FMO DATABASE

FMODB ID: KG3K3

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	OptH
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	-1741265.995561
FMO2-HF: Nuclear repulsion	1673471.541358
FMO2-HF: Total energy	-67794.454203
FMO2-MP2: Total energy	-67987.703549

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.
-5.633	0.598	3.444	-3.431	-6.247	-0.01

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 : -0.017 / q_NPA : -0.016

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	-0.041	-0.021	2.803	-1.720	1.399	1.425	-2.144	-2.401	-0.019
4	A	338	GLY	0	0.012	-0.005	4.984	0.468	0.646	-0.001	-0.007	-0.170	0.000
5	A	339	ASP	-1	-0.770	-0.893	5.942	-0.199	-0.199	0.000	0.000	0.000	0.000
6	A	340	PHE	0	-0.102	-0.059	4.395	-0.268	0.035	0.007	-0.047	-0.264	0.000
7	A	341	SER	0	-0.006	0.003	7.546	-0.179	-0.179	0.000	0.000	0.000	0.000
8	A	342	LYS	1	0.946	0.974	8.346	0.590	0.590	0.000	0.000	0.000	0.000
9	A	343	GLY	0	0.059	0.049	5.187	-0.396	-0.396	0.000	0.000	0.000	0.000
10	A	344	TYR	0	-0.004	-0.007	2.515	-0.682	0.904	0.525	-0.474	-1.637	-0.003
11	A	345	LEU	0	-0.030	-0.004	6.522	-0.073	-0.073	0.000	0.000	0.000	0.000
12	A	346	PHE	0	-0.035	-0.008	9.625	0.060	0.060	0.000	0.000	0.000	0.000
13	A	347	HIS	0	0.024	0.018	8.206	-0.088	-0.088	0.000	0.000	0.000	0.000
14	A	348	THR	0	-0.013	-0.025	6.836	0.248	0.248	0.000	0.000	0.000	0.000
15	A	349	VAL	0	-0.048	-0.012	9.457	0.002	0.002	0.000	0.000	0.000	0.000
16	A	350	ALA	0	0.058	0.033	11.005	0.083	0.083	0.000	0.000	0.000	0.000
17	A	351	GLY	0	0.032	-0.011	11.462	-0.112	-0.112	0.000	0.000	0.000	0.000
18	A	352	LYS	1	0.879	0.940	12.247	-0.139	-0.139	0.000	0.000	0.000	0.000
19	A	353	HIS	0	-0.012	0.005	10.409	0.039	0.039	0.000	0.000	0.000	0.000
20	A	354	GLN	0	0.064	0.014	8.571	0.046	0.046	0.000	0.000	0.000	0.000
21	A	355	ASP	-1	-0.793	-0.879	5.278	0.773	0.773	0.000	0.000	0.000	0.000
22	A	356	LEU	0	-0.059	-0.021	4.826	-0.305	-0.248	-0.001	-0.003	-0.054	0.000
23	A	357	LYS	1	0.921	0.977	2.128	-3.890	-2.902	1.489	-0.756	-1.721	0.012
24	A	358	TYR	0	0.023	0.015	7.297	-0.197	-0.197	0.000	0.000	0.000	0.000
25	A	359	ILE	0	0.030	0.019	11.059	0.009	0.009	0.000	0.000	0.000	0.000
26	A	360	SER	0	0.030	0.013	13.484	0.013	0.013	0.000	0.000	0.000	0.000
27	A	361	PRO	0	0.065	0.014	16.660	-0.025	-0.025	0.000	0.000	0.000	0.000
28	A	362	GLU	-1	-0.782	-0.889	18.606	-0.056	-0.056	0.000	0.000	0.000	0.000
29	A	363	ILE	0	-0.032	-0.006	13.365	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	364	MET	0	0.028	0.024	16.619	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	365	ALA	0	0.032	0.010	18.455	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	366	SER	0	-0.084	-0.052	17.717	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	367	VAL	0	-0.015	-0.012	16.348	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	368	LEU	0	0.002	0.004	19.162	0.001	0.001	0.000	0.000	0.000	0.000
35	A	369	ASN	0	-0.041	-0.009	22.434	0.015	0.015	0.000	0.000	0.000	0.000
36	A	370	GLY	0	0.021	0.014	22.411	0.003	0.003	0.000	0.000	0.000	0.000
37	A	371	LYS	1	0.889	0.961	16.279	0.273	0.273	0.000	0.000	0.000	0.000
38	A	372	PHE	0	0.050	0.000	14.115	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	373	ALA	0	0.036	0.025	18.349	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	374	ASN	0	0.008	-0.008	19.508	0.005	0.005	0.000	0.000	0.000	0.000
41	A	375	LEU	0	-0.033	-0.023	14.749	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	376	ILE	0	-0.044	-0.010	16.072	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	377	LYS	1	0.902	0.973	18.014	0.201	0.201	0.000	0.000	0.000	0.000
44	A	378	GLU	-1	-0.925	-0.974	18.235	-0.122	-0.122	0.000	0.000	0.000	0.000
45	A	379	PHE	0	-0.023	-0.017	15.102	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	380	VAL	0	0.035	0.028	16.787	0.023	0.023	0.000	0.000	0.000	0.000
47	A	381	ILE	0	0.011	0.003	16.750	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	382	ILE	0	0.021	0.003	17.386	0.008	0.008	0.000	0.000	0.000	0.000
49	A	383	ASP	-1	-0.751	-0.858	18.965	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	384	CYS	0	-0.025	-0.020	19.182	0.004	0.004	0.000	0.000	0.000	0.000
51	A	385	ARG	1	0.792	0.886	21.997	0.021	0.021	0.000	0.000	0.000	0.000
52	A	386	TYR	0	0.001	0.005	25.248	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	387	PRO	0	0.094	0.038	28.682	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	388	TYR	0	0.022	0.011	30.357	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	389	GLU	-1	-0.767	-0.907	28.037	0.009	0.009	0.000	0.000	0.000	0.000
56	A	390	TYR	0	-0.086	-0.067	25.826	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	391	GLU	-1	-0.898	-0.943	28.822	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	392	GLY	0	-0.028	-0.018	32.230	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	393	GLY	0	-0.009	-0.003	30.784	0.000	0.000	0.000	0.000	0.000	0.000
60	A	394	HIS	1	0.877	0.946	25.941	0.048	0.048	0.000	0.000	0.000	0.000
61	A	395	ILE	0	-0.003	0.007	21.001	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	396	LYS	1	0.920	0.962	24.940	0.066	0.066	0.000	0.000	0.000	0.000
63	A	397	GLY	0	0.022	0.011	24.555	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	398	ALA	0	-0.061	-0.014	22.420	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	399	VAL	0	0.038	0.031	22.223	0.007	0.007	0.000	0.000	0.000	0.000
66	A	400	ASN	0	-0.059	-0.047	22.744	0.003	0.003	0.000	0.000	0.000	0.000
67	A	401	LEU	0	0.008	0.012	20.310	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	402	HIS	1	0.819	0.903	22.158	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	403	MET	0	-0.030	-0.014	23.734	0.011	0.011	0.000	0.000	0.000	0.000
70	A	404	GLU	-1	-0.837	-0.945	20.342	0.032	0.032	0.000	0.000	0.000	0.000
71	A	405	GLU	-1	-0.927	-0.969	21.950	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	406	GLU	-1	-0.792	-0.896	24.544	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	407	VAL	0	-0.028	-0.025	17.999	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	408	GLU	-1	-0.831	-0.893	20.669	-0.025	-0.025	0.000	0.000	0.000	0.000
75	A	409	ASP	-1	-0.891	-0.966	21.707	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	410	PHE	0	-0.033	-0.010	21.043	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	411	LEU	0	-0.020	-0.016	16.238	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	412	LEU	0	-0.007	0.000	15.848	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	413	LYS	1	0.895	0.972	19.767	0.024	0.024	0.000	0.000	0.000	0.000
80	A	414	LYS	1	0.892	0.976	22.868	0.089	0.089	0.000	0.000	0.000	0.000
81	A	415	PRO	0	0.008	0.008	19.527	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	416	ILE	0	-0.019	-0.022	19.551	0.005	0.005	0.000	0.000	0.000	0.000
83	A	417	VAL	0	0.027	0.022	20.406	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	418	PRO	0	-0.029	-0.021	22.345	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	419	THR	0	0.030	0.003	18.435	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	420	ASP	-1	-0.866	-0.958	19.415	-0.252	-0.252	0.000	0.000	0.000	0.000
87	A	421	GLY	0	-0.001	0.026	18.324	0.000	0.000	0.000	0.000	0.000	0.000
88	A	422	LYS	1	0.848	0.944	17.539	0.187	0.187	0.000	0.000	0.000	0.000
89	A	423	ARG	1	0.771	0.855	8.971	1.022	1.022	0.000	0.000	0.000	0.000
90	A	424	VAL	0	0.061	0.045	14.075	0.036	0.036	0.000	0.000	0.000	0.000
91	A	425	ILE	0	-0.051	-0.024	11.736	-0.050	-0.050	0.000	0.000	0.000	0.000
92	A	426	VAL	0	0.035	0.032	12.196	0.041	0.041	0.000	0.000	0.000	0.000
93	A	427	VAL	0	-0.035	-0.020	12.228	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	428	PHE	0	0.057	0.024	12.094	0.015	0.015	0.000	0.000	0.000	0.000
95	A	429	HIS	0	-0.045	-0.029	15.534	0.013	0.013	0.000	0.000	0.000	0.000
96	A	430	CYS	0	-0.019	0.033	18.175	0.000	0.000	0.000	0.000	0.000	0.000
97	A	431	GLU	-1	-0.825	-0.925	21.246	0.024	0.024	0.000	0.000	0.000	0.000
98	A	432	PHE	0	0.008	-0.007	21.965	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	433	SER	0	-0.042	-0.043	16.672	0.010	0.010	0.000	0.000	0.000	0.000
100	A	434	SER	0	-0.028	-0.006	16.911	0.029	0.029	0.000	0.000	0.000	0.000
101	A	435	GLU	-1	-0.782	-0.910	17.160	0.141	0.141	0.000	0.000	0.000	0.000
102	A	436	ARG	1	0.943	0.987	17.596	-0.031	-0.031	0.000	0.000	0.000	0.000
103	A	437	GLY	0	0.048	0.012	16.963	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	438	PRO	0	-0.007	-0.021	12.996	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	439	ARG	1	0.913	0.970	13.130	-0.065	-0.065	0.000	0.000	0.000	0.000
106	A	440	MET	0	0.069	0.039	15.049	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	441	CYS	0	-0.060	-0.007	10.290	-0.037	-0.037	0.000	0.000	0.000	0.000
108	A	442	ARG	1	0.834	0.888	10.040	-0.284	-0.284	0.000	0.000	0.000	0.000
109	A	443	TYR	0	-0.017	-0.008	11.522	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	444	VAL	0	0.024	-0.003	13.186	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	445	ARG	1	0.865	0.951	5.199	0.595	0.595	0.000	0.000	0.000	0.000
112	A	446	GLU	-1	-0.891	-0.956	10.832	0.105	0.105	0.000	0.000	0.000	0.000
113	A	447	ARG	1	0.887	0.931	12.826	0.015	0.015	0.000	0.000	0.000	0.000
114	A	448	ASP	-1	-0.777	-0.893	12.156	-0.152	-0.152	0.000	0.000	0.000	0.000
115	A	449	ARG	1	0.802	0.897	6.174	0.051	0.051	0.000	0.000	0.000	0.000
116	A	450	LEU	0	-0.016	-0.003	12.874	0.012	0.012	0.000	0.000	0.000	0.000
117	A	451	GLY	0	-0.047	-0.001	16.421	0.008	0.008	0.000	0.000	0.000	0.000
118	A	452	ASN	0	-0.073	-0.043	14.729	-0.017	-0.017	0.000	0.000	0.000	0.000
119	A	453	GLU	-1	-0.935	-0.942	16.158	0.052	0.052	0.000	0.000	0.000	0.000
120	A	454	TYR	0	-0.012	-0.011	8.042	-0.062	-0.062	0.000	0.000	0.000	0.000
121	A	455	PRO	0	-0.036	-0.014	9.280	0.005	0.005	0.000	0.000	0.000	0.000
122	A	456	LYS	1	0.980	0.971	10.521	-0.025	-0.025	0.000	0.000	0.000	0.000
123	A	457	LEU	0	-0.041	-0.014	8.146	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	458	HIS	0	0.046	0.022	12.568	-0.035	-0.035	0.000	0.000	0.000	0.000
125	A	459	TYR	0	-0.076	-0.051	12.410	-0.025	-0.025	0.000	0.000	0.000	0.000
126	A	460	PRO	0	0.032	0.016	8.891	-0.034	-0.034	0.000	0.000	0.000	0.000
127	A	461	GLU	-1	-0.763	-0.838	7.050	-1.017	-1.017	0.000	0.000	0.000	0.000
128	A	462	LEU	0	-0.012	-0.007	7.301	0.099	0.099	0.000	0.000	0.000	0.000
129	A	463	TYR	0	-0.048	-0.078	7.747	-0.030	-0.030	0.000	0.000	0.000	0.000
130	A	464	VAL	0	0.024	0.023	10.161	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	465	LEU	0	-0.004	-0.002	12.759	0.021	0.021	0.000	0.000	0.000	0.000
132	A	466	LYS	1	0.900	0.931	14.797	-0.152	-0.152	0.000	0.000	0.000	0.000
133	A	467	GLY	0	0.036	0.007	16.489	-0.018	-0.018	0.000	0.000	0.000	0.000
134	A	468	GLY	0	-0.042	-0.020	19.045	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	469	TYR	0	0.007	-0.014	20.662	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	470	LYS	1	0.976	1.012	23.691	-0.031	-0.031	0.000	0.000	0.000	0.000
137	A	471	GLU	-1	-0.922	-0.972	22.303	0.014	0.014	0.000	0.000	0.000	0.000
138	A	472	PHE	0	0.007	-0.008	21.569	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	473	PHE	0	0.020	0.016	23.899	-0.007	-0.007	0.000	0.000	0.000	0.000
140	A	474	MET	0	-0.041	-0.027	27.497	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	475	LYS	1	0.858	0.942	22.078	0.011	0.011	0.000	0.000	0.000	0.000
142	A	476	CYS	0	-0.060	-0.031	23.423	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	477	GLN	0	0.093	0.062	27.087	-0.005	-0.005	0.000	0.000	0.000	0.000
144	A	478	SER	0	0.002	-0.002	30.125	0.000	0.000	0.000	0.000	0.000	0.000
145	A	479	TYR	0	-0.032	-0.032	25.057	-0.006	-0.006	0.000	0.000	0.000	0.000
146	A	480	CYS	0	-0.082	-0.021	26.954	-0.003	-0.003	0.000	0.000	0.000	0.000
147	A	481	GLU	-1	-0.944	-0.961	28.610	-0.057	-0.057	0.000	0.000	0.000	0.000
148	A	482	PRO	0	0.045	0.016	30.506	0.001	0.001	0.000	0.000	0.000	0.000
149	A	483	PRO	0	0.013	0.015	31.907	0.001	0.001	0.000	0.000	0.000	0.000
150	A	484	SER	0	-0.032	-0.035	32.358	0.004	0.004	0.000	0.000	0.000	0.000
151	A	485	TYR	0	0.053	0.023	28.340	0.000	0.000	0.000	0.000	0.000	0.000
152	A	486	ARG	1	0.852	0.939	31.675	0.012	0.012	0.000	0.000	0.000	0.000
153	A	487	PRO	0	-0.022	-0.007	30.898	0.000	0.000	0.000	0.000	0.000	0.000
154	A	488	MET	0	-0.010	0.006	30.663	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	489	HIS	0	-0.014	-0.007	32.988	0.003	0.003	0.000	0.000	0.000	0.000
156	A	490	HIS	0	-0.046	-0.034	30.006	0.004	0.004	0.000	0.000	0.000	0.000
157	A	491	GLU	-1	-0.907	-0.956	35.086	0.023	0.023	0.000	0.000	0.000	0.000
158	A	492	ASP	-1	-0.942	-0.956	37.115	0.025	0.025	0.000	0.000	0.000	0.000
159	A	493	PHE	0	-0.007	0.009	38.992	0.002	0.002	0.000	0.000	0.000	0.000
160	A	494	LYS	1	0.947	0.943	35.872	-0.045	-0.045	0.000	0.000	0.000	0.000
161	A	495	GLU	-1	-1.011	-0.979	39.764	0.028	0.028	0.000	0.000	0.000	0.000

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