FMO DATABASE

FMODB ID: K9G33

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1394392.688872
FMO2-HF: Nuclear repulsion	1336533.270646
FMO2-HF: Total energy	-57859.418226
FMO2-MP2: Total energy	-58025.035384

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.
-15.828	-5.399	6.565	-5.935	-11.055	0.02

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 : 0.072 / q_NPA : 0.031

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	0.028	0.032	2.549	-4.894	-0.390	1.495	-2.349	-3.650	0.016
4	B	72	THR	0	-0.013	-0.007	2.200	-0.404	1.530	1.114	-1.030	-2.017	0.001
5	B	73	ALA	0	0.004	0.004	4.619	-0.669	-0.540	-0.001	-0.025	-0.102	0.000
6	B	74	PHE	0	-0.024	-0.009	7.248	-0.297	-0.297	0.000	0.000	0.000	0.000
7	B	75	PHE	0	0.043	-0.002	2.715	-2.549	-1.075	0.449	-0.609	-1.313	0.009
8	B	76	LYS	1	0.903	0.973	7.579	-1.325	-1.325	0.000	0.000	0.000	0.000
9	B	77	LEU	0	-0.063	-0.029	10.258	-0.312	-0.312	0.000	0.000	0.000	0.000
10	B	78	PHE	0	-0.016	-0.009	10.191	-0.206	-0.206	0.000	0.000	0.000	0.000
11	B	79	ASP	-1	-0.864	-0.919	10.513	1.607	1.607	0.000	0.000	0.000	0.000
12	B	80	ASP	-1	-0.838	-0.907	13.683	0.339	0.339	0.000	0.000	0.000	0.000
13	B	81	ASP	-1	-0.908	-0.952	16.761	0.369	0.369	0.000	0.000	0.000	0.000
14	B	82	LEU	0	0.012	-0.002	19.940	-0.013	-0.013	0.000	0.000	0.000	0.000
15	B	83	ILE	0	-0.072	-0.025	15.542	-0.033	-0.033	0.000	0.000	0.000	0.000
16	B	84	GLN	0	-0.028	-0.028	14.461	-0.081	-0.081	0.000	0.000	0.000	0.000
17	B	85	ASP	-1	-0.862	-0.939	18.216	0.279	0.279	0.000	0.000	0.000	0.000
18	B	86	PHE	0	-0.017	-0.009	19.246	-0.028	-0.028	0.000	0.000	0.000	0.000
19	B	87	LEU	0	-0.032	-0.028	15.930	-0.010	-0.010	0.000	0.000	0.000	0.000
20	B	88	TRP	0	-0.054	-0.013	16.983	-0.013	-0.013	0.000	0.000	0.000	0.000
21	B	89	MET	0	-0.020	0.008	22.336	-0.041	-0.041	0.000	0.000	0.000	0.000
22	B	90	ASP	-1	-0.733	-0.869	21.770	0.287	0.287	0.000	0.000	0.000	0.000
23	B	91	CYS	0	-0.017	-0.019	22.461	0.018	0.018	0.000	0.000	0.000	0.000
24	B	92	CYS	0	-0.063	-0.034	24.127	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	93	CYS	0	-0.021	-0.002	20.702	0.002	0.002	0.000	0.000	0.000	0.000
26	B	94	LYS	1	0.865	0.917	22.208	-0.168	-0.168	0.000	0.000	0.000	0.000
27	B	95	ILE	0	-0.005	0.004	22.585	-0.011	-0.011	0.000	0.000	0.000	0.000
28	B	96	ALA	0	-0.014	-0.006	17.975	0.026	0.026	0.000	0.000	0.000	0.000
29	B	97	ASP	-1	-0.806	-0.892	17.951	0.353	0.353	0.000	0.000	0.000	0.000
30	B	98	LYS	1	0.846	0.926	14.149	-0.139	-0.139	0.000	0.000	0.000	0.000
31	B	99	TYR	0	-0.053	-0.059	14.149	0.091	0.091	0.000	0.000	0.000	0.000
32	B	100	LEU	0	-0.013	0.002	16.013	0.032	0.032	0.000	0.000	0.000	0.000
33	B	101	LEU	0	-0.023	-0.017	12.963	0.031	0.031	0.000	0.000	0.000	0.000
34	B	102	ALA	0	0.007	0.006	11.585	0.142	0.142	0.000	0.000	0.000	0.000
35	B	103	MET	0	-0.027	-0.009	12.394	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	104	THR	0	0.008	0.013	13.768	-0.017	-0.017	0.000	0.000	0.000	0.000
37	B	105	PHE	0	0.014	0.012	6.485	0.046	0.046	0.000	0.000	0.000	0.000
38	B	106	VAL	0	0.007	-0.008	11.260	-0.155	-0.155	0.000	0.000	0.000	0.000
39	B	107	TYR	0	-0.045	-0.047	12.604	-0.084	-0.084	0.000	0.000	0.000	0.000
40	B	108	PHE	0	0.014	0.006	11.528	-0.053	-0.053	0.000	0.000	0.000	0.000
41	B	109	LYS	1	0.866	0.922	7.340	0.236	0.236	0.000	0.000	0.000	0.000
42	B	110	ARG	1	0.812	0.886	11.994	-0.207	-0.207	0.000	0.000	0.000	0.000
43	B	111	ALA	0	0.004	0.021	15.454	-0.031	-0.031	0.000	0.000	0.000	0.000
44	B	112	LYS	1	0.818	0.908	13.767	-0.040	-0.040	0.000	0.000	0.000	0.000
45	B	113	PHE	0	-0.021	0.002	13.670	-0.015	-0.015	0.000	0.000	0.000	0.000
46	B	114	THR	0	0.013	-0.021	12.588	-0.052	-0.052	0.000	0.000	0.000	0.000
47	B	115	ILE	0	0.030	0.008	9.852	0.093	0.093	0.000	0.000	0.000	0.000
48	B	116	SER	0	0.001	-0.010	12.615	0.099	0.099	0.000	0.000	0.000	0.000
49	B	117	GLU	-1	-0.779	-0.839	15.769	0.083	0.083	0.000	0.000	0.000	0.000
50	B	118	HIS	0	-0.048	-0.018	10.751	0.103	0.103	0.000	0.000	0.000	0.000
51	B	119	THR	0	-0.029	-0.026	14.744	0.078	0.078	0.000	0.000	0.000	0.000
52	B	120	ARG	1	0.932	0.935	17.303	-0.355	-0.355	0.000	0.000	0.000	0.000
53	B	121	ILE	0	0.012	0.017	18.831	0.004	0.004	0.000	0.000	0.000	0.000
54	B	122	ASN	0	0.008	0.003	17.857	-0.017	-0.017	0.000	0.000	0.000	0.000
55	B	123	PHE	0	0.052	0.027	15.076	0.002	0.002	0.000	0.000	0.000	0.000
56	B	124	PHE	0	0.041	0.021	17.337	-0.014	-0.014	0.000	0.000	0.000	0.000
57	B	125	ILE	0	-0.029	-0.020	20.689	-0.020	-0.020	0.000	0.000	0.000	0.000
58	B	126	ALA	0	0.006	0.006	17.317	-0.027	-0.027	0.000	0.000	0.000	0.000
59	B	127	LEU	0	0.018	0.012	17.400	-0.013	-0.013	0.000	0.000	0.000	0.000
60	B	128	TYR	0	0.026	0.007	19.656	-0.031	-0.031	0.000	0.000	0.000	0.000
61	B	129	LEU	0	-0.027	-0.004	20.992	-0.022	-0.022	0.000	0.000	0.000	0.000
62	B	130	ALA	0	0.020	0.020	19.165	-0.020	-0.020	0.000	0.000	0.000	0.000
63	B	131	ASN	0	-0.020	-0.033	21.301	-0.036	-0.036	0.000	0.000	0.000	0.000
64	B	132	THR	0	-0.046	-0.044	24.260	-0.021	-0.021	0.000	0.000	0.000	0.000
65	B	133	VAL	0	-0.088	-0.041	23.177	-0.018	-0.018	0.000	0.000	0.000	0.000
66	B	134	GLU	-1	-0.907	-0.970	21.531	0.146	0.146	0.000	0.000	0.000	0.000
67	B	135	GLU	-1	-0.844	-0.889	24.231	0.202	0.202	0.000	0.000	0.000	0.000
68	B	136	ASP	-1	-0.897	-0.940	26.974	0.102	0.102	0.000	0.000	0.000	0.000
69	B	137	GLU	-1	-0.856	-0.890	29.529	0.147	0.147	0.000	0.000	0.000	0.000
70	B	138	GLU	-1	-0.848	-0.938	29.745	0.142	0.142	0.000	0.000	0.000	0.000
71	B	139	GLU	-1	-0.887	-0.925	30.935	0.121	0.121	0.000	0.000	0.000	0.000
72	B	140	THR	0	-0.028	-0.051	27.333	0.006	0.006	0.000	0.000	0.000	0.000
73	B	141	LYS	1	0.816	0.901	26.121	-0.149	-0.149	0.000	0.000	0.000	0.000
74	B	142	TYR	0	-0.103	-0.061	27.269	0.012	0.012	0.000	0.000	0.000	0.000
75	B	143	GLU	-1	-0.905	-0.956	27.447	0.187	0.187	0.000	0.000	0.000	0.000
76	B	144	ILE	0	-0.032	-0.011	22.642	0.018	0.018	0.000	0.000	0.000	0.000
77	B	145	PHE	0	-0.036	-0.017	25.540	0.006	0.006	0.000	0.000	0.000	0.000
78	B	146	PRO	0	-0.038	-0.031	28.362	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	147	TRP	0	0.000	0.006	23.829	0.002	0.002	0.000	0.000	0.000	0.000
80	B	148	ALA	0	-0.023	0.007	24.277	0.012	0.012	0.000	0.000	0.000	0.000
81	B	149	LEU	0	-0.054	-0.029	25.206	-0.013	-0.013	0.000	0.000	0.000	0.000
82	B	150	GLY	0	0.034	0.029	28.558	-0.017	-0.017	0.000	0.000	0.000	0.000
83	B	151	LYS	1	0.989	0.962	30.304	-0.179	-0.179	0.000	0.000	0.000	0.000
84	B	152	ASN	0	0.010	0.011	33.771	-0.013	-0.013	0.000	0.000	0.000	0.000
85	B	153	TRP	0	0.110	0.057	31.270	-0.010	-0.010	0.000	0.000	0.000	0.000
86	B	154	ARG	1	0.978	0.995	32.945	-0.120	-0.120	0.000	0.000	0.000	0.000
87	B	155	LYS	1	0.873	0.931	36.106	-0.108	-0.108	0.000	0.000	0.000	0.000
88	B	156	LEU	0	-0.025	-0.008	32.308	-0.005	-0.005	0.000	0.000	0.000	0.000
89	B	157	PHE	0	0.035	0.018	31.145	0.002	0.002	0.000	0.000	0.000	0.000
90	B	158	PRO	0	0.027	0.012	31.604	0.003	0.003	0.000	0.000	0.000	0.000
91	B	159	ASN	0	-0.049	-0.017	30.424	0.005	0.005	0.000	0.000	0.000	0.000
92	B	160	PHE	0	0.047	0.024	24.289	-0.003	-0.003	0.000	0.000	0.000	0.000
93	B	161	LEU	0	0.029	0.019	27.410	0.008	0.008	0.000	0.000	0.000	0.000
94	B	162	LYS	1	0.933	0.968	28.810	-0.090	-0.090	0.000	0.000	0.000	0.000
95	B	163	LEU	0	-0.043	-0.022	25.291	-0.005	-0.005	0.000	0.000	0.000	0.000
96	B	164	ARG	1	0.858	0.912	24.141	-0.145	-0.145	0.000	0.000	0.000	0.000
97	B	165	ASP	-1	-0.818	-0.882	24.638	0.126	0.126	0.000	0.000	0.000	0.000
98	B	166	GLN	0	0.011	0.004	26.226	-0.016	-0.016	0.000	0.000	0.000	0.000
99	B	167	LEU	0	-0.018	0.004	18.597	-0.008	-0.008	0.000	0.000	0.000	0.000
100	B	168	TRP	0	-0.017	-0.019	21.965	-0.004	-0.004	0.000	0.000	0.000	0.000
101	B	169	ASP	-1	-0.882	-0.928	23.924	0.055	0.055	0.000	0.000	0.000	0.000
102	B	170	ARG	1	0.805	0.879	17.692	-0.076	-0.076	0.000	0.000	0.000	0.000
103	B	171	ILE	0	-0.085	-0.026	18.178	-0.010	-0.010	0.000	0.000	0.000	0.000
104	B	172	ASP	-1	-0.880	-0.941	20.283	0.026	0.026	0.000	0.000	0.000	0.000
105	B	173	TYR	0	-0.013	-0.026	23.089	-0.009	-0.009	0.000	0.000	0.000	0.000
106	B	174	ARG	1	0.893	0.962	17.546	-0.036	-0.036	0.000	0.000	0.000	0.000
107	B	175	ALA	0	0.052	0.014	20.118	0.013	0.013	0.000	0.000	0.000	0.000
108	B	176	ILE	0	0.059	0.055	20.854	0.021	0.021	0.000	0.000	0.000	0.000
109	B	177	VAL	0	-0.030	-0.011	15.660	-0.011	-0.011	0.000	0.000	0.000	0.000
110	B	178	SER	0	0.037	0.028	18.837	0.006	0.006	0.000	0.000	0.000	0.000
111	B	179	ARG	1	0.957	0.947	17.486	-0.061	-0.061	0.000	0.000	0.000	0.000
112	B	180	ARG	1	0.868	0.927	15.969	0.061	0.061	0.000	0.000	0.000	0.000
113	B	181	CYS	0	-0.009	0.016	13.348	-0.004	-0.004	0.000	0.000	0.000	0.000
114	B	182	CYS	0	0.030	0.021	12.292	0.059	0.059	0.000	0.000	0.000	0.000
115	B	183	GLU	-1	-0.729	-0.856	11.864	0.159	0.159	0.000	0.000	0.000	0.000
116	B	184	GLU	-1	-0.920	-0.958	10.822	-0.100	-0.100	0.000	0.000	0.000	0.000
117	B	185	VAL	0	-0.023	-0.018	7.418	-0.136	-0.136	0.000	0.000	0.000	0.000
118	B	186	MET	0	-0.009	0.006	7.120	0.334	0.334	0.000	0.000	0.000	0.000
119	B	187	ALA	0	-0.020	-0.012	7.521	-0.103	-0.103	0.000	0.000	0.000	0.000
120	B	188	ILE	0	-0.065	-0.022	2.610	-1.534	-0.941	1.868	-0.567	-1.894	0.000
121	B	189	ALA	0	-0.016	-0.017	2.001	-7.039	-5.382	1.639	-1.298	-1.997	-0.006
122	B	190	PRO	0	0.026	0.013	3.900	1.456	1.594	0.001	-0.057	-0.082	0.000
123	B	191	THR	0	-0.016	-0.009	6.439	0.185	0.185	0.000	0.000	0.000	0.000
124	B	192	HIS	0	0.005	0.018	6.772	-0.133	-0.133	0.000	0.000	0.000	0.000
125	B	193	TYR	0	0.048	0.002	8.714	-0.178	-0.178	0.000	0.000	0.000	0.000
126	B	194	ILE	0	-0.014	0.000	9.112	-0.169	-0.169	0.000	0.000	0.000	0.000
127	B	195	TRP	0	-0.021	-0.021	6.670	-0.204	-0.204	0.000	0.000	0.000	0.000
128	B	196	GLN	0	-0.024	-0.020	11.210	-0.031	-0.031	0.000	0.000	0.000	0.000
129	B	197	ARG	1	0.795	0.910	15.078	-0.523	-0.523	0.000	0.000	0.000	0.000
130	B	198	GLU	-1	-0.842	-0.920	17.403	0.162	0.162	0.000	0.000	0.000	0.000
131	B	199	ARG	1	0.840	0.905	19.442	-0.215	-0.215	0.000	0.000	0.000	0.000
132	B	200	SER	0	-0.022	-0.022	22.963	-0.027	-0.027	0.000	0.000	0.000	0.000
133	B	201	VAL	0	-0.047	-0.011	26.229	0.003	0.003	0.000	0.000	0.000	0.000

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