FMO DATABASE

FMODB ID: L7LJ9

Calculation Name: 1BI7-B-Xray372

Preferred Name: Cyclin-dependent kinase 6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1BI7

Chain ID: B

ChEMBL ID: CHEMBL2508

UniProt ID: Q00534

Base Structure: X-ray

Registration Date: 2023-09-26

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1010019.055435
FMO2-HF: Nuclear repulsion	962585.903888
FMO2-HF: Total energy	-47433.151546
FMO2-MP2: Total energy	-47571.569526

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:10:GLU)

Summations of interaction energy for fragment #1(B:10:GLU)

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.
-16.362	-14.779	-0.009	-0.693	-0.881	0.002

Interaction energy analysis for fragmet #1(B:10:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.950 / q_NPA : -0.984

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

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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	12	SER	0	0.047	0.032	3.861	-5.268	-3.685	-0.009	-0.693	-0.881	0.002
4	B	13	ALA	0	0.036	-0.010	5.459	-4.379	-4.379	0.000	0.000	0.000	0.000
5	B	14	ASP	-1	-0.809	-0.903	7.654	22.396	22.396	0.000	0.000	0.000	0.000
6	B	15	TRP	0	-0.002	0.012	7.063	-3.667	-3.667	0.000	0.000	0.000	0.000
7	B	16	LEU	0	-0.009	0.011	10.674	-2.029	-2.029	0.000	0.000	0.000	0.000
8	B	17	ALA	0	0.017	0.001	12.190	-1.799	-1.799	0.000	0.000	0.000	0.000
9	B	18	THR	0	0.017	-0.003	12.733	-1.622	-1.622	0.000	0.000	0.000	0.000
10	B	19	ALA	0	-0.001	0.009	14.662	-1.319	-1.319	0.000	0.000	0.000	0.000
11	B	20	ALA	0	0.002	-0.009	16.442	-1.224	-1.224	0.000	0.000	0.000	0.000
12	B	21	ALA	0	0.009	0.020	17.748	-0.959	-0.959	0.000	0.000	0.000	0.000
13	B	22	ARG	1	0.844	0.915	17.733	-16.645	-16.645	0.000	0.000	0.000	0.000
14	B	23	GLY	0	0.026	0.019	21.045	-0.645	-0.645	0.000	0.000	0.000	0.000
15	B	24	ARG	1	0.840	0.921	19.259	-13.694	-13.694	0.000	0.000	0.000	0.000
16	B	25	VAL	0	0.025	-0.002	20.186	0.653	0.653	0.000	0.000	0.000	0.000
17	B	26	GLU	-1	-0.722	-0.845	21.134	13.165	13.165	0.000	0.000	0.000	0.000
18	B	27	GLU	-1	-0.812	-0.896	16.734	17.039	17.039	0.000	0.000	0.000	0.000
19	B	28	VAL	0	-0.008	-0.016	16.390	1.085	1.085	0.000	0.000	0.000	0.000
20	B	29	ARG	1	0.853	0.923	16.556	-12.969	-12.969	0.000	0.000	0.000	0.000
21	B	30	ALA	0	-0.030	-0.005	16.881	0.615	0.615	0.000	0.000	0.000	0.000
22	B	31	LEU	0	0.018	0.009	9.758	0.659	0.659	0.000	0.000	0.000	0.000
23	B	32	LEU	0	0.009	0.007	12.349	1.546	1.546	0.000	0.000	0.000	0.000
24	B	33	GLU	-1	-0.887	-0.962	14.407	15.644	15.644	0.000	0.000	0.000	0.000
25	B	34	ALA	0	-0.039	-0.003	12.384	-0.418	-0.418	0.000	0.000	0.000	0.000
26	B	35	GLY	0	-0.008	0.005	10.916	1.972	1.972	0.000	0.000	0.000	0.000
27	B	36	ALA	0	-0.025	-0.007	8.501	2.636	2.636	0.000	0.000	0.000	0.000
28	B	37	ASN	0	0.011	-0.007	7.496	-3.626	-3.626	0.000	0.000	0.000	0.000
29	B	38	PRO	0	0.000	-0.003	10.323	0.196	0.196	0.000	0.000	0.000	0.000
30	B	39	ASN	0	-0.050	-0.034	12.505	0.327	0.327	0.000	0.000	0.000	0.000
31	B	40	ALA	0	0.014	0.009	8.407	-0.330	-0.330	0.000	0.000	0.000	0.000
32	B	41	PRO	0	-0.009	-0.015	9.163	-0.769	-0.769	0.000	0.000	0.000	0.000
33	B	42	ASN	0	-0.025	-0.023	8.665	1.734	1.734	0.000	0.000	0.000	0.000
34	B	43	SER	0	-0.028	-0.001	7.297	-1.138	-1.138	0.000	0.000	0.000	0.000
35	B	44	TYR	0	-0.002	-0.009	9.011	-1.583	-1.583	0.000	0.000	0.000	0.000
36	B	45	GLY	0	-0.001	-0.002	11.835	-1.345	-1.345	0.000	0.000	0.000	0.000
37	B	46	ARG	1	0.812	0.900	13.536	-16.243	-16.243	0.000	0.000	0.000	0.000
38	B	47	ARG	1	0.918	0.958	13.214	-14.967	-14.967	0.000	0.000	0.000	0.000
39	B	48	PRO	0	0.069	0.023	13.525	-1.156	-1.156	0.000	0.000	0.000	0.000
40	B	49	ILE	0	0.004	-0.004	16.415	-0.315	-0.315	0.000	0.000	0.000	0.000
41	B	50	GLN	0	-0.057	-0.037	18.122	-0.044	-0.044	0.000	0.000	0.000	0.000
42	B	51	VAL	0	-0.017	-0.006	15.734	-0.511	-0.511	0.000	0.000	0.000	0.000
43	B	52	MET	0	-0.036	-0.006	19.152	0.286	0.286	0.000	0.000	0.000	0.000
44	B	53	MET	0	-0.002	0.001	20.803	-0.495	-0.495	0.000	0.000	0.000	0.000
45	B	54	MET	0	0.001	0.005	23.642	-0.156	-0.156	0.000	0.000	0.000	0.000
46	B	55	GLY	0	0.080	0.029	26.742	-0.099	-0.099	0.000	0.000	0.000	0.000
47	B	56	SER	0	-0.059	-0.024	24.605	-0.232	-0.232	0.000	0.000	0.000	0.000
48	B	57	ALA	0	0.019	-0.009	25.775	0.414	0.414	0.000	0.000	0.000	0.000
49	B	58	ARG	1	0.863	0.906	26.183	-11.444	-11.444	0.000	0.000	0.000	0.000
50	B	59	VAL	0	-0.003	0.014	20.499	0.368	0.368	0.000	0.000	0.000	0.000
51	B	60	ALA	0	0.056	0.019	21.911	0.502	0.502	0.000	0.000	0.000	0.000
52	B	61	GLU	-1	-0.889	-0.955	23.383	10.644	10.644	0.000	0.000	0.000	0.000
53	B	62	LEU	0	-0.059	-0.017	19.016	0.109	0.109	0.000	0.000	0.000	0.000
54	B	63	LEU	0	0.016	-0.015	16.956	0.390	0.390	0.000	0.000	0.000	0.000
55	B	64	LEU	0	-0.009	0.001	19.677	0.323	0.323	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.046	-0.014	21.974	0.143	0.143	0.000	0.000	0.000	0.000
57	B	66	HIS	1	0.801	0.893	16.781	-16.746	-16.746	0.000	0.000	0.000	0.000
58	B	67	GLY	0	0.013	0.007	17.749	0.937	0.937	0.000	0.000	0.000	0.000
59	B	68	ALA	0	-0.010	0.011	17.527	0.543	0.543	0.000	0.000	0.000	0.000
60	B	69	GLU	-1	-0.781	-0.883	17.487	15.714	15.714	0.000	0.000	0.000	0.000
61	B	70	PRO	0	0.036	0.013	20.716	0.186	0.186	0.000	0.000	0.000	0.000
62	B	71	ASN	0	-0.103	-0.069	22.677	-0.633	-0.633	0.000	0.000	0.000	0.000
63	B	72	CYS	0	-0.011	0.009	19.298	0.065	0.065	0.000	0.000	0.000	0.000
64	B	73	ALA	0	0.041	0.017	21.381	-0.553	-0.553	0.000	0.000	0.000	0.000
65	B	74	ASP	-1	-0.772	-0.864	20.554	14.037	14.037	0.000	0.000	0.000	0.000
66	B	75	PRO	0	-0.025	-0.024	17.311	-0.536	-0.536	0.000	0.000	0.000	0.000
67	B	76	ALA	0	-0.030	0.006	20.601	-0.204	-0.204	0.000	0.000	0.000	0.000
68	B	77	THR	0	-0.014	-0.026	22.916	-0.551	-0.551	0.000	0.000	0.000	0.000
69	B	78	LEU	0	-0.021	-0.021	24.350	-0.439	-0.439	0.000	0.000	0.000	0.000
70	B	79	THR	0	-0.060	-0.025	25.246	-0.102	-0.102	0.000	0.000	0.000	0.000
71	B	80	ARG	1	0.860	0.932	24.416	-10.573	-10.573	0.000	0.000	0.000	0.000
72	B	81	PRO	0	0.053	0.026	22.843	-0.334	-0.334	0.000	0.000	0.000	0.000
73	B	82	VAL	0	-0.028	-0.011	25.301	-0.227	-0.227	0.000	0.000	0.000	0.000
74	B	83	HIS	0	0.010	0.000	28.363	0.001	0.001	0.000	0.000	0.000	0.000
75	B	84	ASP	-1	-0.779	-0.879	25.737	10.848	10.848	0.000	0.000	0.000	0.000
76	B	85	ALA	0	-0.022	-0.025	28.136	-0.163	-0.163	0.000	0.000	0.000	0.000
77	B	86	ALA	0	-0.032	-0.004	29.568	-0.256	-0.256	0.000	0.000	0.000	0.000
78	B	87	ARG	1	0.841	0.892	28.476	-10.186	-10.186	0.000	0.000	0.000	0.000
79	B	88	GLU	-1	-0.917	-0.956	29.115	9.794	9.794	0.000	0.000	0.000	0.000
80	B	89	GLY	0	-0.009	0.007	31.926	-0.069	-0.069	0.000	0.000	0.000	0.000
81	B	90	PHE	0	0.023	0.029	30.065	-0.134	-0.134	0.000	0.000	0.000	0.000
82	B	91	LEU	0	0.028	0.003	32.029	0.262	0.262	0.000	0.000	0.000	0.000
83	B	92	ASP	-1	-0.898	-0.952	31.770	9.274	9.274	0.000	0.000	0.000	0.000
84	B	93	THR	0	-0.025	-0.017	27.003	0.217	0.217	0.000	0.000	0.000	0.000
85	B	94	LEU	0	0.017	0.022	28.978	0.260	0.260	0.000	0.000	0.000	0.000
86	B	95	VAL	0	-0.008	-0.008	31.225	0.032	0.032	0.000	0.000	0.000	0.000
87	B	96	VAL	0	-0.054	-0.015	26.933	0.037	0.037	0.000	0.000	0.000	0.000
88	B	97	LEU	0	0.006	-0.007	25.214	0.213	0.213	0.000	0.000	0.000	0.000
89	B	98	HIS	0	0.004	0.026	28.003	0.082	0.082	0.000	0.000	0.000	0.000
90	B	99	ARG	1	0.888	0.943	30.484	-9.489	-9.489	0.000	0.000	0.000	0.000
91	B	100	ALA	0	0.005	0.016	25.719	-0.041	-0.041	0.000	0.000	0.000	0.000
92	B	101	GLY	0	0.029	0.020	27.074	0.257	0.257	0.000	0.000	0.000	0.000
93	B	102	ALA	0	-0.038	-0.013	27.016	0.065	0.065	0.000	0.000	0.000	0.000
94	B	103	ARG	1	0.918	0.959	28.313	-10.024	-10.024	0.000	0.000	0.000	0.000
95	B	104	LEU	0	0.048	0.015	30.982	0.231	0.231	0.000	0.000	0.000	0.000
96	B	105	ASP	-1	-0.891	-0.938	33.327	8.127	8.127	0.000	0.000	0.000	0.000
97	B	106	VAL	0	-0.049	-0.043	28.716	0.156	0.156	0.000	0.000	0.000	0.000
98	B	107	ARG	1	0.835	0.901	31.814	-8.151	-8.151	0.000	0.000	0.000	0.000
99	B	108	ASP	-1	-0.752	-0.872	29.065	9.668	9.668	0.000	0.000	0.000	0.000
100	B	109	ALA	0	0.009	0.005	28.300	-0.257	-0.257	0.000	0.000	0.000	0.000
101	B	110	TRP	0	-0.068	-0.025	28.088	-0.147	-0.147	0.000	0.000	0.000	0.000
102	B	111	GLY	0	-0.006	0.000	33.314	-0.274	-0.274	0.000	0.000	0.000	0.000
103	B	112	ARG	1	0.792	0.867	33.717	-8.441	-8.441	0.000	0.000	0.000	0.000
104	B	113	LEU	0	-0.046	-0.022	33.300	0.329	0.329	0.000	0.000	0.000	0.000
105	B	114	PRO	0	-0.016	-0.023	31.532	-0.041	-0.041	0.000	0.000	0.000	0.000
106	B	115	VAL	0	0.037	0.014	33.959	-0.053	-0.053	0.000	0.000	0.000	0.000
107	B	116	ASP	-1	-0.742	-0.860	37.054	7.839	7.839	0.000	0.000	0.000	0.000
108	B	117	LEU	0	-0.023	0.002	31.881	-0.088	-0.088	0.000	0.000	0.000	0.000
109	B	118	ALA	0	0.004	0.006	36.105	-0.048	-0.048	0.000	0.000	0.000	0.000
110	B	119	GLU	-1	-0.860	-0.923	37.617	6.941	6.941	0.000	0.000	0.000	0.000
111	B	120	GLU	-1	-0.856	-0.878	37.161	7.902	7.902	0.000	0.000	0.000	0.000
112	B	121	LEU	0	-0.037	-0.021	35.472	-0.110	-0.110	0.000	0.000	0.000	0.000
113	B	122	GLY	0	-0.002	0.019	38.939	-0.060	-0.060	0.000	0.000	0.000	0.000
114	B	123	HIS	0	0.016	0.019	35.327	-0.284	-0.284	0.000	0.000	0.000	0.000
115	B	124	ARG	1	0.926	0.950	39.926	-6.594	-6.594	0.000	0.000	0.000	0.000
116	B	125	ASP	-1	-0.886	-0.947	38.952	7.791	7.791	0.000	0.000	0.000	0.000
117	B	126	VAL	0	0.033	0.018	35.645	-0.016	-0.016	0.000	0.000	0.000	0.000
118	B	127	ALA	0	0.035	0.014	38.305	0.007	0.007	0.000	0.000	0.000	0.000
119	B	128	ARG	1	0.853	0.926	40.703	-7.077	-7.077	0.000	0.000	0.000	0.000
120	B	129	TYR	0	-0.070	-0.060	35.284	-0.116	-0.116	0.000	0.000	0.000	0.000
121	B	130	LEU	0	0.009	0.011	34.850	0.063	0.063	0.000	0.000	0.000	0.000
122	B	131	ARG	1	0.794	0.889	38.969	-7.024	-7.024	0.000	0.000	0.000	0.000
123	B	132	ALA	0	-0.030	-0.021	41.511	-0.246	-0.246	0.000	0.000	0.000	0.000
124	B	133	ALA	0	-0.018	-0.013	39.020	0.159	0.159	0.000	0.000	0.000	0.000
125	B	134	ALA	0	0.012	0.025	38.888	0.132	0.132	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:10:GLU)