FMO DATABASE

FMODB ID: MVN7Z

Calculation Name: 2V5Q-C-Xray372

Preferred Name: Serine/threonine-protein kinase PLK1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2V5Q

Chain ID: C

ChEMBL ID: CHEMBL3024

UniProt ID: P53350

Base Structure: X-ray

Registration Date: 2023-06-22

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1027081.532366
FMO2-HF: Nuclear repulsion	979715.94013
FMO2-HF: Total energy	-47365.592235
FMO2-MP2: Total energy	-47505.802102

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(C:12:SER)

Summations of interaction energy for fragment #1(C:12:SER)

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.
-19.604	-17.124	4.548	-3.055	-3.971	0.029

Interaction energy analysis for fragmet #1(C:12:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.023

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	C	14	LEU	0	0.077	0.030	3.808	-1.209	0.570	-0.004	-0.792	-0.982	0.002
4	C	15	GLY	0	0.053	0.035	3.498	-1.404	-0.752	0.022	-0.211	-0.463	0.001
5	C	16	LYS	1	0.854	0.924	2.065	-17.724	-17.675	4.530	-2.052	-2.526	0.026
6	C	17	LYS	1	0.923	0.945	6.130	-1.382	-1.382	0.000	0.000	0.000	0.000
7	C	18	LEU	0	0.028	0.029	7.653	-0.246	-0.246	0.000	0.000	0.000	0.000
8	C	19	LEU	0	-0.025	-0.003	6.649	-0.176	-0.176	0.000	0.000	0.000	0.000
9	C	20	GLU	-1	-0.959	-0.990	9.667	1.181	1.181	0.000	0.000	0.000	0.000
10	C	21	ALA	0	-0.019	-0.014	11.895	-0.126	-0.126	0.000	0.000	0.000	0.000
11	C	22	ALA	0	-0.001	0.002	12.839	-0.089	-0.089	0.000	0.000	0.000	0.000
12	C	23	ARG	1	0.864	0.922	12.807	-0.677	-0.677	0.000	0.000	0.000	0.000
13	C	24	ALA	0	-0.051	-0.023	15.941	-0.060	-0.060	0.000	0.000	0.000	0.000
14	C	25	GLY	0	0.059	0.040	17.933	-0.034	-0.034	0.000	0.000	0.000	0.000
15	C	26	GLN	0	-0.099	-0.051	16.281	-0.042	-0.042	0.000	0.000	0.000	0.000
16	C	27	ASP	-1	-0.756	-0.880	17.009	0.303	0.303	0.000	0.000	0.000	0.000
17	C	28	ASP	-1	-0.861	-0.925	18.225	0.254	0.254	0.000	0.000	0.000	0.000
18	C	29	GLU	-1	-0.923	-0.969	13.317	0.603	0.603	0.000	0.000	0.000	0.000
19	C	30	VAL	0	0.006	0.006	13.264	0.081	0.081	0.000	0.000	0.000	0.000
20	C	31	ARG	1	0.765	0.857	13.449	-0.228	-0.228	0.000	0.000	0.000	0.000
21	C	32	ILE	0	-0.011	-0.002	13.226	-0.019	-0.019	0.000	0.000	0.000	0.000
22	C	33	LEU	0	0.001	0.000	8.722	0.028	0.028	0.000	0.000	0.000	0.000
23	C	34	ILE	0	0.015	0.012	9.689	0.098	0.098	0.000	0.000	0.000	0.000
24	C	35	ALA	0	-0.047	-0.015	11.453	-0.068	-0.068	0.000	0.000	0.000	0.000
25	C	36	ASN	0	-0.132	-0.074	9.655	-0.155	-0.155	0.000	0.000	0.000	0.000
26	C	37	GLY	0	-0.023	-0.008	8.444	-0.040	-0.040	0.000	0.000	0.000	0.000
27	C	38	ALA	0	-0.069	-0.036	5.810	0.222	0.222	0.000	0.000	0.000	0.000
28	C	39	ASP	-1	-0.863	-0.933	5.450	-0.334	-0.334	0.000	0.000	0.000	0.000
29	C	40	VAL	0	0.024	0.002	7.081	0.231	0.231	0.000	0.000	0.000	0.000
30	C	41	ASN	0	-0.041	-0.015	9.355	0.006	0.006	0.000	0.000	0.000	0.000
31	C	42	ALA	0	-0.027	0.001	5.079	-0.073	-0.073	0.000	0.000	0.000	0.000
32	C	43	VAL	0	0.022	0.008	6.334	-0.045	-0.045	0.000	0.000	0.000	0.000
33	C	44	ASP	-1	-0.734	-0.842	7.270	0.950	0.950	0.000	0.000	0.000	0.000
34	C	45	ASN	0	-0.069	-0.055	9.691	-0.081	-0.081	0.000	0.000	0.000	0.000
35	C	46	THR	0	-0.085	-0.056	11.725	-0.114	-0.114	0.000	0.000	0.000	0.000
36	C	47	GLY	0	0.048	0.017	12.612	-0.064	-0.064	0.000	0.000	0.000	0.000
37	C	48	LEU	0	-0.018	0.011	13.257	-0.035	-0.035	0.000	0.000	0.000	0.000
38	C	49	THR	0	0.051	-0.005	10.702	0.117	0.117	0.000	0.000	0.000	0.000
39	C	50	PRO	0	-0.013	-0.027	9.457	-0.021	-0.021	0.000	0.000	0.000	0.000
40	C	51	LEU	0	0.043	0.033	12.243	-0.032	-0.032	0.000	0.000	0.000	0.000
41	C	52	HIS	0	0.045	0.043	15.011	0.019	0.019	0.000	0.000	0.000	0.000
42	C	53	LEU	0	-0.057	-0.024	12.154	-0.012	-0.012	0.000	0.000	0.000	0.000
43	C	54	ALA	0	0.004	0.010	16.092	-0.019	-0.019	0.000	0.000	0.000	0.000
44	C	55	ALA	0	-0.004	-0.005	17.935	-0.027	-0.027	0.000	0.000	0.000	0.000
45	C	56	VAL	0	-0.028	-0.013	19.021	-0.019	-0.019	0.000	0.000	0.000	0.000
46	C	57	SER	0	-0.068	-0.047	19.013	-0.012	-0.012	0.000	0.000	0.000	0.000
47	C	58	GLY	0	0.040	0.029	21.813	-0.005	-0.005	0.000	0.000	0.000	0.000
48	C	59	HIS	0	-0.040	-0.016	18.886	-0.029	-0.029	0.000	0.000	0.000	0.000
49	C	60	LEU	0	0.041	0.010	20.946	0.015	0.015	0.000	0.000	0.000	0.000
50	C	61	GLU	-1	-0.916	-0.958	22.543	0.191	0.191	0.000	0.000	0.000	0.000
51	C	62	ILE	0	0.002	0.004	16.166	0.007	0.007	0.000	0.000	0.000	0.000
52	C	63	VAL	0	0.012	0.014	17.869	0.015	0.015	0.000	0.000	0.000	0.000
53	C	64	GLU	-1	-0.745	-0.832	19.368	0.126	0.126	0.000	0.000	0.000	0.000
54	C	65	VAL	0	-0.036	-0.018	16.680	-0.016	-0.016	0.000	0.000	0.000	0.000
55	C	66	LEU	0	0.000	0.000	12.980	0.005	0.005	0.000	0.000	0.000	0.000
56	C	67	LEU	0	0.003	0.009	16.400	-0.021	-0.021	0.000	0.000	0.000	0.000
57	C	68	LYS	1	0.761	0.859	19.106	-0.154	-0.154	0.000	0.000	0.000	0.000
58	C	69	HIS	0	-0.133	-0.070	14.379	-0.024	-0.024	0.000	0.000	0.000	0.000
59	C	70	GLY	0	-0.034	-0.013	14.803	-0.006	-0.006	0.000	0.000	0.000	0.000
60	C	71	ALA	0	-0.035	-0.023	14.065	-0.021	-0.021	0.000	0.000	0.000	0.000
61	C	72	ASP	-1	-0.906	-0.964	14.587	0.030	0.030	0.000	0.000	0.000	0.000
62	C	73	VAL	0	-0.011	-0.013	16.461	0.033	0.033	0.000	0.000	0.000	0.000
63	C	74	ASP	-1	-0.797	-0.898	19.174	0.098	0.098	0.000	0.000	0.000	0.000
64	C	75	ALA	0	-0.013	0.013	14.740	-0.012	-0.012	0.000	0.000	0.000	0.000
65	C	76	ALA	0	-0.006	-0.012	16.853	0.027	0.027	0.000	0.000	0.000	0.000
66	C	77	ASP	-1	-0.817	-0.913	16.047	0.202	0.202	0.000	0.000	0.000	0.000
67	C	78	VAL	0	-0.071	-0.047	16.982	-0.035	-0.035	0.000	0.000	0.000	0.000
68	C	79	TYR	0	-0.067	-0.032	18.443	-0.028	-0.028	0.000	0.000	0.000	0.000
69	C	80	GLY	0	-0.009	0.001	20.420	-0.020	-0.020	0.000	0.000	0.000	0.000
70	C	81	PHE	0	-0.038	-0.008	20.658	-0.011	-0.011	0.000	0.000	0.000	0.000
71	C	82	THR	0	0.017	0.012	19.434	0.022	0.022	0.000	0.000	0.000	0.000
72	C	83	PRO	0	0.003	-0.021	17.349	0.010	0.010	0.000	0.000	0.000	0.000
73	C	84	LEU	0	0.030	0.022	20.053	0.003	0.003	0.000	0.000	0.000	0.000
74	C	85	HIS	0	0.002	0.008	23.203	0.007	0.007	0.000	0.000	0.000	0.000
75	C	86	LEU	0	0.011	0.003	19.091	0.002	0.002	0.000	0.000	0.000	0.000
76	C	87	ALA	0	0.014	0.021	23.206	0.002	0.002	0.000	0.000	0.000	0.000
77	C	88	ALA	0	-0.021	-0.016	24.738	-0.006	-0.006	0.000	0.000	0.000	0.000
78	C	89	MET	0	-0.034	-0.016	24.173	-0.008	-0.008	0.000	0.000	0.000	0.000
79	C	90	THR	0	-0.020	-0.028	24.719	0.005	0.005	0.000	0.000	0.000	0.000
80	C	91	GLY	0	0.015	0.021	27.725	0.002	0.002	0.000	0.000	0.000	0.000
81	C	92	HIS	0	0.002	0.002	25.551	-0.005	-0.005	0.000	0.000	0.000	0.000
82	C	93	LEU	0	0.048	0.024	27.994	0.001	0.001	0.000	0.000	0.000	0.000
83	C	94	GLU	-1	-0.893	-0.960	28.293	0.123	0.123	0.000	0.000	0.000	0.000
84	C	95	ILE	0	-0.023	-0.003	22.949	0.001	0.001	0.000	0.000	0.000	0.000
85	C	96	VAL	0	0.025	0.016	25.364	-0.001	-0.001	0.000	0.000	0.000	0.000
86	C	97	GLU	-1	-0.818	-0.900	27.421	0.071	0.071	0.000	0.000	0.000	0.000
87	C	98	VAL	0	-0.060	-0.026	23.830	-0.008	-0.008	0.000	0.000	0.000	0.000
88	C	99	LEU	0	0.032	0.008	20.678	-0.004	-0.004	0.000	0.000	0.000	0.000
89	C	100	LEU	0	0.011	0.012	24.400	-0.011	-0.011	0.000	0.000	0.000	0.000
90	C	101	LYS	1	0.864	0.945	27.623	-0.069	-0.069	0.000	0.000	0.000	0.000
91	C	102	TYR	0	-0.126	-0.097	22.865	-0.011	-0.011	0.000	0.000	0.000	0.000
92	C	103	GLY	0	-0.049	-0.019	24.088	-0.005	-0.005	0.000	0.000	0.000	0.000
93	C	104	ALA	0	-0.013	0.004	24.017	-0.007	-0.007	0.000	0.000	0.000	0.000
94	C	105	ASP	-1	-0.877	-0.948	25.043	0.036	0.036	0.000	0.000	0.000	0.000
95	C	106	VAL	0	-0.038	-0.027	27.261	0.008	0.008	0.000	0.000	0.000	0.000
96	C	107	ASN	0	-0.082	-0.038	29.734	0.005	0.005	0.000	0.000	0.000	0.000
97	C	108	ALA	0	0.041	0.041	24.836	-0.004	-0.004	0.000	0.000	0.000	0.000
98	C	109	PHE	0	-0.050	-0.038	26.567	0.004	0.004	0.000	0.000	0.000	0.000
99	C	110	ASP	-1	-0.757	-0.844	24.447	0.088	0.088	0.000	0.000	0.000	0.000
100	C	111	MET	0	-0.060	-0.059	22.866	-0.018	-0.018	0.000	0.000	0.000	0.000
101	C	112	THR	0	-0.141	-0.083	26.084	-0.008	-0.008	0.000	0.000	0.000	0.000
102	C	113	GLY	0	-0.044	-0.020	28.798	-0.006	-0.006	0.000	0.000	0.000	0.000
103	C	114	SER	0	-0.040	-0.009	29.287	-0.005	-0.005	0.000	0.000	0.000	0.000
104	C	115	THR	0	0.053	0.001	28.525	0.002	0.002	0.000	0.000	0.000	0.000
105	C	116	PRO	0	0.039	0.003	26.371	0.004	0.004	0.000	0.000	0.000	0.000
106	C	117	LEU	0	0.019	0.015	28.832	0.003	0.003	0.000	0.000	0.000	0.000
107	C	118	HIS	0	-0.020	0.011	31.963	0.004	0.004	0.000	0.000	0.000	0.000
108	C	119	LEU	0	0.034	0.014	26.705	0.001	0.001	0.000	0.000	0.000	0.000
109	C	120	ALA	0	-0.003	0.009	30.831	0.003	0.003	0.000	0.000	0.000	0.000
110	C	121	ALA	0	-0.055	-0.041	32.402	-0.001	-0.001	0.000	0.000	0.000	0.000
111	C	122	ASP	-1	-0.996	-0.991	33.084	0.085	0.085	0.000	0.000	0.000	0.000
112	C	123	GLU	-1	-0.909	-0.954	30.337	0.129	0.129	0.000	0.000	0.000	0.000
113	C	124	GLY	0	-0.051	-0.012	33.776	0.000	0.000	0.000	0.000	0.000	0.000
114	C	125	HIS	0	-0.014	0.005	30.674	-0.007	-0.007	0.000	0.000	0.000	0.000
115	C	126	LEU	0	-0.039	-0.045	34.796	-0.002	-0.002	0.000	0.000	0.000	0.000
116	C	127	GLU	-1	-0.906	-0.950	36.076	0.083	0.083	0.000	0.000	0.000	0.000
117	C	128	ILE	0	-0.016	0.005	30.635	-0.002	-0.002	0.000	0.000	0.000	0.000
118	C	129	VAL	0	-0.006	0.006	33.763	-0.003	-0.003	0.000	0.000	0.000	0.000
119	C	130	GLU	-1	-0.950	-0.978	35.934	0.056	0.056	0.000	0.000	0.000	0.000
120	C	131	VAL	0	-0.041	-0.026	32.371	-0.005	-0.005	0.000	0.000	0.000	0.000
121	C	132	LEU	0	0.014	0.011	29.750	-0.003	-0.003	0.000	0.000	0.000	0.000
122	C	133	LEU	0	-0.020	-0.012	33.797	-0.006	-0.006	0.000	0.000	0.000	0.000
123	C	134	LYS	1	0.777	0.904	35.625	-0.071	-0.071	0.000	0.000	0.000	0.000
124	C	135	TYR	0	-0.116	-0.084	33.066	-0.006	-0.006	0.000	0.000	0.000	0.000
125	C	136	GLY	0	-0.015	0.001	34.320	-0.002	-0.002	0.000	0.000	0.000	0.000
126	C	137	ALA	0	0.010	0.010	33.749	-0.003	-0.003	0.000	0.000	0.000	0.000
127	C	138	ASP	-1	-0.854	-0.928	34.964	0.029	0.029	0.000	0.000	0.000	0.000
128	C	139	VAL	0	-0.010	-0.018	36.387	0.002	0.002	0.000	0.000	0.000	0.000
129	C	140	ASN	0	-0.174	-0.092	38.702	0.001	0.001	0.000	0.000	0.000	0.000
130	C	141	ALA	0	-0.001	0.014	33.645	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:12:SER)