FMO DATABASE

FMODB ID: 871GY

Calculation Name: 1C25-A-Xray547

Preferred Name: Dual specificity phosphatase Cdc25A

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1C25

Chain ID: A

ChEMBL ID: CHEMBL3775

UniProt ID: P30304

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	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1741435.698721
FMO2-HF: Nuclear repulsion	1673640.317866
FMO2-HF: Total energy	-67795.380855
FMO2-MP2: Total energy	-67988.53528

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:335:MET)

Summations of interaction energy for fragment #1(A:335:MET)

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.
36.427	43.022	3.163	-3.663	-6.095	-0.037

Interaction energy analysis for fragmet #1(A:335:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.909

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	337	ILE	0	-0.002	0.002	2.425	-12.868	-9.101	2.150	-2.938	-2.979	-0.037
4	A	338	GLY	0	0.010	0.000	4.504	0.335	0.529	-0.001	-0.017	-0.176	0.000
5	A	339	ASP	-1	-0.758	-0.860	5.287	-26.248	-26.195	-0.001	-0.001	-0.051	0.000
10	A	344	TYR	0	-0.008	-0.011	2.519	4.846	6.457	0.686	-0.492	-1.805	0.000
22	A	356	LEU	0	-0.047	-0.015	4.559	-3.865	-3.787	-0.001	-0.005	-0.072	0.000
23	A	357	LYS	1	0.888	0.946	2.644	43.946	44.838	0.330	-0.210	-1.012	0.000
6	A	340	PHE	0	-0.080	-0.049	4.823	1.350	1.350	0.000	0.000	0.000	0.000
7	A	341	SER	0	-0.022	-0.023	7.445	0.162	0.162	0.000	0.000	0.000	0.000
8	A	342	LYS	1	0.946	0.976	8.268	26.057	26.057	0.000	0.000	0.000	0.000
9	A	343	GLY	0	0.032	0.025	4.882	-5.779	-5.779	0.000	0.000	0.000	0.000
11	A	345	LEU	0	-0.055	-0.010	6.322	0.240	0.240	0.000	0.000	0.000	0.000
12	A	346	PHE	0	-0.029	-0.012	9.074	2.029	2.029	0.000	0.000	0.000	0.000
13	A	347	HIS	0	0.020	0.013	8.081	-5.007	-5.007	0.000	0.000	0.000	0.000
14	A	348	THR	0	-0.027	-0.023	6.606	0.162	0.162	0.000	0.000	0.000	0.000
15	A	349	VAL	0	-0.030	-0.013	9.117	0.467	0.467	0.000	0.000	0.000	0.000
16	A	350	ALA	0	0.062	0.038	10.909	-0.922	-0.922	0.000	0.000	0.000	0.000
17	A	351	GLY	0	0.020	-0.004	11.774	1.820	1.820	0.000	0.000	0.000	0.000
18	A	352	LYS	1	0.862	0.925	13.132	14.794	14.794	0.000	0.000	0.000	0.000
19	A	353	HIS	0	-0.020	-0.007	10.555	-0.225	-0.225	0.000	0.000	0.000	0.000
20	A	354	GLN	0	0.041	0.011	8.854	-2.760	-2.760	0.000	0.000	0.000	0.000
21	A	355	ASP	-1	-0.795	-0.864	5.647	-27.676	-27.676	0.000	0.000	0.000	0.000
24	A	358	TYR	0	0.033	0.021	7.038	2.646	2.646	0.000	0.000	0.000	0.000
25	A	359	ILE	0	0.024	0.015	10.781	-1.744	-1.744	0.000	0.000	0.000	0.000
26	A	360	SER	0	-0.009	-0.026	13.010	0.801	0.801	0.000	0.000	0.000	0.000
27	A	361	PRO	0	0.041	0.016	16.274	-0.324	-0.324	0.000	0.000	0.000	0.000
28	A	362	GLU	-1	-0.711	-0.839	18.747	-15.516	-15.516	0.000	0.000	0.000	0.000
29	A	363	ILE	0	-0.044	-0.011	13.035	0.120	0.120	0.000	0.000	0.000	0.000
30	A	364	MET	0	0.040	0.036	16.457	-0.276	-0.276	0.000	0.000	0.000	0.000
31	A	365	ALA	0	0.030	0.015	18.050	0.373	0.373	0.000	0.000	0.000	0.000
32	A	366	SER	0	-0.102	-0.067	17.447	0.165	0.165	0.000	0.000	0.000	0.000
33	A	367	VAL	0	-0.031	-0.021	15.705	0.189	0.189	0.000	0.000	0.000	0.000
34	A	368	LEU	0	-0.004	-0.001	18.776	0.515	0.515	0.000	0.000	0.000	0.000
35	A	369	ASN	0	-0.043	-0.018	22.263	0.949	0.949	0.000	0.000	0.000	0.000
36	A	370	GLY	0	0.038	0.022	22.505	0.311	0.311	0.000	0.000	0.000	0.000
37	A	371	LYS	1	0.897	0.963	16.339	18.369	18.369	0.000	0.000	0.000	0.000
38	A	372	PHE	0	0.049	0.004	13.871	-0.663	-0.663	0.000	0.000	0.000	0.000
39	A	373	ALA	0	0.042	0.027	18.177	-0.427	-0.427	0.000	0.000	0.000	0.000
40	A	374	ASN	0	0.027	0.006	18.975	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	375	LEU	0	-0.015	-0.007	14.276	-0.043	-0.043	0.000	0.000	0.000	0.000
42	A	376	ILE	0	-0.019	-0.002	15.827	-0.878	-0.878	0.000	0.000	0.000	0.000
43	A	377	LYS	1	0.810	0.925	17.717	14.699	14.699	0.000	0.000	0.000	0.000
44	A	378	GLU	-1	-0.870	-0.940	18.126	-13.523	-13.523	0.000	0.000	0.000	0.000
45	A	379	PHE	0	-0.024	-0.031	15.522	-1.535	-1.535	0.000	0.000	0.000	0.000
46	A	380	VAL	0	0.050	0.037	17.072	0.747	0.747	0.000	0.000	0.000	0.000
47	A	381	ILE	0	0.005	-0.001	17.024	-1.040	-1.040	0.000	0.000	0.000	0.000
48	A	382	ILE	0	0.026	0.007	17.181	0.778	0.778	0.000	0.000	0.000	0.000
49	A	383	ASP	-1	-0.724	-0.843	18.861	-12.724	-12.724	0.000	0.000	0.000	0.000
50	A	384	CYS	0	-0.005	-0.011	18.932	0.329	0.329	0.000	0.000	0.000	0.000
51	A	385	ARG	1	0.761	0.860	21.634	11.699	11.699	0.000	0.000	0.000	0.000
52	A	386	TYR	0	0.050	0.016	24.871	0.086	0.086	0.000	0.000	0.000	0.000
53	A	387	PRO	0	0.078	0.035	28.367	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	388	TYR	0	0.019	0.010	30.198	0.038	0.038	0.000	0.000	0.000	0.000
55	A	389	GLU	-1	-0.779	-0.911	27.758	-10.617	-10.617	0.000	0.000	0.000	0.000
56	A	390	TYR	0	-0.073	-0.045	25.822	0.090	0.090	0.000	0.000	0.000	0.000
57	A	391	GLU	-1	-0.844	-0.900	28.808	-8.491	-8.491	0.000	0.000	0.000	0.000
58	A	392	GLY	0	-0.013	-0.011	32.374	0.147	0.147	0.000	0.000	0.000	0.000
59	A	393	GLY	0	-0.017	0.002	30.631	0.113	0.113	0.000	0.000	0.000	0.000
60	A	394	HIS	1	0.816	0.910	26.083	10.234	10.234	0.000	0.000	0.000	0.000
61	A	395	ILE	0	0.010	0.004	20.876	0.169	0.169	0.000	0.000	0.000	0.000
62	A	396	LYS	1	0.870	0.931	24.889	10.557	10.557	0.000	0.000	0.000	0.000
63	A	397	GLY	0	0.033	0.013	24.483	-0.488	-0.488	0.000	0.000	0.000	0.000
64	A	398	ALA	0	-0.057	-0.008	22.613	-0.315	-0.315	0.000	0.000	0.000	0.000
65	A	399	VAL	0	0.021	0.021	22.561	0.635	0.635	0.000	0.000	0.000	0.000
66	A	400	ASN	0	-0.077	-0.051	22.827	-0.073	-0.073	0.000	0.000	0.000	0.000
67	A	401	LEU	0	0.006	0.006	20.832	0.142	0.142	0.000	0.000	0.000	0.000
68	A	402	HIS	1	0.777	0.895	22.424	10.484	10.484	0.000	0.000	0.000	0.000
69	A	403	MET	0	-0.016	-0.021	24.001	-0.280	-0.280	0.000	0.000	0.000	0.000
70	A	404	GLU	-1	-0.771	-0.891	20.420	-13.198	-13.198	0.000	0.000	0.000	0.000
71	A	405	GLU	-1	-0.915	-0.952	21.909	-10.292	-10.292	0.000	0.000	0.000	0.000
72	A	406	GLU	-1	-0.770	-0.888	24.473	-10.858	-10.858	0.000	0.000	0.000	0.000
73	A	407	VAL	0	0.001	-0.011	17.961	-0.256	-0.256	0.000	0.000	0.000	0.000
74	A	408	GLU	-1	-0.783	-0.849	20.514	-13.229	-13.229	0.000	0.000	0.000	0.000
75	A	409	ASP	-1	-0.837	-0.931	21.809	-10.590	-10.590	0.000	0.000	0.000	0.000
76	A	410	PHE	0	-0.004	0.000	21.177	0.041	0.041	0.000	0.000	0.000	0.000
77	A	411	LEU	0	-0.042	-0.026	16.317	-0.183	-0.183	0.000	0.000	0.000	0.000
78	A	412	LEU	0	-0.017	0.002	16.143	-0.272	-0.272	0.000	0.000	0.000	0.000
79	A	413	LYS	1	0.849	0.930	20.036	10.907	10.907	0.000	0.000	0.000	0.000
80	A	414	LYS	1	0.860	0.959	22.552	12.815	12.815	0.000	0.000	0.000	0.000
81	A	415	PRO	0	0.017	0.020	19.062	-0.341	-0.341	0.000	0.000	0.000	0.000
82	A	416	ILE	0	-0.021	-0.017	18.910	0.508	0.508	0.000	0.000	0.000	0.000
83	A	417	VAL	0	0.040	0.028	19.691	-0.395	-0.395	0.000	0.000	0.000	0.000
84	A	418	PRO	0	-0.012	-0.010	21.767	-0.252	-0.252	0.000	0.000	0.000	0.000
85	A	419	THR	0	0.045	0.004	17.806	0.056	0.056	0.000	0.000	0.000	0.000
86	A	420	ASP	-1	-0.861	-0.936	19.202	-15.330	-15.330	0.000	0.000	0.000	0.000
87	A	421	GLY	0	0.027	0.021	17.849	0.248	0.248	0.000	0.000	0.000	0.000
88	A	422	LYS	1	0.780	0.894	16.638	13.766	13.766	0.000	0.000	0.000	0.000
89	A	423	ARG	1	0.754	0.850	8.896	30.796	30.796	0.000	0.000	0.000	0.000
90	A	424	VAL	0	0.079	0.043	14.148	0.958	0.958	0.000	0.000	0.000	0.000
91	A	425	ILE	0	-0.075	-0.036	11.846	-1.714	-1.714	0.000	0.000	0.000	0.000
92	A	426	VAL	0	0.027	0.027	12.242	1.417	1.417	0.000	0.000	0.000	0.000
93	A	427	VAL	0	-0.040	-0.025	12.289	-2.027	-2.027	0.000	0.000	0.000	0.000
94	A	428	PHE	0	0.067	0.030	12.076	1.300	1.300	0.000	0.000	0.000	0.000
95	A	429	HIS	0	-0.056	-0.029	15.320	-0.705	-0.705	0.000	0.000	0.000	0.000
96	A	430	CYS	0	-0.058	0.009	17.903	0.147	0.147	0.000	0.000	0.000	0.000
97	A	431	GLU	-1	-0.788	-0.897	20.776	-12.229	-12.229	0.000	0.000	0.000	0.000
98	A	432	PHE	0	0.000	-0.015	21.720	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	433	SER	0	-0.037	-0.051	16.188	-0.301	-0.301	0.000	0.000	0.000	0.000
100	A	434	SER	0	-0.018	0.001	16.484	-1.035	-1.035	0.000	0.000	0.000	0.000
101	A	435	GLU	-1	-0.744	-0.869	17.367	-14.622	-14.622	0.000	0.000	0.000	0.000
102	A	436	ARG	1	0.910	0.971	17.324	11.254	11.254	0.000	0.000	0.000	0.000
103	A	437	GLY	0	0.059	0.022	16.536	-0.157	-0.157	0.000	0.000	0.000	0.000
104	A	438	PRO	0	-0.032	-0.032	12.776	-0.661	-0.661	0.000	0.000	0.000	0.000
105	A	439	ARG	1	0.825	0.902	12.966	12.169	12.169	0.000	0.000	0.000	0.000
106	A	440	MET	0	0.050	0.037	15.084	-0.160	-0.160	0.000	0.000	0.000	0.000
107	A	441	CYS	0	-0.046	-0.011	9.828	-0.670	-0.670	0.000	0.000	0.000	0.000
108	A	442	ARG	1	0.830	0.868	9.983	19.769	19.769	0.000	0.000	0.000	0.000
109	A	443	TYR	0	-0.001	-0.001	11.742	-0.127	-0.127	0.000	0.000	0.000	0.000
110	A	444	VAL	0	0.023	0.007	12.978	0.198	0.198	0.000	0.000	0.000	0.000
111	A	445	ARG	1	0.805	0.900	5.243	28.325	28.325	0.000	0.000	0.000	0.000
112	A	446	GLU	-1	-0.884	-0.947	10.829	-17.268	-17.268	0.000	0.000	0.000	0.000
113	A	447	ARG	1	0.823	0.881	12.995	13.746	13.746	0.000	0.000	0.000	0.000
114	A	448	ASP	-1	-0.739	-0.874	12.509	-18.394	-18.394	0.000	0.000	0.000	0.000
115	A	449	ARG	1	0.813	0.907	6.687	24.811	24.811	0.000	0.000	0.000	0.000
116	A	450	LEU	0	-0.013	-0.008	13.023	0.513	0.513	0.000	0.000	0.000	0.000
117	A	451	GLY	0	-0.037	-0.001	16.587	0.685	0.685	0.000	0.000	0.000	0.000
118	A	452	ASN	0	-0.080	-0.053	14.655	0.378	0.378	0.000	0.000	0.000	0.000
119	A	453	GLU	-1	-0.839	-0.886	16.390	-14.208	-14.208	0.000	0.000	0.000	0.000
120	A	454	TYR	0	0.020	0.012	8.481	-1.283	-1.283	0.000	0.000	0.000	0.000
121	A	455	PRO	0	-0.036	-0.019	9.369	0.589	0.589	0.000	0.000	0.000	0.000
122	A	456	LYS	1	0.859	0.903	10.333	13.693	13.693	0.000	0.000	0.000	0.000
123	A	457	LEU	0	-0.048	-0.028	8.194	-0.783	-0.783	0.000	0.000	0.000	0.000
124	A	458	HIS	0	0.018	0.008	12.348	-0.174	-0.174	0.000	0.000	0.000	0.000
125	A	459	TYR	0	-0.049	-0.039	12.284	-0.077	-0.077	0.000	0.000	0.000	0.000
126	A	460	PRO	0	0.067	0.039	8.556	-1.595	-1.595	0.000	0.000	0.000	0.000
127	A	461	GLU	-1	-0.759	-0.849	6.820	-36.306	-36.306	0.000	0.000	0.000	0.000
128	A	462	LEU	0	0.010	0.006	7.442	2.518	2.518	0.000	0.000	0.000	0.000
129	A	463	TYR	0	-0.043	-0.051	7.593	-4.667	-4.667	0.000	0.000	0.000	0.000
130	A	464	VAL	0	0.006	0.008	9.971	2.063	2.063	0.000	0.000	0.000	0.000
131	A	465	LEU	0	0.011	0.014	12.425	-1.018	-1.018	0.000	0.000	0.000	0.000
132	A	466	LYS	1	0.890	0.923	14.826	20.170	20.170	0.000	0.000	0.000	0.000
133	A	467	GLY	0	0.061	0.020	16.358	0.388	0.388	0.000	0.000	0.000	0.000
134	A	468	GLY	0	-0.046	-0.012	18.814	0.757	0.757	0.000	0.000	0.000	0.000
135	A	469	TYR	0	-0.005	-0.019	20.394	-0.249	-0.249	0.000	0.000	0.000	0.000
136	A	470	LYS	1	0.983	1.011	23.473	11.194	11.194	0.000	0.000	0.000	0.000
137	A	471	GLU	-1	-0.905	-0.965	21.781	-12.833	-12.833	0.000	0.000	0.000	0.000
138	A	472	PHE	0	0.000	-0.011	21.215	-0.028	-0.028	0.000	0.000	0.000	0.000
139	A	473	PHE	0	0.028	0.015	23.559	0.270	0.270	0.000	0.000	0.000	0.000
140	A	474	MET	0	-0.055	-0.036	27.099	0.239	0.239	0.000	0.000	0.000	0.000
141	A	475	LYS	1	0.840	0.936	21.918	14.271	14.271	0.000	0.000	0.000	0.000
142	A	476	CYS	0	-0.043	-0.021	22.816	0.087	0.087	0.000	0.000	0.000	0.000
143	A	477	GLN	0	0.069	0.051	26.565	0.166	0.166	0.000	0.000	0.000	0.000
144	A	478	SER	0	0.022	0.010	29.579	0.055	0.055	0.000	0.000	0.000	0.000
145	A	479	TYR	0	0.000	0.002	24.630	0.029	0.029	0.000	0.000	0.000	0.000
146	A	480	CYS	0	-0.068	-0.016	26.851	-0.439	-0.439	0.000	0.000	0.000	0.000
147	A	481	GLU	-1	-0.877	-0.925	28.647	-10.008	-10.008	0.000	0.000	0.000	0.000
148	A	482	PRO	0	0.066	0.027	30.491	-0.125	-0.125	0.000	0.000	0.000	0.000
149	A	483	PRO	0	-0.010	0.009	31.777	-0.275	-0.275	0.000	0.000	0.000	0.000
150	A	484	SER	0	-0.018	-0.026	32.200	0.204	0.204	0.000	0.000	0.000	0.000
151	A	485	TYR	0	0.053	0.012	27.776	-0.474	-0.474	0.000	0.000	0.000	0.000
152	A	486	ARG	1	0.802	0.900	31.660	8.865	8.865	0.000	0.000	0.000	0.000
153	A	487	PRO	0	-0.012	-0.003	30.163	-0.136	-0.136	0.000	0.000	0.000	0.000
154	A	488	MET	0	-0.015	0.000	30.246	0.286	0.286	0.000	0.000	0.000	0.000
155	A	489	HIS	0	-0.003	-0.003	32.513	-0.102	-0.102	0.000	0.000	0.000	0.000
156	A	490	HIS	0	-0.063	-0.040	29.501	-0.193	-0.193	0.000	0.000	0.000	0.000
157	A	491	GLU	-1	-0.906	-0.950	34.795	-7.591	-7.591	0.000	0.000	0.000	0.000
158	A	492	ASP	-1	-0.943	-0.965	36.893	-7.516	-7.516	0.000	0.000	0.000	0.000
159	A	493	PHE	0	-0.011	0.004	39.409	0.026	0.026	0.000	0.000	0.000	0.000
160	A	494	LYS	1	0.833	0.890	36.115	7.745	7.745	0.000	0.000	0.000	0.000
161	A	495	GLU	-2	-1.879	-1.909	39.821	-13.901	-13.901	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:335:MET)