FMO DATABASE

FMODB ID: 2JR3R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1101135.940952
FMO2-HF: Nuclear repulsion	1049955.767467
FMO2-HF: Total energy	-51180.173485
FMO2-MP2: Total energy	-51329.504185

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.
0.244	1.843	-0.015	-0.693	-0.892	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 : -0.027 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	874	ASP	-1	-0.815	-0.879	3.883	-0.154	1.445	-0.015	-0.693	-0.892	0.001
4	A	875	ARG	1	0.749	0.818	6.055	0.699	0.699	0.000	0.000	0.000	0.000
5	A	876	THR	0	-0.067	-0.037	9.436	-0.029	-0.029	0.000	0.000	0.000	0.000
6	A	877	ASP	-1	-0.860	-0.925	11.680	-0.020	-0.020	0.000	0.000	0.000	0.000
7	A	878	ASP	-1	-0.840	-0.905	10.471	-0.208	-0.208	0.000	0.000	0.000	0.000
8	A	879	LEU	0	0.028	-0.009	13.198	-0.057	-0.057	0.000	0.000	0.000	0.000
9	A	880	VAL	0	0.009	0.022	14.697	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	881	TYR	0	0.028	0.005	9.052	0.001	0.001	0.000	0.000	0.000	0.000
11	A	882	LEU	0	-0.007	-0.002	12.761	-0.044	-0.044	0.000	0.000	0.000	0.000
12	A	883	ASN	0	0.038	0.010	14.968	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	884	VAL	0	0.006	0.011	13.895	0.004	0.004	0.000	0.000	0.000	0.000
14	A	885	MET	0	-0.037	-0.018	12.128	-0.055	-0.055	0.000	0.000	0.000	0.000
15	A	886	GLU	-1	-0.889	-0.921	15.107	-0.141	-0.141	0.000	0.000	0.000	0.000
16	A	887	LEU	0	0.024	0.015	18.807	0.009	0.009	0.000	0.000	0.000	0.000
17	A	888	VAL	0	0.000	-0.012	15.533	0.014	0.014	0.000	0.000	0.000	0.000
18	A	889	ARG	1	0.930	0.968	14.519	0.354	0.354	0.000	0.000	0.000	0.000
19	A	890	ALA	0	0.062	0.037	19.775	0.016	0.016	0.000	0.000	0.000	0.000
20	A	891	VAL	0	-0.022	-0.020	21.375	0.018	0.018	0.000	0.000	0.000	0.000
21	A	892	LEU	0	-0.041	-0.026	18.013	0.010	0.010	0.000	0.000	0.000	0.000
22	A	893	GLU	-1	-0.917	-0.948	22.504	-0.143	-0.143	0.000	0.000	0.000	0.000
23	A	894	LEU	0	-0.008	-0.010	25.307	0.012	0.012	0.000	0.000	0.000	0.000
24	A	895	LYS	1	0.852	0.913	22.665	0.228	0.228	0.000	0.000	0.000	0.000
25	A	896	ASN	0	-0.062	-0.027	24.296	0.008	0.008	0.000	0.000	0.000	0.000
26	A	897	GLU	-1	-0.854	-0.928	28.107	-0.118	-0.118	0.000	0.000	0.000	0.000
27	A	898	LEU	0	-0.053	-0.039	30.576	0.012	0.012	0.000	0.000	0.000	0.000
28	A	899	ALA	0	-0.052	-0.023	32.566	0.008	0.008	0.000	0.000	0.000	0.000
29	A	900	GLN	0	-0.010	-0.007	34.343	0.011	0.011	0.000	0.000	0.000	0.000
30	A	901	LEU	0	-0.040	0.007	31.964	0.007	0.007	0.000	0.000	0.000	0.000
31	A	902	PRO	0	0.026	0.013	36.288	0.002	0.002	0.000	0.000	0.000	0.000
32	A	903	PRO	0	0.027	-0.015	38.027	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	904	GLU	-1	-0.808	-0.902	37.885	-0.074	-0.074	0.000	0.000	0.000	0.000
34	A	905	GLY	0	0.034	0.016	35.974	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	906	TYR	0	0.048	0.013	33.274	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	907	VAL	0	-0.018	-0.013	33.178	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	908	VAL	0	-0.035	-0.024	32.025	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	909	VAL	0	0.055	0.043	28.605	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	910	VAL	0	-0.009	-0.006	28.615	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	911	LYS	1	0.827	0.921	29.781	0.075	0.075	0.000	0.000	0.000	0.000
41	A	912	ASN	0	0.002	0.001	27.224	0.010	0.010	0.000	0.000	0.000	0.000
42	A	913	VAL	0	0.031	0.020	24.544	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	914	GLY	0	0.011	0.002	25.556	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	915	LEU	0	-0.061	-0.030	27.669	0.007	0.007	0.000	0.000	0.000	0.000
45	A	916	THR	0	-0.026	-0.019	21.966	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	917	LEU	0	0.029	0.012	22.634	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	918	ARG	1	0.930	0.967	23.876	0.087	0.087	0.000	0.000	0.000	0.000
48	A	919	LYS	1	0.841	0.907	21.738	0.141	0.141	0.000	0.000	0.000	0.000
49	A	920	LEU	0	-0.019	-0.003	18.220	0.005	0.005	0.000	0.000	0.000	0.000
50	A	921	ILE	0	-0.002	-0.001	20.840	0.006	0.006	0.000	0.000	0.000	0.000
51	A	922	GLY	0	0.053	0.037	23.167	0.010	0.010	0.000	0.000	0.000	0.000
52	A	923	SER	0	0.010	-0.004	18.965	0.000	0.000	0.000	0.000	0.000	0.000
53	A	924	VAL	0	-0.037	-0.022	18.144	0.006	0.006	0.000	0.000	0.000	0.000
54	A	925	ASP	-1	-0.865	-0.942	20.287	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	926	ASP	-1	-0.938	-0.966	21.882	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	927	LEU	0	-0.040	-0.016	15.505	0.015	0.015	0.000	0.000	0.000	0.000
57	A	928	LEU	0	0.009	0.006	20.108	0.026	0.026	0.000	0.000	0.000	0.000
58	A	929	PRO	0	-0.017	-0.023	21.601	0.018	0.018	0.000	0.000	0.000	0.000
59	A	930	SER	0	-0.043	-0.018	18.986	0.011	0.011	0.000	0.000	0.000	0.000
60	A	931	LEU	0	-0.014	0.009	16.225	0.033	0.033	0.000	0.000	0.000	0.000
61	A	932	PRO	0	0.038	0.016	17.813	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	933	SER	0	0.043	0.004	20.789	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	934	SER	0	-0.007	0.017	21.352	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	935	SER	0	0.054	0.019	17.388	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	936	ARG	1	0.842	0.948	19.405	-0.098	-0.098	0.000	0.000	0.000	0.000
66	A	937	THR	0	0.054	0.013	21.571	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	938	GLU	-1	-0.938	-0.957	19.156	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	939	ILE	0	0.000	-0.005	16.245	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	940	GLU	-1	-0.889	-0.948	20.024	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	941	GLY	0	0.011	0.019	23.531	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	942	THR	0	-0.038	-0.040	18.691	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	943	GLN	0	0.026	-0.008	21.832	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	944	LYS	1	0.855	0.937	23.534	0.025	0.025	0.000	0.000	0.000	0.000
74	A	945	LEU	0	0.005	0.009	22.326	0.001	0.001	0.000	0.000	0.000	0.000
75	A	946	LEU	0	0.042	0.017	19.902	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	947	ASN	0	-0.045	-0.036	24.407	0.000	0.000	0.000	0.000	0.000	0.000
77	A	948	LYS	1	0.906	0.964	27.779	0.102	0.102	0.000	0.000	0.000	0.000
78	A	949	ASH	0	-0.070	-0.064	23.687	0.009	0.009	0.000	0.000	0.000	0.000
79	A	950	LEU	0	0.044	0.032	27.212	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	951	ALA	0	-0.012	-0.008	28.602	0.004	0.004	0.000	0.000	0.000	0.000
81	A	952	GLU	-1	-0.869	-0.918	30.106	-0.081	-0.081	0.000	0.000	0.000	0.000
82	A	953	LEU	0	-0.008	0.004	27.431	0.003	0.003	0.000	0.000	0.000	0.000
83	A	954	ILE	0	0.013	0.002	30.939	0.004	0.004	0.000	0.000	0.000	0.000
84	A	955	ASN	0	0.004	0.002	33.818	0.008	0.008	0.000	0.000	0.000	0.000
85	A	956	LYS	1	0.862	0.918	33.126	0.091	0.091	0.000	0.000	0.000	0.000
86	A	957	MET	0	0.033	0.029	33.923	0.004	0.004	0.000	0.000	0.000	0.000
87	A	958	ARG	1	0.916	0.941	35.840	0.066	0.066	0.000	0.000	0.000	0.000
88	A	959	LEU	0	-0.015	0.000	37.941	0.003	0.003	0.000	0.000	0.000	0.000
89	A	960	ALA	0	0.046	0.010	36.969	0.002	0.002	0.000	0.000	0.000	0.000
90	A	961	GLN	0	-0.017	-0.022	38.796	0.005	0.005	0.000	0.000	0.000	0.000
91	A	962	GLN	0	-0.073	-0.039	41.371	0.004	0.004	0.000	0.000	0.000	0.000
92	A	963	ASN	0	0.007	-0.006	42.100	0.005	0.005	0.000	0.000	0.000	0.000
93	A	964	ALA	0	-0.009	0.006	42.257	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	965	VAL	0	-0.021	-0.003	43.332	0.000	0.000	0.000	0.000	0.000	0.000
95	A	966	THR	0	0.000	-0.005	45.459	0.002	0.002	0.000	0.000	0.000	0.000
96	A	967	SER	0	0.012	-0.002	44.884	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	968	LEU	0	0.002	0.003	42.707	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	969	SER	0	0.002	-0.006	40.869	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	970	GLU	-1	-0.761	-0.859	38.104	-0.090	-0.090	0.000	0.000	0.000	0.000
100	A	971	GLU	-1	-0.834	-0.881	36.795	-0.096	-0.096	0.000	0.000	0.000	0.000
101	A	972	CYS	0	-0.045	-0.013	36.282	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	973	LYS	1	0.873	0.925	34.430	0.084	0.084	0.000	0.000	0.000	0.000
103	A	974	ARG	1	0.910	0.950	32.601	0.087	0.087	0.000	0.000	0.000	0.000
104	A	975	GLN	0	-0.023	-0.027	31.504	-0.009	-0.009	0.000	0.000	0.000	0.000
105	A	976	MET	0	-0.004	0.022	31.127	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	977	LEU	0	0.003	0.027	28.348	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	978	THR	0	-0.034	-0.021	26.845	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	979	ALA	0	-0.023	-0.022	26.572	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	980	SER	0	-0.003	-0.027	25.452	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	981	HIS	0	0.013	0.011	20.901	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	982	THR	0	-0.048	-0.014	21.706	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	983	LEU	0	0.026	0.014	21.829	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	984	ALA	0	0.034	0.012	18.907	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	985	VAL	0	-0.032	-0.015	17.501	-0.044	-0.044	0.000	0.000	0.000	0.000
115	A	986	ASP	-1	-0.767	-0.874	17.115	-0.213	-0.213	0.000	0.000	0.000	0.000
116	A	987	ALA	0	-0.018	0.005	17.774	0.006	0.006	0.000	0.000	0.000	0.000
117	A	988	LYS	1	0.837	0.906	12.346	0.506	0.506	0.000	0.000	0.000	0.000
118	A	989	ASN	0	-0.027	-0.018	13.167	-0.078	-0.078	0.000	0.000	0.000	0.000
119	A	990	LEU	0	0.011	0.016	14.646	0.023	0.023	0.000	0.000	0.000	0.000
120	A	991	LEU	0	0.009	0.004	9.511	0.042	0.042	0.000	0.000	0.000	0.000
121	A	992	ASP	-1	-0.843	-0.915	9.684	-0.748	-0.748	0.000	0.000	0.000	0.000
122	A	993	ALA	0	-0.011	-0.003	10.769	0.128	0.128	0.000	0.000	0.000	0.000
123	A	994	VAL	0	0.013	-0.001	12.720	0.090	0.090	0.000	0.000	0.000	0.000
124	A	995	ASP	-1	-0.769	-0.864	7.718	-0.415	-0.415	0.000	0.000	0.000	0.000
125	A	996	GLN	0	-0.028	-0.011	9.854	0.269	0.269	0.000	0.000	0.000	0.000
126	A	997	ALA	0	-0.001	0.001	11.069	0.111	0.111	0.000	0.000	0.000	0.000
127	A	998	LYS	1	0.831	0.911	10.580	0.111	0.111	0.000	0.000	0.000	0.000
128	A	999	VAL	0	-0.008	0.006	7.820	0.080	0.080	0.000	0.000	0.000	0.000
129	A	1000	LEU	0	-0.005	-0.015	10.810	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	1001	ALA	0	0.002	0.001	14.369	-0.034	-0.034	0.000	0.000	0.000	0.000
131	A	1002	ASN	0	-0.079	-0.042	12.288	-0.048	-0.048	0.000	0.000	0.000	0.000
132	A	1003	LEU	0	-0.050	-0.005	13.991	0.001	0.001	0.000	0.000	0.000	0.000
133	A	1004	ALA	0	-0.082	-0.036	15.529	-0.080	-0.080	0.000	0.000	0.000	0.000

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