FMO DATABASE

FMODB ID: LZNN9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-865682.257791
FMO2-HF: Nuclear repulsion	823372.563798
FMO2-HF: Total energy	-42309.693992
FMO2-MP2: Total energy	-42435.888623

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.
-3.064	-0.726	0.166	-1.101	-1.404	-0.005

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 : -0.018 / q_NPA : -0.024

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	0.033	2.988	-3.205	-0.950	0.167	-1.098	-1.325	-0.005
4	B	74	VAL	0	0.003	0.009	4.695	0.730	0.813	-0.001	-0.003	-0.079	0.000
5	B	75	PRO	0	-0.008	-0.018	6.807	0.089	0.089	0.000	0.000	0.000	0.000
6	B	76	LEU	0	0.026	0.025	10.656	0.009	0.009	0.000	0.000	0.000	0.000
7	B	77	ARG	1	0.850	0.925	10.987	0.431	0.431	0.000	0.000	0.000	0.000
8	B	78	PRO	0	0.032	0.025	15.506	-0.041	-0.041	0.000	0.000	0.000	0.000
9	B	79	MET	0	0.014	0.028	16.360	0.018	0.018	0.000	0.000	0.000	0.000
10	B	80	THR	0	-0.034	-0.034	18.824	0.034	0.034	0.000	0.000	0.000	0.000
11	B	81	TYR	0	0.014	-0.006	21.327	-0.005	-0.005	0.000	0.000	0.000	0.000
12	B	82	LYS	1	0.987	0.989	20.575	0.030	0.030	0.000	0.000	0.000	0.000
13	B	83	ALA	0	0.025	0.025	17.192	0.003	0.003	0.000	0.000	0.000	0.000
14	B	84	ALA	0	0.061	0.026	18.157	-0.016	-0.016	0.000	0.000	0.000	0.000
15	B	85	VAL	0	0.015	0.034	20.386	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	86	ASP	-1	-0.936	-0.970	18.010	-0.046	-0.046	0.000	0.000	0.000	0.000
17	B	87	LEU	0	-0.034	-0.015	14.112	0.004	0.004	0.000	0.000	0.000	0.000
18	B	88	SER	0	-0.018	-0.035	17.251	-0.014	-0.014	0.000	0.000	0.000	0.000
19	B	89	HIS	0	0.004	0.005	20.438	-0.006	-0.006	0.000	0.000	0.000	0.000
20	B	90	PHE	0	0.094	0.053	11.648	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	91	LEU	0	-0.032	-0.027	14.765	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	92	LYS	1	0.823	0.927	18.097	0.089	0.089	0.000	0.000	0.000	0.000
23	B	93	GLU	-1	-0.938	-0.990	18.473	-0.014	-0.014	0.000	0.000	0.000	0.000
24	B	94	LYS	1	0.821	0.922	13.449	0.121	0.121	0.000	0.000	0.000	0.000
25	B	95	GLY	0	0.019	0.031	18.828	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	96	GLY	0	-0.012	-0.012	19.952	-0.021	-0.021	0.000	0.000	0.000	0.000
27	B	97	LEU	0	-0.008	-0.006	19.379	-0.013	-0.013	0.000	0.000	0.000	0.000
28	B	98	GLU	-1	-0.815	-0.911	21.708	-0.108	-0.108	0.000	0.000	0.000	0.000
29	B	99	GLY	0	0.016	0.016	25.120	0.004	0.004	0.000	0.000	0.000	0.000
30	B	100	LEU	0	-0.084	-0.014	21.278	-0.003	-0.003	0.000	0.000	0.000	0.000
31	B	101	ILE	0	0.032	0.001	25.457	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	102	HIS	0	0.002	-0.009	25.390	-0.014	-0.014	0.000	0.000	0.000	0.000
33	B	103	SER	0	0.012	-0.004	25.104	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	104	GLN	0	-0.002	-0.001	23.881	0.005	0.005	0.000	0.000	0.000	0.000
35	B	105	ARG	1	0.954	0.986	19.581	0.395	0.395	0.000	0.000	0.000	0.000
36	B	106	ARG	1	0.902	0.938	20.382	0.213	0.213	0.000	0.000	0.000	0.000
37	B	107	GLN	0	0.063	0.049	19.389	-0.013	-0.013	0.000	0.000	0.000	0.000
38	B	108	ASP	-1	-0.772	-0.900	19.039	-0.382	-0.382	0.000	0.000	0.000	0.000
39	B	109	ILE	0	-0.059	-0.028	15.180	-0.068	-0.068	0.000	0.000	0.000	0.000
40	B	110	LEU	0	-0.031	-0.004	14.694	-0.085	-0.085	0.000	0.000	0.000	0.000
41	B	111	ASP	-1	-0.758	-0.879	14.514	-0.475	-0.475	0.000	0.000	0.000	0.000
42	B	112	LEU	0	-0.003	0.002	12.893	-0.075	-0.075	0.000	0.000	0.000	0.000
43	B	113	TRP	0	-0.017	0.000	8.753	-0.145	-0.145	0.000	0.000	0.000	0.000
44	B	114	ILE	0	0.010	0.011	9.583	-0.115	-0.115	0.000	0.000	0.000	0.000
45	B	115	TYR	0	-0.017	-0.019	10.451	0.019	0.019	0.000	0.000	0.000	0.000
46	B	116	HIS	0	-0.002	-0.024	6.697	-0.311	-0.311	0.000	0.000	0.000	0.000
47	B	117	THR	0	-0.064	-0.039	5.554	-0.483	-0.483	0.000	0.000	0.000	0.000
48	B	118	GLN	0	-0.057	-0.014	6.717	0.284	0.284	0.000	0.000	0.000	0.000
49	B	119	GLY	0	0.060	0.041	9.218	0.139	0.139	0.000	0.000	0.000	0.000
50	B	120	TYR	0	-0.052	-0.047	10.373	0.117	0.117	0.000	0.000	0.000	0.000
51	B	121	PHE	0	0.018	0.003	13.857	-0.077	-0.077	0.000	0.000	0.000	0.000
52	B	122	PRO	0	-0.003	0.002	14.778	0.041	0.041	0.000	0.000	0.000	0.000
53	B	123	ASP	-1	-0.908	-0.948	17.527	-0.262	-0.262	0.000	0.000	0.000	0.000
54	B	124	TRP	0	-0.007	-0.014	16.822	0.055	0.055	0.000	0.000	0.000	0.000
55	B	125	GLN	0	-0.028	0.015	19.397	0.059	0.059	0.000	0.000	0.000	0.000
56	B	126	ASN	0	-0.011	-0.004	21.728	0.006	0.006	0.000	0.000	0.000	0.000
57	B	127	TYR	0	-0.007	-0.025	22.781	0.020	0.020	0.000	0.000	0.000	0.000
58	B	128	THR	0	0.016	0.023	28.356	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	129	PRO	0	0.009	0.009	32.164	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	130	GLY	0	-0.015	0.000	34.477	0.002	0.002	0.000	0.000	0.000	0.000
61	B	131	PRO	0	-0.027	-0.019	36.770	0.001	0.001	0.000	0.000	0.000	0.000
62	B	132	GLY	0	0.019	0.003	37.555	0.005	0.005	0.000	0.000	0.000	0.000
63	B	133	VAL	0	-0.042	-0.028	32.985	-0.007	-0.007	0.000	0.000	0.000	0.000
64	B	134	ARG	1	0.795	0.883	30.285	0.140	0.140	0.000	0.000	0.000	0.000
65	B	135	TYR	0	0.018	-0.002	30.361	-0.004	-0.004	0.000	0.000	0.000	0.000
66	B	136	PRO	0	0.012	0.013	26.070	-0.005	-0.005	0.000	0.000	0.000	0.000
67	B	137	LEU	0	0.017	-0.006	27.117	0.011	0.011	0.000	0.000	0.000	0.000
68	B	138	THR	0	-0.019	-0.032	22.188	0.013	0.013	0.000	0.000	0.000	0.000
69	B	139	PHE	0	0.009	0.006	25.538	0.000	0.000	0.000	0.000	0.000	0.000
70	B	140	GLY	0	0.036	-0.002	25.102	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	141	TRP	0	0.001	0.001	19.216	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	142	CYS	0	-0.075	-0.039	23.646	0.011	0.011	0.000	0.000	0.000	0.000
73	B	143	TYR	0	-0.021	-0.021	21.369	0.006	0.006	0.000	0.000	0.000	0.000
74	B	144	LYS	1	0.883	0.937	25.494	0.097	0.097	0.000	0.000	0.000	0.000
75	B	145	LEU	0	-0.003	0.012	25.837	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	146	VAL	0	-0.006	-0.018	29.470	0.011	0.011	0.000	0.000	0.000	0.000
77	B	147	PRO	0	-0.009	0.009	32.665	-0.006	-0.006	0.000	0.000	0.000	0.000
78	B	148	VAL	0	-0.030	-0.009	34.066	0.006	0.006	0.000	0.000	0.000	0.000
79	B	179	GLU	-1	-0.737	-0.844	35.435	-0.121	-0.121	0.000	0.000	0.000	0.000
80	B	180	VAL	0	-0.043	-0.034	33.012	-0.009	-0.009	0.000	0.000	0.000	0.000
81	B	181	LEU	0	0.011	0.017	30.413	0.007	0.007	0.000	0.000	0.000	0.000
82	B	182	GLU	-1	-0.787	-0.878	28.479	-0.136	-0.136	0.000	0.000	0.000	0.000
83	B	183	TRP	0	-0.003	-0.001	22.450	0.001	0.001	0.000	0.000	0.000	0.000
84	B	184	ARG	1	0.778	0.868	26.657	0.123	0.123	0.000	0.000	0.000	0.000
85	B	185	PHE	0	0.050	0.009	24.013	-0.002	-0.002	0.000	0.000	0.000	0.000
86	B	186	ASP	-1	-0.811	-0.883	27.138	-0.072	-0.072	0.000	0.000	0.000	0.000
87	B	187	SER	0	0.046	0.025	28.146	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	188	ARG	1	0.879	0.906	29.165	0.071	0.071	0.000	0.000	0.000	0.000
89	B	189	LEU	0	0.013	0.015	28.230	0.003	0.003	0.000	0.000	0.000	0.000
90	B	190	ALA	0	-0.001	0.009	27.198	-0.006	-0.006	0.000	0.000	0.000	0.000
91	B	191	PHE	0	-0.059	-0.033	28.940	0.006	0.006	0.000	0.000	0.000	0.000
92	B	192	HIS	0	0.003	0.024	32.737	0.007	0.007	0.000	0.000	0.000	0.000
93	B	193	HIS	0	-0.025	0.000	29.961	0.001	0.001	0.000	0.000	0.000	0.000
94	B	194	VAL	0	0.081	0.021	32.857	-0.002	-0.002	0.000	0.000	0.000	0.000
95	B	195	ALA	0	-0.031	-0.029	31.152	0.001	0.001	0.000	0.000	0.000	0.000
96	B	196	ARG	1	0.858	0.952	32.860	0.083	0.083	0.000	0.000	0.000	0.000
97	B	197	GLU	-1	-0.908	-0.972	35.080	-0.068	-0.068	0.000	0.000	0.000	0.000
98	B	198	LEU	0	-0.048	-0.008	37.073	0.004	0.004	0.000	0.000	0.000	0.000
99	B	199	HIS	0	-0.004	-0.003	35.208	-0.001	-0.001	0.000	0.000	0.000	0.000
100	B	200	PRO	0	0.050	0.015	35.275	-0.006	-0.006	0.000	0.000	0.000	0.000
101	B	201	GLU	-1	-0.832	-0.918	36.196	-0.104	-0.104	0.000	0.000	0.000	0.000
102	B	202	TYR	0	-0.082	-0.046	31.120	-0.003	-0.003	0.000	0.000	0.000	0.000
103	B	203	PHE	0	-0.090	-0.027	29.430	0.001	0.001	0.000	0.000	0.000	0.000

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