FMO DATABASE

FMODB ID: JLQQ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-867220.012794
FMO2-HF: Nuclear repulsion	824911.495439
FMO2-HF: Total energy	-42308.517355
FMO2-MP2: Total energy	-42434.856925

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.
-3.867	-1.829	1.015	-1.314	-1.739	-0.008

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 : -0.020 / q_NPA : -0.026

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	B	73	GLN	0	-0.007	0.012	2.699	-3.648	-1.610	1.015	-1.314	-1.739	-0.008
4	B	74	VAL	0	-0.017	-0.006	4.981	0.683	0.683	0.000	0.000	0.000	0.000
5	B	75	PRO	0	0.009	-0.001	6.959	0.134	0.134	0.000	0.000	0.000	0.000
6	B	76	LEU	0	0.063	0.048	10.750	-0.033	-0.033	0.000	0.000	0.000	0.000
7	B	77	ARG	1	0.880	0.947	10.530	0.736	0.736	0.000	0.000	0.000	0.000
8	B	78	PRO	0	0.023	0.022	15.671	-0.037	-0.037	0.000	0.000	0.000	0.000
9	B	79	MET	0	0.039	0.040	16.570	0.002	0.002	0.000	0.000	0.000	0.000
10	B	80	THR	0	-0.033	-0.030	18.985	0.040	0.040	0.000	0.000	0.000	0.000
11	B	81	TYR	0	0.032	-0.023	21.186	-0.015	-0.015	0.000	0.000	0.000	0.000
12	B	82	LYS	1	0.989	0.990	21.140	0.187	0.187	0.000	0.000	0.000	0.000
13	B	83	ALA	0	-0.012	0.006	17.220	-0.002	-0.002	0.000	0.000	0.000	0.000
14	B	84	ALA	0	0.028	0.006	18.097	-0.026	-0.026	0.000	0.000	0.000	0.000
15	B	85	VAL	0	0.006	-0.001	20.289	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	86	ASP	-1	-0.922	-0.955	18.043	-0.236	-0.236	0.000	0.000	0.000	0.000
17	B	87	LEU	0	-0.030	-0.011	14.221	-0.013	-0.013	0.000	0.000	0.000	0.000
18	B	88	SER	0	0.001	-0.012	17.317	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	89	HIS	0	0.012	-0.001	20.427	0.006	0.006	0.000	0.000	0.000	0.000
20	B	90	PHE	0	0.055	0.039	12.251	-0.008	-0.008	0.000	0.000	0.000	0.000
21	B	91	LEU	0	-0.039	-0.031	14.908	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	92	LYS	1	0.835	0.945	18.198	0.165	0.165	0.000	0.000	0.000	0.000
23	B	93	GLU	-1	-0.973	-0.997	19.339	-0.184	-0.184	0.000	0.000	0.000	0.000
24	B	94	LYS	1	0.866	0.946	13.405	0.398	0.398	0.000	0.000	0.000	0.000
25	B	95	GLY	0	0.032	0.031	18.819	0.018	0.018	0.000	0.000	0.000	0.000
26	B	96	GLY	0	0.002	-0.010	20.021	-0.014	-0.014	0.000	0.000	0.000	0.000
27	B	97	LEU	0	-0.009	-0.009	19.373	0.006	0.006	0.000	0.000	0.000	0.000
28	B	98	GLU	-1	-0.869	-0.950	21.556	-0.132	-0.132	0.000	0.000	0.000	0.000
29	B	99	GLY	0	0.017	0.013	24.900	0.007	0.007	0.000	0.000	0.000	0.000
30	B	100	LEU	0	-0.064	-0.007	21.420	0.009	0.009	0.000	0.000	0.000	0.000
31	B	101	ILE	0	0.056	0.014	25.572	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	102	HIS	0	-0.041	-0.029	24.999	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	103	SER	0	0.010	-0.002	24.020	0.012	0.012	0.000	0.000	0.000	0.000
34	B	104	GLN	0	0.071	0.032	23.399	-0.006	-0.006	0.000	0.000	0.000	0.000
35	B	105	ARG	1	0.954	0.998	19.494	0.180	0.180	0.000	0.000	0.000	0.000
36	B	106	ARG	1	0.878	0.912	19.751	0.147	0.147	0.000	0.000	0.000	0.000
37	B	107	GLN	0	0.072	0.061	19.016	-0.015	-0.015	0.000	0.000	0.000	0.000
38	B	108	ASP	-1	-0.817	-0.932	18.654	-0.301	-0.301	0.000	0.000	0.000	0.000
39	B	109	ILE	0	-0.075	-0.037	14.629	-0.038	-0.038	0.000	0.000	0.000	0.000
40	B	110	LEU	0	-0.060	-0.010	14.273	-0.080	-0.080	0.000	0.000	0.000	0.000
41	B	111	ASP	-1	-0.806	-0.901	14.143	-0.462	-0.462	0.000	0.000	0.000	0.000
42	B	112	LEU	0	0.011	-0.003	12.164	-0.079	-0.079	0.000	0.000	0.000	0.000
43	B	113	TRP	0	-0.010	0.008	9.014	-0.136	-0.136	0.000	0.000	0.000	0.000
44	B	114	ILE	0	-0.025	-0.005	9.554	-0.200	-0.200	0.000	0.000	0.000	0.000
45	B	115	TYR	0	-0.008	0.002	10.389	-0.139	-0.139	0.000	0.000	0.000	0.000
46	B	116	HIS	0	-0.024	-0.018	6.117	-0.356	-0.356	0.000	0.000	0.000	0.000
47	B	117	THR	0	-0.071	-0.043	5.562	-0.420	-0.420	0.000	0.000	0.000	0.000
48	B	118	GLN	0	0.019	0.008	6.650	-0.081	-0.081	0.000	0.000	0.000	0.000
49	B	119	GLY	0	0.053	0.021	9.553	0.087	0.087	0.000	0.000	0.000	0.000
50	B	120	TYR	0	-0.089	-0.065	10.535	0.112	0.112	0.000	0.000	0.000	0.000
51	B	121	PHE	0	-0.021	-0.008	14.175	-0.038	-0.038	0.000	0.000	0.000	0.000
52	B	122	PRO	0	-0.014	-0.001	14.591	0.030	0.030	0.000	0.000	0.000	0.000
53	B	123	ASP	-1	-0.868	-0.938	17.118	-0.299	-0.299	0.000	0.000	0.000	0.000
54	B	124	TRP	0	0.020	-0.001	16.052	0.048	0.048	0.000	0.000	0.000	0.000
55	B	125	GLN	0	-0.015	0.004	18.925	0.051	0.051	0.000	0.000	0.000	0.000
56	B	126	ASN	0	0.023	0.013	21.863	0.012	0.012	0.000	0.000	0.000	0.000
57	B	127	TYR	0	0.006	0.003	22.704	0.008	0.008	0.000	0.000	0.000	0.000
58	B	128	THR	0	0.032	0.024	28.165	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	129	PRO	0	-0.025	-0.004	31.831	-0.003	-0.003	0.000	0.000	0.000	0.000
60	B	130	GLY	0	-0.028	-0.009	34.144	0.003	0.003	0.000	0.000	0.000	0.000
61	B	131	PRO	0	-0.016	-0.020	36.069	0.001	0.001	0.000	0.000	0.000	0.000
62	B	132	GLY	0	0.032	-0.004	37.340	0.001	0.001	0.000	0.000	0.000	0.000
63	B	133	VAL	0	-0.056	-0.045	33.111	-0.004	-0.004	0.000	0.000	0.000	0.000
64	B	134	ARG	1	0.871	0.965	29.933	0.122	0.122	0.000	0.000	0.000	0.000
65	B	135	TYR	0	0.014	0.004	30.095	-0.008	-0.008	0.000	0.000	0.000	0.000
66	B	136	PRO	0	0.003	0.004	26.123	0.000	0.000	0.000	0.000	0.000	0.000
67	B	137	LEU	0	0.024	-0.008	27.225	0.009	0.009	0.000	0.000	0.000	0.000
68	B	138	THR	0	-0.036	-0.028	22.479	0.007	0.007	0.000	0.000	0.000	0.000
69	B	139	PHE	0	0.004	0.005	25.744	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	140	GLY	0	0.051	0.001	24.694	-0.010	-0.010	0.000	0.000	0.000	0.000
71	B	141	TRP	0	-0.007	0.010	18.833	-0.018	-0.018	0.000	0.000	0.000	0.000
72	B	142	CYS	0	-0.050	-0.039	23.584	0.019	0.019	0.000	0.000	0.000	0.000
73	B	143	TYR	0	0.006	0.001	21.339	0.016	0.016	0.000	0.000	0.000	0.000
74	B	144	LYS	1	0.929	0.969	25.623	0.115	0.115	0.000	0.000	0.000	0.000
75	B	145	LEU	0	-0.047	-0.017	26.003	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	146	VAL	0	0.006	-0.005	29.585	0.009	0.009	0.000	0.000	0.000	0.000
77	B	147	PRO	0	0.010	0.007	32.543	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	148	VAL	0	0.002	0.012	33.820	0.004	0.004	0.000	0.000	0.000	0.000
79	B	179	GLU	-1	-0.847	-0.929	35.182	-0.091	-0.091	0.000	0.000	0.000	0.000
80	B	180	VAL	0	-0.011	-0.006	32.623	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	181	LEU	0	0.004	0.010	30.300	0.003	0.003	0.000	0.000	0.000	0.000
82	B	182	GLU	-1	-0.843	-0.938	28.290	-0.116	-0.116	0.000	0.000	0.000	0.000
83	B	183	TRP	0	-0.011	-0.001	22.155	0.003	0.003	0.000	0.000	0.000	0.000
84	B	184	ARG	1	0.828	0.932	26.555	0.120	0.120	0.000	0.000	0.000	0.000
85	B	185	PHE	0	0.032	0.016	23.959	-0.004	-0.004	0.000	0.000	0.000	0.000
86	B	186	ASP	-1	-0.815	-0.900	27.073	-0.100	-0.100	0.000	0.000	0.000	0.000
87	B	187	SER	0	0.025	0.003	28.418	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	188	ARG	1	0.905	0.930	29.399	0.099	0.099	0.000	0.000	0.000	0.000
89	B	189	LEU	0	0.005	0.007	27.932	0.003	0.003	0.000	0.000	0.000	0.000
90	B	190	ALA	0	-0.018	-0.007	27.544	-0.006	-0.006	0.000	0.000	0.000	0.000
91	B	191	PHE	0	-0.049	0.002	28.982	0.001	0.001	0.000	0.000	0.000	0.000
92	B	192	HIS	0	0.002	0.017	32.565	0.007	0.007	0.000	0.000	0.000	0.000
93	B	193	HIS	0	-0.003	0.014	30.021	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	194	VAL	0	0.113	0.032	32.932	0.002	0.002	0.000	0.000	0.000	0.000
95	B	195	ALA	0	-0.051	-0.034	31.269	0.005	0.005	0.000	0.000	0.000	0.000
96	B	196	ARG	1	0.899	0.969	33.137	0.119	0.119	0.000	0.000	0.000	0.000
97	B	197	GLU	-1	-0.988	-0.991	35.261	-0.094	-0.094	0.000	0.000	0.000	0.000
98	B	198	LEU	0	-0.064	-0.031	36.594	0.005	0.005	0.000	0.000	0.000	0.000
99	B	199	HIS	0	0.031	0.014	35.044	-0.001	-0.001	0.000	0.000	0.000	0.000
100	B	200	PRO	0	0.022	-0.001	35.542	-0.008	-0.008	0.000	0.000	0.000	0.000
101	B	201	GLU	-1	-0.860	-0.939	36.504	-0.109	-0.109	0.000	0.000	0.000	0.000
102	B	202	TYR	0	-0.057	-0.026	31.439	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	203	PHE	0	-0.063	-0.013	29.555	-0.010	-0.010	0.000	0.000	0.000	0.000

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