FMO DATABASE

FMODB ID: 94862

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1026477.934661
FMO2-HF: Nuclear repulsion	979112.51458
FMO2-HF: Total energy	-47365.420081
FMO2-MP2: Total energy	-47505.654826

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.
-21.605	-16.661	2.603	-3.289	-4.258	0.026

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 : 0.053 / q_NPA : 0.013

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	0.086	0.041	3.311	-2.609	-0.002	0.058	-1.249	-1.416	0.004
4	C	15	GLY	0	0.055	0.036	3.167	-3.129	-2.066	0.114	-0.452	-0.725	0.004
5	C	16	LYS	1	0.885	0.932	2.299	-15.786	-14.512	2.431	-1.588	-2.117	0.018
6	C	17	LYS	1	0.919	0.938	5.845	-1.599	-1.599	0.000	0.000	0.000	0.000
7	C	18	LEU	0	0.016	0.021	7.277	-0.283	-0.283	0.000	0.000	0.000	0.000
8	C	19	LEU	0	-0.036	-0.015	6.450	-0.195	-0.195	0.000	0.000	0.000	0.000
9	C	20	GLU	-1	-0.966	-0.983	9.656	1.076	1.076	0.000	0.000	0.000	0.000
10	C	21	ALA	0	-0.010	-0.010	11.553	-0.134	-0.134	0.000	0.000	0.000	0.000
11	C	22	ALA	0	-0.006	-0.006	12.559	-0.097	-0.097	0.000	0.000	0.000	0.000
12	C	23	ARG	1	0.922	0.965	13.350	-0.618	-0.618	0.000	0.000	0.000	0.000
13	C	24	ALA	0	-0.053	-0.024	15.734	-0.057	-0.057	0.000	0.000	0.000	0.000
14	C	25	GLY	0	0.033	0.023	17.495	-0.038	-0.038	0.000	0.000	0.000	0.000
15	C	26	GLN	0	-0.061	-0.036	16.340	-0.039	-0.039	0.000	0.000	0.000	0.000
16	C	27	ASP	-1	-0.789	-0.897	16.922	0.317	0.317	0.000	0.000	0.000	0.000
17	C	28	ASP	-1	-0.902	-0.958	17.951	0.287	0.287	0.000	0.000	0.000	0.000
18	C	29	GLU	-1	-0.911	-0.970	13.103	0.710	0.710	0.000	0.000	0.000	0.000
19	C	30	VAL	0	0.017	0.017	13.261	0.097	0.097	0.000	0.000	0.000	0.000
20	C	31	ARG	1	0.830	0.905	13.330	-0.230	-0.230	0.000	0.000	0.000	0.000
21	C	32	ILE	0	-0.011	-0.006	13.301	-0.018	-0.018	0.000	0.000	0.000	0.000
22	C	33	LEU	0	-0.005	-0.004	8.473	0.060	0.060	0.000	0.000	0.000	0.000
23	C	34	ILE	0	0.011	0.007	9.592	0.130	0.130	0.000	0.000	0.000	0.000
24	C	35	ALA	0	-0.045	-0.010	11.535	-0.079	-0.079	0.000	0.000	0.000	0.000
25	C	36	ASN	0	-0.132	-0.073	9.754	-0.166	-0.166	0.000	0.000	0.000	0.000
26	C	37	GLY	0	-0.021	-0.001	8.453	0.013	0.013	0.000	0.000	0.000	0.000
27	C	38	ALA	0	-0.069	-0.028	5.666	0.144	0.144	0.000	0.000	0.000	0.000
28	C	39	ASP	-1	-0.878	-0.944	5.143	-0.753	-0.753	0.000	0.000	0.000	0.000
29	C	40	VAL	0	0.013	-0.011	6.677	0.203	0.203	0.000	0.000	0.000	0.000
30	C	41	ASN	0	-0.030	0.004	9.034	0.071	0.071	0.000	0.000	0.000	0.000
31	C	42	ALA	0	-0.028	-0.003	5.124	-0.106	-0.106	0.000	0.000	0.000	0.000
32	C	43	VAL	0	0.014	0.019	6.476	0.007	0.007	0.000	0.000	0.000	0.000
33	C	44	ASP	-1	-0.801	-0.908	7.285	0.901	0.901	0.000	0.000	0.000	0.000
34	C	45	ASN	0	-0.073	-0.058	9.514	-0.135	-0.135	0.000	0.000	0.000	0.000
35	C	46	THR	0	-0.067	-0.028	11.486	-0.113	-0.113	0.000	0.000	0.000	0.000
36	C	47	GLY	0	0.054	0.010	12.530	-0.056	-0.056	0.000	0.000	0.000	0.000
37	C	48	LEU	0	-0.022	0.007	13.070	-0.036	-0.036	0.000	0.000	0.000	0.000
38	C	49	THR	0	0.047	-0.008	10.601	0.113	0.113	0.000	0.000	0.000	0.000
39	C	50	PRO	0	0.003	-0.022	9.355	0.004	0.004	0.000	0.000	0.000	0.000
40	C	51	LEU	0	0.030	0.030	12.096	-0.018	-0.018	0.000	0.000	0.000	0.000
41	C	52	HIS	0	0.059	0.051	14.913	0.024	0.024	0.000	0.000	0.000	0.000
42	C	53	LEU	0	-0.058	-0.022	12.054	-0.006	-0.006	0.000	0.000	0.000	0.000
43	C	54	ALA	0	0.007	0.007	15.952	-0.016	-0.016	0.000	0.000	0.000	0.000
44	C	55	ALA	0	0.003	0.000	17.783	-0.025	-0.025	0.000	0.000	0.000	0.000
45	C	56	VAL	0	-0.038	-0.016	18.802	-0.016	-0.016	0.000	0.000	0.000	0.000
46	C	57	SER	0	-0.083	-0.051	18.899	-0.008	-0.008	0.000	0.000	0.000	0.000
47	C	58	GLY	0	0.024	0.019	21.591	-0.004	-0.004	0.000	0.000	0.000	0.000
48	C	59	HIS	0	-0.034	-0.014	18.696	-0.026	-0.026	0.000	0.000	0.000	0.000
49	C	60	LEU	0	0.023	0.004	20.890	0.011	0.011	0.000	0.000	0.000	0.000
50	C	61	GLU	-1	-0.903	-0.959	22.453	0.185	0.185	0.000	0.000	0.000	0.000
51	C	62	ILE	0	-0.017	-0.004	16.084	0.007	0.007	0.000	0.000	0.000	0.000
52	C	63	VAL	0	0.032	0.020	17.737	0.012	0.012	0.000	0.000	0.000	0.000
53	C	64	GLU	-1	-0.760	-0.860	19.003	0.112	0.112	0.000	0.000	0.000	0.000
54	C	65	VAL	0	-0.053	-0.029	16.576	-0.017	-0.017	0.000	0.000	0.000	0.000
55	C	66	LEU	0	-0.004	0.003	12.750	0.004	0.004	0.000	0.000	0.000	0.000
56	C	67	LEU	0	0.006	0.004	16.187	-0.027	-0.027	0.000	0.000	0.000	0.000
57	C	68	LYS	1	0.768	0.881	18.872	-0.150	-0.150	0.000	0.000	0.000	0.000
58	C	69	HIS	0	-0.139	-0.072	14.329	-0.025	-0.025	0.000	0.000	0.000	0.000
59	C	70	GLY	0	-0.012	-0.005	14.533	-0.007	-0.007	0.000	0.000	0.000	0.000
60	C	71	ALA	0	-0.030	-0.012	13.883	-0.030	-0.030	0.000	0.000	0.000	0.000
61	C	72	ASP	-1	-0.920	-0.974	14.333	-0.034	-0.034	0.000	0.000	0.000	0.000
62	C	73	VAL	0	-0.016	-0.012	16.281	0.030	0.030	0.000	0.000	0.000	0.000
63	C	74	ASP	-1	-0.850	-0.921	19.165	0.052	0.052	0.000	0.000	0.000	0.000
64	C	75	ALA	0	-0.023	0.002	14.704	-0.012	-0.012	0.000	0.000	0.000	0.000
65	C	76	ALA	0	-0.007	-0.014	16.797	0.027	0.027	0.000	0.000	0.000	0.000
66	C	77	ASP	-1	-0.823	-0.910	15.865	0.155	0.155	0.000	0.000	0.000	0.000
67	C	78	VAL	0	-0.043	-0.037	16.900	-0.034	-0.034	0.000	0.000	0.000	0.000
68	C	79	TYR	0	-0.072	-0.034	18.465	-0.025	-0.025	0.000	0.000	0.000	0.000
69	C	80	GLY	0	-0.017	-0.007	20.362	-0.016	-0.016	0.000	0.000	0.000	0.000
70	C	81	PHE	0	-0.028	-0.002	20.426	-0.009	-0.009	0.000	0.000	0.000	0.000
71	C	82	THR	0	0.076	0.034	19.397	0.016	0.016	0.000	0.000	0.000	0.000
72	C	83	PRO	0	0.011	-0.011	17.290	0.015	0.015	0.000	0.000	0.000	0.000
73	C	84	LEU	0	0.032	0.020	19.967	0.008	0.008	0.000	0.000	0.000	0.000
74	C	85	HIS	0	0.030	0.011	23.102	0.007	0.007	0.000	0.000	0.000	0.000
75	C	86	LEU	0	0.006	0.008	18.975	0.005	0.005	0.000	0.000	0.000	0.000
76	C	87	ALA	0	-0.012	0.005	23.109	0.005	0.005	0.000	0.000	0.000	0.000
77	C	88	ALA	0	-0.012	-0.018	24.732	-0.004	-0.004	0.000	0.000	0.000	0.000
78	C	89	MET	0	-0.022	-0.010	23.982	-0.004	-0.004	0.000	0.000	0.000	0.000
79	C	90	THR	0	-0.030	-0.029	24.556	0.001	0.001	0.000	0.000	0.000	0.000
80	C	91	GLY	0	0.003	0.014	27.602	0.001	0.001	0.000	0.000	0.000	0.000
81	C	92	HIS	0	-0.008	-0.007	25.530	-0.002	-0.002	0.000	0.000	0.000	0.000
82	C	93	LEU	0	0.043	0.012	27.821	-0.001	-0.001	0.000	0.000	0.000	0.000
83	C	94	GLU	-1	-0.875	-0.952	28.337	0.112	0.112	0.000	0.000	0.000	0.000
84	C	95	ILE	0	-0.035	-0.002	22.616	0.000	0.000	0.000	0.000	0.000	0.000
85	C	96	VAL	0	0.029	0.012	25.168	-0.004	-0.004	0.000	0.000	0.000	0.000
86	C	97	GLU	-1	-0.865	-0.932	27.237	0.063	0.063	0.000	0.000	0.000	0.000
87	C	98	VAL	0	-0.050	-0.024	23.382	-0.009	-0.009	0.000	0.000	0.000	0.000
88	C	99	LEU	0	0.028	0.009	20.572	-0.005	-0.005	0.000	0.000	0.000	0.000
89	C	100	LEU	0	0.018	0.013	24.214	-0.012	-0.012	0.000	0.000	0.000	0.000
90	C	101	LYS	1	0.869	0.950	27.246	-0.056	-0.056	0.000	0.000	0.000	0.000
91	C	102	TYR	0	-0.132	-0.093	22.320	-0.008	-0.008	0.000	0.000	0.000	0.000
92	C	103	GLY	0	-0.034	-0.011	23.607	-0.007	-0.007	0.000	0.000	0.000	0.000
93	C	104	ALA	0	-0.001	0.006	23.722	-0.007	-0.007	0.000	0.000	0.000	0.000
94	C	105	ASP	-1	-0.877	-0.942	24.613	0.013	0.013	0.000	0.000	0.000	0.000
95	C	106	VAL	0	-0.049	-0.035	26.796	0.008	0.008	0.000	0.000	0.000	0.000
96	C	107	ASN	0	-0.072	-0.032	29.332	0.008	0.008	0.000	0.000	0.000	0.000
97	C	108	ALA	0	0.048	0.048	24.698	-0.005	-0.005	0.000	0.000	0.000	0.000
98	C	109	PHE	0	-0.050	-0.035	26.784	0.005	0.005	0.000	0.000	0.000	0.000
99	C	110	ASP	-1	-0.757	-0.843	24.541	0.058	0.058	0.000	0.000	0.000	0.000
100	C	111	MET	0	-0.060	-0.060	22.922	-0.017	-0.017	0.000	0.000	0.000	0.000
101	C	112	THR	0	-0.142	-0.083	26.287	-0.005	-0.005	0.000	0.000	0.000	0.000
102	C	113	GLY	0	-0.045	-0.017	28.908	-0.004	-0.004	0.000	0.000	0.000	0.000
103	C	114	SER	0	-0.038	-0.014	29.194	-0.002	-0.002	0.000	0.000	0.000	0.000
104	C	115	THR	0	0.046	0.003	28.379	0.003	0.003	0.000	0.000	0.000	0.000
105	C	116	PRO	0	0.018	-0.008	26.382	0.005	0.005	0.000	0.000	0.000	0.000
106	C	117	LEU	0	0.015	0.012	28.796	0.005	0.005	0.000	0.000	0.000	0.000
107	C	118	HIS	0	0.012	0.028	31.801	0.004	0.004	0.000	0.000	0.000	0.000
108	C	119	LEU	0	0.036	0.025	26.516	0.002	0.002	0.000	0.000	0.000	0.000
109	C	120	ALA	0	0.005	0.015	30.681	0.004	0.004	0.000	0.000	0.000	0.000
110	C	121	ALA	0	-0.055	-0.041	32.185	0.000	0.000	0.000	0.000	0.000	0.000
111	C	122	ASP	-1	-0.996	-0.990	32.893	0.074	0.074	0.000	0.000	0.000	0.000
112	C	123	GLU	-1	-0.969	-0.979	30.166	0.115	0.115	0.000	0.000	0.000	0.000
113	C	124	GLY	0	-0.062	-0.021	33.592	0.002	0.002	0.000	0.000	0.000	0.000
114	C	125	HIS	0	0.014	0.014	30.798	-0.006	-0.006	0.000	0.000	0.000	0.000
115	C	126	LEU	0	-0.021	-0.039	34.772	-0.003	-0.003	0.000	0.000	0.000	0.000
116	C	127	GLU	-1	-0.909	-0.949	36.001	0.074	0.074	0.000	0.000	0.000	0.000
117	C	128	ILE	0	-0.003	0.014	30.530	-0.002	-0.002	0.000	0.000	0.000	0.000
118	C	129	VAL	0	-0.017	-0.007	33.557	-0.004	-0.004	0.000	0.000	0.000	0.000
119	C	130	GLU	-1	-0.947	-0.977	35.748	0.048	0.048	0.000	0.000	0.000	0.000
120	C	131	VAL	0	-0.043	-0.021	32.304	-0.005	-0.005	0.000	0.000	0.000	0.000
121	C	132	LEU	0	0.020	0.010	29.615	-0.004	-0.004	0.000	0.000	0.000	0.000
122	C	133	LEU	0	-0.013	-0.003	33.608	-0.006	-0.006	0.000	0.000	0.000	0.000
123	C	134	LYS	1	0.830	0.938	36.040	-0.059	-0.059	0.000	0.000	0.000	0.000
124	C	135	TYR	0	-0.133	-0.086	32.931	-0.006	-0.006	0.000	0.000	0.000	0.000
125	C	136	GLY	0	0.003	0.008	33.844	-0.002	-0.002	0.000	0.000	0.000	0.000
126	C	137	ALA	0	0.006	0.008	33.457	-0.003	-0.003	0.000	0.000	0.000	0.000
127	C	138	ASP	-1	-0.918	-0.972	34.606	0.014	0.014	0.000	0.000	0.000	0.000
128	C	139	VAL	0	-0.018	-0.019	36.148	0.002	0.002	0.000	0.000	0.000	0.000
129	C	140	ASN	0	-0.145	-0.069	38.414	0.002	0.002	0.000	0.000	0.000	0.000
130	C	141	ALA	0	0.023	0.028	33.865	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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