FMO DATABASE

FMODB ID: K9LV3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-838323.414094
FMO2-HF: Nuclear repulsion	796258.056873
FMO2-HF: Total energy	-42065.357221
FMO2-MP2: Total energy	-42188.116913

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.
-5.293	-1.029	0.541	-1.748	-3.056	-0.004

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 : 0.006 / q_NPA : -0.003

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	0.050	-0.004	3.332	-3.478	-1.843	0.037	-0.908	-0.764	0.002
4	A	523	SER	0	-0.067	-0.028	5.117	0.390	0.390	0.000	0.000	0.000	0.000
5	A	524	GLY	0	0.050	0.035	3.801	0.594	1.170	0.024	-0.171	-0.428	0.001
6	A	525	TYR	0	-0.026	-0.006	2.618	-4.980	-2.977	0.481	-0.669	-1.815	-0.007
7	A	526	PRO	0	0.046	0.023	5.385	0.929	0.979	-0.001	0.000	-0.049	0.000
8	A	527	TRP	0	0.044	0.023	7.254	0.483	0.483	0.000	0.000	0.000	0.000
9	A	528	PHE	0	-0.030	-0.020	8.631	0.305	0.305	0.000	0.000	0.000	0.000
10	A	529	HIS	0	-0.028	-0.042	10.494	0.273	0.273	0.000	0.000	0.000	0.000
11	A	530	GLY	0	0.030	0.024	12.126	0.182	0.182	0.000	0.000	0.000	0.000
12	A	531	MET	0	-0.020	0.012	13.180	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	532	LEU	0	0.017	0.026	16.618	0.074	0.074	0.000	0.000	0.000	0.000
14	A	533	SER	0	0.090	0.036	18.556	-0.035	-0.035	0.000	0.000	0.000	0.000
15	A	534	ARG	1	0.959	0.973	22.096	0.255	0.255	0.000	0.000	0.000	0.000
16	A	535	LEU	0	0.019	-0.002	23.752	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	536	LYS	1	1.012	1.022	21.621	0.189	0.189	0.000	0.000	0.000	0.000
18	A	537	ALA	0	0.021	-0.003	20.132	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	538	ALA	0	-0.045	-0.038	21.296	-0.032	-0.032	0.000	0.000	0.000	0.000
20	A	539	GLN	0	0.005	-0.016	24.368	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	540	LEU	0	0.017	0.017	18.675	0.007	0.007	0.000	0.000	0.000	0.000
22	A	541	VAL	0	-0.025	0.000	19.739	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	542	LEU	0	-0.049	-0.021	22.189	0.000	0.000	0.000	0.000	0.000	0.000
24	A	543	GLU	-1	-0.905	-0.920	23.711	-0.215	-0.215	0.000	0.000	0.000	0.000
25	A	544	GLY	0	0.028	0.041	25.064	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	545	GLY	0	-0.009	-0.006	27.522	0.007	0.007	0.000	0.000	0.000	0.000
27	A	546	THR	0	-0.011	-0.036	28.211	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	547	GLY	0	0.020	0.026	28.717	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	548	SER	0	-0.020	-0.044	23.937	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	549	HIS	0	0.003	0.025	23.844	-0.036	-0.036	0.000	0.000	0.000	0.000
31	A	550	GLY	0	0.030	0.007	22.330	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	551	VAL	0	-0.028	0.006	19.185	-0.094	-0.094	0.000	0.000	0.000	0.000
33	A	552	PHE	0	-0.010	-0.028	12.991	0.030	0.030	0.000	0.000	0.000	0.000
34	A	553	LEU	0	0.010	0.017	14.531	-0.040	-0.040	0.000	0.000	0.000	0.000
35	A	554	VAL	0	-0.004	-0.002	12.306	0.072	0.072	0.000	0.000	0.000	0.000
36	A	555	ARG	1	0.851	0.931	13.764	0.456	0.456	0.000	0.000	0.000	0.000
37	A	556	GLN	0	0.030	-0.024	12.264	0.022	0.022	0.000	0.000	0.000	0.000
38	A	557	SER	0	-0.075	-0.027	15.798	0.077	0.077	0.000	0.000	0.000	0.000
39	A	558	GLU	-1	-0.877	-0.953	19.032	-0.163	-0.163	0.000	0.000	0.000	0.000
40	A	559	THR	0	-0.020	-0.019	21.342	0.027	0.027	0.000	0.000	0.000	0.000
41	A	560	ARG	1	0.873	0.955	22.016	0.276	0.276	0.000	0.000	0.000	0.000
42	A	561	ARG	1	1.042	1.002	19.213	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	562	GLY	0	0.025	0.015	16.771	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	563	GLU	-1	-0.792	-0.876	17.560	-0.435	-0.435	0.000	0.000	0.000	0.000
45	A	564	CYS	0	-0.020	-0.004	12.762	0.045	0.045	0.000	0.000	0.000	0.000
46	A	565	VAL	0	-0.063	-0.031	16.481	0.081	0.081	0.000	0.000	0.000	0.000
47	A	566	LEU	0	0.041	0.028	15.934	-0.079	-0.079	0.000	0.000	0.000	0.000
48	A	567	THR	0	-0.017	-0.024	18.148	0.096	0.096	0.000	0.000	0.000	0.000
49	A	568	PHE	0	0.032	0.004	19.211	-0.055	-0.055	0.000	0.000	0.000	0.000
50	A	569	ASN	0	-0.030	0.002	21.451	0.070	0.070	0.000	0.000	0.000	0.000
51	A	570	PHE	0	0.011	-0.002	24.386	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	571	GLN	0	0.036	-0.014	27.154	0.043	0.043	0.000	0.000	0.000	0.000
53	A	572	GLY	0	0.010	0.000	28.514	0.029	0.029	0.000	0.000	0.000	0.000
54	A	573	LYS	1	0.886	0.955	29.231	0.287	0.287	0.000	0.000	0.000	0.000
55	A	574	ALA	0	0.026	0.022	25.251	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	575	LYS	1	0.864	0.953	24.676	0.373	0.373	0.000	0.000	0.000	0.000
57	A	576	HIS	0	0.016	0.001	22.714	-0.059	-0.059	0.000	0.000	0.000	0.000
58	A	577	LEU	0	0.045	0.028	20.838	0.046	0.046	0.000	0.000	0.000	0.000
59	A	578	ARG	1	0.786	0.875	20.218	0.288	0.288	0.000	0.000	0.000	0.000
60	A	579	LEU	0	0.033	0.020	15.172	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	580	SER	0	-0.036	-0.005	18.135	0.051	0.051	0.000	0.000	0.000	0.000
62	A	581	LEU	0	0.046	0.018	11.567	-0.079	-0.079	0.000	0.000	0.000	0.000
63	A	582	ASN	0	-0.009	-0.014	14.766	0.065	0.065	0.000	0.000	0.000	0.000
64	A	583	ALA	0	0.013	-0.009	13.396	-0.080	-0.080	0.000	0.000	0.000	0.000
65	A	584	ALA	0	-0.017	0.000	11.810	0.086	0.086	0.000	0.000	0.000	0.000
66	A	585	GLY	0	0.008	0.012	10.291	-0.124	-0.124	0.000	0.000	0.000	0.000
67	A	586	GLN	0	-0.034	0.008	11.279	-0.178	-0.178	0.000	0.000	0.000	0.000
68	A	587	CYS	0	-0.047	-0.027	14.154	0.060	0.060	0.000	0.000	0.000	0.000
69	A	588	ARG	1	0.922	0.972	16.067	0.436	0.436	0.000	0.000	0.000	0.000
70	A	589	VAL	0	0.011	-0.005	19.194	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	590	GLN	0	-0.047	-0.031	21.534	0.011	0.011	0.000	0.000	0.000	0.000
72	A	591	HIS	0	0.090	0.039	25.126	0.006	0.006	0.000	0.000	0.000	0.000
73	A	592	LEU	0	-0.020	0.013	22.479	0.006	0.006	0.000	0.000	0.000	0.000
74	A	593	HIS	0	0.010	-0.012	20.708	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	594	PHE	0	0.034	0.021	16.373	0.001	0.001	0.000	0.000	0.000	0.000
76	A	595	GLN	0	0.084	0.029	14.373	0.084	0.084	0.000	0.000	0.000	0.000
77	A	596	SER	0	0.011	0.008	10.427	-0.172	-0.172	0.000	0.000	0.000	0.000
78	A	597	ILE	0	0.014	-0.006	9.262	0.164	0.164	0.000	0.000	0.000	0.000
79	A	598	PHE	0	0.030	0.002	5.412	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	599	ASP	-1	-0.786	-0.887	10.517	-1.373	-1.373	0.000	0.000	0.000	0.000
81	A	600	MET	0	-0.091	-0.018	13.934	0.191	0.191	0.000	0.000	0.000	0.000
82	A	601	LEU	0	-0.011	-0.030	10.499	0.149	0.149	0.000	0.000	0.000	0.000
83	A	602	GLU	-1	-0.971	-0.989	11.352	-1.883	-1.883	0.000	0.000	0.000	0.000
84	A	603	HIS	0	0.010	0.015	15.092	0.126	0.126	0.000	0.000	0.000	0.000
85	A	604	PHE	0	0.014	-0.019	17.809	0.114	0.114	0.000	0.000	0.000	0.000
86	A	605	ARG	1	0.916	0.987	13.427	1.444	1.444	0.000	0.000	0.000	0.000
87	A	606	VAL	0	-0.025	-0.006	18.797	0.060	0.060	0.000	0.000	0.000	0.000
88	A	607	HIS	0	-0.039	-0.013	21.665	0.114	0.114	0.000	0.000	0.000	0.000
89	A	608	PRO	0	0.036	0.003	22.874	-0.046	-0.046	0.000	0.000	0.000	0.000
90	A	609	ILE	0	-0.024	-0.013	20.895	0.004	0.004	0.000	0.000	0.000	0.000
91	A	610	PRO	0	0.000	0.007	24.447	0.037	0.037	0.000	0.000	0.000	0.000
92	A	611	LEU	0	-0.072	-0.041	25.623	0.018	0.018	0.000	0.000	0.000	0.000
93	A	612	GLU	-1	-0.847	-0.929	28.914	-0.263	-0.263	0.000	0.000	0.000	0.000
94	A	613	SER	0	-0.100	-0.045	30.416	0.015	0.015	0.000	0.000	0.000	0.000
95	A	614	GLY	0	-0.022	-0.018	30.559	0.003	0.003	0.000	0.000	0.000	0.000
96	A	615	GLY	0	0.034	0.012	31.327	0.008	0.008	0.000	0.000	0.000	0.000
97	A	616	SER	0	-0.016	-0.006	34.561	0.011	0.011	0.000	0.000	0.000	0.000
98	A	617	SER	0	-0.046	-0.013	31.944	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	618	ASP	-1	-0.849	-0.914	28.209	-0.390	-0.390	0.000	0.000	0.000	0.000
100	A	619	VAL	0	-0.058	-0.054	23.423	0.008	0.008	0.000	0.000	0.000	0.000
101	A	620	VAL	0	0.030	0.053	21.686	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	621	LEU	0	-0.082	-0.048	16.142	0.028	0.028	0.000	0.000	0.000	0.000
103	A	622	VAL	0	0.014	0.009	18.818	-0.037	-0.037	0.000	0.000	0.000	0.000
104	A	623	SER	0	-0.021	-0.012	16.506	-0.059	-0.059	0.000	0.000	0.000	0.000
105	A	624	TYR	0	0.025	0.004	10.652	-0.019	-0.019	0.000	0.000	0.000	0.000
106	A	625	VAL	0	0.007	0.013	15.502	0.067	0.067	0.000	0.000	0.000	0.000
107	A	626	PRO	0	-0.013	0.003	12.830	-0.129	-0.129	0.000	0.000	0.000	0.000
108	A	627	SER	0	0.013	0.014	10.126	0.218	0.218	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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