000
94	A	197	GLU	-1	-0.905	-0.964	29.377	-0.094	-0.094	0.000	0.000	0.000	0.000
95	A	198	LEU	0	-0.048	-0.018	31.897	0.007	0.007	0.000	0.000	0.000	0.000
96	A	199	HIS	0	-0.006	0.001	29.884	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	200	PRO	0	0.052	0.017	29.759	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	201	GLU	-1	-0.837	-0.914	30.645	-0.135	-0.135	0.000	0.000	0.000	0.000
99	A	202	TYR	0	-0.082	-0.051	25.647	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	203	PHE	0	-0.075	-0.025	23.804	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:74:VAL)