FMO DATABASE

FMODB ID: 94882

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

Total energy (hartree)

FMO2-HF: Electronic energy	-837039.916043
FMO2-HF: Nuclear repulsion	795866.423058
FMO2-HF: Total energy	-41173.492986
FMO2-MP2: Total energy	-41296.449393

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.
-11.735	-6.911	4.122	-3.309	-5.638	-0.031

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 : -0.017 / q_NPA : -0.014

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

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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	0.018	0.012	3.896	-2.218	-0.912	-0.011	-0.580	-0.715	0.002
4	A	77	ARG	1	0.894	0.950	4.863	2.269	2.269	0.000	0.000	0.000	0.000
5	A	78	PRO	0	-0.010	-0.004	8.464	-0.183	-0.183	0.000	0.000	0.000	0.000
6	A	79	MET	0	0.036	0.013	11.294	0.070	0.070	0.000	0.000	0.000	0.000
7	A	80	THR	0	-0.024	-0.005	12.691	0.112	0.112	0.000	0.000	0.000	0.000
8	A	81	TYR	0	0.015	-0.028	15.313	-0.037	-0.037	0.000	0.000	0.000	0.000
9	A	82	LYS	1	0.981	0.984	14.340	-0.026	-0.026	0.000	0.000	0.000	0.000
10	A	83	ALA	0	0.004	0.017	11.532	0.005	0.005	0.000	0.000	0.000	0.000
11	A	84	ALA	0	0.046	0.019	13.115	-0.070	-0.070	0.000	0.000	0.000	0.000
12	A	85	VAL	0	0.010	0.020	15.114	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	86	ASP	-1	-0.923	-0.959	13.195	-0.173	-0.173	0.000	0.000	0.000	0.000
14	A	87	LEU	0	-0.045	-0.010	10.577	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	88	SER	0	-0.010	-0.045	13.280	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	89	HIS	0	-0.001	0.006	16.486	0.004	0.004	0.000	0.000	0.000	0.000
17	A	90	PHE	0	0.059	0.040	9.975	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	91	LEU	0	-0.058	-0.046	12.236	0.017	0.017	0.000	0.000	0.000	0.000
19	A	92	LYS	1	0.864	0.965	15.777	0.239	0.239	0.000	0.000	0.000	0.000
20	A	93	GLU	-1	-0.978	-0.993	16.931	-0.170	-0.170	0.000	0.000	0.000	0.000
21	A	94	LYS	1	0.860	0.938	12.301	0.476	0.476	0.000	0.000	0.000	0.000
22	A	95	GLY	0	0.049	0.037	17.385	0.020	0.020	0.000	0.000	0.000	0.000
23	A	96	GLY	0	-0.018	-0.021	18.426	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	97	LEU	0	-0.008	-0.007	16.872	0.005	0.005	0.000	0.000	0.000	0.000
25	A	98	GLU	-1	-0.850	-0.942	19.734	-0.219	-0.219	0.000	0.000	0.000	0.000
26	A	99	GLY	0	0.020	0.014	22.869	0.010	0.010	0.000	0.000	0.000	0.000
27	A	100	LEU	0	-0.070	-0.005	20.027	0.009	0.009	0.000	0.000	0.000	0.000
28	A	101	ILE	0	0.041	0.012	24.060	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	102	HIS	0	-0.031	-0.043	22.475	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	103	SER	0	-0.012	-0.014	22.787	0.019	0.019	0.000	0.000	0.000	0.000
31	A	104	GLN	0	0.076	0.030	21.128	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	105	ARG	1	0.989	1.014	19.253	0.404	0.404	0.000	0.000	0.000	0.000
33	A	106	ARG	1	0.882	0.936	18.676	0.302	0.302	0.000	0.000	0.000	0.000
34	A	107	GLN	0	0.059	0.044	17.529	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	108	ASP	-1	-0.845	-0.925	16.510	-0.584	-0.584	0.000	0.000	0.000	0.000
36	A	109	ILE	0	-0.068	-0.043	14.446	-0.097	-0.097	0.000	0.000	0.000	0.000
37	A	110	LEU	0	-0.050	-0.016	12.942	-0.146	-0.146	0.000	0.000	0.000	0.000
38	A	111	ASP	-1	-0.822	-0.916	11.898	-0.955	-0.955	0.000	0.000	0.000	0.000
39	A	112	LEU	0	-0.006	-0.008	10.176	-0.236	-0.236	0.000	0.000	0.000	0.000
40	A	113	TRP	0	-0.010	0.001	8.352	-0.398	-0.398	0.000	0.000	0.000	0.000
41	A	114	ILE	0	-0.008	-0.006	7.288	-0.465	-0.465	0.000	0.000	0.000	0.000
42	A	115	TYR	0	-0.013	0.012	5.988	-0.785	-0.785	0.000	0.000	0.000	0.000
43	A	116	HIS	0	-0.004	-0.010	4.247	-1.300	-1.127	-0.001	-0.037	-0.135	0.000
44	A	117	THR	0	-0.066	-0.032	2.402	-5.375	-3.776	1.885	-1.354	-2.130	-0.016
45	A	118	GLN	0	-0.016	-0.011	2.633	-2.346	-1.077	2.229	-1.191	-2.307	-0.016
46	A	119	GLY	0	0.059	0.052	3.643	-0.703	-0.291	0.021	-0.137	-0.297	-0.001
47	A	120	TYR	0	-0.047	-0.042	4.346	0.981	1.046	-0.001	-0.010	-0.054	0.000
48	A	121	PHE	0	0.003	0.001	8.027	-0.075	-0.075	0.000	0.000	0.000	0.000
49	A	122	PRO	0	-0.009	-0.003	9.989	0.092	0.092	0.000	0.000	0.000	0.000
50	A	123	ASP	-1	-0.894	-0.945	12.740	-0.527	-0.527	0.000	0.000	0.000	0.000
51	A	124	TRP	0	0.030	0.011	11.247	0.138	0.138	0.000	0.000	0.000	0.000
52	A	125	GLN	0	0.009	0.010	15.446	0.125	0.125	0.000	0.000	0.000	0.000
53	A	126	ASN	0	0.020	0.009	17.295	0.009	0.009	0.000	0.000	0.000	0.000
54	A	127	TYR	0	-0.016	-0.007	19.210	0.027	0.027	0.000	0.000	0.000	0.000
55	A	128	THR	0	0.058	0.036	23.863	0.000	0.000	0.000	0.000	0.000	0.000
56	A	129	PRO	0	-0.030	-0.004	27.467	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	130	GLY	0	-0.018	0.010	30.152	0.006	0.006	0.000	0.000	0.000	0.000
58	A	131	PRO	0	-0.012	-0.028	32.354	0.004	0.004	0.000	0.000	0.000	0.000
59	A	132	GLY	0	0.036	0.006	34.020	0.005	0.005	0.000	0.000	0.000	0.000
60	A	133	VAL	0	-0.059	-0.053	29.224	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	134	ARG	1	0.850	0.954	26.013	0.216	0.216	0.000	0.000	0.000	0.000
62	A	135	TYR	0	0.006	-0.006	25.902	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	136	PRO	0	-0.006	0.002	21.190	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	137	LEU	0	0.018	-0.005	22.065	0.022	0.022	0.000	0.000	0.000	0.000
65	A	138	THR	0	-0.025	-0.017	16.738	0.031	0.031	0.000	0.000	0.000	0.000
66	A	139	PHE	0	0.001	0.011	20.115	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	140	GLY	0	0.060	0.005	19.218	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	141	TRP	0	-0.010	0.004	15.276	-0.033	-0.033	0.000	0.000	0.000	0.000
69	A	142	CYS	0	-0.069	-0.044	18.692	0.038	0.038	0.000	0.000	0.000	0.000
70	A	143	TYR	0	0.015	0.001	17.929	0.025	0.025	0.000	0.000	0.000	0.000
71	A	144	LYS	1	0.945	0.983	21.857	0.186	0.186	0.000	0.000	0.000	0.000
72	A	145	LEU	0	-0.022	0.000	22.884	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	146	VAL	0	-0.009	-0.012	26.331	0.018	0.018	0.000	0.000	0.000	0.000
74	A	147	PRO	0	0.005	0.008	29.756	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	148	VAL	0	-0.022	-0.005	31.373	0.008	0.008	0.000	0.000	0.000	0.000
76	A	179	GLU	-1	-0.856	-0.930	33.324	-0.169	-0.169	0.000	0.000	0.000	0.000
77	A	180	VAL	0	0.019	-0.001	30.734	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	181	LEU	0	0.023	0.018	27.447	0.007	0.007	0.000	0.000	0.000	0.000
79	A	182	GLU	-1	-0.824	-0.924	26.163	-0.222	-0.222	0.000	0.000	0.000	0.000
80	A	183	TRP	0	-0.014	-0.007	19.663	0.007	0.007	0.000	0.000	0.000	0.000
81	A	184	ARG	1	0.829	0.930	24.007	0.215	0.215	0.000	0.000	0.000	0.000
82	A	185	PHE	0	0.016	-0.002	20.366	0.000	0.000	0.000	0.000	0.000	0.000
83	A	186	ASP	-1	-0.829	-0.918	23.988	-0.141	-0.141	0.000	0.000	0.000	0.000
84	A	187	SER	0	0.031	0.002	24.232	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	188	ARG	1	0.897	0.944	25.265	0.143	0.143	0.000	0.000	0.000	0.000
86	A	189	LEU	0	-0.005	0.006	24.105	0.009	0.009	0.000	0.000	0.000	0.000
87	A	190	ALA	0	-0.006	0.011	22.607	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	191	PHE	0	-0.055	-0.012	24.086	0.013	0.013	0.000	0.000	0.000	0.000
89	A	192	HIS	0	0.017	0.020	27.657	0.010	0.010	0.000	0.000	0.000	0.000
90	A	193	HIS	0	-0.003	0.002	24.273	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	194	VAL	0	0.092	0.026	27.629	0.001	0.001	0.000	0.000	0.000	0.000
92	A	195	ALA	0	-0.033	-0.019	26.026	0.006	0.006	0.000	0.000	0.000	0.000
93	A	196	ARG	1	0.903	0.967	27.051	0.138	0.138	0.000	0.000	0.000	0.000
94	A	197	GLU	-1	-0.988	-0.992	29.722	-0.115	-0.115	0.000	0.000	0.000	0.000
95	A	198	LEU	0	-0.052	-0.037	31.703	0.007	0.007	0.000	0.000	0.000	0.000
96	A	199	HIS	0	0.017	0.020	29.791	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	200	PRO	0	0.027	0.003	30.246	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	201	GLU	-1	-0.836	-0.928	30.992	-0.157	-0.157	0.000	0.000	0.000	0.000
99	A	202	TYR	0	-0.076	-0.029	25.968	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	203	PHE	0	-0.074	-0.027	24.219	-0.008	-0.008	0.000	0.000	0.000	0.000

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