FMO DATABASE

FMODB ID: 49VYN

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-838407.039989
FMO2-HF: Nuclear repulsion	796341.321673
FMO2-HF: Total energy	-42065.718316
FMO2-MP2: Total energy	-42188.446503

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.
-5.508	-0.764	0.504	-1.936	-3.312	-0.003

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 : -0.002

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	0.045	-0.006	3.404	-3.674	-1.967	0.027	-0.938	-0.796	0.002
4	A	523	SER	0	-0.043	-0.023	4.723	-0.068	0.090	-0.001	-0.006	-0.151	0.000
5	A	524	GLY	0	0.025	0.028	3.456	0.509	1.220	0.072	-0.246	-0.537	0.002
6	A	525	TYR	0	-0.031	-0.004	2.687	-4.402	-2.303	0.407	-0.745	-1.761	-0.007
7	A	526	PRO	0	0.050	0.022	5.165	1.010	1.079	-0.001	-0.001	-0.067	0.000
8	A	527	TRP	0	0.040	0.023	7.263	0.511	0.511	0.000	0.000	0.000	0.000
9	A	528	PHE	0	-0.026	-0.020	8.341	0.332	0.332	0.000	0.000	0.000	0.000
10	A	529	HIS	0	-0.021	-0.040	10.269	0.255	0.255	0.000	0.000	0.000	0.000
11	A	530	GLY	0	0.031	0.031	12.199	0.183	0.183	0.000	0.000	0.000	0.000
12	A	531	MET	0	-0.030	0.007	13.157	-0.053	-0.053	0.000	0.000	0.000	0.000
13	A	532	LEU	0	0.028	0.032	16.591	0.074	0.074	0.000	0.000	0.000	0.000
14	A	533	SER	0	0.068	0.025	18.536	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	534	ARG	1	0.962	0.983	22.011	0.241	0.241	0.000	0.000	0.000	0.000
16	A	535	LEU	0	0.024	-0.001	23.746	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	536	LYS	1	0.970	1.006	21.362	0.210	0.210	0.000	0.000	0.000	0.000
18	A	537	ALA	0	0.043	0.007	19.923	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	538	ALA	0	-0.038	-0.033	21.069	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	539	GLN	0	0.019	-0.009	24.161	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	540	LEU	0	0.012	0.014	18.382	0.007	0.007	0.000	0.000	0.000	0.000
22	A	541	VAL	0	-0.017	0.002	19.514	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	542	LEU	0	-0.046	-0.017	22.011	0.002	0.002	0.000	0.000	0.000	0.000
24	A	543	GLU	-1	-0.912	-0.924	23.517	-0.219	-0.219	0.000	0.000	0.000	0.000
25	A	544	GLY	0	0.024	0.028	24.882	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	545	GLY	0	-0.006	-0.004	27.351	0.007	0.007	0.000	0.000	0.000	0.000
27	A	546	THR	0	-0.005	-0.032	28.079	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	547	GLY	0	0.008	0.021	28.615	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	548	SER	0	-0.009	-0.028	23.809	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	549	HIS	0	-0.024	0.011	23.737	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	550	GLY	0	0.035	0.013	22.270	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	551	VAL	0	-0.028	0.004	19.033	-0.090	-0.090	0.000	0.000	0.000	0.000
33	A	552	PHE	0	-0.005	-0.028	13.003	0.033	0.033	0.000	0.000	0.000	0.000
34	A	553	LEU	0	0.010	0.016	14.370	-0.045	-0.045	0.000	0.000	0.000	0.000
35	A	554	VAL	0	-0.004	0.000	12.162	0.078	0.078	0.000	0.000	0.000	0.000
36	A	555	ARG	1	0.822	0.916	13.586	0.386	0.386	0.000	0.000	0.000	0.000
37	A	556	GLN	0	0.035	-0.022	12.624	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	557	SER	0	-0.039	-0.023	15.882	0.068	0.068	0.000	0.000	0.000	0.000
39	A	558	GLU	-1	-0.811	-0.919	19.015	-0.222	-0.222	0.000	0.000	0.000	0.000
40	A	559	THR	0	-0.020	-0.018	21.311	0.030	0.030	0.000	0.000	0.000	0.000
41	A	560	ARG	1	0.884	0.968	22.222	0.247	0.247	0.000	0.000	0.000	0.000
42	A	561	ARG	1	1.024	0.995	19.280	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	562	GLY	0	0.044	0.022	16.753	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	563	GLU	-1	-0.800	-0.855	17.560	-0.390	-0.390	0.000	0.000	0.000	0.000
45	A	564	CYS	0	-0.030	-0.005	14.056	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	565	VAL	0	-0.061	-0.033	16.566	0.074	0.074	0.000	0.000	0.000	0.000
47	A	566	LEU	0	0.035	0.029	15.842	-0.080	-0.080	0.000	0.000	0.000	0.000
48	A	567	THR	0	-0.024	-0.031	18.027	0.087	0.087	0.000	0.000	0.000	0.000
49	A	568	PHE	0	0.030	0.001	19.067	-0.056	-0.056	0.000	0.000	0.000	0.000
50	A	569	ASN	0	-0.033	-0.004	21.325	0.073	0.073	0.000	0.000	0.000	0.000
51	A	570	PHE	0	0.024	0.006	24.263	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	571	GLN	0	0.041	-0.009	27.058	0.049	0.049	0.000	0.000	0.000	0.000
53	A	572	GLY	0	0.041	0.022	28.394	0.030	0.030	0.000	0.000	0.000	0.000
54	A	573	LYS	1	0.849	0.928	29.102	0.277	0.277	0.000	0.000	0.000	0.000
55	A	574	ALA	0	0.025	0.022	25.105	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	575	LYS	1	0.855	0.948	24.583	0.359	0.359	0.000	0.000	0.000	0.000
57	A	576	HIS	0	-0.011	-0.022	22.571	-0.053	-0.053	0.000	0.000	0.000	0.000
58	A	577	LEU	0	0.038	0.025	20.891	0.044	0.044	0.000	0.000	0.000	0.000
59	A	578	ARG	1	0.788	0.858	20.307	0.259	0.259	0.000	0.000	0.000	0.000
60	A	579	LEU	0	0.024	0.017	15.257	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	580	SER	0	-0.043	-0.014	18.213	0.048	0.048	0.000	0.000	0.000	0.000
62	A	581	LEU	0	0.058	0.022	11.780	-0.065	-0.065	0.000	0.000	0.000	0.000
63	A	582	ASN	0	-0.015	-0.015	15.113	0.073	0.073	0.000	0.000	0.000	0.000
64	A	583	ALA	0	0.012	-0.005	13.536	-0.063	-0.063	0.000	0.000	0.000	0.000
65	A	584	ALA	0	-0.013	0.001	11.952	0.096	0.096	0.000	0.000	0.000	0.000
66	A	585	GLY	0	0.004	0.010	10.420	-0.091	-0.091	0.000	0.000	0.000	0.000
67	A	586	GLN	0	-0.022	-0.001	11.410	-0.171	-0.171	0.000	0.000	0.000	0.000
68	A	587	CYS	0	-0.056	-0.029	14.165	0.021	0.021	0.000	0.000	0.000	0.000
69	A	588	ARG	1	0.922	0.972	16.127	0.387	0.387	0.000	0.000	0.000	0.000
70	A	589	VAL	0	0.016	-0.004	19.100	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	590	GLN	0	-0.036	-0.025	21.608	0.008	0.008	0.000	0.000	0.000	0.000
72	A	591	HIS	0	0.096	0.043	25.198	0.009	0.009	0.000	0.000	0.000	0.000
73	A	592	LEU	0	-0.014	0.014	22.567	0.007	0.007	0.000	0.000	0.000	0.000
74	A	593	HIS	0	-0.016	-0.025	20.805	0.006	0.006	0.000	0.000	0.000	0.000
75	A	594	PHE	0	0.036	0.020	16.505	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	595	GLN	0	0.070	0.029	14.462	0.082	0.082	0.000	0.000	0.000	0.000
77	A	596	SER	0	0.010	-0.017	10.474	-0.157	-0.157	0.000	0.000	0.000	0.000
78	A	597	ILE	0	0.014	-0.009	9.366	0.125	0.125	0.000	0.000	0.000	0.000
79	A	598	PHE	0	0.045	0.009	5.715	-0.096	-0.096	0.000	0.000	0.000	0.000
80	A	599	ASP	-1	-0.806	-0.866	10.608	-1.237	-1.237	0.000	0.000	0.000	0.000
81	A	600	MET	0	-0.091	-0.018	14.064	0.180	0.180	0.000	0.000	0.000	0.000
82	A	601	LEU	0	-0.001	-0.020	10.574	0.129	0.129	0.000	0.000	0.000	0.000
83	A	602	GLU	-1	-0.896	-0.941	11.913	-1.615	-1.615	0.000	0.000	0.000	0.000
84	A	603	HIS	0	0.021	0.024	15.197	0.120	0.120	0.000	0.000	0.000	0.000
85	A	604	PHE	0	-0.003	-0.023	17.865	0.107	0.107	0.000	0.000	0.000	0.000
86	A	605	ARG	1	0.848	0.941	14.248	1.369	1.369	0.000	0.000	0.000	0.000
87	A	606	VAL	0	-0.031	-0.011	18.855	0.058	0.058	0.000	0.000	0.000	0.000
88	A	607	HIS	0	-0.031	-0.015	21.760	0.101	0.101	0.000	0.000	0.000	0.000
89	A	608	PRO	0	0.037	0.005	22.925	-0.044	-0.044	0.000	0.000	0.000	0.000
90	A	609	ILE	0	-0.032	-0.018	21.043	0.005	0.005	0.000	0.000	0.000	0.000
91	A	610	PRO	0	0.002	0.008	24.452	0.034	0.034	0.000	0.000	0.000	0.000
92	A	611	LEU	0	-0.077	-0.040	25.380	0.017	0.017	0.000	0.000	0.000	0.000
93	A	612	GLU	-1	-0.851	-0.926	28.884	-0.246	-0.246	0.000	0.000	0.000	0.000
94	A	613	SER	0	-0.068	-0.039	30.596	0.010	0.010	0.000	0.000	0.000	0.000
95	A	614	GLY	0	-0.045	-0.023	30.517	0.003	0.003	0.000	0.000	0.000	0.000
96	A	615	GLY	0	0.035	0.010	31.278	0.007	0.007	0.000	0.000	0.000	0.000
97	A	616	SER	0	-0.016	-0.003	34.542	0.009	0.009	0.000	0.000	0.000	0.000
98	A	617	SER	0	-0.026	-0.004	31.731	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	618	ASP	-1	-0.847	-0.919	28.260	-0.374	-0.374	0.000	0.000	0.000	0.000
100	A	619	VAL	0	-0.075	-0.060	23.491	0.006	0.006	0.000	0.000	0.000	0.000
101	A	620	VAL	0	0.041	0.056	21.665	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	621	LEU	0	-0.086	-0.046	16.099	0.026	0.026	0.000	0.000	0.000	0.000
103	A	622	VAL	0	0.011	0.004	18.829	-0.033	-0.033	0.000	0.000	0.000	0.000
104	A	623	SER	0	-0.014	-0.009	16.435	-0.056	-0.056	0.000	0.000	0.000	0.000
105	A	624	TYR	0	0.016	0.003	10.769	-0.111	-0.111	0.000	0.000	0.000	0.000
106	A	625	VAL	0	0.018	0.012	15.380	0.063	0.063	0.000	0.000	0.000	0.000
107	A	626	PRO	0	-0.018	0.008	12.613	-0.129	-0.129	0.000	0.000	0.000	0.000
108	A	627	SER	0	0.003	0.009	9.878	0.198	0.198	0.000	0.000	0.000	0.000

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