FMO DATABASE

FMODB ID: VVY11

Calculation Name: 1D1Q-A-Xray547

Preferred Name: Low molecular weight phosphotyrosine protein phosphatase

Target Type: SINGLE PROTEIN

Ligand Name: 4-nitrophenyl phosphate | phosphate ion

Ligand 3-letter code: 4NP | PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1D1Q

Chain ID: A

ChEMBL ID: CHEMBL5397

UniProt ID: P40347

Base Structure: X-ray

Registration Date: 2025-09-02

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1708545.950961
FMO2-HF: Nuclear repulsion	1644064.289821
FMO2-HF: Total energy	-64481.66114
FMO2-MP2: Total energy	-64670.609027

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:2:ILE)

Summations of interaction energy for fragment #1(A:2:ILE)

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.
42.912	46.919	4.655	-2.325	-6.338	-0.01

Interaction energy analysis for fragmet #1(A:2:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.903

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	4	LYS	1	0.824	0.898	2.062	39.819	41.668	3.293	-1.756	-3.387	0.003
4	A	5	PRO	0	0.012	0.009	2.679	-4.047	-1.592	1.307	-1.058	-2.704	-0.013
5	A	6	LYS	1	0.890	0.950	3.258	31.029	30.732	0.055	0.489	-0.247	0.000
6	A	7	ILE	0	0.020	0.021	6.471	0.457	0.457	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.034	-0.017	9.481	1.756	1.756	0.000	0.000	0.000	0.000
8	A	9	VAL	0	0.023	0.009	12.800	0.080	0.080	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.010	0.007	15.961	0.524	0.524	0.000	0.000	0.000	0.000
10	A	11	PHE	0	0.027	0.014	19.399	0.201	0.201	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.023	-0.028	22.576	0.425	0.425	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.025	0.015	25.650	0.168	0.168	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.080	0.036	29.386	-0.112	-0.112	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.019	0.013	32.569	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.031	-0.007	27.003	0.098	0.098	0.000	0.000	0.000	0.000
16	A	17	PHE	0	0.066	0.042	30.480	-0.073	-0.073	0.000	0.000	0.000	0.000
17	A	18	CYS	0	0.000	0.017	32.994	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.778	0.880	29.945	9.008	9.008	0.000	0.000	0.000	0.000
19	A	20	SER	0	0.044	0.009	25.845	-0.046	-0.046	0.000	0.000	0.000	0.000
20	A	21	PRO	0	-0.020	-0.007	25.679	-0.408	-0.408	0.000	0.000	0.000	0.000
21	A	22	MET	0	-0.006	0.016	26.659	-0.193	-0.193	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.003	-0.001	23.883	-0.182	-0.182	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.786	-0.870	21.466	-12.723	-12.723	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.024	-0.008	22.095	-0.391	-0.391	0.000	0.000	0.000	0.000
25	A	26	ILE	0	0.002	-0.002	23.916	-0.148	-0.148	0.000	0.000	0.000	0.000
26	A	27	PHE	0	0.008	0.011	15.472	-0.174	-0.174	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.840	0.905	19.133	13.005	13.005	0.000	0.000	0.000	0.000
28	A	29	HIS	0	0.034	0.025	19.848	-0.411	-0.411	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.800	-0.899	20.273	-12.039	-12.039	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.018	0.002	14.554	-0.390	-0.390	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.841	-0.903	16.600	-13.203	-13.203	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.825	0.899	18.919	11.536	11.536	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.038	-0.007	16.438	0.230	0.230	0.000	0.000	0.000	0.000
34	A	35	ASN	0	-0.033	-0.001	15.505	-0.262	-0.262	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.027	0.012	11.377	-1.265	-1.265	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.818	-0.922	11.738	-18.094	-18.094	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.101	-0.057	8.892	-2.272	-2.272	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.857	0.907	6.009	26.820	26.820	0.000	0.000	0.000	0.000
39	A	40	PHE	0	0.015	0.006	8.538	-0.981	-0.981	0.000	0.000	0.000	0.000
40	A	41	ASN	0	-0.082	-0.030	9.207	0.867	0.867	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.861	0.925	10.977	20.246	20.246	0.000	0.000	0.000	0.000
42	A	43	ILE	0	0.049	0.030	14.508	-0.407	-0.407	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.797	-0.861	17.187	-13.968	-13.968	0.000	0.000	0.000	0.000
44	A	45	SER	0	-0.008	-0.006	20.464	0.077	0.077	0.000	0.000	0.000	0.000
45	A	46	PHE	0	0.025	-0.002	20.656	0.125	0.125	0.000	0.000	0.000	0.000
46	A	47	GLY	0	-0.016	0.002	25.864	0.136	0.136	0.000	0.000	0.000	0.000
47	A	48	THR	0	0.067	0.027	28.515	-0.119	-0.119	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.075	-0.028	30.208	0.193	0.193	0.000	0.000	0.000	0.000
49	A	50	ASN	0	0.022	-0.009	32.106	-0.193	-0.193	0.000	0.000	0.000	0.000
50	A	51	TYR	0	0.003	-0.015	34.056	0.034	0.034	0.000	0.000	0.000	0.000
51	A	52	HIS	1	0.880	0.938	34.224	8.361	8.361	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.021	-0.005	31.550	-0.225	-0.225	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.005	0.006	32.111	0.232	0.232	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.852	-0.902	33.401	-7.976	-7.976	0.000	0.000	0.000	0.000
55	A	56	SER	0	-0.018	-0.015	32.671	-0.403	-0.403	0.000	0.000	0.000	0.000
56	A	57	PRO	0	-0.003	-0.002	30.425	0.140	0.140	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.765	-0.859	33.185	-7.703	-7.703	0.000	0.000	0.000	0.000
58	A	59	HIS	0	0.053	0.017	35.765	-0.197	-0.197	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.829	0.912	37.996	7.595	7.595	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.034	-0.006	31.324	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.009	-0.002	33.116	-0.170	-0.170	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.051	-0.033	34.386	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	64	ILE	0	0.018	0.018	32.948	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	65	CYS	0	-0.065	-0.040	30.480	-0.234	-0.234	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.970	0.985	31.854	7.710	7.710	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.029	-0.007	34.150	0.114	0.114	0.000	0.000	0.000	0.000
67	A	68	HIS	1	0.767	0.867	30.674	9.019	9.019	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.008	0.011	30.438	-0.233	-0.233	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.060	-0.019	26.331	-0.287	-0.287	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.832	0.890	23.229	12.194	12.194	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.026	0.003	26.539	-0.359	-0.359	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.044	-0.026	27.291	0.503	0.503	0.000	0.000	0.000	0.000
73	A	74	HIS	0	0.032	0.013	25.739	-0.451	-0.451	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.859	0.912	27.935	9.722	9.722	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.032	0.041	28.461	-0.323	-0.323	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.850	0.906	22.091	12.728	12.728	0.000	0.000	0.000	0.000
77	A	78	GLN	0	-0.027	-0.030	28.129	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.031	-0.007	21.743	-0.225	-0.225	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.918	0.939	24.467	10.757	10.757	0.000	0.000	0.000	0.000
80	A	81	THR	0	0.046	0.010	23.649	-0.370	-0.370	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.869	0.916	21.752	12.846	12.846	0.000	0.000	0.000	0.000
82	A	83	HIS	0	0.035	0.016	19.623	-0.429	-0.429	0.000	0.000	0.000	0.000
83	A	84	PHE	0	0.013	-0.010	18.313	-0.613	-0.613	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.813	-0.899	15.669	-19.289	-19.289	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.883	-0.916	14.659	-15.666	-15.666	0.000	0.000	0.000	0.000
86	A	87	TYR	0	-0.122	-0.100	14.307	-0.729	-0.729	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.755	-0.859	10.368	-25.777	-25.777	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.044	-0.045	11.577	0.244	0.244	0.000	0.000	0.000	0.000
89	A	90	ILE	0	-0.010	-0.006	16.081	0.356	0.356	0.000	0.000	0.000	0.000
90	A	91	ILE	0	0.012	0.013	17.706	0.265	0.265	0.000	0.000	0.000	0.000
91	A	92	GLY	0	-0.013	-0.002	21.725	0.360	0.360	0.000	0.000	0.000	0.000
92	A	93	MET	0	-0.064	-0.025	24.744	-0.060	-0.060	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.710	-0.826	28.105	-9.160	-9.160	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.788	-0.924	29.901	-10.488	-10.488	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.098	-0.058	31.434	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.024	-0.020	28.393	-0.233	-0.233	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.051	0.031	25.473	-0.257	-0.257	0.000	0.000	0.000	0.000
98	A	99	ASN	0	0.007	0.013	28.279	-0.137	-0.137	0.000	0.000	0.000	0.000
99	A	100	ASN	0	-0.027	-0.019	30.817	0.116	0.116	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.000	-0.003	24.233	-0.067	-0.067	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.977	0.985	25.961	11.212	11.212	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.861	0.933	27.389	9.360	9.360	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.044	-0.007	26.365	0.180	0.180	0.000	0.000	0.000	0.000
104	A	105	GLN	0	0.039	0.026	20.876	0.248	0.248	0.000	0.000	0.000	0.000
105	A	106	PRO	0	-0.054	-0.010	21.733	0.370	0.370	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.842	-0.928	22.389	-13.737	-13.737	0.000	0.000	0.000	0.000
107	A	108	GLY	0	-0.042	-0.018	20.126	-0.096	-0.096	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.091	-0.047	17.918	-0.894	-0.894	0.000	0.000	0.000	0.000
109	A	110	LYS	1	0.849	0.912	10.366	24.147	24.147	0.000	0.000	0.000	0.000
110	A	111	ALA	0	-0.060	-0.011	14.803	-0.573	-0.573	0.000	0.000	0.000	0.000
111	A	112	LYS	1	0.931	0.967	15.899	17.509	17.509	0.000	0.000	0.000	0.000
112	A	113	VAL	0	-0.013	-0.001	17.709	0.269	0.269	0.000	0.000	0.000	0.000
113	A	114	CYS	0	-0.099	-0.046	19.556	-0.182	-0.182	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.010	0.019	22.176	0.245	0.245	0.000	0.000	0.000	0.000
115	A	116	PHE	0	0.003	-0.022	20.859	-0.304	-0.304	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.039	0.012	23.807	-0.173	-0.173	0.000	0.000	0.000	0.000
117	A	118	ASP	-1	-0.844	-0.925	22.209	-12.482	-12.482	0.000	0.000	0.000	0.000
118	A	119	TRP	0	-0.106	-0.072	16.903	-0.138	-0.138	0.000	0.000	0.000	0.000
119	A	120	ASN	0	-0.009	-0.030	22.629	0.001	0.001	0.000	0.000	0.000	0.000
120	A	121	THR	0	-0.053	-0.020	25.577	-0.136	-0.136	0.000	0.000	0.000	0.000
121	A	122	ASN	0	-0.049	-0.035	27.330	0.299	0.299	0.000	0.000	0.000	0.000
122	A	123	ASP	-1	-0.788	-0.861	29.894	-9.640	-9.640	0.000	0.000	0.000	0.000
123	A	124	GLY	0	0.040	0.027	32.251	0.270	0.270	0.000	0.000	0.000	0.000
124	A	125	THR	0	-0.100	-0.066	30.971	0.244	0.244	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.060	-0.048	28.761	0.124	0.124	0.000	0.000	0.000	0.000
126	A	127	GLN	0	0.065	0.041	31.977	-0.270	-0.270	0.000	0.000	0.000	0.000
127	A	128	THR	0	0.036	0.031	28.478	-0.183	-0.183	0.000	0.000	0.000	0.000
128	A	129	ILE	0	0.018	0.024	29.277	-0.352	-0.352	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.008	0.014	26.788	0.191	0.191	0.000	0.000	0.000	0.000
130	A	131	GLU	-1	-0.901	-0.960	31.149	-8.259	-8.259	0.000	0.000	0.000	0.000
131	A	132	ASP	-1	-0.851	-0.937	34.654	-8.609	-8.609	0.000	0.000	0.000	0.000
132	A	133	PRO	0	0.038	0.032	34.835	0.218	0.218	0.000	0.000	0.000	0.000
133	A	134	TRP	0	-0.063	-0.024	37.831	0.127	0.127	0.000	0.000	0.000	0.000
134	A	135	TYR	0	-0.023	-0.028	39.462	0.161	0.161	0.000	0.000	0.000	0.000
135	A	136	GLY	0	0.043	0.046	41.277	0.160	0.160	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.856	-0.938	42.256	-6.962	-6.962	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.030	-0.035	38.952	-0.213	-0.213	0.000	0.000	0.000	0.000
138	A	139	GLN	0	-0.031	-0.022	38.917	-0.251	-0.251	0.000	0.000	0.000	0.000
139	A	140	ASP	-1	-0.811	-0.894	38.071	-7.748	-7.748	0.000	0.000	0.000	0.000
140	A	141	PHE	0	-0.016	-0.022	34.769	-0.332	-0.332	0.000	0.000	0.000	0.000
141	A	142	GLU	-1	-0.785	-0.871	33.949	-8.899	-8.899	0.000	0.000	0.000	0.000
142	A	143	TYR	0	0.020	0.012	33.973	-0.325	-0.325	0.000	0.000	0.000	0.000
143	A	144	ASN	0	0.009	-0.010	31.255	-0.237	-0.237	0.000	0.000	0.000	0.000
144	A	145	PHE	0	0.065	0.011	28.923	-0.425	-0.425	0.000	0.000	0.000	0.000
145	A	146	LYS	1	0.884	0.964	29.045	8.642	8.642	0.000	0.000	0.000	0.000
146	A	147	GLN	0	-0.025	-0.041	29.111	-0.184	-0.184	0.000	0.000	0.000	0.000
147	A	148	ILE	0	0.038	0.024	24.618	-0.430	-0.430	0.000	0.000	0.000	0.000
148	A	149	THR	0	-0.052	-0.020	24.486	-0.611	-0.611	0.000	0.000	0.000	0.000
149	A	150	TYR	0	-0.057	-0.034	24.341	-0.555	-0.555	0.000	0.000	0.000	0.000
150	A	151	PHE	0	0.039	0.002	23.223	-0.416	-0.416	0.000	0.000	0.000	0.000
151	A	152	SER	0	-0.006	-0.019	20.337	-0.794	-0.794	0.000	0.000	0.000	0.000
152	A	153	LYS	1	0.821	0.915	19.097	11.262	11.262	0.000	0.000	0.000	0.000
153	A	154	GLN	0	-0.036	-0.004	19.258	-0.944	-0.944	0.000	0.000	0.000	0.000
154	A	155	PHE	0	0.029	0.009	13.588	-0.626	-0.626	0.000	0.000	0.000	0.000
155	A	156	LEU	0	-0.023	-0.015	14.553	-1.086	-1.086	0.000	0.000	0.000	0.000
156	A	157	LYS	1	0.924	0.972	14.398	12.850	12.850	0.000	0.000	0.000	0.000
157	A	158	LYS	1	0.884	0.940	16.078	14.507	14.507	0.000	0.000	0.000	0.000
158	A	159	GLU	-1	-0.758	-0.849	12.710	-18.921	-18.921	0.000	0.000	0.000	0.000
159	A	160	LEU	-1	-0.833	-0.853	8.631	-29.535	-29.535	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ILE)