FMO DATABASE

FMODB ID: J2M39

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:

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1017223.607435
FMO2-HF: Nuclear repulsion	969793.327203
FMO2-HF: Total energy	-47430.280231
FMO2-MP2: Total energy	-47569.268515

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.
-8.233	-6.512	-0.012	-0.839	-0.87	0

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 : -0.946 / q_NPA : -0.986

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].
3	B	12	SER	0	0.049	0.025	3.885	-2.700	-0.979	-0.012	-0.839	-0.870
4	B	13	ALA	0	0.027	-0.018	5.952	-4.381	-4.381	0.000	0.000	0.000
5	B	14	ASP	-1	-0.899	-0.951	7.593	25.036	25.036	0.000	0.000	0.000
6	B	15	TRP	0	-0.015	0.025	6.634	-3.410	-3.410	0.000	0.000	0.000
7	B	16	LEU	0	0.040	0.010	10.850	-2.035	-2.035	0.000	0.000	0.000
8	B	17	ALA	0	0.016	0.022	12.432	-1.570	-1.570	0.000	0.000	0.000
9	B	18	THR	0	0.036	0.018	13.165	-1.640	-1.640	0.000	0.000	0.000
10	B	19	ALA	0	0.053	0.031	15.042	-1.196	-1.196	0.000	0.000	0.000
11	B	20	ALA	0	0.066	0.012	16.780	-1.157	-1.157	0.000	0.000	0.000
12	B	21	ALA	0	-0.042	-0.002	17.879	-0.866	-0.866	0.000	0.000	0.000
13	B	22	ARG	1	0.872	0.944	18.624	-15.578	-15.578	0.000	0.000	0.000
14	B	23	GLY	0	0.011	-0.034	21.074	-0.627	-0.627	0.000	0.000	0.000
15	B	24	ARG	1	0.851	0.923	19.314	-13.424	-13.424	0.000	0.000	0.000
16	B	25	VAL	0	0.001	-0.005	20.182	0.553	0.553	0.000	0.000	0.000
17	B	26	GLU	-1	-0.812	-0.912	20.780	13.287	13.287	0.000	0.000	0.000
18	B	27	GLU	-1	-0.900	-0.938	16.676	17.084	17.084	0.000	0.000	0.000
19	B	28	VAL	0	0.015	-0.002	16.460	0.981	0.981	0.000	0.000	0.000
20	B	29	ARG	1	0.893	0.936	16.434	-12.517	-12.517	0.000	0.000	0.000
21	B	30	ALA	0	-0.010	0.012	16.903	0.679	0.679	0.000	0.000	0.000
22	B	31	LEU	0	0.010	-0.015	10.690	0.722	0.722	0.000	0.000	0.000
23	B	32	LEU	0	0.015	-0.001	12.637	1.262	1.262	0.000	0.000	0.000
24	B	33	GLU	-1	-1.041	-1.020	13.941	15.711	15.711	0.000	0.000	0.000
25	B	34	ALA	0	-0.022	-0.011	12.755	-0.693	-0.693	0.000	0.000	0.000
26	B	35	GLY	0	-0.065	-0.018	10.952	1.895	1.895	0.000	0.000	0.000
27	B	36	ALA	0	-0.002	0.006	8.946	3.217	3.217	0.000	0.000	0.000
28	B	37	ASN	0	-0.004	-0.033	8.047	-3.754	-3.754	0.000	0.000	0.000
29	B	38	PRO	0	-0.002	0.023	10.177	0.269	0.269	0.000	0.000	0.000
30	B	39	ASN	0	0.036	0.011	12.153	-1.296	-1.296	0.000	0.000	0.000
31	B	40	ALA	0	-0.092	-0.041	8.312	-0.327	-0.327	0.000	0.000	0.000
32	B	41	PRO	0	0.002	-0.009	8.516	-1.305	-1.305	0.000	0.000	0.000
33	B	42	ASN	0	0.091	0.026	9.033	1.679	1.679	0.000	0.000	0.000
34	B	43	SER	0	-0.060	-0.004	7.627	-0.812	-0.812	0.000	0.000	0.000
35	B	44	TYR	0	-0.012	-0.013	9.052	-1.476	-1.476	0.000	0.000	0.000
36	B	45	GLY	0	-0.062	-0.028	11.641	-1.120	-1.120	0.000	0.000	0.000
37	B	46	ARG	1	0.848	0.889	13.155	-16.082	-16.082	0.000	0.000	0.000
38	B	47	ARG	1	0.942	1.001	13.747	-15.347	-15.347	0.000	0.000	0.000
39	B	48	PRO	0	0.071	-0.007	13.735	-0.854	-0.854	0.000	0.000	0.000
40	B	49	ILE	0	-0.012	-0.038	16.618	-0.318	-0.318	0.000	0.000	0.000
41	B	50	GLN	0	-0.028	0.003	17.273	0.233	0.233	0.000	0.000	0.000
42	B	51	VAL	0	0.047	0.030	16.251	-0.421	-0.421	0.000	0.000	0.000
43	B	52	MET	0	-0.049	0.016	19.310	0.166	0.166	0.000	0.000	0.000
44	B	53	MET	0	0.029	0.064	20.951	-0.487	-0.487	0.000	0.000	0.000
45	B	54	MET	0	0.001	0.010	23.470	-0.225	-0.225	0.000	0.000	0.000
46	B	55	GLY	0	0.058	0.001	26.749	-0.073	-0.073	0.000	0.000	0.000
47	B	56	SER	0	-0.040	-0.019	24.852	-0.172	-0.172	0.000	0.000	0.000
48	B	57	ALA	0	0.027	0.007	25.586	0.432	0.432	0.000	0.000	0.000
49	B	58	ARG	1	0.958	0.979	26.298	-10.950	-10.950	0.000	0.000	0.000
50	B	59	VAL	0	0.018	0.010	20.577	0.348	0.348	0.000	0.000	0.000
51	B	60	ALA	0	0.053	0.015	21.903	0.501	0.501	0.000	0.000	0.000
52	B	61	GLU	-1	-0.979	-1.010	23.043	10.784	10.784	0.000	0.000	0.000
53	B	62	LEU	0	-0.089	-0.026	19.224	0.160	0.160	0.000	0.000	0.000
54	B	63	LEU	0	0.013	-0.013	16.714	0.416	0.416	0.000	0.000	0.000
55	B	64	LEU	0	0.016	0.007	19.652	0.119	0.119	0.000	0.000	0.000
56	B	65	LEU	0	-0.037	0.001	21.876	0.165	0.165	0.000	0.000	0.000
57	B	66	HIS	1	0.832	0.906	16.894	-16.195	-16.195	0.000	0.000	0.000
58	B	67	GLY	0	-0.035	-0.004	17.694	0.865	0.865	0.000	0.000	0.000
59	B	68	ALA	0	0.055	0.037	17.065	0.713	0.713	0.000	0.000	0.000
60	B	69	GLU	-1	-0.897	-0.953	17.007	15.684	15.684	0.000	0.000	0.000
61	B	70	PRO	0	0.068	0.032	20.286	0.159	0.159	0.000	0.000	0.000
62	B	71	ASN	0	-0.021	-0.022	22.519	-0.527	-0.527	0.000	0.000	0.000
63	B	72	CYS	0	-0.051	-0.040	19.073	0.379	0.379	0.000	0.000	0.000
64	B	73	ALA	0	0.012	0.023	21.169	-0.273	-0.273	0.000	0.000	0.000
65	B	74	ASP	-1	-0.815	-0.898	20.206	14.142	14.142	0.000	0.000	0.000
66	B	75	PRO	0	-0.038	-0.011	17.006	-0.433	-0.433	0.000	0.000	0.000
67	B	76	ALA	0	-0.036	0.000	20.004	-0.390	-0.390	0.000	0.000	0.000
68	B	77	THR	0	0.085	0.035	22.826	-0.239	-0.239	0.000	0.000	0.000
69	B	78	LEU	0	-0.032	-0.021	23.653	-0.471	-0.471	0.000	0.000	0.000
70	B	79	THR	0	0.002	-0.009	24.638	-0.164	-0.164	0.000	0.000	0.000
71	B	80	ARG	1	0.908	0.956	24.008	-10.472	-10.472	0.000	0.000	0.000
72	B	81	PRO	0	0.089	0.048	22.899	-0.355	-0.355	0.000	0.000	0.000
73	B	82	VAL	0	-0.002	-0.037	25.247	-0.278	-0.278	0.000	0.000	0.000
74	B	83	HIS	0	-0.025	-0.016	28.064	-0.018	-0.018	0.000	0.000	0.000
75	B	84	ASP	-1	-0.812	-0.915	25.176	10.952	10.952	0.000	0.000	0.000
76	B	85	ALA	0	-0.087	-0.042	28.428	-0.205	-0.205	0.000	0.000	0.000
77	B	86	ALA	0	-0.009	-0.013	29.804	-0.251	-0.251	0.000	0.000	0.000
78	B	87	ARG	1	0.930	0.963	28.276	-10.204	-10.204	0.000	0.000	0.000
79	B	88	GLU	-1	-0.930	-0.954	29.277	9.672	9.672	0.000	0.000	0.000
80	B	89	GLY	0	-0.004	0.019	32.286	-0.138	-0.138	0.000	0.000	0.000
81	B	90	PHE	0	0.004	0.015	29.544	-0.074	-0.074	0.000	0.000	0.000
82	B	91	LEU	0	0.044	0.012	32.085	0.240	0.240	0.000	0.000	0.000
83	B	92	ASP	-1	-0.893	-0.940	31.653	9.230	9.230	0.000	0.000	0.000
84	B	93	THR	0	-0.002	0.006	26.433	0.176	0.176	0.000	0.000	0.000
85	B	94	LEU	0	0.020	0.039	28.896	0.242	0.242	0.000	0.000	0.000
86	B	95	VAL	0	0.020	-0.002	30.640	0.115	0.115	0.000	0.000	0.000
87	B	96	VAL	0	-0.048	0.000	26.612	0.045	0.045	0.000	0.000	0.000
88	B	97	LEU	0	0.011	-0.024	24.819	0.260	0.260	0.000	0.000	0.000
89	B	98	HIS	0	-0.037	-0.002	27.761	0.025	0.025	0.000	0.000	0.000
90	B	99	ARG	1	0.915	0.944	30.681	-8.939	-8.939	0.000	0.000	0.000
91	B	100	ALA	0	0.007	0.020	25.751	-0.007	-0.007	0.000	0.000	0.000
92	B	101	GLY	0	0.015	0.005	27.099	0.262	0.262	0.000	0.000	0.000
93	B	102	ALA	0	-0.081	-0.026	26.137	-0.168	-0.168	0.000	0.000	0.000
94	B	103	ARG	1	0.926	0.955	27.785	-10.238	-10.238	0.000	0.000	0.000
95	B	104	LEU	0	0.022	-0.001	30.821	0.186	0.186	0.000	0.000	0.000
96	B	105	ASP	-1	-0.842	-0.924	32.689	7.914	7.914	0.000	0.000	0.000
97	B	106	VAL	0	-0.143	-0.044	27.893	0.150	0.150	0.000	0.000	0.000
98	B	107	ARG	1	0.935	0.982	30.754	-8.297	-8.297	0.000	0.000	0.000
99	B	108	ASP	-1	-0.772	-0.886	28.619	9.663	9.663	0.000	0.000	0.000
100	B	109	ALA	0	0.038	0.022	28.009	-0.278	-0.278	0.000	0.000	0.000
101	B	110	TRP	0	-0.104	-0.032	27.961	-0.113	-0.113	0.000	0.000	0.000
102	B	111	GLY	0	-0.018	-0.025	32.472	-0.269	-0.269	0.000	0.000	0.000
103	B	112	ARG	1	0.925	0.947	32.936	-8.553	-8.553	0.000	0.000	0.000
104	B	113	LEU	0	-0.001	0.014	32.782	0.353	0.353	0.000	0.000	0.000
105	B	114	PRO	0	-0.031	-0.031	31.261	-0.050	-0.050	0.000	0.000	0.000
106	B	115	VAL	0	0.035	0.019	33.517	-0.027	-0.027	0.000	0.000	0.000
107	B	116	ASP	-1	-0.773	-0.881	36.802	7.715	7.715	0.000	0.000	0.000
108	B	117	LEU	0	-0.028	-0.002	31.622	-0.056	-0.056	0.000	0.000	0.000
109	B	118	ALA	0	0.012	-0.004	35.894	-0.102	-0.102	0.000	0.000	0.000
110	B	119	GLU	-1	-1.023	-1.022	37.330	7.017	7.017	0.000	0.000	0.000
111	B	120	GLU	-1	-1.012	-0.998	37.965	7.766	7.766	0.000	0.000	0.000
112	B	121	LEU	0	-0.048	-0.037	35.834	-0.134	-0.134	0.000	0.000	0.000
113	B	122	GLY	0	0.013	0.032	39.089	-0.089	-0.089	0.000	0.000	0.000
114	B	123	HIS	0	-0.028	-0.008	35.153	-0.285	-0.285	0.000	0.000	0.000
115	B	124	ARG	1	0.937	0.958	40.023	-6.621	-6.621	0.000	0.000	0.000
116	B	125	ASP	-1	-0.834	-0.930	38.839	7.785	7.785	0.000	0.000	0.000
117	B	126	VAL	0	0.021	0.018	35.386	-0.033	-0.033	0.000	0.000	0.000
118	B	127	ALA	0	0.039	0.011	38.450	-0.015	-0.015	0.000	0.000	0.000
119	B	128	ARG	1	0.834	0.903	40.806	-6.954	-6.954	0.000	0.000	0.000
120	B	129	TYR	0	-0.103	-0.066	34.872	-0.101	-0.101	0.000	0.000	0.000
121	B	130	LEU	0	0.066	0.044	34.656	0.147	0.147	0.000	0.000	0.000
122	B	131	ARG	1	0.911	0.995	38.835	-6.989	-6.989	0.000	0.000	0.000
123	B	132	ALA	0	-0.060	-0.066	41.289	-0.249	-0.249	0.000	0.000	0.000
124	B	133	ALA	0	-0.032	-0.003	38.740	0.139	0.139	0.000	0.000	0.000
125	B	134	ALA	0	0.020	0.020	38.107	0.139	0.139	0.000	0.000	0.000

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