FMO DATABASE

FMODB ID: 4J3QN

Calculation Name: 1C25-A-Xray372

Preferred Name: Dual specificity phosphatase Cdc25A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1C25

Chain ID: A

ChEMBL ID: CHEMBL3775

UniProt ID: P30304

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1742535.268434
FMO2-HF: Nuclear repulsion	1674739.867636
FMO2-HF: Total energy	-67795.400799
FMO2-MP2: Total energy	-67988.670635

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: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.
-27.242	-26.448	16.58	-8.294	-9.08	0.052

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 : 0 / q_Mulliken : 0.039 / q_NPA : 0.039

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	-0.025	-0.016	2.524	-5.595	-2.464	2.316	-2.625	-2.821	-0.027
4	A	338	GLY	0	0.028	0.004	4.596	-0.570	-0.449	-0.001	-0.009	-0.112	0.000
5	A	339	ASP	-1	-0.771	-0.862	5.545	-1.502	-1.502	0.000	0.000	0.000	0.000
6	A	340	PHE	0	-0.101	-0.062	3.348	-0.151	0.227	0.015	-0.060	-0.333	0.000
7	A	341	SER	0	-0.017	-0.023	6.736	0.179	0.179	0.000	0.000	0.000	0.000
8	A	342	LYS	1	0.947	0.975	8.206	1.535	1.535	0.000	0.000	0.000	0.000
9	A	343	GLY	0	0.048	0.041	5.246	-1.049	-1.040	-0.001	-0.020	0.012	0.000
10	A	344	TYR	0	-0.007	-0.010	2.414	0.225	1.699	0.481	-0.359	-1.596	0.000
11	A	345	LEU	0	-0.044	-0.009	6.645	-0.093	-0.093	0.000	0.000	0.000	0.000
12	A	346	PHE	0	-0.037	-0.018	9.722	0.042	0.042	0.000	0.000	0.000	0.000
13	A	347	HIS	0	0.028	0.020	8.293	0.065	0.065	0.000	0.000	0.000	0.000
14	A	348	THR	0	0.003	-0.011	6.933	0.307	0.307	0.000	0.000	0.000	0.000
15	A	349	VAL	0	-0.068	-0.029	9.531	-0.072	-0.072	0.000	0.000	0.000	0.000
16	A	350	ALA	0	0.070	0.039	10.610	0.274	0.274	0.000	0.000	0.000	0.000
17	A	351	GLY	0	0.043	0.000	11.585	-0.297	-0.297	0.000	0.000	0.000	0.000
18	A	352	LYS	1	0.867	0.922	12.875	-0.601	-0.601	0.000	0.000	0.000	0.000
19	A	353	HIS	0	-0.028	-0.005	11.609	0.034	0.034	0.000	0.000	0.000	0.000
20	A	354	GLN	0	0.026	0.000	9.183	0.359	0.359	0.000	0.000	0.000	0.000
21	A	355	ASP	-1	-0.793	-0.857	6.354	3.308	3.308	0.000	0.000	0.000	0.000
22	A	356	LEU	0	-0.057	-0.024	6.115	0.384	0.384	0.000	0.000	0.000	0.000
23	A	357	LYS	1	0.854	0.920	2.289	-22.959	-27.278	13.770	-5.221	-4.230	0.079
24	A	358	TYR	0	0.032	0.015	7.815	-0.677	-0.677	0.000	0.000	0.000	0.000
25	A	359	ILE	0	0.020	0.015	10.725	0.014	0.014	0.000	0.000	0.000	0.000
26	A	360	SER	0	-0.020	-0.035	13.180	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	361	PRO	0	0.051	0.017	16.538	-0.034	-0.034	0.000	0.000	0.000	0.000
28	A	362	GLU	-1	-0.711	-0.842	18.762	0.247	0.247	0.000	0.000	0.000	0.000
29	A	363	ILE	0	-0.039	-0.008	13.378	-0.064	-0.064	0.000	0.000	0.000	0.000
30	A	364	MET	0	0.032	0.030	16.703	-0.054	-0.054	0.000	0.000	0.000	0.000
31	A	365	ALA	0	0.039	0.017	18.563	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	366	SER	0	-0.088	-0.058	17.792	-0.051	-0.051	0.000	0.000	0.000	0.000
33	A	367	VAL	0	-0.018	-0.015	16.414	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	368	LEU	0	0.001	0.008	19.266	-0.026	-0.026	0.000	0.000	0.000	0.000
35	A	369	ASN	0	-0.055	-0.026	22.516	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	370	GLY	0	0.023	0.016	22.493	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	371	LYS	1	0.886	0.960	16.379	0.125	0.125	0.000	0.000	0.000	0.000
38	A	372	PHE	0	0.047	-0.003	14.198	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	373	ALA	0	0.037	0.028	18.435	-0.038	-0.038	0.000	0.000	0.000	0.000
40	A	374	ASN	0	0.034	0.006	19.654	0.000	0.000	0.000	0.000	0.000	0.000
41	A	375	LEU	0	-0.016	-0.015	14.703	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	376	ILE	0	-0.044	-0.014	15.869	-0.064	-0.064	0.000	0.000	0.000	0.000
43	A	377	LYS	1	0.805	0.910	18.099	0.313	0.313	0.000	0.000	0.000	0.000
44	A	378	GLU	-1	-0.893	-0.953	18.393	-0.090	-0.090	0.000	0.000	0.000	0.000
45	A	379	PHE	0	-0.018	-0.020	15.804	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	380	VAL	0	0.024	0.016	17.228	0.023	0.023	0.000	0.000	0.000	0.000
47	A	381	ILE	0	0.013	0.009	17.310	0.041	0.041	0.000	0.000	0.000	0.000
48	A	382	ILE	0	0.030	0.003	18.040	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	383	ASP	-1	-0.755	-0.869	19.697	0.260	0.260	0.000	0.000	0.000	0.000
50	A	384	CYS	0	-0.020	-0.020	19.973	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	385	ARG	1	0.789	0.886	22.740	-0.186	-0.186	0.000	0.000	0.000	0.000
52	A	386	TYR	0	0.024	0.014	26.042	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	387	PRO	0	0.102	0.041	29.444	0.001	0.001	0.000	0.000	0.000	0.000
54	A	388	TYR	0	0.026	0.019	31.076	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	389	GLU	-1	-0.798	-0.911	28.972	0.209	0.209	0.000	0.000	0.000	0.000
56	A	390	TYR	0	-0.074	-0.054	26.408	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	391	GLU	-1	-0.855	-0.904	29.601	0.071	0.071	0.000	0.000	0.000	0.000
58	A	392	GLY	0	-0.019	-0.012	32.981	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	393	GLY	0	-0.011	-0.005	31.601	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	394	HIS	1	0.797	0.893	26.780	-0.064	-0.064	0.000	0.000	0.000	0.000
61	A	395	ILE	0	-0.008	0.005	21.751	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	396	LYS	1	0.888	0.938	25.710	-0.045	-0.045	0.000	0.000	0.000	0.000
63	A	397	GLY	0	0.026	0.014	25.206	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	398	ALA	0	-0.059	-0.012	23.061	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	399	VAL	0	0.035	0.031	22.877	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	400	ASN	0	-0.068	-0.052	23.382	0.016	0.016	0.000	0.000	0.000	0.000
67	A	401	LEU	0	-0.004	0.003	21.003	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	402	HIS	1	0.781	0.888	22.785	-0.167	-0.167	0.000	0.000	0.000	0.000
69	A	403	MET	0	-0.015	-0.017	24.448	0.037	0.037	0.000	0.000	0.000	0.000
70	A	404	GLU	-1	-0.769	-0.886	20.451	0.269	0.269	0.000	0.000	0.000	0.000
71	A	405	GLU	-1	-0.925	-0.959	22.664	0.092	0.092	0.000	0.000	0.000	0.000
72	A	406	GLU	-1	-0.793	-0.896	25.034	0.104	0.104	0.000	0.000	0.000	0.000
73	A	407	VAL	0	-0.009	-0.018	18.497	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	408	GLU	-1	-0.810	-0.860	21.057	0.002	0.002	0.000	0.000	0.000	0.000
75	A	409	ASP	-1	-0.838	-0.936	22.252	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	410	PHE	0	0.031	0.012	21.403	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	411	LEU	0	-0.032	-0.009	16.464	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	412	LEU	0	-0.014	-0.003	16.377	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	413	LYS	1	0.852	0.949	20.031	-0.026	-0.026	0.000	0.000	0.000	0.000
80	A	414	LYS	1	0.829	0.937	22.881	0.044	0.044	0.000	0.000	0.000	0.000
81	A	415	PRO	0	-0.002	0.007	19.370	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	416	ILE	0	-0.015	-0.022	19.402	0.005	0.005	0.000	0.000	0.000	0.000
83	A	417	VAL	0	0.032	0.023	20.248	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	418	PRO	0	-0.013	-0.013	22.130	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	419	THR	0	0.043	0.007	18.117	0.001	0.001	0.000	0.000	0.000	0.000
86	A	420	ASP	-1	-0.836	-0.912	19.194	-0.388	-0.388	0.000	0.000	0.000	0.000
87	A	421	GLY	0	0.007	0.022	18.055	0.002	0.002	0.000	0.000	0.000	0.000
88	A	422	LYS	1	0.808	0.920	17.372	0.263	0.263	0.000	0.000	0.000	0.000
89	A	423	ARG	1	0.777	0.853	9.011	1.313	1.313	0.000	0.000	0.000	0.000
90	A	424	VAL	0	0.056	0.042	14.088	0.083	0.083	0.000	0.000	0.000	0.000
91	A	425	ILE	0	-0.057	-0.027	12.116	-0.063	-0.063	0.000	0.000	0.000	0.000
92	A	426	VAL	0	0.032	0.030	12.639	0.030	0.030	0.000	0.000	0.000	0.000
93	A	427	VAL	0	-0.035	-0.020	12.834	0.099	0.099	0.000	0.000	0.000	0.000
94	A	428	PHE	0	0.049	0.021	12.814	-0.046	-0.046	0.000	0.000	0.000	0.000
95	A	429	HIS	0	-0.043	-0.025	16.360	0.080	0.080	0.000	0.000	0.000	0.000
96	A	430	CYS	0	-0.043	0.006	19.033	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	431	GLU	-1	-0.776	-0.891	22.112	0.317	0.317	0.000	0.000	0.000	0.000
98	A	432	PHE	0	-0.002	-0.013	22.999	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	433	SER	0	-0.047	-0.049	17.753	0.027	0.027	0.000	0.000	0.000	0.000
100	A	434	SER	0	-0.030	-0.007	18.127	0.121	0.121	0.000	0.000	0.000	0.000
101	A	435	GLU	-1	-0.752	-0.876	18.503	0.646	0.646	0.000	0.000	0.000	0.000
102	A	436	ARG	1	0.941	0.990	18.689	-0.254	-0.254	0.000	0.000	0.000	0.000
103	A	437	GLY	0	0.033	0.009	17.848	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	438	PRO	0	-0.003	-0.023	14.094	0.007	0.007	0.000	0.000	0.000	0.000
105	A	439	ARG	1	0.832	0.913	14.039	-0.301	-0.301	0.000	0.000	0.000	0.000
106	A	440	MET	0	0.047	0.030	15.920	-0.026	-0.026	0.000	0.000	0.000	0.000
107	A	441	CYS	0	-0.055	-0.008	11.089	-0.048	-0.048	0.000	0.000	0.000	0.000
108	A	442	ARG	1	0.834	0.864	10.595	-1.383	-1.383	0.000	0.000	0.000	0.000
109	A	443	TYR	0	-0.016	-0.010	12.362	-0.076	-0.076	0.000	0.000	0.000	0.000
110	A	444	VAL	0	0.026	-0.002	13.315	-0.066	-0.066	0.000	0.000	0.000	0.000
111	A	445	ARG	1	0.827	0.919	5.550	0.407	0.407	0.000	0.000	0.000	0.000
112	A	446	GLU	-1	-0.895	-0.946	11.536	0.070	0.070	0.000	0.000	0.000	0.000
113	A	447	ARG	1	0.834	0.883	13.388	-0.067	-0.067	0.000	0.000	0.000	0.000
114	A	448	ASP	-1	-0.750	-0.881	12.711	-0.386	-0.386	0.000	0.000	0.000	0.000
115	A	449	ARG	1	0.815	0.906	6.630	0.968	0.968	0.000	0.000	0.000	0.000
116	A	450	LEU	0	-0.010	-0.003	13.194	-0.026	-0.026	0.000	0.000	0.000	0.000
117	A	451	GLY	0	-0.048	-0.002	16.726	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	452	ASN	0	-0.073	-0.046	14.948	-0.037	-0.037	0.000	0.000	0.000	0.000
119	A	453	GLU	-1	-0.851	-0.889	16.234	-0.351	-0.351	0.000	0.000	0.000	0.000
120	A	454	TYR	0	0.010	-0.002	7.647	-0.111	-0.111	0.000	0.000	0.000	0.000
121	A	455	PRO	0	-0.043	-0.016	8.932	0.028	0.028	0.000	0.000	0.000	0.000
122	A	456	LYS	1	0.879	0.906	10.362	0.301	0.301	0.000	0.000	0.000	0.000
123	A	457	LEU	0	-0.040	-0.013	8.302	0.002	0.002	0.000	0.000	0.000	0.000
124	A	458	HIS	0	0.029	0.014	12.419	-0.066	-0.066	0.000	0.000	0.000	0.000
125	A	459	TYR	0	-0.062	-0.046	12.436	0.002	0.002	0.000	0.000	0.000	0.000
126	A	460	PRO	0	0.057	0.037	8.599	0.057	0.057	0.000	0.000	0.000	0.000
127	A	461	GLU	-1	-0.760	-0.849	7.021	-1.211	-1.211	0.000	0.000	0.000	0.000
128	A	462	LEU	0	0.003	0.002	7.787	0.097	0.097	0.000	0.000	0.000	0.000
129	A	463	TYR	0	-0.043	-0.054	8.480	0.409	0.409	0.000	0.000	0.000	0.000
130	A	464	VAL	0	0.027	0.023	10.975	-0.180	-0.180	0.000	0.000	0.000	0.000
131	A	465	LEU	0	0.006	0.004	13.664	0.081	0.081	0.000	0.000	0.000	0.000
132	A	466	LYS	1	0.895	0.932	14.790	-0.857	-0.857	0.000	0.000	0.000	0.000
133	A	467	GLY	0	0.040	0.009	16.728	-0.067	-0.067	0.000	0.000	0.000	0.000
134	A	468	GLY	0	-0.041	-0.017	19.604	-0.045	-0.045	0.000	0.000	0.000	0.000
135	A	469	TYR	0	0.014	-0.012	21.400	-0.016	-0.016	0.000	0.000	0.000	0.000
136	A	470	LYS	1	0.991	1.013	24.476	-0.281	-0.281	0.000	0.000	0.000	0.000
137	A	471	GLU	-1	-0.885	-0.955	22.233	0.294	0.294	0.000	0.000	0.000	0.000
138	A	472	PHE	0	0.012	-0.004	21.560	-0.021	-0.021	0.000	0.000	0.000	0.000
139	A	473	PHE	0	0.017	0.016	24.036	-0.026	-0.026	0.000	0.000	0.000	0.000
140	A	474	MET	0	-0.049	-0.031	27.759	-0.012	-0.012	0.000	0.000	0.000	0.000
141	A	475	LYS	1	0.818	0.931	22.010	-0.304	-0.304	0.000	0.000	0.000	0.000
142	A	476	CYS	0	-0.064	-0.037	24.661	-0.016	-0.016	0.000	0.000	0.000	0.000
143	A	477	GLN	0	0.079	0.059	27.181	-0.016	-0.016	0.000	0.000	0.000	0.000
144	A	478	SER	0	0.012	0.003	30.098	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	479	TYR	0	0.001	0.001	24.969	-0.016	-0.016	0.000	0.000	0.000	0.000
146	A	480	CYS	0	-0.061	-0.012	27.567	0.005	0.005	0.000	0.000	0.000	0.000
147	A	481	GLU	-1	-0.877	-0.913	29.344	0.030	0.030	0.000	0.000	0.000	0.000
148	A	482	PRO	0	0.058	0.022	31.257	0.004	0.004	0.000	0.000	0.000	0.000
149	A	483	PRO	0	0.012	0.015	32.588	0.010	0.010	0.000	0.000	0.000	0.000
150	A	484	SER	0	-0.031	-0.035	33.197	0.003	0.003	0.000	0.000	0.000	0.000
151	A	485	TYR	0	0.060	0.025	29.200	0.014	0.014	0.000	0.000	0.000	0.000
152	A	486	ARG	1	0.801	0.891	32.551	-0.104	-0.104	0.000	0.000	0.000	0.000
153	A	487	PRO	0	-0.009	-0.002	31.786	0.005	0.005	0.000	0.000	0.000	0.000
154	A	488	MET	0	0.001	0.009	31.652	-0.016	-0.016	0.000	0.000	0.000	0.000
155	A	489	HIS	0	-0.013	-0.007	33.933	0.010	0.010	0.000	0.000	0.000	0.000
156	A	490	HIS	0	-0.045	-0.033	30.947	0.013	0.013	0.000	0.000	0.000	0.000
157	A	491	GLU	-1	-0.903	-0.955	36.371	0.133	0.133	0.000	0.000	0.000	0.000
158	A	492	ASP	-1	-0.929	-0.953	38.407	0.140	0.140	0.000	0.000	0.000	0.000
159	A	493	PHE	0	-0.031	0.000	40.763	0.000	0.000	0.000	0.000	0.000	0.000
160	A	494	LYS	1	0.920	0.926	37.573	-0.169	-0.169	0.000	0.000	0.000	0.000
161	A	495	GLU	-1	-0.979	-0.960	41.025	0.127	0.127	0.000	0.000	0.000	0.000

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