FMO DATABASE

FMODB ID: 1YQ8Z

Calculation Name: 1DG9-A-Xray547

Preferred Name: Low molecular weight phosphotyrosine protein phosphatase

Target Type: SINGLE PROTEIN

Ligand Name: 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid

Ligand 3-letter code: EPE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DG9

Chain ID: A

ChEMBL ID: CHEMBL1075054

UniProt ID: P11064

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1625733.581867
FMO2-HF: Nuclear repulsion	1561567.682201
FMO2-HF: Total energy	-64165.899666
FMO2-MP2: Total energy	-64348.908245

3D Structure Molmil

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:1:ALA)

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

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.
-18.1	-16.141	-0.025	-0.983	-0.951	-0.004

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.807 / q_NPA : 0.889

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	3	GLN	0	-0.077	-0.031	3.843	4.043	6.002	-0.025	-0.983	-0.951	-0.004
4	A	4	VAL	0	-0.001	0.007	7.026	1.418	1.418	0.000	0.000	0.000	0.000
5	A	5	THR	0	-0.014	-0.009	10.113	-0.423	-0.423	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.883	0.946	11.709	24.420	24.420	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.006	-0.020	14.302	0.192	0.192	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.039	-0.025	17.332	0.643	0.643	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.025	0.009	19.816	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.015	-0.004	20.033	0.442	0.442	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.016	-0.010	25.152	0.221	0.221	0.000	0.000	0.000	0.000
12	A	12	CYS	-1	-0.813	-0.760	28.975	-9.487	-9.487	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.059	0.022	32.162	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.017	-0.010	34.873	0.111	0.111	0.000	0.000	0.000	0.000
15	A	15	ASN	0	0.026	-0.031	27.993	0.028	0.028	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.031	0.013	31.239	-0.190	-0.190	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.040	0.002	32.698	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.830	0.880	30.918	8.517	8.517	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.018	-0.106	27.576	-0.361	-0.361	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.000	-0.004	26.051	-0.489	-0.489	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.003	0.012	25.393	-0.421	-0.421	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.036	0.009	24.258	-0.413	-0.413	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.777	-0.845	21.354	-13.484	-13.484	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.022	-0.011	20.369	-0.762	-0.762	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.017	0.007	20.301	-0.569	-0.569	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.025	0.003	15.535	-0.445	-0.445	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.843	0.899	16.082	14.301	14.301	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.807	0.909	15.387	14.745	14.745	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.003	-0.006	15.500	-0.702	-0.702	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.035	0.025	11.089	-1.019	-1.019	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.042	-0.025	10.730	-2.120	-2.120	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.839	-0.897	11.341	-18.399	-18.399	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.082	-0.053	10.601	-1.687	-1.687	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.080	-0.038	6.577	-2.877	-2.877	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.031	0.013	5.807	-4.524	-4.524	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.030	-0.007	7.449	0.833	0.833	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.922	-0.944	6.624	-32.316	-32.316	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.067	-0.017	5.718	-2.614	-2.614	0.000	0.000	0.000	0.000
39	A	39	TRP	0	0.045	0.013	9.113	2.707	2.707	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.004	0.014	12.488	0.661	0.661	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.007	-0.005	14.726	0.655	0.655	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.776	-0.878	18.217	-12.363	-12.363	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.072	-0.065	21.975	0.243	0.243	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.041	0.021	25.472	0.048	0.048	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.045	-0.021	28.933	0.041	0.041	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.061	-0.033	32.609	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.048	-0.016	35.092	0.195	0.195	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.855	-0.941	36.374	-7.962	-7.962	0.000	0.000	0.000	0.000
49	A	49	TRP	0	-0.011	0.000	38.180	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.040	-0.025	36.359	0.222	0.222	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.020	0.014	34.575	-0.213	-0.213	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.021	-0.007	33.732	0.206	0.206	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.920	0.974	34.513	7.741	7.741	0.000	0.000	0.000	0.000
54	A	54	SER	0	0.015	0.009	32.165	-0.310	-0.310	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.001	-0.001	29.163	0.213	0.213	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.775	-0.862	32.302	-8.072	-8.072	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.017	0.000	33.718	-0.262	-0.262	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.813	0.898	34.889	7.721	7.721	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.030	0.020	30.779	-0.173	-0.173	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.041	-0.026	29.868	-0.336	-0.336	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.050	-0.042	30.278	-0.216	-0.216	0.000	0.000	0.000	0.000
62	A	62	CYS	0	0.003	0.022	30.822	-0.216	-0.216	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.005	-0.017	25.386	-0.271	-0.271	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.951	0.984	26.922	9.379	9.379	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.010	-0.001	28.621	-0.139	-0.139	0.000	0.000	0.000	0.000
66	A	66	HIS	1	0.770	0.873	25.651	10.455	10.455	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.013	0.017	24.550	-0.461	-0.461	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.050	-0.018	21.886	-0.611	-0.611	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.018	-0.024	23.152	0.948	0.948	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.021	-0.002	23.314	-0.516	-0.516	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.022	0.012	24.801	0.409	0.409	0.000	0.000	0.000	0.000
72	A	72	HIS	1	0.800	0.919	24.643	11.723	11.723	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.910	0.942	26.883	9.863	9.863	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.003	0.011	29.342	-0.240	-0.240	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.746	0.833	25.138	11.740	11.740	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.012	-0.001	31.393	0.162	0.162	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.010	0.008	29.250	-0.316	-0.316	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.064	-0.057	30.326	0.336	0.336	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.935	0.959	31.087	8.351	8.351	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.793	-0.886	28.090	-10.038	-10.038	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.719	-0.804	26.082	-11.770	-11.770	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.010	-0.013	25.763	-0.378	-0.378	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.004	0.001	26.928	-0.061	-0.061	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.061	-0.044	22.843	-0.448	-0.448	0.000	0.000	0.000	0.000
85	A	85	PHE	0	0.007	0.012	20.496	-0.768	-0.768	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.781	-0.855	17.722	-16.160	-16.160	0.000	0.000	0.000	0.000
87	A	87	TYR	0	-0.011	-0.005	17.960	0.366	0.366	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.017	0.003	22.495	-0.132	-0.132	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.007	0.011	21.864	0.409	0.409	0.000	0.000	0.000	0.000
90	A	90	CYS	0	-0.088	-0.040	25.890	0.161	0.161	0.000	0.000	0.000	0.000
91	A	91	MET	0	-0.006	0.003	26.977	-0.071	-0.071	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.718	-0.855	31.466	-8.298	-8.298	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.847	-0.952	34.818	-7.890	-7.890	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.030	-0.008	36.969	0.133	0.133	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.007	0.001	33.170	-0.206	-0.206	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.065	0.039	31.997	-0.093	-0.093	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.918	0.973	34.407	7.584	7.584	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.808	-0.900	36.727	-7.849	-7.849	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.044	-0.006	30.319	0.008	0.008	0.000	0.000	0.000	0.000
100	A	100	ASN	0	0.010	-0.001	33.539	-0.112	-0.112	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.848	0.919	35.214	7.731	7.731	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.898	0.935	34.595	8.802	8.802	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.012	-0.009	32.403	-0.051	-0.051	0.000	0.000	0.000	0.000
104	A	104	ASN	0	0.046	0.013	34.041	-0.161	-0.161	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.097	-0.040	37.012	0.037	0.037	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.028	-0.014	31.236	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.965	0.987	34.214	8.949	8.949	0.000	0.000	0.000	0.000
108	A	108	ASN	0	-0.036	-0.031	30.034	0.216	0.216	0.000	0.000	0.000	0.000
109	A	109	CYS	0	0.013	0.018	29.120	-0.390	-0.390	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.811	0.891	19.922	14.479	14.479	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.003	0.023	24.257	-0.315	-0.315	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.836	0.897	24.314	12.382	12.382	0.000	0.000	0.000	0.000
113	A	113	ILE	0	-0.007	-0.001	25.702	-0.222	-0.222	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.785	-0.863	24.994	-11.561	-11.561	0.000	0.000	0.000	0.000
115	A	115	LEU	0	0.036	0.029	28.501	-0.102	-0.102	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.010	0.011	23.859	-0.210	-0.210	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.083	0.022	26.819	-0.254	-0.254	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.100	-0.068	28.093	0.089	0.089	0.000	0.000	0.000	0.000
119	A	119	TYR	0	-0.047	-0.045	22.230	-0.224	-0.224	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.723	-0.854	25.900	-10.307	-10.307	0.000	0.000	0.000	0.000
121	A	121	PRO	0	-0.022	-0.012	25.999	0.337	0.337	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.045	-0.038	28.733	0.419	0.419	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.847	0.927	30.300	10.084	10.084	0.000	0.000	0.000	0.000
124	A	124	GLN	0	0.051	0.036	32.446	0.118	0.118	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.002	-0.014	32.072	-0.212	-0.212	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.018	0.009	32.588	-0.230	-0.230	0.000	0.000	0.000	0.000
127	A	127	ILE	0	0.004	0.017	28.625	-0.011	-0.011	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.847	-0.939	33.120	-7.969	-7.969	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.875	-0.941	35.716	-8.419	-8.419	0.000	0.000	0.000	0.000
130	A	130	PRO	0	0.023	0.019	34.566	0.196	0.196	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.011	0.001	37.842	0.167	0.167	0.000	0.000	0.000	0.000
132	A	132	TYR	0	-0.008	-0.019	39.441	0.122	0.122	0.000	0.000	0.000	0.000
133	A	133	GLY	0	0.026	0.035	40.903	0.173	0.173	0.000	0.000	0.000	0.000
134	A	134	ASN	0	-0.023	-0.029	40.918	-0.118	-0.118	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.840	-0.947	37.085	-8.097	-8.097	0.000	0.000	0.000	0.000
136	A	136	ALA	0	-0.024	-0.006	36.161	-0.272	-0.272	0.000	0.000	0.000	0.000
137	A	137	ASP	-1	-0.814	-0.891	36.500	-7.787	-7.787	0.000	0.000	0.000	0.000
138	A	138	PHE	0	0.010	-0.012	33.285	-0.308	-0.308	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.771	-0.858	31.219	-10.125	-10.125	0.000	0.000	0.000	0.000
140	A	140	THR	0	-0.071	-0.044	31.799	-0.275	-0.275	0.000	0.000	0.000	0.000
141	A	141	VAL	0	0.060	0.028	30.324	-0.275	-0.275	0.000	0.000	0.000	0.000
142	A	142	TYR	0	0.028	0.009	25.004	-0.570	-0.570	0.000	0.000	0.000	0.000
143	A	143	GLN	0	-0.049	-0.043	27.270	-0.633	-0.633	0.000	0.000	0.000	0.000
144	A	144	GLN	0	-0.055	-0.032	28.093	-0.147	-0.147	0.000	0.000	0.000	0.000
145	A	145	CYS	0	-0.022	-0.005	25.041	-0.345	-0.345	0.000	0.000	0.000	0.000
146	A	146	VAL	0	-0.011	-0.011	22.759	-0.572	-0.572	0.000	0.000	0.000	0.000
147	A	147	ARG	1	0.788	0.893	22.863	9.440	9.440	0.000	0.000	0.000	0.000
148	A	148	CYS	0	-0.038	-0.012	23.671	-0.245	-0.245	0.000	0.000	0.000	0.000
149	A	149	CYS	0	-0.031	-0.014	20.054	-0.249	-0.249	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.983	1.001	18.696	12.877	12.877	0.000	0.000	0.000	0.000
151	A	151	ALA	0	-0.007	0.004	18.957	-0.548	-0.548	0.000	0.000	0.000	0.000
152	A	152	PHE	0	-0.015	-0.014	18.457	-0.200	-0.200	0.000	0.000	0.000	0.000
153	A	153	LEU	0	0.021	0.018	12.801	-0.282	-0.282	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.838	-0.925	15.040	-19.064	-19.064	0.000	0.000	0.000	0.000
155	A	155	LYS	1	0.869	0.946	16.669	13.328	13.328	0.000	0.000	0.000	0.000
156	A	156	VAL	0	-0.091	-0.044	15.716	0.502	0.502	0.000	0.000	0.000	0.000
157	A	157	ARG	0	0.001	0.028	8.983	-0.046	-0.046	0.000	0.000	0.000	0.000

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