FMO DATABASE

FMODB ID: R9858

Calculation Name: 5UQ2-B-Xray372

Preferred Name: Cyclin-dependent kinase 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5UQ2

Chain ID: B

ChEMBL ID: CHEMBL301

UniProt ID: P24941

Base Structure: X-ray

Registration Date: 2023-06-21

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

DOI:

Apendix: None

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1389406.697843
FMO2-HF: Nuclear repulsion	1331548.683279
FMO2-HF: Total energy	-57858.014564
FMO2-MP2: Total energy	-58023.651916

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(B:69:GLN)

Summations of interaction energy for fragment #1(B:69:GLN)

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.
-6.662	-1.476	9.143	-4.136	-10.19	-0.008

Interaction energy analysis for fragmet #1(B:69:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.024

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	B	71	MET	0	0.017	0.008	2.109	-2.401	0.386	1.954	-1.370	-3.371	-0.007
4	B	72	THR	0	0.027	0.039	2.166	1.618	2.741	3.901	-1.543	-3.481	0.000
5	B	73	ALA	0	0.031	0.016	3.899	-0.131	0.087	0.006	-0.062	-0.162	0.000
6	B	74	PHE	0	-0.021	-0.016	5.751	-0.087	-0.087	0.000	0.000	0.000	0.000
7	B	75	PHE	0	0.031	-0.018	3.689	-1.024	-0.320	0.011	-0.238	-0.477	0.001
8	B	76	LYS	1	0.847	0.960	7.817	-1.110	-1.110	0.000	0.000	0.000	0.000
9	B	77	LEU	0	-0.049	-0.033	10.267	-0.226	-0.226	0.000	0.000	0.000	0.000
10	B	78	PHE	0	-0.022	-0.009	10.470	-0.189	-0.189	0.000	0.000	0.000	0.000
11	B	79	ASP	-1	-0.885	-0.933	10.682	2.119	2.119	0.000	0.000	0.000	0.000
12	B	80	ASP	-1	-0.951	-0.988	13.702	0.444	0.444	0.000	0.000	0.000	0.000
13	B	81	ASP	-1	-0.868	-0.928	16.839	0.487	0.487	0.000	0.000	0.000	0.000
14	B	82	LEU	0	0.001	-0.014	20.010	-0.034	-0.034	0.000	0.000	0.000	0.000
15	B	83	ILE	0	-0.083	-0.028	15.795	-0.052	-0.052	0.000	0.000	0.000	0.000
16	B	84	GLN	0	0.009	-0.011	14.661	-0.106	-0.106	0.000	0.000	0.000	0.000
17	B	85	ASP	-1	-0.876	-0.932	18.700	0.353	0.353	0.000	0.000	0.000	0.000
18	B	86	PHE	0	-0.049	-0.031	19.663	-0.046	-0.046	0.000	0.000	0.000	0.000
19	B	87	LEU	0	-0.041	-0.033	16.205	-0.033	-0.033	0.000	0.000	0.000	0.000
20	B	88	TRP	0	-0.046	-0.018	17.268	-0.040	-0.040	0.000	0.000	0.000	0.000
21	B	89	MET	0	-0.048	-0.007	22.738	-0.042	-0.042	0.000	0.000	0.000	0.000
22	B	90	ASP	-1	-0.717	-0.858	22.418	0.165	0.165	0.000	0.000	0.000	0.000
23	B	91	CYS	0	-0.019	-0.013	22.979	0.007	0.007	0.000	0.000	0.000	0.000
24	B	92	CYS	0	-0.072	-0.037	24.286	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	93	CYS	0	-0.031	0.006	21.286	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	94	LYS	1	0.961	0.968	22.996	-0.124	-0.124	0.000	0.000	0.000	0.000
27	B	95	ILE	0	0.000	0.013	22.922	-0.015	-0.015	0.000	0.000	0.000	0.000
28	B	96	ALA	0	-0.028	-0.016	18.780	0.006	0.006	0.000	0.000	0.000	0.000
29	B	97	ASP	-1	-0.775	-0.894	18.776	0.097	0.097	0.000	0.000	0.000	0.000
30	B	98	LYS	1	0.953	0.988	15.035	0.092	0.092	0.000	0.000	0.000	0.000
31	B	99	TYR	0	-0.043	-0.040	14.802	-0.015	-0.015	0.000	0.000	0.000	0.000
32	B	100	LEU	0	0.017	0.017	16.167	-0.026	-0.026	0.000	0.000	0.000	0.000
33	B	101	LEU	0	-0.032	-0.030	13.429	0.008	0.008	0.000	0.000	0.000	0.000
34	B	102	ALA	0	0.006	0.013	11.775	0.046	0.046	0.000	0.000	0.000	0.000
35	B	103	MET	0	-0.015	-0.017	12.428	-0.078	-0.078	0.000	0.000	0.000	0.000
36	B	104	THR	0	-0.006	0.009	13.089	-0.026	-0.026	0.000	0.000	0.000	0.000
37	B	105	PHE	0	0.031	0.020	5.823	-0.062	-0.062	0.000	0.000	0.000	0.000
38	B	106	VAL	0	-0.031	-0.023	11.146	-0.093	-0.093	0.000	0.000	0.000	0.000
39	B	107	TYR	0	-0.059	-0.080	12.553	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	108	PHE	0	0.016	0.016	10.793	0.025	0.025	0.000	0.000	0.000	0.000
41	B	109	LYS	1	0.982	0.997	6.571	0.377	0.377	0.000	0.000	0.000	0.000
42	B	110	ARG	1	0.773	0.872	11.287	0.205	0.205	0.000	0.000	0.000	0.000
43	B	111	ALA	0	0.024	0.035	14.622	0.014	0.014	0.000	0.000	0.000	0.000
44	B	112	LYS	1	0.910	0.944	13.136	0.075	0.075	0.000	0.000	0.000	0.000
45	B	113	PHE	0	-0.001	0.009	13.433	0.028	0.028	0.000	0.000	0.000	0.000
46	B	114	THR	0	0.039	0.021	12.486	-0.022	-0.022	0.000	0.000	0.000	0.000
47	B	115	ILE	0	0.044	0.016	9.796	0.016	0.016	0.000	0.000	0.000	0.000
48	B	116	SER	0	-0.004	-0.016	12.548	0.078	0.078	0.000	0.000	0.000	0.000
49	B	117	GLU	-1	-0.807	-0.855	15.497	0.107	0.107	0.000	0.000	0.000	0.000
50	B	118	HIS	0	-0.033	-0.008	10.120	-0.026	-0.026	0.000	0.000	0.000	0.000
51	B	119	THR	0	0.014	-0.002	13.991	0.086	0.086	0.000	0.000	0.000	0.000
52	B	120	ARG	1	1.052	1.002	16.389	-0.376	-0.376	0.000	0.000	0.000	0.000
53	B	121	ILE	0	-0.012	0.003	18.283	-0.011	-0.011	0.000	0.000	0.000	0.000
54	B	122	ASN	0	0.048	0.006	17.135	-0.022	-0.022	0.000	0.000	0.000	0.000
55	B	123	PHE	0	0.042	0.029	14.212	-0.027	-0.027	0.000	0.000	0.000	0.000
56	B	124	PHE	0	0.049	0.012	16.661	-0.025	-0.025	0.000	0.000	0.000	0.000
57	B	125	ILE	0	-0.040	-0.011	20.155	-0.025	-0.025	0.000	0.000	0.000	0.000
58	B	126	ALA	0	0.020	0.009	16.868	-0.029	-0.029	0.000	0.000	0.000	0.000
59	B	127	LEU	0	0.003	0.009	17.634	-0.029	-0.029	0.000	0.000	0.000	0.000
60	B	128	TYR	0	0.033	0.009	19.279	-0.028	-0.028	0.000	0.000	0.000	0.000
61	B	129	LEU	0	-0.034	-0.011	20.582	-0.016	-0.016	0.000	0.000	0.000	0.000
62	B	130	ALA	0	-0.005	0.002	18.939	-0.017	-0.017	0.000	0.000	0.000	0.000
63	B	131	ASN	0	-0.010	-0.029	21.058	-0.020	-0.020	0.000	0.000	0.000	0.000
64	B	132	THR	0	-0.045	-0.038	23.901	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	133	VAL	0	-0.101	-0.039	22.956	-0.007	-0.007	0.000	0.000	0.000	0.000
66	B	134	GLU	-1	-0.938	-0.976	22.135	-0.082	-0.082	0.000	0.000	0.000	0.000
67	B	135	GLU	-1	-0.906	-0.934	24.612	0.032	0.032	0.000	0.000	0.000	0.000
68	B	136	ASP	-1	-0.876	-0.930	27.129	-0.004	-0.004	0.000	0.000	0.000	0.000
69	B	137	GLU	-1	-0.871	-0.869	30.349	0.071	0.071	0.000	0.000	0.000	0.000
70	B	138	GLU	-1	-0.990	-1.001	30.064	0.042	0.042	0.000	0.000	0.000	0.000
71	B	139	GLU	-1	-0.910	-0.964	30.999	0.068	0.068	0.000	0.000	0.000	0.000
72	B	140	THR	0	-0.049	-0.098	27.828	0.010	0.010	0.000	0.000	0.000	0.000
73	B	141	LYS	1	0.874	0.942	26.030	-0.045	-0.045	0.000	0.000	0.000	0.000
74	B	142	TYR	0	-0.047	-0.022	27.085	0.012	0.012	0.000	0.000	0.000	0.000
75	B	143	GLU	-1	-0.907	-0.956	27.535	0.156	0.156	0.000	0.000	0.000	0.000
76	B	144	ILE	0	-0.039	-0.014	22.399	0.020	0.020	0.000	0.000	0.000	0.000
77	B	145	PHE	0	-0.039	-0.025	25.688	0.012	0.012	0.000	0.000	0.000	0.000
78	B	146	PRO	0	-0.009	-0.019	28.320	0.004	0.004	0.000	0.000	0.000	0.000
79	B	147	TRP	0	0.028	0.034	23.881	0.010	0.010	0.000	0.000	0.000	0.000
80	B	148	ALA	0	-0.019	0.013	23.744	0.019	0.019	0.000	0.000	0.000	0.000
81	B	149	LEU	0	-0.048	-0.023	24.954	-0.007	-0.007	0.000	0.000	0.000	0.000
82	B	150	GLY	0	-0.031	-0.013	28.498	-0.006	-0.006	0.000	0.000	0.000	0.000
83	B	151	LYS	1	1.002	0.974	30.257	-0.208	-0.208	0.000	0.000	0.000	0.000
84	B	152	ASN	0	0.008	-0.005	33.531	-0.013	-0.013	0.000	0.000	0.000	0.000
85	B	153	TRP	0	0.097	0.054	31.174	-0.009	-0.009	0.000	0.000	0.000	0.000
86	B	154	ARG	1	0.986	1.000	32.756	-0.105	-0.105	0.000	0.000	0.000	0.000
87	B	155	LYS	1	0.896	0.943	35.651	-0.100	-0.100	0.000	0.000	0.000	0.000
88	B	156	LEU	0	-0.025	-0.012	31.510	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	157	PHE	0	0.016	0.015	30.542	0.003	0.003	0.000	0.000	0.000	0.000
90	B	158	PRO	0	0.030	0.015	30.957	-0.002	-0.002	0.000	0.000	0.000	0.000
91	B	159	ASN	0	-0.026	-0.011	29.883	0.004	0.004	0.000	0.000	0.000	0.000
92	B	160	PHE	0	0.041	0.029	23.648	-0.002	-0.002	0.000	0.000	0.000	0.000
93	B	161	LEU	0	0.045	0.010	26.770	0.000	0.000	0.000	0.000	0.000	0.000
94	B	162	LYS	1	0.962	1.003	28.523	-0.068	-0.068	0.000	0.000	0.000	0.000
95	B	163	LEU	0	-0.040	-0.030	24.642	-0.007	-0.007	0.000	0.000	0.000	0.000
96	B	164	ARG	1	0.858	0.929	23.846	-0.056	-0.056	0.000	0.000	0.000	0.000
97	B	165	ASP	-1	-0.830	-0.901	24.597	0.035	0.035	0.000	0.000	0.000	0.000
98	B	166	GLN	0	-0.043	-0.024	25.656	-0.013	-0.013	0.000	0.000	0.000	0.000
99	B	167	LEU	0	-0.023	0.005	18.366	-0.006	-0.006	0.000	0.000	0.000	0.000
100	B	168	TRP	0	-0.006	-0.010	21.528	-0.013	-0.013	0.000	0.000	0.000	0.000
101	B	169	ASP	-1	-0.913	-0.965	23.583	-0.007	-0.007	0.000	0.000	0.000	0.000
102	B	170	ARG	1	0.795	0.868	17.960	-0.056	-0.056	0.000	0.000	0.000	0.000
103	B	171	ILE	0	-0.108	-0.041	17.855	-0.011	-0.011	0.000	0.000	0.000	0.000
104	B	172	ASP	-1	-0.906	-0.950	20.040	-0.062	-0.062	0.000	0.000	0.000	0.000
105	B	173	TYR	0	-0.010	-0.017	23.128	-0.011	-0.011	0.000	0.000	0.000	0.000
106	B	174	ARG	1	0.896	0.966	16.626	0.151	0.151	0.000	0.000	0.000	0.000
107	B	175	ALA	0	0.030	0.011	19.701	-0.017	-0.017	0.000	0.000	0.000	0.000
108	B	176	ILE	0	0.064	0.075	20.758	-0.003	-0.003	0.000	0.000	0.000	0.000
109	B	177	VAL	0	-0.014	-0.010	15.570	-0.032	-0.032	0.000	0.000	0.000	0.000
110	B	178	SER	0	0.021	0.017	18.214	-0.005	-0.005	0.000	0.000	0.000	0.000
111	B	179	ARG	1	1.013	0.985	17.168	0.209	0.209	0.000	0.000	0.000	0.000
112	B	180	ARG	1	0.958	0.983	15.843	0.346	0.346	0.000	0.000	0.000	0.000
113	B	181	CYS	0	0.002	0.003	12.238	-0.065	-0.065	0.000	0.000	0.000	0.000
114	B	182	CYS	0	0.013	0.012	11.999	-0.071	-0.071	0.000	0.000	0.000	0.000
115	B	183	GLU	-1	-0.772	-0.898	12.205	-0.395	-0.395	0.000	0.000	0.000	0.000
116	B	184	GLU	-1	-0.995	-0.992	10.146	-0.856	-0.856	0.000	0.000	0.000	0.000
117	B	185	VAL	0	-0.059	-0.034	7.395	-0.423	-0.423	0.000	0.000	0.000	0.000
118	B	186	MET	0	-0.007	0.004	7.564	0.025	0.025	0.000	0.000	0.000	0.000
119	B	187	ALA	0	-0.011	0.006	8.896	0.062	0.062	0.000	0.000	0.000	0.000
120	B	188	ILE	0	-0.073	-0.029	2.190	-1.557	-1.903	3.252	-0.725	-2.180	-0.002
121	B	189	ALA	0	-0.002	-0.015	3.194	-3.087	-2.406	0.020	-0.197	-0.503	0.000
122	B	190	PRO	0	0.026	0.012	5.001	1.075	1.094	-0.001	-0.001	-0.016	0.000
123	B	191	THR	0	-0.041	-0.018	7.216	0.256	0.256	0.000	0.000	0.000	0.000
124	B	192	HIS	0	0.034	0.028	6.684	-0.356	-0.356	0.000	0.000	0.000	0.000
125	B	193	TYR	0	0.083	0.030	9.231	-0.390	-0.390	0.000	0.000	0.000	0.000
126	B	194	ILE	0	-0.026	-0.007	9.843	-0.194	-0.194	0.000	0.000	0.000	0.000
127	B	195	TRP	0	-0.016	-0.018	7.779	-0.208	-0.208	0.000	0.000	0.000	0.000
128	B	196	GLN	0	-0.034	-0.024	12.219	-0.040	-0.040	0.000	0.000	0.000	0.000
129	B	197	ARG	1	0.800	0.906	16.038	-0.360	-0.360	0.000	0.000	0.000	0.000
130	B	198	GLU	-1	-0.973	-0.980	18.290	-0.068	-0.068	0.000	0.000	0.000	0.000
131	B	199	ARG	1	0.898	0.941	20.435	-0.040	-0.040	0.000	0.000	0.000	0.000
132	B	200	SER	0	-0.033	-0.034	23.827	-0.027	-0.027	0.000	0.000	0.000	0.000
133	B	201	VAL	0	-0.017	0.007	26.985	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:69:GLN)