FMO DATABASE

FMODB ID: MVNNZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-836460.077733
FMO2-HF: Nuclear repulsion	795286.045677
FMO2-HF: Total energy	-41174.032056
FMO2-MP2: Total energy	-41296.940661

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.
-11.282	-5.897	2.945	-3.054	-5.276	-0.028

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 : -0.022 / q_NPA : -0.019

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	0.007	0.012	3.896	-2.127	-0.852	-0.011	-0.558	-0.707	0.002
4	A	77	ARG	1	0.874	0.942	4.665	2.070	2.227	-0.001	-0.009	-0.147	0.000
5	A	78	PRO	0	0.004	0.004	8.485	-0.161	-0.161	0.000	0.000	0.000	0.000
6	A	79	MET	0	0.028	0.012	11.254	0.067	0.067	0.000	0.000	0.000	0.000
7	A	80	THR	0	-0.026	-0.006	12.810	0.104	0.104	0.000	0.000	0.000	0.000
8	A	81	TYR	0	0.035	-0.001	15.416	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	82	LYS	1	0.970	0.977	14.063	-0.038	-0.038	0.000	0.000	0.000	0.000
10	A	83	ALA	0	0.011	0.023	11.686	0.003	0.003	0.000	0.000	0.000	0.000
11	A	84	ALA	0	0.041	0.013	13.190	-0.065	-0.065	0.000	0.000	0.000	0.000
12	A	85	VAL	0	0.004	0.014	15.200	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	86	ASP	-1	-0.926	-0.960	13.322	-0.162	-0.162	0.000	0.000	0.000	0.000
14	A	87	LEU	0	-0.039	-0.010	10.456	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	88	SER	0	-0.027	-0.035	13.440	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	89	HIS	0	0.014	0.005	16.672	0.004	0.004	0.000	0.000	0.000	0.000
17	A	90	PHE	0	0.102	0.055	10.214	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	91	LEU	0	-0.050	-0.042	12.328	0.017	0.017	0.000	0.000	0.000	0.000
19	A	92	LYS	1	0.804	0.924	15.862	0.232	0.232	0.000	0.000	0.000	0.000
20	A	93	GLU	-1	-0.973	-0.988	16.560	-0.171	-0.171	0.000	0.000	0.000	0.000
21	A	94	LYS	1	0.824	0.923	12.126	0.456	0.456	0.000	0.000	0.000	0.000
22	A	95	GLY	0	0.056	0.042	17.425	0.019	0.019	0.000	0.000	0.000	0.000
23	A	96	GLY	0	-0.020	-0.021	18.481	-0.037	-0.037	0.000	0.000	0.000	0.000
24	A	97	LEU	0	-0.015	-0.008	16.924	0.005	0.005	0.000	0.000	0.000	0.000
25	A	98	GLU	-1	-0.804	-0.903	19.822	-0.214	-0.214	0.000	0.000	0.000	0.000
26	A	99	GLY	0	0.021	0.014	22.959	0.010	0.010	0.000	0.000	0.000	0.000
27	A	100	LEU	0	-0.066	-0.006	20.199	0.010	0.010	0.000	0.000	0.000	0.000
28	A	101	ILE	0	0.035	0.004	24.147	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	102	HIS	0	-0.014	-0.027	22.515	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	103	SER	0	0.007	-0.010	23.503	0.011	0.011	0.000	0.000	0.000	0.000
31	A	104	GLN	0	0.045	0.027	20.971	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	105	ARG	1	0.993	1.015	19.234	0.386	0.386	0.000	0.000	0.000	0.000
33	A	106	ARG	1	0.889	0.937	18.715	0.285	0.285	0.000	0.000	0.000	0.000
34	A	107	GLN	0	0.067	0.045	17.572	-0.026	-0.026	0.000	0.000	0.000	0.000
35	A	108	ASP	-1	-0.844	-0.931	16.583	-0.554	-0.554	0.000	0.000	0.000	0.000
36	A	109	ILE	0	-0.053	-0.036	14.465	-0.094	-0.094	0.000	0.000	0.000	0.000
37	A	110	LEU	0	-0.048	-0.016	12.977	-0.139	-0.139	0.000	0.000	0.000	0.000
38	A	111	ASP	-1	-0.784	-0.898	11.941	-0.947	-0.947	0.000	0.000	0.000	0.000
39	A	112	LEU	0	-0.005	-0.003	10.238	-0.218	-0.218	0.000	0.000	0.000	0.000
40	A	113	TRP	0	-0.014	-0.004	8.404	-0.359	-0.359	0.000	0.000	0.000	0.000
41	A	114	ILE	0	0.010	0.012	7.393	-0.450	-0.450	0.000	0.000	0.000	0.000
42	A	115	TYR	0	-0.010	0.014	6.048	-0.713	-0.713	0.000	0.000	0.000	0.000
43	A	116	HIS	0	-0.017	-0.014	4.312	-1.164	-1.010	-0.001	-0.032	-0.121	0.000
44	A	117	THR	0	-0.061	-0.042	2.440	-5.111	-3.463	1.599	-1.239	-2.008	-0.015
45	A	118	GLN	0	-0.034	-0.020	2.767	-2.276	-0.523	1.347	-1.092	-2.007	-0.014
46	A	119	GLY	0	0.076	0.058	3.749	-0.675	-0.333	0.013	-0.116	-0.239	-0.001
47	A	120	TYR	0	-0.028	-0.038	4.470	0.881	0.937	-0.001	-0.008	-0.047	0.000
48	A	121	PHE	0	0.014	0.005	8.147	-0.071	-0.071	0.000	0.000	0.000	0.000
49	A	122	PRO	0	-0.016	-0.002	10.050	0.089	0.089	0.000	0.000	0.000	0.000
50	A	123	ASP	-1	-0.910	-0.954	12.841	-0.492	-0.492	0.000	0.000	0.000	0.000
51	A	124	TRP	0	0.033	0.011	11.701	0.121	0.121	0.000	0.000	0.000	0.000
52	A	125	GLN	0	-0.006	0.025	15.592	0.125	0.125	0.000	0.000	0.000	0.000
53	A	126	ASN	0	0.000	0.004	17.386	0.016	0.016	0.000	0.000	0.000	0.000
54	A	127	TYR	0	-0.037	-0.038	19.252	0.029	0.029	0.000	0.000	0.000	0.000
55	A	128	THR	0	0.073	0.046	23.952	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	129	PRO	0	-0.050	-0.022	27.561	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	130	GLY	0	-0.029	0.023	30.242	0.007	0.007	0.000	0.000	0.000	0.000
58	A	131	PRO	0	-0.008	-0.023	32.435	0.004	0.004	0.000	0.000	0.000	0.000
59	A	132	GLY	0	0.006	-0.016	34.092	0.004	0.004	0.000	0.000	0.000	0.000
60	A	133	VAL	0	-0.053	-0.033	29.361	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	134	ARG	1	0.801	0.890	26.142	0.208	0.208	0.000	0.000	0.000	0.000
62	A	135	TYR	0	0.026	-0.001	25.978	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	136	PRO	0	-0.007	0.007	21.241	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	137	LEU	0	0.022	0.001	22.036	0.021	0.021	0.000	0.000	0.000	0.000
65	A	138	THR	0	-0.031	-0.038	16.766	0.031	0.031	0.000	0.000	0.000	0.000
66	A	139	PHE	0	0.006	0.009	20.221	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	140	GLY	0	0.058	0.006	19.303	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	141	TRP	0	-0.020	0.000	15.552	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	142	CYS	0	-0.068	-0.048	18.773	0.037	0.037	0.000	0.000	0.000	0.000
70	A	143	TYR	0	0.002	-0.004	18.390	0.021	0.021	0.000	0.000	0.000	0.000
71	A	144	LYS	1	0.903	0.947	21.918	0.178	0.178	0.000	0.000	0.000	0.000
72	A	145	LEU	0	-0.029	-0.005	22.602	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	146	VAL	0	0.006	-0.005	26.391	0.017	0.017	0.000	0.000	0.000	0.000
74	A	147	PRO	0	0.008	0.010	29.810	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	148	VAL	0	-0.028	-0.008	31.484	0.008	0.008	0.000	0.000	0.000	0.000
76	A	179	GLU	-1	-0.796	-0.885	33.431	-0.167	-0.167	0.000	0.000	0.000	0.000
77	A	180	VAL	0	0.028	0.004	30.866	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	181	LEU	0	0.029	0.022	27.683	0.007	0.007	0.000	0.000	0.000	0.000
79	A	182	GLU	-1	-0.771	-0.874	26.271	-0.209	-0.209	0.000	0.000	0.000	0.000
80	A	183	TRP	0	-0.015	-0.001	19.549	0.010	0.010	0.000	0.000	0.000	0.000
81	A	184	ARG	1	0.780	0.882	24.095	0.206	0.206	0.000	0.000	0.000	0.000
82	A	185	PHE	0	0.033	0.006	20.424	0.002	0.002	0.000	0.000	0.000	0.000
83	A	186	ASP	-1	-0.785	-0.862	24.031	-0.132	-0.132	0.000	0.000	0.000	0.000
84	A	187	SER	0	0.040	0.012	24.293	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	188	ARG	1	0.868	0.904	25.331	0.136	0.136	0.000	0.000	0.000	0.000
86	A	189	LEU	0	0.007	0.014	24.136	0.009	0.009	0.000	0.000	0.000	0.000
87	A	190	ALA	0	-0.012	0.007	22.713	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	191	PHE	0	-0.062	-0.033	24.165	0.013	0.013	0.000	0.000	0.000	0.000
89	A	192	HIS	0	0.002	0.012	27.740	0.010	0.010	0.000	0.000	0.000	0.000
90	A	193	HIS	0	-0.033	-0.011	24.392	0.001	0.001	0.000	0.000	0.000	0.000
91	A	194	VAL	0	0.109	0.033	27.728	0.000	0.000	0.000	0.000	0.000	0.000
92	A	195	ALA	0	-0.051	-0.022	26.123	0.006	0.006	0.000	0.000	0.000	0.000
93	A	196	ARG	1	0.896	0.964	27.405	0.132	0.132	0.000	0.000	0.000	0.000
94	A	197	GLU	-1	-0.943	-0.977	29.830	-0.116	-0.116	0.000	0.000	0.000	0.000
95	A	198	LEU	0	-0.058	-0.034	31.890	0.007	0.007	0.000	0.000	0.000	0.000
96	A	199	HIS	0	0.001	0.010	30.009	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	200	PRO	0	0.021	-0.002	30.358	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	201	GLU	-1	-0.839	-0.921	31.111	-0.151	-0.151	0.000	0.000	0.000	0.000
99	A	202	TYR	0	-0.079	-0.031	26.109	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	203	PHE	0	-0.052	-0.022	24.059	-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)