FMO DATABASE

FMODB ID: 72NVK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1096020.54207
FMO2-HF: Nuclear repulsion	1044840.718073
FMO2-HF: Total energy	-51179.823997
FMO2-MP2: Total energy	-51329.186726

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.
-0.067	1.581	-0.018	-0.732	-0.898	0.001

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 : -0.033

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	A	874	ASP	-1	-0.818	-0.878	3.855	-0.822	0.826	-0.018	-0.732	-0.898	0.001
4	A	875	ARG	1	0.739	0.825	6.389	0.568	0.568	0.000	0.000	0.000	0.000
5	A	876	THR	0	-0.052	-0.047	9.139	-0.001	-0.001	0.000	0.000	0.000	0.000
6	A	877	ASP	-1	-0.897	-0.943	11.528	-0.021	-0.021	0.000	0.000	0.000	0.000
7	A	878	ASP	-1	-0.852	-0.915	10.589	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	879	LEU	0	0.048	0.008	13.353	-0.051	-0.051	0.000	0.000	0.000	0.000
9	A	880	VAL	0	0.024	0.022	14.476	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	881	TYR	0	0.015	0.001	9.222	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	882	LEU	0	0.018	0.001	12.818	-0.062	-0.062	0.000	0.000	0.000	0.000
12	A	883	ASN	0	0.014	0.002	15.150	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	884	VAL	0	0.020	0.022	13.739	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	885	MET	0	-0.043	-0.018	12.126	-0.052	-0.052	0.000	0.000	0.000	0.000
15	A	886	GLU	-1	-0.865	-0.910	15.135	-0.131	-0.131	0.000	0.000	0.000	0.000
16	A	887	LEU	0	0.019	0.015	18.685	0.009	0.009	0.000	0.000	0.000	0.000
17	A	888	VAL	0	-0.003	-0.015	15.718	0.011	0.011	0.000	0.000	0.000	0.000
18	A	889	ARG	1	0.926	0.961	14.274	0.370	0.370	0.000	0.000	0.000	0.000
19	A	890	ALA	0	0.050	0.030	19.533	0.013	0.013	0.000	0.000	0.000	0.000
20	A	891	VAL	0	-0.026	-0.022	21.402	0.015	0.015	0.000	0.000	0.000	0.000
21	A	892	LEU	0	-0.057	-0.036	17.977	0.011	0.011	0.000	0.000	0.000	0.000
22	A	893	GLU	-1	-0.929	-0.946	22.486	-0.140	-0.140	0.000	0.000	0.000	0.000
23	A	894	LEU	0	0.009	0.002	25.129	0.013	0.013	0.000	0.000	0.000	0.000
24	A	895	LYS	1	0.861	0.906	22.528	0.207	0.207	0.000	0.000	0.000	0.000
25	A	896	ASN	0	-0.073	-0.043	24.104	0.009	0.009	0.000	0.000	0.000	0.000
26	A	897	GLU	-1	-0.873	-0.923	27.983	-0.111	-0.111	0.000	0.000	0.000	0.000
27	A	898	LEU	0	-0.076	-0.052	30.522	0.011	0.011	0.000	0.000	0.000	0.000
28	A	899	ALA	0	-0.059	-0.027	32.509	0.007	0.007	0.000	0.000	0.000	0.000
29	A	900	GLN	0	0.014	0.006	34.246	0.011	0.011	0.000	0.000	0.000	0.000
30	A	901	LEU	0	-0.029	0.017	32.145	0.005	0.005	0.000	0.000	0.000	0.000
31	A	902	PRO	0	0.010	0.002	36.384	0.002	0.002	0.000	0.000	0.000	0.000
32	A	903	PRO	0	0.028	-0.020	38.013	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	904	GLU	-1	-0.917	-0.958	38.213	-0.061	-0.061	0.000	0.000	0.000	0.000
34	A	905	GLY	0	0.020	0.005	36.093	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	906	TYR	0	0.067	0.022	33.086	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	907	VAL	0	0.014	0.003	32.982	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	908	VAL	0	-0.041	-0.016	32.253	0.000	0.000	0.000	0.000	0.000	0.000
38	A	909	VAL	0	0.066	0.039	28.659	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	910	VAL	0	0.013	-0.005	28.629	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	911	LYS	1	0.913	0.972	29.738	0.066	0.066	0.000	0.000	0.000	0.000
41	A	912	ASN	0	0.028	0.008	27.027	0.010	0.010	0.000	0.000	0.000	0.000
42	A	913	VAL	0	0.018	0.019	24.733	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	914	GLY	0	-0.012	-0.012	25.643	0.001	0.001	0.000	0.000	0.000	0.000
44	A	915	LEU	0	-0.057	-0.035	27.347	0.006	0.006	0.000	0.000	0.000	0.000
45	A	916	THR	0	0.014	0.005	21.966	0.003	0.003	0.000	0.000	0.000	0.000
46	A	917	LEU	0	0.029	0.027	22.484	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	918	ARG	1	0.935	0.962	23.792	0.064	0.064	0.000	0.000	0.000	0.000
48	A	919	LYS	1	0.822	0.905	21.600	0.120	0.120	0.000	0.000	0.000	0.000
49	A	920	LEU	0	-0.029	-0.012	17.691	0.008	0.008	0.000	0.000	0.000	0.000
50	A	921	ILE	0	-0.005	-0.017	20.772	0.013	0.013	0.000	0.000	0.000	0.000
51	A	922	GLY	0	0.046	0.035	23.038	0.013	0.013	0.000	0.000	0.000	0.000
52	A	923	SER	0	0.003	-0.007	19.356	0.002	0.002	0.000	0.000	0.000	0.000
53	A	924	VAL	0	-0.038	-0.027	17.913	0.015	0.015	0.000	0.000	0.000	0.000
54	A	925	ASP	-1	-0.850	-0.919	20.092	0.036	0.036	0.000	0.000	0.000	0.000
55	A	926	ASP	-1	-0.944	-0.963	22.108	0.027	0.027	0.000	0.000	0.000	0.000
56	A	927	LEU	0	-0.055	-0.025	15.255	0.016	0.016	0.000	0.000	0.000	0.000
57	A	928	LEU	0	0.009	-0.008	19.714	0.032	0.032	0.000	0.000	0.000	0.000
58	A	929	PRO	0	-0.037	-0.029	21.380	0.023	0.023	0.000	0.000	0.000	0.000
59	A	930	SER	0	-0.037	-0.002	18.982	0.003	0.003	0.000	0.000	0.000	0.000
60	A	931	LEU	0	-0.009	0.008	15.718	0.045	0.045	0.000	0.000	0.000	0.000
61	A	932	PRO	0	0.039	0.012	17.616	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	933	SER	0	0.029	0.002	20.674	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	934	SER	0	-0.004	0.002	21.148	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	935	SER	0	0.044	0.023	17.511	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	936	ARG	1	0.904	0.971	19.650	-0.158	-0.158	0.000	0.000	0.000	0.000
66	A	937	THR	0	0.035	0.009	21.946	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	938	GLU	-1	-0.926	-0.950	19.437	0.039	0.039	0.000	0.000	0.000	0.000
68	A	939	ILE	0	0.003	-0.009	16.549	-0.022	-0.022	0.000	0.000	0.000	0.000
69	A	940	GLU	-1	-0.882	-0.944	20.321	0.040	0.040	0.000	0.000	0.000	0.000
70	A	941	GLY	0	-0.036	-0.014	23.768	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	942	THR	0	-0.030	-0.031	19.146	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	943	GLN	0	0.016	-0.014	22.100	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	944	LYS	1	0.896	0.961	23.495	-0.031	-0.031	0.000	0.000	0.000	0.000
74	A	945	LEU	0	0.000	0.009	22.223	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	946	LEU	0	0.036	0.015	19.637	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	947	ASN	0	-0.022	-0.026	24.117	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	948	LYS	1	0.919	0.977	27.563	0.059	0.059	0.000	0.000	0.000	0.000
78	A	949	ASH	0	-0.081	-0.085	23.578	0.004	0.004	0.000	0.000	0.000	0.000
79	A	950	LEU	0	0.055	0.039	27.225	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	951	ALA	0	-0.013	-0.015	28.547	0.001	0.001	0.000	0.000	0.000	0.000
81	A	952	GLU	-1	-0.903	-0.947	29.972	-0.055	-0.055	0.000	0.000	0.000	0.000
82	A	953	LEU	0	-0.017	-0.005	27.451	0.000	0.000	0.000	0.000	0.000	0.000
83	A	954	ILE	0	0.007	-0.006	30.870	0.001	0.001	0.000	0.000	0.000	0.000
84	A	955	ASN	0	-0.028	-0.021	33.842	0.005	0.005	0.000	0.000	0.000	0.000
85	A	956	LYS	1	0.887	0.943	33.332	0.065	0.065	0.000	0.000	0.000	0.000
86	A	957	MET	0	0.027	0.025	33.936	0.002	0.002	0.000	0.000	0.000	0.000
87	A	958	ARG	1	0.928	0.968	35.855	0.047	0.047	0.000	0.000	0.000	0.000
88	A	959	LEU	0	-0.026	-0.009	38.020	0.002	0.002	0.000	0.000	0.000	0.000
89	A	960	ALA	0	0.036	-0.001	36.981	0.002	0.002	0.000	0.000	0.000	0.000
90	A	961	GLN	0	-0.021	-0.013	38.759	0.003	0.003	0.000	0.000	0.000	0.000
91	A	962	GLN	0	-0.051	-0.025	41.362	0.003	0.003	0.000	0.000	0.000	0.000
92	A	963	ASN	0	-0.030	-0.018	42.393	0.004	0.004	0.000	0.000	0.000	0.000
93	A	964	ALA	0	0.028	0.018	42.660	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	965	VAL	0	-0.017	-0.007	43.632	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	966	THR	0	0.002	0.010	45.822	0.001	0.001	0.000	0.000	0.000	0.000
96	A	967	SER	0	0.018	-0.002	45.234	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	968	LEU	0	-0.013	-0.007	43.099	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	969	SER	0	0.012	0.005	41.202	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	970	GLU	-1	-0.789	-0.887	38.457	-0.077	-0.077	0.000	0.000	0.000	0.000
100	A	971	GLU	-1	-0.835	-0.889	37.028	-0.078	-0.078	0.000	0.000	0.000	0.000
101	A	972	CYS	0	-0.032	-0.018	36.451	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	973	LYS	1	0.902	0.940	34.591	0.073	0.073	0.000	0.000	0.000	0.000
103	A	974	ARG	1	0.921	0.951	32.670	0.071	0.071	0.000	0.000	0.000	0.000
104	A	975	GLN	0	-0.046	-0.034	31.581	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	976	MET	0	0.006	0.036	31.295	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	977	LEU	0	0.007	0.040	28.113	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	978	THR	0	-0.025	-0.018	26.895	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	979	ALA	0	-0.019	-0.007	26.607	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	980	SER	0	-0.005	-0.019	25.514	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	981	HIS	0	0.027	0.018	21.020	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	982	THR	0	-0.036	-0.024	21.860	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	983	LEU	0	0.004	0.009	21.971	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	984	ALA	0	0.025	0.011	19.089	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	985	VAL	0	-0.023	-0.011	17.451	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	986	ASP	-1	-0.801	-0.880	17.044	-0.127	-0.127	0.000	0.000	0.000	0.000
116	A	987	ALA	0	-0.016	0.000	17.530	0.014	0.014	0.000	0.000	0.000	0.000
117	A	988	LYS	1	0.868	0.933	12.250	0.401	0.401	0.000	0.000	0.000	0.000
118	A	989	ASN	0	-0.034	-0.029	12.725	-0.067	-0.067	0.000	0.000	0.000	0.000
119	A	990	LEU	0	0.025	0.028	14.146	0.040	0.040	0.000	0.000	0.000	0.000
120	A	991	LEU	0	-0.004	-0.001	9.409	0.048	0.048	0.000	0.000	0.000	0.000
121	A	992	ASP	-1	-0.853	-0.929	9.096	-0.487	-0.487	0.000	0.000	0.000	0.000
122	A	993	ALA	0	-0.002	0.007	10.436	0.175	0.175	0.000	0.000	0.000	0.000
123	A	994	VAL	0	0.006	-0.004	12.534	0.091	0.091	0.000	0.000	0.000	0.000
124	A	995	ASP	-1	-0.776	-0.868	7.490	0.049	0.049	0.000	0.000	0.000	0.000
125	A	996	GLN	0	-0.038	-0.020	9.623	0.281	0.281	0.000	0.000	0.000	0.000
126	A	997	ALA	0	0.000	-0.001	10.934	0.094	0.094	0.000	0.000	0.000	0.000
127	A	998	LYS	1	0.863	0.928	10.508	-0.180	-0.180	0.000	0.000	0.000	0.000
128	A	999	VAL	0	-0.010	0.010	7.628	0.034	0.034	0.000	0.000	0.000	0.000
129	A	1000	LEU	0	-0.002	-0.010	10.772	-0.060	-0.060	0.000	0.000	0.000	0.000
130	A	1001	ALA	0	0.000	0.003	14.210	-0.072	-0.072	0.000	0.000	0.000	0.000
131	A	1002	ASN	0	-0.083	-0.038	12.298	-0.091	-0.091	0.000	0.000	0.000	0.000
132	A	1003	LEU	0	-0.049	-0.004	14.173	-0.034	-0.034	0.000	0.000	0.000	0.000
133	A	1004	ALA	0	-0.078	-0.040	15.734	-0.100	-0.100	0.000	0.000	0.000	0.000

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