FMO DATABASE

FMODB ID: QYV1Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1389048.083802
FMO2-HF: Nuclear repulsion	1331189.209457
FMO2-HF: Total energy	-57858.874345
FMO2-MP2: Total energy	-58024.485468

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.
-10.742	-1.346	5.198	-4.827	-9.767	0.024

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 : 0.064 / q_NPA : 0.028

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	0.024	0.017	2.556	-4.362	0.218	1.536	-2.301	-3.816	0.014
4	B	72	THR	0	0.023	0.034	2.182	-0.136	1.715	1.779	-1.146	-2.484	0.005
5	B	73	ALA	0	-0.001	0.000	4.451	-1.007	-0.838	0.002	-0.065	-0.106	0.000
6	B	74	PHE	0	-0.003	0.000	6.719	-0.471	-0.471	0.000	0.000	0.000	0.000
7	B	75	PHE	0	0.026	-0.017	3.000	-1.894	-0.640	0.150	-0.466	-0.938	0.005
8	B	76	LYS	1	0.883	0.966	7.597	-1.275	-1.275	0.000	0.000	0.000	0.000
9	B	77	LEU	0	-0.032	-0.021	10.219	-0.282	-0.282	0.000	0.000	0.000	0.000
10	B	78	PHE	0	-0.022	-0.007	10.260	-0.204	-0.204	0.000	0.000	0.000	0.000
11	B	79	ASP	-1	-0.883	-0.931	10.759	1.605	1.605	0.000	0.000	0.000	0.000
12	B	80	ASP	-1	-0.861	-0.928	13.747	0.348	0.348	0.000	0.000	0.000	0.000
13	B	81	ASP	-1	-0.889	-0.943	16.795	0.391	0.391	0.000	0.000	0.000	0.000
14	B	82	LEU	0	0.013	-0.008	20.008	-0.016	-0.016	0.000	0.000	0.000	0.000
15	B	83	ILE	0	-0.081	-0.027	15.673	-0.031	-0.031	0.000	0.000	0.000	0.000
16	B	84	GLN	0	0.005	-0.013	14.620	-0.079	-0.079	0.000	0.000	0.000	0.000
17	B	85	ASP	-1	-0.873	-0.932	18.611	0.302	0.302	0.000	0.000	0.000	0.000
18	B	86	PHE	0	-0.053	-0.029	19.368	-0.031	-0.031	0.000	0.000	0.000	0.000
19	B	87	LEU	0	-0.036	-0.027	16.081	-0.012	-0.012	0.000	0.000	0.000	0.000
20	B	88	TRP	0	-0.048	-0.016	17.341	-0.021	-0.021	0.000	0.000	0.000	0.000
21	B	89	MET	0	-0.054	-0.009	22.614	-0.040	-0.040	0.000	0.000	0.000	0.000
22	B	90	ASP	-1	-0.712	-0.847	22.210	0.281	0.281	0.000	0.000	0.000	0.000
23	B	91	CYS	0	-0.008	-0.005	22.722	0.018	0.018	0.000	0.000	0.000	0.000
24	B	92	CYS	0	-0.054	-0.032	24.059	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	93	CYS	0	-0.040	-0.012	20.885	0.007	0.007	0.000	0.000	0.000	0.000
26	B	94	LYS	1	0.956	0.960	22.646	-0.179	-0.179	0.000	0.000	0.000	0.000
27	B	95	ILE	0	-0.005	0.006	22.827	-0.010	-0.010	0.000	0.000	0.000	0.000
28	B	96	ALA	0	-0.024	-0.013	18.461	0.025	0.025	0.000	0.000	0.000	0.000
29	B	97	ASP	-1	-0.790	-0.891	18.386	0.362	0.362	0.000	0.000	0.000	0.000
30	B	98	LYS	1	0.911	0.957	14.655	-0.194	-0.194	0.000	0.000	0.000	0.000
31	B	99	TYR	0	-0.032	-0.057	14.608	0.071	0.071	0.000	0.000	0.000	0.000
32	B	100	LEU	0	-0.002	0.009	15.983	0.019	0.019	0.000	0.000	0.000	0.000
33	B	101	LEU	0	-0.039	-0.032	13.315	0.023	0.023	0.000	0.000	0.000	0.000
34	B	102	ALA	0	0.006	0.013	11.536	0.167	0.167	0.000	0.000	0.000	0.000
35	B	103	MET	0	-0.016	-0.012	12.202	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	104	THR	0	0.021	0.012	13.512	-0.048	-0.048	0.000	0.000	0.000	0.000
37	B	105	PHE	0	-0.006	0.007	6.045	0.016	0.016	0.000	0.000	0.000	0.000
38	B	106	VAL	0	-0.004	-0.014	11.014	-0.149	-0.149	0.000	0.000	0.000	0.000
39	B	107	TYR	0	-0.043	-0.050	12.484	-0.084	-0.084	0.000	0.000	0.000	0.000
40	B	108	PHE	0	0.002	0.007	11.229	-0.048	-0.048	0.000	0.000	0.000	0.000
41	B	109	LYS	1	0.906	0.955	6.118	0.618	0.618	0.000	0.000	0.000	0.000
42	B	110	ARG	1	0.788	0.875	11.278	-0.179	-0.179	0.000	0.000	0.000	0.000
43	B	111	ALA	0	0.014	0.033	14.614	-0.026	-0.026	0.000	0.000	0.000	0.000
44	B	112	LYS	1	0.924	0.953	13.108	0.090	0.090	0.000	0.000	0.000	0.000
45	B	113	PHE	0	-0.012	0.008	13.423	-0.016	-0.016	0.000	0.000	0.000	0.000
46	B	114	THR	0	0.013	-0.012	12.464	-0.071	-0.071	0.000	0.000	0.000	0.000
47	B	115	ILE	0	0.029	0.008	9.761	0.103	0.103	0.000	0.000	0.000	0.000
48	B	116	SER	0	0.002	-0.013	12.840	0.103	0.103	0.000	0.000	0.000	0.000
49	B	117	GLU	-1	-0.789	-0.850	15.861	0.041	0.041	0.000	0.000	0.000	0.000
50	B	118	HIS	0	-0.054	-0.024	10.823	0.121	0.121	0.000	0.000	0.000	0.000
51	B	119	THR	0	-0.014	-0.013	14.790	0.085	0.085	0.000	0.000	0.000	0.000
52	B	120	ARG	1	0.951	0.944	17.202	-0.348	-0.348	0.000	0.000	0.000	0.000
53	B	121	ILE	0	0.002	0.008	18.866	0.005	0.005	0.000	0.000	0.000	0.000
54	B	122	ASN	0	0.038	0.004	17.801	-0.016	-0.016	0.000	0.000	0.000	0.000
55	B	123	PHE	0	0.048	0.026	14.967	0.002	0.002	0.000	0.000	0.000	0.000
56	B	124	PHE	0	0.048	0.017	17.376	-0.005	-0.005	0.000	0.000	0.000	0.000
57	B	125	ILE	0	-0.040	-0.014	20.723	-0.019	-0.019	0.000	0.000	0.000	0.000
58	B	126	ALA	0	0.000	0.003	17.016	-0.028	-0.028	0.000	0.000	0.000	0.000
59	B	127	LEU	0	0.018	0.015	17.667	-0.012	-0.012	0.000	0.000	0.000	0.000
60	B	128	TYR	0	0.039	0.013	19.556	-0.029	-0.029	0.000	0.000	0.000	0.000
61	B	129	LEU	0	-0.035	-0.006	20.618	-0.023	-0.023	0.000	0.000	0.000	0.000
62	B	130	ALA	0	-0.003	0.003	18.791	-0.019	-0.019	0.000	0.000	0.000	0.000
63	B	131	ASN	0	-0.015	-0.035	20.896	-0.029	-0.029	0.000	0.000	0.000	0.000
64	B	132	THR	0	-0.052	-0.045	23.836	-0.020	-0.020	0.000	0.000	0.000	0.000
65	B	133	VAL	0	-0.092	-0.034	22.728	-0.017	-0.017	0.000	0.000	0.000	0.000
66	B	134	GLU	-1	-0.928	-0.973	21.873	0.147	0.147	0.000	0.000	0.000	0.000
67	B	135	GLU	-1	-0.854	-0.891	24.318	0.204	0.204	0.000	0.000	0.000	0.000
68	B	136	ASP	-1	-0.895	-0.937	26.906	0.102	0.102	0.000	0.000	0.000	0.000
69	B	137	GLU	-1	-0.895	-0.924	30.186	0.140	0.140	0.000	0.000	0.000	0.000
70	B	138	GLU	-1	-0.888	-0.938	30.060	0.133	0.133	0.000	0.000	0.000	0.000
71	B	139	GLU	-1	-0.925	-0.982	31.146	0.119	0.119	0.000	0.000	0.000	0.000
72	B	140	THR	0	-0.029	-0.048	27.653	0.007	0.007	0.000	0.000	0.000	0.000
73	B	141	LYS	1	0.815	0.907	26.313	-0.137	-0.137	0.000	0.000	0.000	0.000
74	B	142	TYR	0	-0.049	-0.022	27.346	0.011	0.011	0.000	0.000	0.000	0.000
75	B	143	GLU	-1	-0.908	-0.954	27.528	0.188	0.188	0.000	0.000	0.000	0.000
76	B	144	ILE	0	-0.049	-0.019	22.911	0.014	0.014	0.000	0.000	0.000	0.000
77	B	145	PHE	0	-0.033	-0.021	25.873	0.005	0.005	0.000	0.000	0.000	0.000
78	B	146	PRO	0	0.002	-0.016	28.649	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	147	TRP	0	0.034	0.034	23.897	0.002	0.002	0.000	0.000	0.000	0.000
80	B	148	ALA	0	-0.020	0.013	24.218	0.012	0.012	0.000	0.000	0.000	0.000
81	B	149	LEU	0	-0.058	-0.026	25.327	-0.015	-0.015	0.000	0.000	0.000	0.000
82	B	150	GLY	0	-0.016	-0.002	28.911	-0.014	-0.014	0.000	0.000	0.000	0.000
83	B	151	LYS	1	0.992	0.967	30.472	-0.180	-0.180	0.000	0.000	0.000	0.000
84	B	152	ASN	0	-0.016	-0.019	33.817	-0.012	-0.012	0.000	0.000	0.000	0.000
85	B	153	TRP	0	0.120	0.063	31.524	-0.008	-0.008	0.000	0.000	0.000	0.000
86	B	154	ARG	1	0.978	0.991	33.143	-0.118	-0.118	0.000	0.000	0.000	0.000
87	B	155	LYS	1	0.889	0.946	36.148	-0.101	-0.101	0.000	0.000	0.000	0.000
88	B	156	LEU	0	-0.012	-0.007	32.174	-0.005	-0.005	0.000	0.000	0.000	0.000
89	B	157	PHE	0	0.027	0.019	31.219	0.003	0.003	0.000	0.000	0.000	0.000
90	B	158	PRO	0	0.029	0.018	31.506	0.002	0.002	0.000	0.000	0.000	0.000
91	B	159	ASN	0	-0.032	-0.016	30.583	0.005	0.005	0.000	0.000	0.000	0.000
92	B	160	PHE	0	0.045	0.027	24.333	-0.004	-0.004	0.000	0.000	0.000	0.000
93	B	161	LEU	0	0.037	0.012	27.262	0.007	0.007	0.000	0.000	0.000	0.000
94	B	162	LYS	1	0.917	0.967	28.795	-0.079	-0.079	0.000	0.000	0.000	0.000
95	B	163	LEU	0	-0.032	-0.021	25.161	-0.007	-0.007	0.000	0.000	0.000	0.000
96	B	164	ARG	1	0.849	0.917	24.109	-0.134	-0.134	0.000	0.000	0.000	0.000
97	B	165	ASP	-1	-0.818	-0.889	24.689	0.107	0.107	0.000	0.000	0.000	0.000
98	B	166	GLN	0	0.010	0.009	25.732	-0.014	-0.014	0.000	0.000	0.000	0.000
99	B	167	LEU	0	-0.016	0.006	18.339	-0.012	-0.012	0.000	0.000	0.000	0.000
100	B	168	TRP	0	0.001	-0.009	21.525	-0.008	-0.008	0.000	0.000	0.000	0.000
101	B	169	ASP	-1	-0.875	-0.922	23.583	0.033	0.033	0.000	0.000	0.000	0.000
102	B	170	ARG	1	0.791	0.880	17.420	-0.026	-0.026	0.000	0.000	0.000	0.000
103	B	171	ILE	0	-0.103	-0.035	17.834	-0.015	-0.015	0.000	0.000	0.000	0.000
104	B	172	ASP	-1	-0.927	-0.964	20.033	-0.004	-0.004	0.000	0.000	0.000	0.000
105	B	173	TYR	0	-0.036	-0.050	23.119	-0.004	-0.004	0.000	0.000	0.000	0.000
106	B	174	ARG	1	0.889	0.962	16.834	-0.018	-0.018	0.000	0.000	0.000	0.000
107	B	175	ALA	0	0.036	0.013	19.706	0.011	0.011	0.000	0.000	0.000	0.000
108	B	176	ILE	0	0.061	0.053	20.635	0.022	0.022	0.000	0.000	0.000	0.000
109	B	177	VAL	0	-0.015	-0.001	15.396	-0.017	-0.017	0.000	0.000	0.000	0.000
110	B	178	SER	0	0.026	0.023	18.253	0.008	0.008	0.000	0.000	0.000	0.000
111	B	179	ARG	1	0.992	0.961	17.218	-0.092	-0.092	0.000	0.000	0.000	0.000
112	B	180	ARG	1	0.935	0.975	16.019	0.011	0.011	0.000	0.000	0.000	0.000
113	B	181	CYS	0	-0.019	0.006	12.519	0.002	0.002	0.000	0.000	0.000	0.000
114	B	182	CYS	0	0.027	0.006	12.083	0.050	0.050	0.000	0.000	0.000	0.000
115	B	183	GLU	-1	-0.750	-0.863	12.252	0.216	0.216	0.000	0.000	0.000	0.000
116	B	184	GLU	-1	-0.964	-0.985	10.377	-0.009	-0.009	0.000	0.000	0.000	0.000
117	B	185	VAL	0	-0.057	-0.035	7.500	-0.054	-0.054	0.000	0.000	0.000	0.000
118	B	186	MET	0	-0.019	0.005	7.543	0.350	0.350	0.000	0.000	0.000	0.000
119	B	187	ALA	0	-0.014	0.004	8.803	-0.063	-0.063	0.000	0.000	0.000	0.000
120	B	188	ILE	0	-0.077	-0.031	2.489	-1.405	-0.727	1.652	-0.582	-1.748	0.001
121	B	189	ALA	0	-0.007	-0.016	2.708	-3.069	-2.233	0.080	-0.261	-0.654	-0.001
122	B	190	PRO	0	0.034	0.016	4.669	0.849	0.877	-0.001	-0.006	-0.021	0.000
123	B	191	THR	0	-0.035	-0.016	6.392	0.157	0.157	0.000	0.000	0.000	0.000
124	B	192	HIS	0	0.014	0.018	6.639	-0.282	-0.282	0.000	0.000	0.000	0.000
125	B	193	TYR	0	0.099	0.037	8.936	-0.190	-0.190	0.000	0.000	0.000	0.000
126	B	194	ILE	0	-0.037	-0.011	9.462	-0.154	-0.154	0.000	0.000	0.000	0.000
127	B	195	TRP	0	-0.012	-0.015	7.319	-0.139	-0.139	0.000	0.000	0.000	0.000
128	B	196	GLN	0	-0.041	-0.027	11.630	-0.045	-0.045	0.000	0.000	0.000	0.000
129	B	197	ARG	1	0.799	0.904	15.599	-0.509	-0.509	0.000	0.000	0.000	0.000
130	B	198	GLU	-1	-0.930	-0.947	17.949	0.172	0.172	0.000	0.000	0.000	0.000
131	B	199	ARG	1	0.873	0.923	20.029	-0.227	-0.227	0.000	0.000	0.000	0.000
132	B	200	SER	0	-0.017	-0.022	23.424	-0.023	-0.023	0.000	0.000	0.000	0.000
133	B	201	VAL	0	-0.049	-0.012	26.595	0.000	0.000	0.000	0.000	0.000	0.000

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