FMO DATABASE

FMODB ID: 5J3RZ

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	OptAll
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	-1744488.132553
FMO2-HF: Nuclear repulsion	1676692.26201
FMO2-HF: Total energy	-67795.870543
FMO2-MP2: Total energy	-67989.08275

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.
-15.008	-12.066	9.412	-4.224	-8.13	-0.011

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 : -0.009 / q_NPA : -0.010

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	-0.027	-0.010	2.587	-5.407	-2.324	1.633	-2.331	-2.385	-0.023
4	A	338	GLY	0	0.016	0.000	4.687	-0.472	-0.355	-0.001	-0.010	-0.107	0.000
5	A	339	ASP	-1	-0.773	-0.867	5.638	-1.337	-1.337	0.000	0.000	0.000	0.000
6	A	340	PHE	0	-0.077	-0.050	3.661	0.084	0.355	0.003	-0.032	-0.241	0.000
7	A	341	SER	0	-0.043	-0.038	7.344	0.074	0.074	0.000	0.000	0.000	0.000
8	A	342	LYS	1	0.944	0.974	8.495	1.340	1.340	0.000	0.000	0.000	0.000
9	A	343	GLY	0	0.053	0.038	4.890	-0.878	-0.878	0.000	0.000	0.000	0.000
10	A	344	TYR	0	-0.002	-0.005	2.315	-0.103	1.578	0.858	-0.505	-2.034	0.000
11	A	345	LEU	0	-0.060	-0.013	6.170	-0.118	-0.118	0.000	0.000	0.000	0.000
12	A	346	PHE	0	-0.039	-0.022	9.033	0.023	0.023	0.000	0.000	0.000	0.000
13	A	347	HIS	0	0.018	0.004	7.962	0.230	0.230	0.000	0.000	0.000	0.000
14	A	348	THR	0	-0.006	0.003	5.801	0.304	0.304	0.000	0.000	0.000	0.000
15	A	349	VAL	0	-0.039	-0.023	8.739	-0.106	-0.106	0.000	0.000	0.000	0.000
16	A	350	ALA	0	0.052	0.030	10.481	0.235	0.235	0.000	0.000	0.000	0.000
17	A	351	GLY	0	0.032	0.003	11.394	-0.277	-0.277	0.000	0.000	0.000	0.000
18	A	352	LYS	1	0.859	0.926	12.976	-0.606	-0.606	0.000	0.000	0.000	0.000
19	A	353	HIS	0	-0.017	-0.004	11.253	0.020	0.020	0.000	0.000	0.000	0.000
20	A	354	GLN	0	0.022	-0.004	8.622	0.368	0.368	0.000	0.000	0.000	0.000
21	A	355	ASP	-1	-0.786	-0.861	5.847	3.279	3.367	-0.001	-0.005	-0.081	0.000
22	A	356	LEU	0	-0.043	-0.007	5.342	1.117	1.294	-0.001	-0.014	-0.162	0.000
23	A	357	LYS	1	0.887	0.944	2.756	-11.986	-14.461	6.921	-1.327	-3.120	0.012
24	A	358	TYR	0	0.024	0.010	7.392	-0.692	-0.692	0.000	0.000	0.000	0.000
25	A	359	ILE	0	0.013	0.012	10.063	0.083	0.083	0.000	0.000	0.000	0.000
26	A	360	SER	0	-0.012	-0.031	12.629	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	361	PRO	0	0.046	0.019	16.127	-0.031	-0.031	0.000	0.000	0.000	0.000
28	A	362	GLU	-1	-0.700	-0.826	18.816	0.302	0.302	0.000	0.000	0.000	0.000
29	A	363	ILE	0	-0.036	-0.009	13.101	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	364	MET	0	0.036	0.040	16.469	-0.053	-0.053	0.000	0.000	0.000	0.000
31	A	365	ALA	0	0.053	0.020	18.008	-0.047	-0.047	0.000	0.000	0.000	0.000
32	A	366	SER	0	-0.086	-0.055	17.211	-0.053	-0.053	0.000	0.000	0.000	0.000
33	A	367	VAL	0	-0.029	-0.018	15.858	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	368	LEU	0	-0.002	-0.001	18.692	-0.031	-0.031	0.000	0.000	0.000	0.000
35	A	369	ASN	0	-0.066	-0.033	22.266	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	370	GLY	0	0.035	0.022	22.300	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	371	LYS	1	0.867	0.945	15.740	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	372	PHE	0	0.053	0.010	13.594	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	373	ALA	0	0.040	0.025	17.997	-0.036	-0.036	0.000	0.000	0.000	0.000
40	A	374	ASN	0	0.028	0.008	18.852	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	375	LEU	0	0.001	0.005	14.109	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	376	ILE	0	-0.009	0.005	15.480	-0.056	-0.056	0.000	0.000	0.000	0.000
43	A	377	LYS	1	0.815	0.919	17.523	0.264	0.264	0.000	0.000	0.000	0.000
44	A	378	GLU	-1	-0.859	-0.932	18.132	-0.054	-0.054	0.000	0.000	0.000	0.000
45	A	379	PHE	0	-0.033	-0.037	15.318	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	380	VAL	0	0.059	0.039	17.589	0.033	0.033	0.000	0.000	0.000	0.000
47	A	381	ILE	0	0.008	0.003	17.493	0.050	0.050	0.000	0.000	0.000	0.000
48	A	382	ILE	0	0.021	0.004	17.538	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	383	ASP	-1	-0.708	-0.834	19.739	0.270	0.270	0.000	0.000	0.000	0.000
50	A	384	CYS	0	-0.005	-0.010	19.845	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	385	ARG	1	0.736	0.856	22.574	-0.201	-0.201	0.000	0.000	0.000	0.000
52	A	386	TYR	0	0.053	0.018	25.877	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	387	PRO	0	0.085	0.036	29.351	0.001	0.001	0.000	0.000	0.000	0.000
54	A	388	TYR	0	0.010	0.008	31.125	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	389	GLU	-1	-0.790	-0.917	28.850	0.216	0.216	0.000	0.000	0.000	0.000
56	A	390	TYR	0	-0.076	-0.052	26.553	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	391	GLU	-1	-0.834	-0.893	29.804	0.080	0.080	0.000	0.000	0.000	0.000
58	A	392	GLY	0	-0.010	-0.008	33.333	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	393	GLY	0	-0.017	-0.002	31.324	0.000	0.000	0.000	0.000	0.000	0.000
60	A	394	HIS	1	0.817	0.909	26.750	-0.083	-0.083	0.000	0.000	0.000	0.000
61	A	395	ILE	0	0.012	0.003	21.346	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	396	LYS	1	0.858	0.920	25.390	-0.072	-0.072	0.000	0.000	0.000	0.000
63	A	397	GLY	0	0.008	0.008	25.002	0.000	0.000	0.000	0.000	0.000	0.000
64	A	398	ALA	0	-0.057	-0.008	23.341	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	399	VAL	0	0.015	0.018	23.175	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	400	ASN	0	-0.083	-0.055	23.562	0.013	0.013	0.000	0.000	0.000	0.000
67	A	401	LEU	0	-0.003	-0.003	21.389	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	402	HIS	1	0.750	0.880	23.166	-0.168	-0.168	0.000	0.000	0.000	0.000
69	A	403	MET	0	-0.016	-0.010	24.706	0.035	0.035	0.000	0.000	0.000	0.000
70	A	404	GLU	-1	-0.772	-0.889	19.895	0.254	0.254	0.000	0.000	0.000	0.000
71	A	405	GLU	-1	-0.925	-0.953	22.438	0.088	0.088	0.000	0.000	0.000	0.000
72	A	406	GLU	-1	-0.772	-0.891	24.952	0.111	0.111	0.000	0.000	0.000	0.000
73	A	407	VAL	0	0.012	-0.009	18.389	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	408	GLU	-1	-0.772	-0.835	20.855	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	409	ASP	-1	-0.809	-0.905	22.159	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	410	PHE	0	0.033	0.016	21.656	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	411	LEU	0	-0.046	-0.023	16.701	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	412	LEU	0	-0.013	0.000	16.479	-0.035	-0.035	0.000	0.000	0.000	0.000
79	A	413	LYS	1	0.811	0.908	20.314	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	414	LYS	1	0.802	0.925	22.741	0.029	0.029	0.000	0.000	0.000	0.000
81	A	415	PRO	0	0.023	0.024	19.366	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	416	ILE	0	-0.015	-0.012	19.100	0.005	0.005	0.000	0.000	0.000	0.000
83	A	417	VAL	0	0.037	0.022	19.921	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	418	PRO	0	-0.004	-0.007	22.068	-0.026	-0.026	0.000	0.000	0.000	0.000
85	A	419	THR	0	0.014	-0.015	17.948	0.009	0.009	0.000	0.000	0.000	0.000
86	A	420	ASP	-1	-0.838	-0.904	19.497	-0.343	-0.343	0.000	0.000	0.000	0.000
87	A	421	GLY	0	0.015	0.009	18.190	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	422	LYS	1	0.754	0.873	16.693	0.193	0.193	0.000	0.000	0.000	0.000
89	A	423	ARG	1	0.755	0.854	8.685	1.162	1.162	0.000	0.000	0.000	0.000
90	A	424	VAL	0	0.072	0.039	14.563	0.087	0.087	0.000	0.000	0.000	0.000
91	A	425	ILE	0	-0.072	-0.034	11.992	-0.060	-0.060	0.000	0.000	0.000	0.000
92	A	426	VAL	0	0.015	0.019	12.653	0.023	0.023	0.000	0.000	0.000	0.000
93	A	427	VAL	0	-0.035	-0.026	12.831	0.111	0.111	0.000	0.000	0.000	0.000
94	A	428	PHE	0	0.064	0.032	12.559	-0.050	-0.050	0.000	0.000	0.000	0.000
95	A	429	HIS	0	-0.053	-0.027	16.311	0.071	0.071	0.000	0.000	0.000	0.000
96	A	430	CYS	0	-0.052	0.018	19.025	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	431	GLU	-1	-0.729	-0.855	21.948	0.313	0.313	0.000	0.000	0.000	0.000
98	A	432	PHE	0	-0.003	-0.017	22.536	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	433	SER	0	-0.032	-0.052	17.130	0.024	0.024	0.000	0.000	0.000	0.000
100	A	434	SER	0	-0.016	-0.001	17.329	0.123	0.123	0.000	0.000	0.000	0.000
101	A	435	GLU	-1	-0.745	-0.875	18.249	0.600	0.600	0.000	0.000	0.000	0.000
102	A	436	ARG	1	0.883	0.943	18.479	-0.254	-0.254	0.000	0.000	0.000	0.000
103	A	437	GLY	0	0.048	0.011	17.836	-0.016	-0.016	0.000	0.000	0.000	0.000
104	A	438	PRO	0	-0.031	-0.030	14.052	0.012	0.012	0.000	0.000	0.000	0.000
105	A	439	ARG	1	0.825	0.897	13.866	-0.266	-0.266	0.000	0.000	0.000	0.000
106	A	440	MET	0	0.033	0.031	15.666	-0.028	-0.028	0.000	0.000	0.000	0.000
107	A	441	CYS	0	-0.034	-0.011	10.787	-0.056	-0.056	0.000	0.000	0.000	0.000
108	A	442	ARG	1	0.836	0.873	10.408	-1.232	-1.232	0.000	0.000	0.000	0.000
109	A	443	TYR	0	-0.003	-0.009	12.474	-0.078	-0.078	0.000	0.000	0.000	0.000
110	A	444	VAL	0	0.022	0.007	13.254	-0.063	-0.063	0.000	0.000	0.000	0.000
111	A	445	ARG	1	0.815	0.905	5.605	0.433	0.433	0.000	0.000	0.000	0.000
112	A	446	GLU	-1	-0.884	-0.947	11.494	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	447	ARG	1	0.824	0.876	13.443	-0.046	-0.046	0.000	0.000	0.000	0.000
114	A	448	ASP	-1	-0.748	-0.878	12.759	-0.361	-0.361	0.000	0.000	0.000	0.000
115	A	449	ARG	1	0.815	0.909	7.338	0.902	0.902	0.000	0.000	0.000	0.000
116	A	450	LEU	0	-0.025	-0.014	13.421	-0.019	-0.019	0.000	0.000	0.000	0.000
117	A	451	GLY	0	-0.024	0.007	16.692	0.017	0.017	0.000	0.000	0.000	0.000
118	A	452	ASN	0	-0.085	-0.058	14.842	-0.040	-0.040	0.000	0.000	0.000	0.000
119	A	453	GLU	-1	-0.842	-0.885	16.603	-0.350	-0.350	0.000	0.000	0.000	0.000
120	A	454	TYR	0	0.030	0.014	8.267	-0.100	-0.100	0.000	0.000	0.000	0.000
121	A	455	PRO	0	-0.027	-0.012	9.481	0.043	0.043	0.000	0.000	0.000	0.000
122	A	456	LYS	1	0.859	0.905	10.503	0.309	0.309	0.000	0.000	0.000	0.000
123	A	457	LEU	0	-0.049	-0.028	8.422	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	458	HIS	0	-0.003	0.003	12.629	-0.051	-0.051	0.000	0.000	0.000	0.000
125	A	459	TYR	0	-0.049	-0.040	12.717	0.019	0.019	0.000	0.000	0.000	0.000
126	A	460	PRO	0	0.067	0.038	8.927	0.055	0.055	0.000	0.000	0.000	0.000
127	A	461	GLU	-1	-0.746	-0.836	7.232	-0.950	-0.950	0.000	0.000	0.000	0.000
128	A	462	LEU	0	0.003	0.002	7.867	0.117	0.117	0.000	0.000	0.000	0.000
129	A	463	TYR	0	-0.036	-0.045	8.073	0.483	0.483	0.000	0.000	0.000	0.000
130	A	464	VAL	0	0.003	0.003	10.812	-0.186	-0.186	0.000	0.000	0.000	0.000
131	A	465	LEU	0	0.019	0.013	13.296	0.095	0.095	0.000	0.000	0.000	0.000
132	A	466	LYS	1	0.890	0.930	14.465	-0.871	-0.871	0.000	0.000	0.000	0.000
133	A	467	GLY	0	0.056	0.018	16.331	-0.060	-0.060	0.000	0.000	0.000	0.000
134	A	468	GLY	0	-0.043	-0.011	19.265	-0.047	-0.047	0.000	0.000	0.000	0.000
135	A	469	TYR	0	0.002	-0.017	21.052	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	470	LYS	1	0.980	1.008	24.032	-0.290	-0.290	0.000	0.000	0.000	0.000
137	A	471	GLU	-1	-0.836	-0.917	21.535	0.333	0.333	0.000	0.000	0.000	0.000
138	A	472	PHE	0	0.017	0.000	20.986	-0.017	-0.017	0.000	0.000	0.000	0.000
139	A	473	PHE	0	0.016	0.011	23.470	-0.026	-0.026	0.000	0.000	0.000	0.000
140	A	474	MET	0	-0.055	-0.040	26.940	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	475	LYS	1	0.786	0.894	21.774	-0.335	-0.335	0.000	0.000	0.000	0.000
142	A	476	CYS	0	-0.056	-0.028	24.032	-0.011	-0.011	0.000	0.000	0.000	0.000
143	A	477	GLN	0	0.063	0.051	26.500	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	478	SER	0	0.015	0.006	29.651	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	479	TYR	0	-0.011	-0.002	24.961	-0.017	-0.017	0.000	0.000	0.000	0.000
146	A	480	CYS	0	-0.052	-0.010	26.866	0.009	0.009	0.000	0.000	0.000	0.000
147	A	481	GLU	-1	-0.827	-0.889	28.821	0.050	0.050	0.000	0.000	0.000	0.000
148	A	482	PRO	0	0.051	0.022	31.092	0.004	0.004	0.000	0.000	0.000	0.000
149	A	483	PRO	0	0.007	0.010	31.901	0.011	0.011	0.000	0.000	0.000	0.000
150	A	484	SER	0	-0.017	-0.024	32.425	0.001	0.001	0.000	0.000	0.000	0.000
151	A	485	TYR	0	0.048	0.010	28.436	0.017	0.017	0.000	0.000	0.000	0.000
152	A	486	ARG	1	0.795	0.900	32.210	-0.111	-0.111	0.000	0.000	0.000	0.000
153	A	487	PRO	0	-0.011	-0.004	31.007	0.002	0.002	0.000	0.000	0.000	0.000
154	A	488	MET	0	-0.010	0.000	31.455	-0.015	-0.015	0.000	0.000	0.000	0.000
155	A	489	HIS	0	0.002	0.000	33.579	0.010	0.010	0.000	0.000	0.000	0.000
156	A	490	HIS	0	-0.053	-0.035	30.403	0.010	0.010	0.000	0.000	0.000	0.000
157	A	491	GLU	-1	-0.907	-0.951	35.822	0.131	0.131	0.000	0.000	0.000	0.000
158	A	492	ASP	-1	-0.907	-0.946	37.687	0.136	0.136	0.000	0.000	0.000	0.000
159	A	493	PHE	0	-0.034	-0.012	40.208	0.001	0.001	0.000	0.000	0.000	0.000
160	A	494	LYS	1	0.912	0.941	37.315	-0.159	-0.159	0.000	0.000	0.000	0.000
161	A	495	GLU	-1	-0.987	-0.971	40.757	0.121	0.121	0.000	0.000	0.000	0.000

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