FMO DATABASE

FMODB ID: YRQM2

Calculation Name: 1MKP-A-Xray547

Preferred Name: Dual specificity protein phosphatase 6

Target Type: SINGLE PROTEIN

Ligand Name: (4s)-2-methyl-2,4-pentanediol | chloride ion

Ligand 3-letter code: MPD | CL

Ligand of Interest (LOI):

PDB ID: 1MKP

Chain ID: A

ChEMBL ID: CHEMBL1250381

UniProt ID: Q16828

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1385015.532474
FMO2-HF: Nuclear repulsion	1327824.992302
FMO2-HF: Total energy	-57190.540172
FMO2-MP2: Total energy	-57356.585337

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:204:ALA)

Summations of interaction energy for fragment #1(A:204: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.
-108.958	-104.705	3.728	-4.315	-3.663	-0.037

Interaction energy analysis for fragmet #1(A:204:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.908

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	206	PHE	0	0.044	0.028	3.148	-21.169	-18.001	0.046	-1.956	-1.257	-0.012
18	A	221	ASP	-1	-0.757	-0.842	4.630	-48.211	-48.118	-0.001	-0.013	-0.078	0.000
19	A	222	SER	0	-0.042	-0.053	2.139	-12.497	-11.596	3.684	-2.303	-2.281	-0.025
20	A	223	THR	0	-0.008	0.004	4.474	2.297	2.388	-0.001	-0.043	-0.047	0.000
4	A	207	PRO	0	0.013	0.003	5.913	3.242	3.242	0.000	0.000	0.000	0.000
5	A	208	VAL	0	0.010	0.006	9.457	-0.006	-0.006	0.000	0.000	0.000	0.000
6	A	209	GLU	-1	-0.797	-0.882	12.074	-16.549	-16.549	0.000	0.000	0.000	0.000
7	A	210	ILE	0	-0.042	-0.020	15.393	0.530	0.530	0.000	0.000	0.000	0.000
8	A	211	LEU	0	0.020	0.001	18.285	0.828	0.828	0.000	0.000	0.000	0.000
9	A	212	PRO	0	0.049	0.028	19.687	-0.617	-0.617	0.000	0.000	0.000	0.000
10	A	213	PHE	0	0.046	0.028	18.973	0.742	0.742	0.000	0.000	0.000	0.000
11	A	214	LEU	0	-0.016	0.004	18.814	0.065	0.065	0.000	0.000	0.000	0.000
12	A	215	TYR	0	0.010	-0.007	12.375	-0.948	-0.948	0.000	0.000	0.000	0.000
13	A	216	LEU	0	0.005	0.007	14.001	0.403	0.403	0.000	0.000	0.000	0.000
14	A	217	GLY	0	0.001	-0.011	10.360	-2.344	-2.344	0.000	0.000	0.000	0.000
15	A	218	CYS	-1	-0.819	-0.858	8.755	-26.765	-26.765	0.000	0.000	0.000	0.000
16	A	219	ALA	0	0.006	0.010	9.325	-2.155	-2.155	0.000	0.000	0.000	0.000
17	A	220	LYS	1	0.757	0.819	5.199	36.207	36.207	0.000	0.000	0.000	0.000
21	A	224	ASN	0	-0.009	-0.008	7.309	3.840	3.840	0.000	0.000	0.000	0.000
22	A	225	LEU	0	0.048	0.013	8.988	-0.090	-0.090	0.000	0.000	0.000	0.000
23	A	226	ASP	-1	-0.849	-0.917	11.023	-22.442	-22.442	0.000	0.000	0.000	0.000
24	A	227	VAL	0	-0.008	-0.004	6.330	-0.251	-0.251	0.000	0.000	0.000	0.000
25	A	228	LEU	0	-0.062	-0.026	9.724	1.092	1.092	0.000	0.000	0.000	0.000
26	A	229	GLU	-1	-0.815	-0.895	12.558	-16.305	-16.305	0.000	0.000	0.000	0.000
27	A	230	GLU	-1	-0.973	-0.976	10.495	-27.387	-27.387	0.000	0.000	0.000	0.000
28	A	231	PHE	0	-0.083	-0.048	8.249	0.084	0.084	0.000	0.000	0.000	0.000
29	A	232	GLY	0	0.031	0.026	13.885	1.018	1.018	0.000	0.000	0.000	0.000
30	A	233	ILE	0	-0.100	-0.040	12.950	1.049	1.049	0.000	0.000	0.000	0.000
31	A	234	LYS	1	0.805	0.885	16.842	16.930	16.930	0.000	0.000	0.000	0.000
32	A	235	TYR	0	-0.075	-0.042	19.282	0.560	0.560	0.000	0.000	0.000	0.000
33	A	236	ILE	0	0.008	-0.001	15.168	-1.012	-1.012	0.000	0.000	0.000	0.000
34	A	237	LEU	0	-0.009	-0.001	18.024	0.933	0.933	0.000	0.000	0.000	0.000
35	A	238	ASN	0	0.017	0.018	17.519	-1.204	-1.204	0.000	0.000	0.000	0.000
36	A	239	VAL	0	0.021	-0.010	18.083	1.044	1.044	0.000	0.000	0.000	0.000
37	A	240	THR	0	-0.029	-0.024	17.181	-0.478	-0.478	0.000	0.000	0.000	0.000
38	A	241	PRO	0	-0.060	-0.021	19.293	0.469	0.469	0.000	0.000	0.000	0.000
39	A	242	ASN	0	-0.022	-0.051	22.486	0.033	0.033	0.000	0.000	0.000	0.000
40	A	243	LEU	0	-0.006	0.021	19.715	0.022	0.022	0.000	0.000	0.000	0.000
41	A	244	PRO	0	0.009	0.006	24.443	0.336	0.336	0.000	0.000	0.000	0.000
42	A	245	ASN	0	0.012	0.001	25.793	-0.587	-0.587	0.000	0.000	0.000	0.000
43	A	246	LEU	0	-0.016	-0.010	23.867	0.261	0.261	0.000	0.000	0.000	0.000
44	A	247	PHE	0	0.013	-0.020	25.598	-0.356	-0.356	0.000	0.000	0.000	0.000
45	A	248	GLU	-1	-0.895	-0.922	25.021	-10.594	-10.594	0.000	0.000	0.000	0.000
46	A	249	ASN	0	-0.021	-0.014	24.374	-0.648	-0.648	0.000	0.000	0.000	0.000
47	A	250	ALA	0	-0.002	0.003	20.343	0.308	0.308	0.000	0.000	0.000	0.000
48	A	251	GLY	0	0.000	-0.005	20.438	-0.799	-0.799	0.000	0.000	0.000	0.000
49	A	252	GLU	-1	-0.902	-0.954	19.399	-13.502	-13.502	0.000	0.000	0.000	0.000
50	A	253	PHE	0	-0.038	-0.013	15.406	0.103	0.103	0.000	0.000	0.000	0.000
51	A	254	LYS	1	0.893	0.948	20.394	12.951	12.951	0.000	0.000	0.000	0.000
52	A	255	TYR	0	-0.001	-0.011	17.412	-0.936	-0.936	0.000	0.000	0.000	0.000
53	A	256	LYS	1	0.889	0.943	21.218	12.661	12.661	0.000	0.000	0.000	0.000
54	A	257	GLN	0	0.006	0.005	21.193	-1.534	-1.534	0.000	0.000	0.000	0.000
55	A	258	ILE	0	0.023	0.018	22.946	0.601	0.601	0.000	0.000	0.000	0.000
56	A	259	PRO	0	-0.015	0.010	24.834	-0.349	-0.349	0.000	0.000	0.000	0.000
57	A	260	ILE	0	-0.034	-0.006	22.837	0.351	0.351	0.000	0.000	0.000	0.000
58	A	261	SER	0	0.039	0.022	25.827	-0.195	-0.195	0.000	0.000	0.000	0.000
59	A	262	ASP	-1	-0.914	-0.984	23.883	-12.735	-12.735	0.000	0.000	0.000	0.000
60	A	263	HIS	0	0.049	0.057	25.940	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	264	TRP	0	0.012	-0.007	29.426	-0.075	-0.075	0.000	0.000	0.000	0.000
62	A	265	SER	0	-0.043	-0.034	30.476	0.076	0.076	0.000	0.000	0.000	0.000
63	A	266	GLN	0	-0.040	-0.010	27.783	0.155	0.155	0.000	0.000	0.000	0.000
64	A	267	ASN	0	0.044	0.038	29.735	-0.345	-0.345	0.000	0.000	0.000	0.000
65	A	268	LEU	0	-0.004	-0.013	23.549	-0.145	-0.145	0.000	0.000	0.000	0.000
66	A	269	SER	0	0.031	-0.010	28.036	-0.083	-0.083	0.000	0.000	0.000	0.000
67	A	270	GLN	0	-0.007	-0.006	30.029	0.102	0.102	0.000	0.000	0.000	0.000
68	A	271	PHE	0	0.003	-0.002	27.109	0.075	0.075	0.000	0.000	0.000	0.000
69	A	272	PHE	0	0.002	0.015	25.799	-0.388	-0.388	0.000	0.000	0.000	0.000
70	A	273	PRO	0	0.035	0.024	28.474	-0.205	-0.205	0.000	0.000	0.000	0.000
71	A	274	GLU	-1	-0.849	-0.933	28.082	-10.970	-10.970	0.000	0.000	0.000	0.000
72	A	275	ALA	0	-0.010	-0.009	24.194	-0.271	-0.271	0.000	0.000	0.000	0.000
73	A	276	ILE	0	-0.002	-0.002	25.142	-0.423	-0.423	0.000	0.000	0.000	0.000
74	A	277	SER	0	-0.025	-0.003	27.191	-0.105	-0.105	0.000	0.000	0.000	0.000
75	A	278	PHE	0	0.000	-0.005	20.974	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	279	ILE	0	-0.002	0.000	21.593	-0.380	-0.380	0.000	0.000	0.000	0.000
77	A	280	ASP	-1	-0.784	-0.854	24.076	-11.354	-11.354	0.000	0.000	0.000	0.000
78	A	281	GLU	-1	-0.858	-0.882	27.205	-11.311	-11.311	0.000	0.000	0.000	0.000
79	A	282	ALA	0	0.005	0.011	22.639	0.142	0.142	0.000	0.000	0.000	0.000
80	A	283	ARG	1	0.872	0.900	22.424	13.604	13.604	0.000	0.000	0.000	0.000
81	A	284	GLY	0	-0.011	0.004	24.712	0.129	0.129	0.000	0.000	0.000	0.000
82	A	285	LYS	1	0.806	0.881	26.423	11.364	11.364	0.000	0.000	0.000	0.000
83	A	286	ASN	0	-0.066	-0.028	24.540	-0.169	-0.169	0.000	0.000	0.000	0.000
84	A	287	CYS	0	-0.031	0.003	21.876	-0.339	-0.339	0.000	0.000	0.000	0.000
85	A	288	GLY	0	0.027	0.014	17.936	0.031	0.031	0.000	0.000	0.000	0.000
86	A	289	VAL	0	-0.006	-0.013	18.706	0.066	0.066	0.000	0.000	0.000	0.000
87	A	290	LEU	0	-0.020	0.002	11.950	-0.758	-0.758	0.000	0.000	0.000	0.000
88	A	291	VAL	0	0.001	0.008	15.631	1.026	1.026	0.000	0.000	0.000	0.000
89	A	292	HIS	0	-0.024	-0.023	9.814	0.354	0.354	0.000	0.000	0.000	0.000
90	A	293	SER	0	0.019	-0.008	13.791	1.748	1.748	0.000	0.000	0.000	0.000
91	A	294	LEU	0	0.034	0.003	12.203	-1.542	-1.542	0.000	0.000	0.000	0.000
92	A	295	ALA	0	-0.029	-0.008	14.129	-0.232	-0.232	0.000	0.000	0.000	0.000
93	A	296	GLY	0	-0.001	-0.001	13.376	0.593	0.593	0.000	0.000	0.000	0.000
94	A	297	ILE	0	0.025	0.005	12.604	0.343	0.343	0.000	0.000	0.000	0.000
95	A	298	SER	0	0.032	-0.003	14.746	0.430	0.430	0.000	0.000	0.000	0.000
96	A	299	ARG	1	0.948	1.010	18.451	14.689	14.689	0.000	0.000	0.000	0.000
97	A	300	SER	0	0.043	0.027	14.596	0.934	0.934	0.000	0.000	0.000	0.000
98	A	301	VAL	0	0.023	0.011	17.308	0.383	0.383	0.000	0.000	0.000	0.000
99	A	302	THR	0	-0.014	-0.016	18.901	0.835	0.835	0.000	0.000	0.000	0.000
100	A	303	VAL	0	0.021	0.004	21.061	0.544	0.544	0.000	0.000	0.000	0.000
101	A	304	THR	0	-0.032	-0.020	18.773	0.109	0.109	0.000	0.000	0.000	0.000
102	A	305	VAL	0	0.001	-0.009	21.192	0.373	0.373	0.000	0.000	0.000	0.000
103	A	306	ALA	0	0.047	0.027	23.939	0.471	0.471	0.000	0.000	0.000	0.000
104	A	307	TYR	0	-0.022	-0.038	23.764	0.267	0.267	0.000	0.000	0.000	0.000
105	A	308	LEU	0	-0.040	-0.024	21.952	0.319	0.319	0.000	0.000	0.000	0.000
106	A	309	MET	0	-0.030	0.015	26.042	0.155	0.155	0.000	0.000	0.000	0.000
107	A	310	GLN	0	0.044	0.024	29.262	0.321	0.321	0.000	0.000	0.000	0.000
108	A	311	LYS	1	0.778	0.872	27.566	11.148	11.148	0.000	0.000	0.000	0.000
109	A	312	LEU	0	-0.055	-0.040	26.138	0.107	0.107	0.000	0.000	0.000	0.000
110	A	313	ASN	0	-0.050	-0.012	30.399	0.348	0.348	0.000	0.000	0.000	0.000
111	A	314	LEU	0	-0.007	0.004	28.257	0.078	0.078	0.000	0.000	0.000	0.000
112	A	315	SER	0	0.029	-0.005	31.719	-0.096	-0.096	0.000	0.000	0.000	0.000
113	A	316	MET	0	0.009	-0.023	27.399	-0.498	-0.498	0.000	0.000	0.000	0.000
114	A	317	ASN	0	-0.051	-0.028	27.004	-0.780	-0.780	0.000	0.000	0.000	0.000
115	A	318	ASP	-1	-0.780	-0.862	27.015	-10.693	-10.693	0.000	0.000	0.000	0.000
116	A	319	ALA	0	0.002	0.007	25.848	-0.496	-0.496	0.000	0.000	0.000	0.000
117	A	320	TYR	0	0.007	-0.019	19.757	-1.064	-1.064	0.000	0.000	0.000	0.000
118	A	321	ASP	-1	-0.874	-0.935	22.284	-13.077	-13.077	0.000	0.000	0.000	0.000
119	A	322	ILE	0	0.008	-0.003	22.496	-0.604	-0.604	0.000	0.000	0.000	0.000
120	A	323	VAL	0	-0.036	-0.019	17.932	-0.835	-0.835	0.000	0.000	0.000	0.000
121	A	324	LYS	1	0.832	0.916	18.394	12.750	12.750	0.000	0.000	0.000	0.000
122	A	325	MET	0	-0.035	-0.009	19.032	-0.412	-0.412	0.000	0.000	0.000	0.000
123	A	326	LYS	1	0.817	0.926	17.072	16.907	16.907	0.000	0.000	0.000	0.000
124	A	327	LYS	1	0.823	0.907	9.838	27.270	27.270	0.000	0.000	0.000	0.000
125	A	328	SER	0	0.033	0.019	14.934	-0.188	-0.188	0.000	0.000	0.000	0.000
126	A	329	ASN	0	-0.066	-0.033	11.187	0.066	0.066	0.000	0.000	0.000	0.000
127	A	330	ILE	0	-0.027	-0.001	13.984	-0.503	-0.503	0.000	0.000	0.000	0.000
128	A	331	SER	0	0.012	0.001	14.969	0.783	0.783	0.000	0.000	0.000	0.000
129	A	332	PRO	0	-0.008	0.011	16.655	-0.458	-0.458	0.000	0.000	0.000	0.000
130	A	333	ASN	0	-0.020	-0.002	18.702	0.668	0.668	0.000	0.000	0.000	0.000
131	A	334	PHE	0	0.073	0.011	21.616	-0.078	-0.078	0.000	0.000	0.000	0.000
132	A	335	ASN	0	-0.024	-0.009	24.625	0.372	0.372	0.000	0.000	0.000	0.000
133	A	336	PHE	0	0.039	0.009	22.068	0.262	0.262	0.000	0.000	0.000	0.000
134	A	337	MET	0	0.018	0.019	25.561	0.276	0.276	0.000	0.000	0.000	0.000
135	A	338	GLY	0	0.028	0.016	28.203	0.236	0.236	0.000	0.000	0.000	0.000
136	A	339	GLN	0	0.040	0.019	28.815	0.192	0.192	0.000	0.000	0.000	0.000
137	A	340	LEU	0	-0.008	-0.002	24.847	0.085	0.085	0.000	0.000	0.000	0.000
138	A	341	LEU	0	0.038	0.005	29.574	0.184	0.184	0.000	0.000	0.000	0.000
139	A	342	ASP	-1	-0.954	-0.973	32.672	-8.445	-8.445	0.000	0.000	0.000	0.000
140	A	343	PHE	0	-0.014	-0.018	29.659	0.136	0.136	0.000	0.000	0.000	0.000
141	A	344	GLU	-1	-0.839	-0.929	32.547	-9.654	-9.654	0.000	0.000	0.000	0.000
142	A	345	ARG	1	0.868	0.943	34.255	8.472	8.472	0.000	0.000	0.000	0.000
143	A	346	THR	0	-0.103	-0.047	35.340	0.243	0.243	0.000	0.000	0.000	0.000
144	A	347	LEU	-1	-0.958	-0.954	32.267	-8.462	-8.462	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:204:ALA)