FMO DATABASE

FMODB ID: 37NQL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1016331.906618
FMO2-HF: Nuclear repulsion	968900.234273
FMO2-HF: Total energy	-47431.672345
FMO2-MP2: Total energy	-47570.484798

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.
-9.306	-7.529	-0.013	-0.845	-0.918	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 : -0.966 / q_NPA : -0.993

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	0.047	3.885	-3.070	-1.293	-0.013	-0.845	-0.918
4	B	13	ALA	0	0.019	-0.020	6.057	-4.688	-4.688	0.000	0.000	0.000
5	B	14	ASP	-1	-0.900	-0.936	7.695	25.305	25.305	0.000	0.000	0.000
6	B	15	TRP	0	-0.003	0.000	7.007	-3.605	-3.605	0.000	0.000	0.000
7	B	16	LEU	0	0.030	0.009	10.941	-2.104	-2.104	0.000	0.000	0.000
8	B	17	ALA	0	0.004	0.016	12.443	-1.635	-1.635	0.000	0.000	0.000
9	B	18	THR	0	0.057	0.024	13.396	-1.609	-1.609	0.000	0.000	0.000
10	B	19	ALA	0	0.055	0.037	15.102	-1.257	-1.257	0.000	0.000	0.000
11	B	20	ALA	0	0.059	0.007	16.866	-1.185	-1.185	0.000	0.000	0.000
12	B	21	ALA	0	-0.034	-0.001	17.948	-0.895	-0.895	0.000	0.000	0.000
13	B	22	ARG	1	0.788	0.899	18.034	-16.406	-16.406	0.000	0.000	0.000
14	B	23	GLY	0	0.038	0.012	21.121	-0.645	-0.645	0.000	0.000	0.000
15	B	24	ARG	1	0.779	0.897	19.221	-13.646	-13.646	0.000	0.000	0.000
16	B	25	VAL	0	0.017	0.003	20.280	0.586	0.586	0.000	0.000	0.000
17	B	26	GLU	-1	-0.751	-0.855	20.845	13.295	13.295	0.000	0.000	0.000
18	B	27	GLU	-1	-0.801	-0.892	16.728	16.942	16.942	0.000	0.000	0.000
19	B	28	VAL	0	0.017	-0.005	16.511	1.018	1.018	0.000	0.000	0.000
20	B	29	ARG	1	0.896	0.925	16.510	-12.739	-12.739	0.000	0.000	0.000
21	B	30	ALA	0	-0.028	0.003	16.845	0.691	0.691	0.000	0.000	0.000
22	B	31	LEU	0	0.017	-0.007	10.317	0.658	0.658	0.000	0.000	0.000
23	B	32	LEU	0	0.027	0.018	12.678	1.352	1.352	0.000	0.000	0.000
24	B	33	GLU	-1	-0.967	-0.972	14.037	16.039	16.039	0.000	0.000	0.000
25	B	34	ALA	0	-0.026	-0.017	12.719	-0.739	-0.739	0.000	0.000	0.000
26	B	35	GLY	0	-0.066	-0.016	10.976	1.930	1.930	0.000	0.000	0.000
27	B	36	ALA	0	0.003	0.004	9.042	3.310	3.310	0.000	0.000	0.000
28	B	37	ASN	0	0.011	-0.021	7.924	-3.566	-3.566	0.000	0.000	0.000
29	B	38	PRO	0	-0.005	0.017	10.279	0.187	0.187	0.000	0.000	0.000
30	B	39	ASN	0	-0.019	-0.019	11.902	0.270	0.270	0.000	0.000	0.000
31	B	40	ALA	0	-0.040	-0.008	8.526	-0.400	-0.400	0.000	0.000	0.000
32	B	41	PRO	0	0.001	-0.007	8.598	-1.386	-1.386	0.000	0.000	0.000
33	B	42	ASN	0	0.071	0.010	9.211	1.580	1.580	0.000	0.000	0.000
34	B	43	SER	0	-0.068	-0.026	7.348	-0.842	-0.842	0.000	0.000	0.000
35	B	44	TYR	0	0.001	-0.001	9.019	-1.495	-1.495	0.000	0.000	0.000
36	B	45	GLY	0	-0.062	-0.032	11.602	-1.177	-1.177	0.000	0.000	0.000
37	B	46	ARG	1	0.891	0.921	13.294	-16.288	-16.288	0.000	0.000	0.000
38	B	47	ARG	1	0.892	0.978	13.882	-15.308	-15.308	0.000	0.000	0.000
39	B	48	PRO	0	0.062	-0.001	13.618	-0.960	-0.960	0.000	0.000	0.000
40	B	49	ILE	0	-0.025	-0.029	16.618	-0.328	-0.328	0.000	0.000	0.000
41	B	50	GLN	0	-0.047	-0.010	18.002	0.187	0.187	0.000	0.000	0.000
42	B	51	VAL	0	0.028	0.004	15.996	-0.403	-0.403	0.000	0.000	0.000
43	B	52	MET	0	-0.039	0.008	19.296	0.150	0.150	0.000	0.000	0.000
44	B	53	MET	0	0.012	0.030	20.946	-0.498	-0.498	0.000	0.000	0.000
45	B	54	MET	0	0.011	0.007	23.588	-0.216	-0.216	0.000	0.000	0.000
46	B	55	GLY	0	0.071	0.011	26.743	-0.070	-0.070	0.000	0.000	0.000
47	B	56	SER	0	-0.055	-0.024	24.923	-0.061	-0.061	0.000	0.000	0.000
48	B	57	ALA	0	0.038	0.004	25.649	0.446	0.446	0.000	0.000	0.000
49	B	58	ARG	1	0.903	0.943	26.350	-11.244	-11.244	0.000	0.000	0.000
50	B	59	VAL	0	0.016	0.008	20.609	0.344	0.344	0.000	0.000	0.000
51	B	60	ALA	0	0.050	0.014	21.978	0.508	0.508	0.000	0.000	0.000
52	B	61	GLU	-1	-0.955	-0.996	23.126	10.810	10.810	0.000	0.000	0.000
53	B	62	LEU	0	-0.080	-0.029	19.119	0.145	0.145	0.000	0.000	0.000
54	B	63	LEU	0	0.008	-0.013	16.829	0.443	0.443	0.000	0.000	0.000
55	B	64	LEU	0	0.004	-0.002	19.740	0.118	0.118	0.000	0.000	0.000
56	B	65	LEU	0	-0.039	0.003	21.976	0.145	0.145	0.000	0.000	0.000
57	B	66	HIS	1	0.796	0.863	17.124	-16.307	-16.307	0.000	0.000	0.000
58	B	67	GLY	0	-0.034	-0.001	17.800	0.902	0.902	0.000	0.000	0.000
59	B	68	ALA	0	0.040	0.018	17.167	0.777	0.777	0.000	0.000	0.000
60	B	69	GLU	-1	-0.838	-0.916	16.929	15.821	15.821	0.000	0.000	0.000
61	B	70	PRO	0	0.061	0.031	20.456	0.186	0.186	0.000	0.000	0.000
62	B	71	ASN	0	-0.054	-0.048	22.711	-0.615	-0.615	0.000	0.000	0.000
63	B	72	CYS	0	-0.028	-0.021	19.201	0.310	0.310	0.000	0.000	0.000
64	B	73	ALA	0	0.028	0.027	21.381	-0.281	-0.281	0.000	0.000	0.000
65	B	74	ASP	-1	-0.792	-0.873	20.433	14.083	14.083	0.000	0.000	0.000
66	B	75	PRO	0	-0.022	-0.003	17.251	-0.430	-0.430	0.000	0.000	0.000
67	B	76	ALA	0	-0.040	0.002	20.258	-0.365	-0.365	0.000	0.000	0.000
68	B	77	THR	0	0.021	-0.019	23.013	-0.435	-0.435	0.000	0.000	0.000
69	B	78	LEU	0	-0.012	-0.019	23.904	-0.454	-0.454	0.000	0.000	0.000
70	B	79	THR	0	-0.013	-0.009	24.990	-0.129	-0.129	0.000	0.000	0.000
71	B	80	ARG	1	0.882	0.950	24.246	-10.510	-10.510	0.000	0.000	0.000
72	B	81	PRO	0	0.096	0.040	23.010	-0.350	-0.350	0.000	0.000	0.000
73	B	82	VAL	0	-0.034	-0.024	25.430	-0.269	-0.269	0.000	0.000	0.000
74	B	83	HIS	0	-0.009	-0.005	28.294	-0.014	-0.014	0.000	0.000	0.000
75	B	84	ASP	-1	-0.778	-0.888	25.758	10.843	10.843	0.000	0.000	0.000
76	B	85	ALA	0	-0.070	-0.031	28.420	-0.201	-0.201	0.000	0.000	0.000
77	B	86	ALA	0	-0.009	-0.013	29.804	-0.250	-0.250	0.000	0.000	0.000
78	B	87	ARG	1	0.867	0.918	28.209	-10.292	-10.292	0.000	0.000	0.000
79	B	88	GLU	-1	-0.943	-0.970	29.592	9.663	9.663	0.000	0.000	0.000
80	B	89	GLY	0	0.012	0.028	32.274	-0.134	-0.134	0.000	0.000	0.000
81	B	90	PHE	0	0.004	0.022	29.881	-0.098	-0.098	0.000	0.000	0.000
82	B	91	LEU	0	0.041	0.012	32.145	0.246	0.246	0.000	0.000	0.000
83	B	92	ASP	-1	-0.895	-0.941	31.679	9.309	9.309	0.000	0.000	0.000
84	B	93	THR	0	-0.012	0.005	26.888	0.197	0.197	0.000	0.000	0.000
85	B	94	LEU	0	0.011	0.026	28.968	0.238	0.238	0.000	0.000	0.000
86	B	95	VAL	0	0.023	-0.002	30.715	0.111	0.111	0.000	0.000	0.000
87	B	96	VAL	0	-0.073	-0.019	27.130	0.061	0.061	0.000	0.000	0.000
88	B	97	LEU	0	0.012	-0.009	24.986	0.259	0.259	0.000	0.000	0.000
89	B	98	HIS	0	-0.022	0.006	27.841	0.042	0.042	0.000	0.000	0.000
90	B	99	ARG	1	0.920	0.952	30.769	-9.103	-9.103	0.000	0.000	0.000
91	B	100	ALA	0	0.004	0.014	25.789	-0.001	-0.001	0.000	0.000	0.000
92	B	101	GLY	0	0.022	0.010	27.195	0.262	0.262	0.000	0.000	0.000
93	B	102	ALA	0	-0.089	-0.029	26.322	-0.162	-0.162	0.000	0.000	0.000
94	B	103	ARG	1	0.954	0.965	27.963	-10.155	-10.155	0.000	0.000	0.000
95	B	104	LEU	0	0.008	-0.001	31.008	0.184	0.184	0.000	0.000	0.000
96	B	105	ASP	-1	-0.868	-0.933	32.894	7.966	7.966	0.000	0.000	0.000
97	B	106	VAL	0	-0.092	-0.041	28.207	0.126	0.126	0.000	0.000	0.000
98	B	107	ARG	1	0.858	0.939	31.010	-8.269	-8.269	0.000	0.000	0.000
99	B	108	ASP	-1	-0.781	-0.900	28.879	9.771	9.771	0.000	0.000	0.000
100	B	109	ALA	0	0.038	0.031	28.232	-0.285	-0.285	0.000	0.000	0.000
101	B	110	TRP	0	-0.089	-0.032	28.054	-0.142	-0.142	0.000	0.000	0.000
102	B	111	GLY	0	-0.007	-0.020	32.728	-0.271	-0.271	0.000	0.000	0.000
103	B	112	ARG	1	0.805	0.869	33.162	-8.524	-8.524	0.000	0.000	0.000
104	B	113	LEU	0	-0.030	-0.012	33.018	0.330	0.330	0.000	0.000	0.000
105	B	114	PRO	0	-0.039	-0.033	31.402	-0.065	-0.065	0.000	0.000	0.000
106	B	115	VAL	0	0.046	0.020	33.741	-0.054	-0.054	0.000	0.000	0.000
107	B	116	ASP	-1	-0.723	-0.839	36.992	7.817	7.817	0.000	0.000	0.000
108	B	117	LEU	0	-0.023	-0.001	31.732	-0.075	-0.075	0.000	0.000	0.000
109	B	118	ALA	0	0.030	0.009	35.921	-0.105	-0.105	0.000	0.000	0.000
110	B	119	GLU	-1	-0.890	-0.943	37.309	6.948	6.948	0.000	0.000	0.000
111	B	120	GLU	-1	-0.882	-0.904	37.653	7.831	7.831	0.000	0.000	0.000
112	B	121	LEU	0	-0.055	-0.035	35.629	-0.141	-0.141	0.000	0.000	0.000
113	B	122	GLY	0	0.015	0.029	39.069	-0.087	-0.087	0.000	0.000	0.000
114	B	123	HIS	0	-0.004	0.006	35.425	-0.266	-0.266	0.000	0.000	0.000
115	B	124	ARG	1	0.934	0.952	40.008	-6.615	-6.615	0.000	0.000	0.000
116	B	125	ASP	-1	-0.843	-0.923	38.905	7.832	7.832	0.000	0.000	0.000
117	B	126	VAL	0	0.025	0.016	35.423	-0.031	-0.031	0.000	0.000	0.000
118	B	127	ALA	0	0.031	0.009	38.450	-0.007	-0.007	0.000	0.000	0.000
119	B	128	ARG	1	0.862	0.920	40.894	-7.010	-7.010	0.000	0.000	0.000
120	B	129	TYR	0	-0.110	-0.082	35.126	-0.088	-0.088	0.000	0.000	0.000
121	B	130	LEU	0	0.056	0.045	34.919	0.156	0.156	0.000	0.000	0.000
122	B	131	ARG	1	0.777	0.903	39.035	-7.044	-7.044	0.000	0.000	0.000
123	B	132	ALA	0	-0.057	-0.061	41.485	-0.248	-0.248	0.000	0.000	0.000
124	B	133	ALA	0	-0.032	-0.005	38.858	0.148	0.148	0.000	0.000	0.000
125	B	134	ALA	0	0.028	0.022	38.361	0.163	0.163	0.000	0.000	0.000

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