FMO DATABASE

FMODB ID: 52V5Z

Calculation Name: 2HDX-A-Xray372

Preferred Name: Tyrosine-protein kinase JAK2

Target Type: SINGLE PROTEIN

Ligand Name: o-phosphotyrosine

ligand 3-letter code: PTR

PDB ID: 2HDX

Chain ID: A

ChEMBL ID: CHEMBL1649049

UniProt ID: Q62120

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-839789.791344
FMO2-HF: Nuclear repulsion	797723.891049
FMO2-HF: Total energy	-42065.900295
FMO2-MP2: Total energy	-42188.627245

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:520:GLN)

Summations of interaction energy for fragment #1(A:520:GLN)

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.
-12.239	-6.906	6.736	-4.181	-7.887	-0.024

Interaction energy analysis for fragmet #1(A:520:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.000

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	522	LEU	0	0.048	-0.005	3.448	-2.627	-0.897	0.036	-0.929	-0.837	0.001
4	A	523	SER	0	-0.038	-0.025	5.253	-0.221	-0.221	0.000	0.000	0.000	0.000
5	A	524	GLY	0	0.025	0.036	2.728	0.952	1.882	1.097	-0.804	-1.223	0.007
6	A	525	TYR	0	-0.028	-0.004	2.264	-13.481	-10.912	5.604	-2.434	-5.738	-0.032
7	A	526	PRO	0	0.037	0.020	4.432	1.475	1.579	-0.001	-0.014	-0.089	0.000
8	A	527	TRP	0	0.066	0.040	6.669	0.575	0.575	0.000	0.000	0.000	0.000
9	A	528	PHE	0	-0.020	-0.014	7.708	0.412	0.412	0.000	0.000	0.000	0.000
10	A	529	HIS	0	-0.015	-0.027	9.628	0.263	0.263	0.000	0.000	0.000	0.000
11	A	530	GLY	0	0.042	0.031	11.539	0.226	0.226	0.000	0.000	0.000	0.000
12	A	531	MET	0	-0.045	-0.009	12.842	-0.051	-0.051	0.000	0.000	0.000	0.000
13	A	532	LEU	0	0.033	0.031	16.121	0.090	0.090	0.000	0.000	0.000	0.000
14	A	533	SER	0	0.024	0.009	17.860	-0.046	-0.046	0.000	0.000	0.000	0.000
15	A	534	ARG	1	0.968	0.978	21.385	0.311	0.311	0.000	0.000	0.000	0.000
16	A	535	LEU	0	0.017	0.000	22.933	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	536	LYS	1	0.955	0.988	20.676	0.288	0.288	0.000	0.000	0.000	0.000
18	A	537	ALA	0	0.047	0.012	19.172	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	538	ALA	0	-0.018	-0.024	20.327	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	539	GLN	0	0.023	0.008	23.574	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	540	LEU	0	0.027	0.014	17.566	0.007	0.007	0.000	0.000	0.000	0.000
22	A	541	VAL	0	-0.030	0.005	19.016	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	542	LEU	0	-0.044	-0.018	21.418	0.010	0.010	0.000	0.000	0.000	0.000
24	A	543	GLU	-1	-0.902	-0.927	22.399	-0.271	-0.271	0.000	0.000	0.000	0.000
25	A	544	GLY	0	0.029	0.032	24.125	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	545	GLY	0	-0.014	-0.010	26.762	0.010	0.010	0.000	0.000	0.000	0.000
27	A	546	THR	0	0.006	-0.023	27.371	-0.030	-0.030	0.000	0.000	0.000	0.000
28	A	547	GLY	0	0.000	0.014	28.064	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	548	SER	0	-0.004	-0.018	23.126	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	549	HIS	0	-0.030	-0.004	23.342	-0.043	-0.043	0.000	0.000	0.000	0.000
31	A	550	GLY	0	0.030	0.011	21.765	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	551	VAL	0	-0.035	0.004	18.390	-0.092	-0.092	0.000	0.000	0.000	0.000
33	A	552	PHE	0	-0.014	-0.029	12.361	0.039	0.039	0.000	0.000	0.000	0.000
34	A	553	LEU	0	-0.001	0.007	13.921	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	554	VAL	0	-0.015	-0.006	11.367	0.090	0.090	0.000	0.000	0.000	0.000
36	A	555	ARG	1	0.827	0.910	12.811	0.471	0.471	0.000	0.000	0.000	0.000
37	A	556	GLN	0	0.039	-0.023	12.940	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	557	SER	0	-0.037	-0.018	15.878	0.073	0.073	0.000	0.000	0.000	0.000
39	A	558	GLU	-1	-0.769	-0.889	19.327	-0.333	-0.333	0.000	0.000	0.000	0.000
40	A	559	THR	0	-0.027	-0.018	21.281	0.038	0.038	0.000	0.000	0.000	0.000
41	A	560	ARG	1	0.889	0.970	21.783	0.306	0.306	0.000	0.000	0.000	0.000
42	A	561	ARG	1	1.019	0.998	19.239	0.018	0.018	0.000	0.000	0.000	0.000
43	A	562	GLY	0	0.057	0.033	17.040	0.015	0.015	0.000	0.000	0.000	0.000
44	A	563	GLU	-1	-0.819	-0.871	17.900	-0.459	-0.459	0.000	0.000	0.000	0.000
45	A	564	CYS	0	-0.048	-0.011	14.032	-0.037	-0.037	0.000	0.000	0.000	0.000
46	A	565	VAL	0	-0.046	-0.027	16.361	0.084	0.084	0.000	0.000	0.000	0.000
47	A	566	LEU	0	0.053	0.042	15.246	-0.093	-0.093	0.000	0.000	0.000	0.000
48	A	567	THR	0	-0.019	-0.020	17.213	0.106	0.106	0.000	0.000	0.000	0.000
49	A	568	PHE	0	0.023	-0.005	18.259	-0.073	-0.073	0.000	0.000	0.000	0.000
50	A	569	ASN	0	-0.045	-0.011	20.582	0.086	0.086	0.000	0.000	0.000	0.000
51	A	570	PHE	0	0.013	0.001	23.681	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	571	GLN	0	0.046	-0.002	26.641	0.052	0.052	0.000	0.000	0.000	0.000
53	A	572	GLY	0	0.017	0.018	27.883	0.033	0.033	0.000	0.000	0.000	0.000
54	A	573	LYS	1	0.852	0.917	28.051	0.314	0.314	0.000	0.000	0.000	0.000
55	A	574	ALA	0	0.030	0.024	24.316	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	575	LYS	1	0.842	0.935	23.674	0.411	0.411	0.000	0.000	0.000	0.000
57	A	576	HIS	0	-0.019	-0.026	21.662	-0.061	-0.061	0.000	0.000	0.000	0.000
58	A	577	LEU	0	0.024	0.024	20.248	0.052	0.052	0.000	0.000	0.000	0.000
59	A	578	ARG	1	0.791	0.857	19.692	0.318	0.318	0.000	0.000	0.000	0.000
60	A	579	LEU	0	0.019	0.013	14.627	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	580	SER	0	-0.024	-0.002	17.624	0.031	0.031	0.000	0.000	0.000	0.000
62	A	581	LEU	0	0.043	0.006	12.178	-0.076	-0.076	0.000	0.000	0.000	0.000
63	A	582	ASN	0	-0.007	-0.021	14.848	0.084	0.084	0.000	0.000	0.000	0.000
64	A	583	ALA	0	0.005	-0.009	13.337	-0.084	-0.084	0.000	0.000	0.000	0.000
65	A	584	ALA	0	-0.006	0.013	12.172	0.124	0.124	0.000	0.000	0.000	0.000
66	A	585	GLY	0	0.002	0.004	10.027	-0.074	-0.074	0.000	0.000	0.000	0.000
67	A	586	GLN	0	-0.019	0.004	10.996	-0.208	-0.208	0.000	0.000	0.000	0.000
68	A	587	CYS	0	-0.071	-0.025	13.949	0.008	0.008	0.000	0.000	0.000	0.000
69	A	588	ARG	1	0.909	0.956	15.874	0.468	0.468	0.000	0.000	0.000	0.000
70	A	589	VAL	0	0.009	-0.002	18.738	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	590	GLN	0	-0.021	-0.018	21.319	0.013	0.013	0.000	0.000	0.000	0.000
72	A	591	HIS	0	0.078	0.039	24.901	0.011	0.011	0.000	0.000	0.000	0.000
73	A	592	LEU	0	0.005	0.023	22.226	0.012	0.012	0.000	0.000	0.000	0.000
74	A	593	HIS	0	-0.024	-0.034	20.332	0.003	0.003	0.000	0.000	0.000	0.000
75	A	594	PHE	0	0.036	0.018	16.218	0.002	0.002	0.000	0.000	0.000	0.000
76	A	595	GLN	0	0.080	0.035	14.207	0.030	0.030	0.000	0.000	0.000	0.000
77	A	596	SER	0	0.008	-0.019	10.146	-0.149	-0.149	0.000	0.000	0.000	0.000
78	A	597	ILE	0	0.026	-0.009	9.325	0.113	0.113	0.000	0.000	0.000	0.000
79	A	598	PHE	0	0.036	0.008	5.265	-0.146	-0.146	0.000	0.000	0.000	0.000
80	A	599	ASP	-1	-0.841	-0.885	10.331	-1.244	-1.244	0.000	0.000	0.000	0.000
81	A	600	MET	0	-0.075	-0.011	13.731	0.189	0.189	0.000	0.000	0.000	0.000
82	A	601	LEU	0	0.001	-0.016	10.041	0.135	0.135	0.000	0.000	0.000	0.000
83	A	602	GLU	-1	-0.827	-0.892	12.194	-1.510	-1.510	0.000	0.000	0.000	0.000
84	A	603	HIS	0	0.014	0.024	14.746	0.142	0.142	0.000	0.000	0.000	0.000
85	A	604	PHE	0	-0.010	-0.017	17.435	0.108	0.108	0.000	0.000	0.000	0.000
86	A	605	ARG	1	0.830	0.895	14.064	1.419	1.419	0.000	0.000	0.000	0.000
87	A	606	VAL	0	-0.041	-0.003	18.214	0.065	0.065	0.000	0.000	0.000	0.000
88	A	607	HIS	0	-0.033	-0.025	21.267	0.107	0.107	0.000	0.000	0.000	0.000
89	A	608	PRO	0	0.037	0.016	22.276	-0.054	-0.054	0.000	0.000	0.000	0.000
90	A	609	ILE	0	-0.027	-0.016	20.344	0.001	0.001	0.000	0.000	0.000	0.000
91	A	610	PRO	0	-0.009	0.000	23.920	0.037	0.037	0.000	0.000	0.000	0.000
92	A	611	LEU	0	-0.056	-0.026	24.970	0.012	0.012	0.000	0.000	0.000	0.000
93	A	612	GLU	-1	-0.826	-0.917	28.416	-0.275	-0.275	0.000	0.000	0.000	0.000
94	A	613	SER	0	-0.058	-0.028	29.669	0.011	0.011	0.000	0.000	0.000	0.000
95	A	614	GLY	0	-0.040	-0.031	29.946	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	615	GLY	0	0.039	0.015	30.958	0.003	0.003	0.000	0.000	0.000	0.000
97	A	616	SER	0	-0.002	0.005	33.655	0.017	0.017	0.000	0.000	0.000	0.000
98	A	617	SER	0	-0.052	-0.025	31.338	0.007	0.007	0.000	0.000	0.000	0.000
99	A	618	ASP	-1	-0.841	-0.910	27.618	-0.406	-0.406	0.000	0.000	0.000	0.000
100	A	619	VAL	0	-0.062	-0.045	22.960	0.005	0.005	0.000	0.000	0.000	0.000
101	A	620	VAL	0	0.040	0.034	21.046	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	621	LEU	0	-0.055	-0.031	15.337	0.029	0.029	0.000	0.000	0.000	0.000
103	A	622	VAL	0	0.000	0.011	17.298	-0.085	-0.085	0.000	0.000	0.000	0.000
104	A	623	SER	0	-0.022	-0.010	16.069	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	624	TYR	0	0.002	-0.008	10.223	-0.131	-0.131	0.000	0.000	0.000	0.000
106	A	625	VAL	0	0.021	0.011	14.827	0.068	0.068	0.000	0.000	0.000	0.000
107	A	626	PRO	0	-0.014	0.005	11.708	-0.181	-0.181	0.000	0.000	0.000	0.000
108	A	627	SER	0	-0.029	-0.015	8.884	0.235	0.235	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:520:GLN)