FMO DATABASE

FMODB ID: 39JJL

Calculation Name: 1AVZ-B-Xray372

Preferred Name: Tyrosine-protein kinase FYN

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1AVZ

Chain ID: B

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	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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-866704.516185
FMO2-HF: Nuclear repulsion	824395.255645
FMO2-HF: Total energy	-42309.260539
FMO2-MP2: Total energy	-42435.549236

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(B:71:THR)

Summations of interaction energy for fragment #1(B:71:THR)

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.
-4.473	-2.087	0.746	-1.372	-1.759	-0.009

Interaction energy analysis for fragmet #1(B:71:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.027

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	B	73	GLN	0	0.020	0.036	2.631	-4.658	-2.272	0.746	-1.372	-1.759	-0.009
4	B	74	VAL	0	-0.025	-0.008	5.138	0.868	0.868	0.000	0.000	0.000	0.000
5	B	75	PRO	0	0.000	-0.010	7.015	0.035	0.035	0.000	0.000	0.000	0.000
6	B	76	LEU	0	0.046	0.047	10.813	-0.047	-0.047	0.000	0.000	0.000	0.000
7	B	77	ARG	1	0.854	0.915	10.774	0.460	0.460	0.000	0.000	0.000	0.000
8	B	78	PRO	0	0.025	0.022	15.633	-0.047	-0.047	0.000	0.000	0.000	0.000
9	B	79	MET	0	0.025	0.034	16.348	0.024	0.024	0.000	0.000	0.000	0.000
10	B	80	THR	0	-0.013	-0.021	18.817	0.037	0.037	0.000	0.000	0.000	0.000
11	B	81	TYR	0	0.046	0.009	21.173	-0.007	-0.007	0.000	0.000	0.000	0.000
12	B	82	LYS	1	0.977	0.986	20.934	0.048	0.048	0.000	0.000	0.000	0.000
13	B	83	ALA	0	-0.012	0.007	17.230	0.003	0.003	0.000	0.000	0.000	0.000
14	B	84	ALA	0	0.025	0.005	18.170	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	85	VAL	0	0.012	0.008	20.409	-0.007	-0.007	0.000	0.000	0.000	0.000
16	B	86	ASP	-1	-0.928	-0.956	18.021	-0.079	-0.079	0.000	0.000	0.000	0.000
17	B	87	LEU	0	-0.019	-0.005	14.281	-0.004	-0.004	0.000	0.000	0.000	0.000
18	B	88	SER	0	-0.016	-0.027	17.390	-0.020	-0.020	0.000	0.000	0.000	0.000
19	B	89	HIS	0	0.027	0.002	20.529	-0.010	-0.010	0.000	0.000	0.000	0.000
20	B	90	PHE	0	0.106	0.064	11.953	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	91	LEU	0	-0.032	-0.031	14.946	-0.009	-0.009	0.000	0.000	0.000	0.000
22	B	92	LYS	1	0.791	0.913	18.304	0.124	0.124	0.000	0.000	0.000	0.000
23	B	93	GLU	-1	-0.972	-0.994	19.135	-0.063	-0.063	0.000	0.000	0.000	0.000
24	B	94	LYS	1	0.800	0.913	13.531	0.224	0.224	0.000	0.000	0.000	0.000
25	B	95	GLY	0	0.040	0.036	18.846	0.002	0.002	0.000	0.000	0.000	0.000
26	B	96	GLY	0	0.000	-0.011	20.146	-0.021	-0.021	0.000	0.000	0.000	0.000
27	B	97	LEU	0	-0.018	-0.010	19.461	-0.006	-0.006	0.000	0.000	0.000	0.000
28	B	98	GLU	-1	-0.821	-0.920	21.785	-0.137	-0.137	0.000	0.000	0.000	0.000
29	B	99	GLY	0	0.017	0.012	25.092	0.003	0.003	0.000	0.000	0.000	0.000
30	B	100	LEU	0	-0.067	-0.005	21.718	0.000	0.000	0.000	0.000	0.000	0.000
31	B	101	ILE	0	0.041	0.003	25.853	0.000	0.000	0.000	0.000	0.000	0.000
32	B	102	HIS	0	-0.023	-0.029	25.579	-0.016	-0.016	0.000	0.000	0.000	0.000
33	B	103	SER	0	0.020	-0.001	25.226	0.003	0.003	0.000	0.000	0.000	0.000
34	B	104	GLN	0	0.024	0.014	23.721	0.001	0.001	0.000	0.000	0.000	0.000
35	B	105	ARG	1	0.961	0.997	19.791	0.409	0.409	0.000	0.000	0.000	0.000
36	B	106	ARG	1	0.897	0.937	20.489	0.244	0.244	0.000	0.000	0.000	0.000
37	B	107	GLN	0	0.067	0.050	19.600	-0.018	-0.018	0.000	0.000	0.000	0.000
38	B	108	ASP	-1	-0.795	-0.920	19.170	-0.405	-0.405	0.000	0.000	0.000	0.000
39	B	109	ILE	0	-0.056	-0.027	15.485	-0.061	-0.061	0.000	0.000	0.000	0.000
40	B	110	LEU	0	-0.026	-0.010	14.877	-0.093	-0.093	0.000	0.000	0.000	0.000
41	B	111	ASP	-1	-0.777	-0.894	14.552	-0.516	-0.516	0.000	0.000	0.000	0.000
42	B	112	LEU	0	0.018	0.008	12.849	-0.064	-0.064	0.000	0.000	0.000	0.000
43	B	113	TRP	0	-0.016	0.005	9.213	-0.124	-0.124	0.000	0.000	0.000	0.000
44	B	114	ILE	0	-0.020	-0.003	9.856	-0.125	-0.125	0.000	0.000	0.000	0.000
45	B	115	TYR	0	-0.025	-0.011	10.375	0.000	0.000	0.000	0.000	0.000	0.000
46	B	116	HIS	0	-0.016	-0.018	6.680	-0.365	-0.365	0.000	0.000	0.000	0.000
47	B	117	THR	0	-0.056	-0.038	5.784	-0.318	-0.318	0.000	0.000	0.000	0.000
48	B	118	GLN	0	-0.037	-0.015	6.744	0.179	0.179	0.000	0.000	0.000	0.000
49	B	119	GLY	0	0.087	0.045	9.495	0.119	0.119	0.000	0.000	0.000	0.000
50	B	120	TYR	0	-0.070	-0.058	10.341	0.105	0.105	0.000	0.000	0.000	0.000
51	B	121	PHE	0	-0.006	-0.002	13.953	-0.068	-0.068	0.000	0.000	0.000	0.000
52	B	122	PRO	0	-0.018	-0.003	14.552	0.040	0.040	0.000	0.000	0.000	0.000
53	B	123	ASP	-1	-0.903	-0.951	17.272	-0.279	-0.279	0.000	0.000	0.000	0.000
54	B	124	TRP	0	0.011	-0.003	16.711	0.055	0.055	0.000	0.000	0.000	0.000
55	B	125	GLN	0	-0.030	0.020	19.617	0.059	0.059	0.000	0.000	0.000	0.000
56	B	126	ASN	0	0.007	0.015	22.012	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	127	TYR	0	-0.006	-0.024	22.954	0.020	0.020	0.000	0.000	0.000	0.000
58	B	128	THR	0	0.050	0.032	28.364	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	129	PRO	0	-0.026	-0.011	32.032	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	130	GLY	0	-0.029	0.006	34.440	0.005	0.005	0.000	0.000	0.000	0.000
61	B	131	PRO	0	-0.014	-0.015	36.414	0.003	0.003	0.000	0.000	0.000	0.000
62	B	132	GLY	0	0.008	-0.017	37.674	0.005	0.005	0.000	0.000	0.000	0.000
63	B	133	VAL	0	-0.037	-0.023	33.452	-0.007	-0.007	0.000	0.000	0.000	0.000
64	B	134	ARG	1	0.786	0.878	30.280	0.151	0.151	0.000	0.000	0.000	0.000
65	B	135	TYR	0	0.027	0.009	30.379	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	136	PRO	0	0.000	0.006	26.270	-0.004	-0.004	0.000	0.000	0.000	0.000
67	B	137	LEU	0	0.015	-0.009	27.269	0.013	0.013	0.000	0.000	0.000	0.000
68	B	138	THR	0	-0.022	-0.028	22.324	0.014	0.014	0.000	0.000	0.000	0.000
69	B	139	PHE	0	0.007	0.004	25.694	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	140	GLY	0	0.050	-0.001	24.814	-0.003	-0.003	0.000	0.000	0.000	0.000
71	B	141	TRP	0	-0.016	0.008	19.336	-0.008	-0.008	0.000	0.000	0.000	0.000
72	B	142	CYS	0	-0.053	-0.040	23.765	0.012	0.012	0.000	0.000	0.000	0.000
73	B	143	TYR	0	0.002	-0.004	21.504	0.007	0.007	0.000	0.000	0.000	0.000
74	B	144	LYS	1	0.893	0.937	25.838	0.114	0.114	0.000	0.000	0.000	0.000
75	B	145	LEU	0	-0.040	-0.014	26.097	-0.006	-0.006	0.000	0.000	0.000	0.000
76	B	146	VAL	0	0.005	-0.001	29.889	0.012	0.012	0.000	0.000	0.000	0.000
77	B	147	PRO	0	-0.006	0.009	32.845	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	148	VAL	0	-0.026	-0.006	34.174	0.006	0.006	0.000	0.000	0.000	0.000
79	B	179	GLU	-1	-0.737	-0.857	35.885	-0.130	-0.130	0.000	0.000	0.000	0.000
80	B	180	VAL	0	-0.032	-0.020	32.966	-0.010	-0.010	0.000	0.000	0.000	0.000
81	B	181	LEU	0	0.008	0.008	30.707	0.007	0.007	0.000	0.000	0.000	0.000
82	B	182	GLU	-1	-0.785	-0.888	28.611	-0.159	-0.159	0.000	0.000	0.000	0.000
83	B	183	TRP	0	-0.006	0.009	22.588	0.004	0.004	0.000	0.000	0.000	0.000
84	B	184	ARG	1	0.805	0.894	26.831	0.144	0.144	0.000	0.000	0.000	0.000
85	B	185	PHE	0	0.037	0.022	23.902	0.000	0.000	0.000	0.000	0.000	0.000
86	B	186	ASP	-1	-0.783	-0.867	27.235	-0.088	-0.088	0.000	0.000	0.000	0.000
87	B	187	SER	0	0.033	0.011	28.506	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	188	ARG	1	0.897	0.920	29.487	0.088	0.088	0.000	0.000	0.000	0.000
89	B	189	LEU	0	0.001	0.007	28.587	0.004	0.004	0.000	0.000	0.000	0.000
90	B	190	ALA	0	-0.024	-0.006	27.600	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	191	PHE	0	-0.049	-0.029	29.079	0.006	0.006	0.000	0.000	0.000	0.000
92	B	192	HIS	0	-0.003	0.018	32.683	0.008	0.008	0.000	0.000	0.000	0.000
93	B	193	HIS	0	-0.028	0.004	30.016	0.000	0.000	0.000	0.000	0.000	0.000
94	B	194	VAL	0	0.123	0.035	33.085	0.000	0.000	0.000	0.000	0.000	0.000
95	B	195	ALA	0	-0.060	-0.033	31.299	0.002	0.002	0.000	0.000	0.000	0.000
96	B	196	ARG	1	0.884	0.963	32.904	0.091	0.091	0.000	0.000	0.000	0.000
97	B	197	GLU	-1	-0.953	-0.978	35.196	-0.078	-0.078	0.000	0.000	0.000	0.000
98	B	198	LEU	0	-0.067	-0.028	36.921	0.004	0.004	0.000	0.000	0.000	0.000
99	B	199	HIS	0	0.018	0.005	35.170	0.000	0.000	0.000	0.000	0.000	0.000
100	B	200	PRO	0	0.024	0.010	35.534	-0.006	-0.006	0.000	0.000	0.000	0.000
101	B	201	GLU	-1	-0.843	-0.933	36.568	-0.107	-0.107	0.000	0.000	0.000	0.000
102	B	202	TYR	0	-0.063	-0.032	31.449	-0.003	-0.003	0.000	0.000	0.000	0.000
103	B	203	PHE	0	-0.076	-0.023	29.484	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:71:THR)