FMO DATABASE

FMODB ID: MV81Z

Calculation Name: 3GM3-A-Xray372

Preferred Name: Protein tyrosine kinase 2 beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3GM3

Chain ID: A

ChEMBL ID: CHEMBL5469

UniProt ID: Q14289

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1095662.700362
FMO2-HF: Nuclear repulsion	1044483.870293
FMO2-HF: Total energy	-51178.83007
FMO2-MP2: Total energy	-51328.276647

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:872:ASN)

Summations of interaction energy for fragment #1(A:872:ASN)

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.
0.181	1.638	-0.016	-0.61	-0.831	0

Interaction energy analysis for fragmet #1(A:872:ASN)

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 : -0.029

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].
3	A	874	ASP	-1	-0.837	-0.887	3.855	-0.593	0.864	-0.016	-0.610	-0.831
4	A	875	ARG	1	0.770	0.871	6.305	0.525	0.525	0.000	0.000	0.000
5	A	876	THR	0	-0.041	-0.041	8.963	0.023	0.023	0.000	0.000	0.000
6	A	877	ASP	-1	-0.910	-0.951	11.439	-0.016	-0.016	0.000	0.000	0.000
7	A	878	ASP	-1	-0.921	-0.953	10.296	-0.009	-0.009	0.000	0.000	0.000
8	A	879	LEU	0	0.049	0.003	13.121	-0.043	-0.043	0.000	0.000	0.000
9	A	880	VAL	0	0.020	0.019	14.633	-0.024	-0.024	0.000	0.000	0.000
10	A	881	TYR	0	0.035	0.009	9.199	-0.020	-0.020	0.000	0.000	0.000
11	A	882	LEU	0	0.011	-0.005	12.799	-0.055	-0.055	0.000	0.000	0.000
12	A	883	ASN	0	0.012	-0.001	14.936	-0.023	-0.023	0.000	0.000	0.000
13	A	884	VAL	0	0.015	0.024	14.224	-0.004	-0.004	0.000	0.000	0.000
14	A	885	MET	0	-0.041	-0.021	11.997	-0.036	-0.036	0.000	0.000	0.000
15	A	886	GLU	-1	-0.874	-0.922	15.579	-0.123	-0.123	0.000	0.000	0.000
16	A	887	LEU	0	0.018	0.016	18.945	0.006	0.006	0.000	0.000	0.000
17	A	888	VAL	0	-0.003	-0.016	15.943	0.008	0.008	0.000	0.000	0.000
18	A	889	ARG	1	0.917	0.954	14.347	0.345	0.345	0.000	0.000	0.000
19	A	890	ALA	0	0.051	0.031	19.918	0.011	0.011	0.000	0.000	0.000
20	A	891	VAL	0	-0.027	-0.021	21.774	0.013	0.013	0.000	0.000	0.000
21	A	892	LEU	0	-0.067	-0.043	18.258	0.009	0.009	0.000	0.000	0.000
22	A	893	GLU	-1	-0.940	-0.962	22.804	-0.133	-0.133	0.000	0.000	0.000
23	A	894	LEU	0	0.006	0.011	25.474	0.012	0.012	0.000	0.000	0.000
24	A	895	LYS	1	0.878	0.928	22.737	0.212	0.212	0.000	0.000	0.000
25	A	896	ASN	0	-0.051	-0.026	24.331	0.010	0.010	0.000	0.000	0.000
26	A	897	GLU	-1	-0.867	-0.916	28.260	-0.108	-0.108	0.000	0.000	0.000
27	A	898	LEU	0	-0.086	-0.062	30.828	0.011	0.011	0.000	0.000	0.000
28	A	899	ALA	0	-0.048	-0.024	32.816	0.007	0.007	0.000	0.000	0.000
29	A	900	GLN	0	0.024	0.012	34.537	0.010	0.010	0.000	0.000	0.000
30	A	901	LEU	0	-0.050	0.003	32.448	0.005	0.005	0.000	0.000	0.000
31	A	902	PRO	0	0.018	0.004	36.718	0.002	0.002	0.000	0.000	0.000
32	A	903	PRO	0	0.023	-0.026	38.373	-0.003	-0.003	0.000	0.000	0.000
33	A	904	GLU	-1	-0.921	-0.952	38.592	-0.060	-0.060	0.000	0.000	0.000
34	A	905	GLY	0	0.026	0.008	36.483	-0.001	-0.001	0.000	0.000	0.000
35	A	906	TYR	0	0.066	0.020	33.501	-0.004	-0.004	0.000	0.000	0.000
36	A	907	VAL	0	0.030	-0.041	33.372	-0.003	-0.003	0.000	0.000	0.000
37	A	908	VAL	0	-0.016	-0.011	32.683	0.000	0.000	0.000	0.000	0.000
38	A	909	VAL	0	0.044	0.032	29.149	-0.001	-0.001	0.000	0.000	0.000
39	A	910	VAL	0	0.020	0.002	29.042	-0.006	-0.006	0.000	0.000	0.000
40	A	911	LYS	1	0.914	0.973	30.159	0.063	0.063	0.000	0.000	0.000
41	A	912	ASN	0	0.025	0.002	27.319	0.009	0.009	0.000	0.000	0.000
42	A	913	VAL	0	0.014	0.018	25.135	-0.004	-0.004	0.000	0.000	0.000
43	A	914	GLY	0	-0.019	-0.019	26.078	0.001	0.001	0.000	0.000	0.000
44	A	915	LEU	0	-0.044	-0.033	27.700	0.006	0.006	0.000	0.000	0.000
45	A	916	THR	0	0.026	0.020	22.243	0.003	0.003	0.000	0.000	0.000
46	A	917	LEU	0	0.040	0.030	22.856	0.000	0.000	0.000	0.000	0.000
47	A	918	ARG	1	0.927	0.959	24.271	0.063	0.063	0.000	0.000	0.000
48	A	919	LYS	1	0.847	0.930	21.435	0.109	0.109	0.000	0.000	0.000
49	A	920	LEU	0	-0.033	-0.014	18.012	0.009	0.009	0.000	0.000	0.000
50	A	921	ILE	0	-0.009	-0.016	21.147	0.013	0.013	0.000	0.000	0.000
51	A	922	GLY	0	0.047	0.035	23.627	0.012	0.012	0.000	0.000	0.000
52	A	923	SER	0	0.008	-0.007	19.101	0.002	0.002	0.000	0.000	0.000
53	A	924	VAL	0	-0.041	-0.029	18.631	0.014	0.014	0.000	0.000	0.000
54	A	925	ASP	-1	-0.853	-0.922	20.610	0.032	0.032	0.000	0.000	0.000
55	A	926	ASP	-1	-0.946	-0.967	21.954	0.026	0.026	0.000	0.000	0.000
56	A	927	LEU	0	-0.064	-0.029	15.626	0.017	0.017	0.000	0.000	0.000
57	A	928	LEU	0	0.014	-0.004	19.849	0.032	0.032	0.000	0.000	0.000
58	A	929	PRO	0	-0.038	-0.024	21.501	0.022	0.022	0.000	0.000	0.000
59	A	930	SER	0	-0.034	-0.006	18.940	0.002	0.002	0.000	0.000	0.000
60	A	931	LEU	0	-0.010	0.010	15.950	0.044	0.044	0.000	0.000	0.000
61	A	932	PRO	0	0.066	0.031	17.592	-0.036	-0.036	0.000	0.000	0.000
62	A	933	SER	0	0.038	-0.001	20.739	-0.016	-0.016	0.000	0.000	0.000
63	A	934	SER	0	0.000	0.001	21.436	-0.013	-0.013	0.000	0.000	0.000
64	A	935	SER	0	0.033	0.023	17.626	0.000	0.000	0.000	0.000	0.000
65	A	936	ARG	1	0.897	0.957	20.025	-0.158	-0.158	0.000	0.000	0.000
66	A	937	THR	0	0.020	0.009	22.313	-0.016	-0.016	0.000	0.000	0.000
67	A	938	GLU	-1	-0.930	-0.953	19.703	0.027	0.027	0.000	0.000	0.000
68	A	939	ILE	0	-0.014	-0.018	16.930	-0.022	-0.022	0.000	0.000	0.000
69	A	940	GLU	-1	-0.891	-0.952	20.830	0.036	0.036	0.000	0.000	0.000
70	A	941	GLY	0	-0.060	-0.025	24.236	-0.014	-0.014	0.000	0.000	0.000
71	A	942	THR	0	0.000	-0.011	19.758	-0.022	-0.022	0.000	0.000	0.000
72	A	943	GLN	0	0.019	-0.006	22.536	-0.011	-0.011	0.000	0.000	0.000
73	A	944	LYS	1	0.883	0.948	24.073	-0.025	-0.025	0.000	0.000	0.000
74	A	945	LEU	0	-0.016	-0.001	22.491	-0.003	-0.003	0.000	0.000	0.000
75	A	946	LEU	0	0.032	0.016	20.277	-0.010	-0.010	0.000	0.000	0.000
76	A	947	ASN	0	0.017	-0.003	24.678	-0.011	-0.011	0.000	0.000	0.000
77	A	948	LYS	1	0.938	0.987	28.199	0.062	0.062	0.000	0.000	0.000
78	A	949	ASH	0	-0.077	-0.091	24.095	0.004	0.004	0.000	0.000	0.000
79	A	950	LEU	0	0.033	0.026	27.695	-0.004	-0.004	0.000	0.000	0.000
80	A	951	ALA	0	-0.023	-0.016	29.116	0.001	0.001	0.000	0.000	0.000
81	A	952	GLU	-1	-0.942	-0.978	30.525	-0.057	-0.057	0.000	0.000	0.000
82	A	953	LEU	0	-0.025	-0.008	27.814	0.000	0.000	0.000	0.000	0.000
83	A	954	ILE	0	0.013	-0.003	31.315	0.002	0.002	0.000	0.000	0.000
84	A	955	ASN	0	-0.073	-0.042	34.265	0.005	0.005	0.000	0.000	0.000
85	A	956	LYS	1	0.945	0.976	33.719	0.070	0.070	0.000	0.000	0.000
86	A	957	MET	0	0.018	0.078	33.961	0.002	0.002	0.000	0.000	0.000
87	A	958	ARG	1	0.904	0.958	36.204	0.048	0.048	0.000	0.000	0.000
88	A	959	LEU	0	-0.008	0.000	38.683	0.001	0.001	0.000	0.000	0.000
89	A	960	ALA	0	0.030	-0.001	37.296	0.002	0.002	0.000	0.000	0.000
90	A	961	GLN	0	-0.005	-0.009	39.426	0.001	0.001	0.000	0.000	0.000
91	A	962	GLN	0	-0.047	-0.024	41.709	0.002	0.002	0.000	0.000	0.000
92	A	963	ASN	0	-0.005	0.001	42.703	0.004	0.004	0.000	0.000	0.000
93	A	964	ALA	0	0.035	0.023	42.978	-0.002	-0.002	0.000	0.000	0.000
94	A	965	VAL	0	-0.015	-0.005	43.946	-0.001	-0.001	0.000	0.000	0.000
95	A	966	THR	0	-0.011	-0.002	45.940	0.001	0.001	0.000	0.000	0.000
96	A	967	SER	0	0.009	-0.007	45.500	-0.002	-0.002	0.000	0.000	0.000
97	A	968	LEU	0	-0.014	-0.006	43.274	-0.003	-0.003	0.000	0.000	0.000
98	A	969	SER	0	0.016	0.015	41.402	-0.004	-0.004	0.000	0.000	0.000
99	A	970	GLU	-1	-0.899	-0.968	38.165	-0.080	-0.080	0.000	0.000	0.000
100	A	971	GLU	-1	-0.854	-0.913	37.278	-0.083	-0.083	0.000	0.000	0.000
101	A	972	CYS	0	-0.029	-0.020	36.694	-0.003	-0.003	0.000	0.000	0.000
102	A	973	LYS	1	0.989	1.008	34.909	0.077	0.077	0.000	0.000	0.000
103	A	974	ARG	1	0.939	0.960	32.869	0.075	0.075	0.000	0.000	0.000
104	A	975	GLN	0	-0.063	-0.040	31.819	-0.006	-0.006	0.000	0.000	0.000
105	A	976	MET	0	0.008	0.028	31.639	-0.001	-0.001	0.000	0.000	0.000
106	A	977	LEU	0	0.018	0.035	28.225	-0.008	-0.008	0.000	0.000	0.000
107	A	978	THR	0	-0.016	0.001	27.160	-0.014	-0.014	0.000	0.000	0.000
108	A	979	ALA	0	-0.020	-0.009	27.010	-0.008	-0.008	0.000	0.000	0.000
109	A	980	SER	0	0.005	-0.012	25.814	-0.007	-0.007	0.000	0.000	0.000
110	A	981	HIS	0	-0.002	-0.005	21.022	-0.014	-0.014	0.000	0.000	0.000
111	A	982	THR	0	-0.041	-0.024	22.269	-0.014	-0.014	0.000	0.000	0.000
112	A	983	LEU	0	0.018	0.018	22.420	-0.002	-0.002	0.000	0.000	0.000
113	A	984	ALA	0	0.030	0.012	19.374	-0.003	-0.003	0.000	0.000	0.000
114	A	985	VAL	0	-0.045	-0.019	17.864	-0.033	-0.033	0.000	0.000	0.000
115	A	986	ASP	-1	-0.804	-0.868	17.489	-0.136	-0.136	0.000	0.000	0.000
116	A	987	ALA	0	-0.007	0.002	18.089	0.014	0.014	0.000	0.000	0.000
117	A	988	LYS	1	0.943	0.972	12.761	0.409	0.409	0.000	0.000	0.000
118	A	989	ASN	0	-0.013	-0.023	13.225	-0.077	-0.077	0.000	0.000	0.000
119	A	990	LEU	0	0.013	0.019	14.603	0.039	0.039	0.000	0.000	0.000
120	A	991	LEU	0	-0.012	-0.006	10.064	0.046	0.046	0.000	0.000	0.000
121	A	992	ASP	-1	-0.877	-0.932	9.130	-0.477	-0.477	0.000	0.000	0.000
122	A	993	ALA	0	-0.025	-0.005	10.908	0.165	0.165	0.000	0.000	0.000
123	A	994	VAL	0	-0.013	-0.013	13.153	0.087	0.087	0.000	0.000	0.000
124	A	995	ASP	-1	-0.809	-0.902	8.021	0.063	0.063	0.000	0.000	0.000
125	A	996	GLN	0	-0.039	-0.027	9.873	0.276	0.276	0.000	0.000	0.000
126	A	997	ALA	0	-0.007	-0.002	11.280	0.092	0.092	0.000	0.000	0.000
127	A	998	LYS	1	0.955	0.971	10.910	-0.169	-0.169	0.000	0.000	0.000
128	A	999	VAL	0	-0.002	0.008	7.578	0.033	0.033	0.000	0.000	0.000
129	A	1000	LEU	0	-0.016	-0.018	10.796	-0.048	-0.048	0.000	0.000	0.000
130	A	1001	ALA	0	-0.023	-0.011	14.221	-0.068	-0.068	0.000	0.000	0.000
131	A	1002	ASN	0	-0.082	-0.034	12.102	-0.091	-0.091	0.000	0.000	0.000
132	A	1003	LEU	0	-0.052	-0.005	14.142	-0.030	-0.030	0.000	0.000	0.000
133	A	1004	ALA	0	-0.046	-0.014	15.678	-0.080	-0.080	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:872:ASN)