FMO DATABASE

FMODB ID: LZN29

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1024822.048801
FMO2-HF: Nuclear repulsion	977457.13755
FMO2-HF: Total energy	-47364.911251
FMO2-MP2: Total energy	-47505.081964

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.
-15.257	-10.095	0.339	-2.338	-3.162	0.009

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 : 0.028 / q_NPA : -0.001

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	0.023	0.009	3.168	-3.828	-1.326	0.059	-1.211	-1.350	0.003
4	C	15	GLY	0	0.049	0.035	2.493	-1.037	-0.247	0.173	-0.281	-0.682	-0.001
5	C	16	LYS	1	0.947	0.969	2.915	-8.647	-6.891	0.109	-0.842	-1.023	0.007
6	C	17	LYS	1	1.009	1.004	5.854	-1.115	-1.115	0.000	0.000	0.000	0.000
7	C	18	LEU	0	0.004	0.017	6.994	0.011	0.011	0.000	0.000	0.000	0.000
8	C	19	LEU	0	-0.033	-0.015	6.585	0.074	0.074	0.000	0.000	0.000	0.000
9	C	20	GLU	-1	-0.980	-0.988	9.675	0.675	0.675	0.000	0.000	0.000	0.000
10	C	21	ALA	0	-0.008	-0.009	11.582	-0.024	-0.024	0.000	0.000	0.000	0.000
11	C	22	ALA	0	0.002	-0.003	12.586	-0.012	-0.012	0.000	0.000	0.000	0.000
12	C	23	ARG	1	0.965	0.987	13.938	-0.163	-0.163	0.000	0.000	0.000	0.000
13	C	24	ALA	0	-0.062	-0.038	15.753	-0.005	-0.005	0.000	0.000	0.000	0.000
14	C	25	GLY	0	0.030	0.020	17.515	-0.001	-0.001	0.000	0.000	0.000	0.000
15	C	26	GLN	0	-0.041	-0.025	15.961	-0.001	-0.001	0.000	0.000	0.000	0.000
16	C	27	ASP	-1	-0.847	-0.938	16.266	0.021	0.021	0.000	0.000	0.000	0.000
17	C	28	ASP	-1	-0.951	-0.984	17.067	0.060	0.060	0.000	0.000	0.000	0.000
18	C	29	GLU	-1	-0.923	-0.977	12.510	0.302	0.302	0.000	0.000	0.000	0.000
19	C	30	VAL	0	0.027	0.024	12.380	-0.004	-0.004	0.000	0.000	0.000	0.000
20	C	31	ARG	1	0.937	0.968	12.396	-0.044	-0.044	0.000	0.000	0.000	0.000
21	C	32	ILE	0	-0.024	-0.010	12.641	-0.019	-0.019	0.000	0.000	0.000	0.000
22	C	33	LEU	0	-0.023	-0.017	7.873	0.037	0.037	0.000	0.000	0.000	0.000
23	C	34	ILE	0	0.005	0.006	8.725	-0.050	-0.050	0.000	0.000	0.000	0.000
24	C	35	ALA	0	-0.048	-0.012	10.586	-0.042	-0.042	0.000	0.000	0.000	0.000
25	C	36	ASN	0	-0.082	-0.040	9.405	-0.023	-0.023	0.000	0.000	0.000	0.000
26	C	37	GLY	0	-0.024	-0.007	7.995	0.171	0.171	0.000	0.000	0.000	0.000
27	C	38	ALA	0	-0.069	-0.029	4.765	-0.382	-0.330	-0.001	-0.001	-0.050	0.000
28	C	39	ASP	-1	-0.893	-0.951	4.454	-1.295	-1.233	-0.001	-0.003	-0.057	0.000
29	C	40	VAL	0	0.015	-0.010	6.230	0.060	0.060	0.000	0.000	0.000	0.000
30	C	41	ASN	0	-0.014	0.017	8.811	0.204	0.204	0.000	0.000	0.000	0.000
31	C	42	ALA	0	-0.022	-0.001	5.170	-0.019	-0.019	0.000	0.000	0.000	0.000
32	C	43	VAL	0	0.008	0.027	6.478	0.146	0.146	0.000	0.000	0.000	0.000
33	C	44	ASP	-1	-0.829	-0.921	7.270	0.460	0.460	0.000	0.000	0.000	0.000
34	C	45	ASN	0	-0.083	-0.061	9.500	-0.101	-0.101	0.000	0.000	0.000	0.000
35	C	46	THR	0	-0.061	-0.023	11.455	-0.056	-0.056	0.000	0.000	0.000	0.000
36	C	47	GLY	0	0.061	0.007	12.505	-0.033	-0.033	0.000	0.000	0.000	0.000
37	C	48	LEU	0	-0.020	0.000	12.983	-0.048	-0.048	0.000	0.000	0.000	0.000
38	C	49	THR	0	0.031	-0.013	10.609	0.027	0.027	0.000	0.000	0.000	0.000
39	C	50	PRO	0	0.000	-0.021	9.382	0.069	0.069	0.000	0.000	0.000	0.000
40	C	51	LEU	0	0.026	0.026	12.118	0.045	0.045	0.000	0.000	0.000	0.000
41	C	52	HIS	0	0.050	0.046	14.929	0.020	0.020	0.000	0.000	0.000	0.000
42	C	53	LEU	0	-0.045	-0.018	12.016	0.032	0.032	0.000	0.000	0.000	0.000
43	C	54	ALA	0	0.012	0.013	15.966	0.020	0.020	0.000	0.000	0.000	0.000
44	C	55	ALA	0	0.006	0.001	17.805	0.010	0.010	0.000	0.000	0.000	0.000
45	C	56	VAL	0	-0.039	-0.017	18.988	0.008	0.008	0.000	0.000	0.000	0.000
46	C	57	SER	0	-0.086	-0.055	18.899	0.016	0.016	0.000	0.000	0.000	0.000
47	C	58	GLY	0	0.015	0.013	21.607	0.007	0.007	0.000	0.000	0.000	0.000
48	C	59	HIS	0	-0.018	-0.001	18.760	-0.005	-0.005	0.000	0.000	0.000	0.000
49	C	60	LEU	0	0.036	0.011	20.806	-0.015	-0.015	0.000	0.000	0.000	0.000
50	C	61	GLU	-1	-0.912	-0.962	22.102	-0.013	-0.013	0.000	0.000	0.000	0.000
51	C	62	ILE	0	-0.010	-0.002	15.692	-0.015	-0.015	0.000	0.000	0.000	0.000
52	C	63	VAL	0	0.025	0.017	17.288	-0.030	-0.030	0.000	0.000	0.000	0.000
53	C	64	GLU	-1	-0.913	-0.952	18.657	-0.084	-0.084	0.000	0.000	0.000	0.000
54	C	65	VAL	0	-0.089	-0.049	15.577	-0.013	-0.013	0.000	0.000	0.000	0.000
55	C	66	LEU	0	-0.009	-0.006	12.421	-0.031	-0.031	0.000	0.000	0.000	0.000
56	C	67	LEU	0	0.018	0.011	15.602	-0.036	-0.036	0.000	0.000	0.000	0.000
57	C	68	LYS	1	0.890	0.949	18.386	0.061	0.061	0.000	0.000	0.000	0.000
58	C	69	HIS	0	-0.131	-0.062	13.690	0.015	0.015	0.000	0.000	0.000	0.000
59	C	70	GLY	0	-0.008	-0.002	14.103	-0.056	-0.056	0.000	0.000	0.000	0.000
60	C	71	ALA	0	-0.025	-0.012	13.654	-0.046	-0.046	0.000	0.000	0.000	0.000
61	C	72	ASP	-1	-0.930	-0.983	14.359	-0.236	-0.236	0.000	0.000	0.000	0.000
62	C	73	VAL	0	-0.012	-0.008	16.300	0.012	0.012	0.000	0.000	0.000	0.000
63	C	74	ASP	-1	-0.842	-0.918	19.186	-0.116	-0.116	0.000	0.000	0.000	0.000
64	C	75	ALA	0	-0.020	-0.002	14.759	0.002	0.002	0.000	0.000	0.000	0.000
65	C	76	ALA	0	-0.002	-0.011	16.803	0.029	0.029	0.000	0.000	0.000	0.000
66	C	77	ASP	-1	-0.824	-0.907	15.866	-0.061	-0.061	0.000	0.000	0.000	0.000
67	C	78	VAL	0	-0.042	-0.039	16.892	-0.009	-0.009	0.000	0.000	0.000	0.000
68	C	79	TYR	0	-0.071	-0.035	18.448	0.004	0.004	0.000	0.000	0.000	0.000
69	C	80	GLY	0	-0.020	-0.009	20.350	-0.001	-0.001	0.000	0.000	0.000	0.000
70	C	81	PHE	0	-0.019	0.002	20.346	-0.003	-0.003	0.000	0.000	0.000	0.000
71	C	82	THR	0	0.057	0.029	19.398	-0.007	-0.007	0.000	0.000	0.000	0.000
72	C	83	PRO	0	0.010	-0.014	17.360	0.022	0.022	0.000	0.000	0.000	0.000
73	C	84	LEU	0	0.029	0.023	19.980	0.016	0.016	0.000	0.000	0.000	0.000
74	C	85	HIS	0	0.010	0.001	23.046	0.006	0.006	0.000	0.000	0.000	0.000
75	C	86	LEU	0	0.003	0.005	18.962	0.011	0.011	0.000	0.000	0.000	0.000
76	C	87	ALA	0	0.001	0.011	23.117	0.010	0.010	0.000	0.000	0.000	0.000
77	C	88	ALA	0	-0.016	-0.016	24.747	0.007	0.007	0.000	0.000	0.000	0.000
78	C	89	MET	0	-0.020	-0.011	23.738	0.005	0.005	0.000	0.000	0.000	0.000
79	C	90	THR	0	-0.044	-0.041	24.616	0.005	0.005	0.000	0.000	0.000	0.000
80	C	91	GLY	0	0.003	0.014	27.613	0.004	0.004	0.000	0.000	0.000	0.000
81	C	92	HIS	0	-0.017	-0.007	24.999	0.005	0.005	0.000	0.000	0.000	0.000
82	C	93	LEU	0	0.032	0.007	27.841	-0.008	-0.008	0.000	0.000	0.000	0.000
83	C	94	GLU	-1	-0.864	-0.943	28.314	-0.018	-0.018	0.000	0.000	0.000	0.000
84	C	95	ILE	0	-0.051	-0.006	22.807	-0.008	-0.008	0.000	0.000	0.000	0.000
85	C	96	VAL	0	0.023	0.008	25.192	-0.011	-0.011	0.000	0.000	0.000	0.000
86	C	97	GLU	-1	-0.940	-0.978	27.259	-0.040	-0.040	0.000	0.000	0.000	0.000
87	C	98	VAL	0	-0.038	-0.017	23.415	-0.008	-0.008	0.000	0.000	0.000	0.000
88	C	99	LEU	0	0.030	0.005	20.620	-0.013	-0.013	0.000	0.000	0.000	0.000
89	C	100	LEU	0	0.019	0.013	24.238	-0.009	-0.009	0.000	0.000	0.000	0.000
90	C	101	LYS	1	0.866	0.948	26.862	0.063	0.063	0.000	0.000	0.000	0.000
91	C	102	TYR	0	-0.096	-0.065	21.767	-0.004	-0.004	0.000	0.000	0.000	0.000
92	C	103	GLY	0	-0.034	-0.011	23.470	-0.015	-0.015	0.000	0.000	0.000	0.000
93	C	104	ALA	0	-0.001	0.005	23.690	-0.005	-0.005	0.000	0.000	0.000	0.000
94	C	105	ASP	-1	-0.899	-0.948	24.631	-0.086	-0.086	0.000	0.000	0.000	0.000
95	C	106	VAL	0	-0.041	-0.034	26.809	0.004	0.004	0.000	0.000	0.000	0.000
96	C	107	ASN	0	-0.068	-0.027	29.345	0.012	0.012	0.000	0.000	0.000	0.000
97	C	108	ALA	0	0.053	0.048	24.709	0.000	0.000	0.000	0.000	0.000	0.000
98	C	109	PHE	0	-0.037	-0.029	26.776	0.009	0.009	0.000	0.000	0.000	0.000
99	C	110	ASP	-1	-0.767	-0.852	24.541	-0.055	-0.055	0.000	0.000	0.000	0.000
100	C	111	MET	0	-0.068	-0.061	23.297	-0.004	-0.004	0.000	0.000	0.000	0.000
101	C	112	THR	0	-0.135	-0.078	26.274	0.005	0.005	0.000	0.000	0.000	0.000
102	C	113	GLY	0	-0.049	-0.020	28.897	0.003	0.003	0.000	0.000	0.000	0.000
103	C	114	SER	0	-0.025	-0.005	29.132	0.003	0.003	0.000	0.000	0.000	0.000
104	C	115	THR	0	0.042	0.018	28.378	-0.005	-0.005	0.000	0.000	0.000	0.000
105	C	116	PRO	0	0.023	-0.009	26.471	0.008	0.008	0.000	0.000	0.000	0.000
106	C	117	LEU	0	0.017	0.013	28.803	0.006	0.006	0.000	0.000	0.000	0.000
107	C	118	HIS	0	0.012	0.019	31.709	0.003	0.003	0.000	0.000	0.000	0.000
108	C	119	LEU	0	0.029	0.018	26.534	0.004	0.004	0.000	0.000	0.000	0.000
109	C	120	ALA	0	0.007	0.018	30.684	0.005	0.005	0.000	0.000	0.000	0.000
110	C	121	ALA	0	-0.062	-0.042	32.193	0.004	0.004	0.000	0.000	0.000	0.000
111	C	122	ASP	-1	-1.004	-0.998	32.958	-0.002	-0.002	0.000	0.000	0.000	0.000
112	C	123	GLU	-1	-0.952	-0.963	30.170	0.012	0.012	0.000	0.000	0.000	0.000
113	C	124	GLY	0	-0.066	-0.024	33.596	0.003	0.003	0.000	0.000	0.000	0.000
114	C	125	HIS	0	0.021	0.016	30.970	0.000	0.000	0.000	0.000	0.000	0.000
115	C	126	LEU	0	-0.027	-0.043	34.784	-0.004	-0.004	0.000	0.000	0.000	0.000
116	C	127	GLU	-1	-0.908	-0.949	35.998	-0.009	-0.009	0.000	0.000	0.000	0.000
117	C	128	ILE	0	0.005	0.020	30.560	-0.004	-0.004	0.000	0.000	0.000	0.000
118	C	129	VAL	0	-0.023	-0.007	33.573	-0.005	-0.005	0.000	0.000	0.000	0.000
119	C	130	GLU	-1	-0.950	-0.983	35.761	-0.020	-0.020	0.000	0.000	0.000	0.000
120	C	131	VAL	0	-0.038	-0.013	32.412	-0.003	-0.003	0.000	0.000	0.000	0.000
121	C	132	LEU	0	0.020	0.006	29.639	-0.004	-0.004	0.000	0.000	0.000	0.000
122	C	133	LEU	0	-0.008	0.001	33.624	-0.004	-0.004	0.000	0.000	0.000	0.000
123	C	134	LYS	1	0.878	0.956	36.810	0.028	0.028	0.000	0.000	0.000	0.000
124	C	135	TYR	0	-0.076	-0.047	33.110	0.000	0.000	0.000	0.000	0.000	0.000
125	C	136	GLY	0	0.001	0.006	33.861	-0.005	-0.005	0.000	0.000	0.000	0.000
126	C	137	ALA	0	0.000	0.006	33.395	-0.002	-0.002	0.000	0.000	0.000	0.000
127	C	138	ASP	-1	-0.919	-0.975	34.617	-0.044	-0.044	0.000	0.000	0.000	0.000
128	C	139	VAL	0	-0.023	-0.023	36.153	0.001	0.001	0.000	0.000	0.000	0.000
129	C	140	ASN	0	-0.137	-0.062	38.416	0.003	0.003	0.000	0.000	0.000	0.000
130	C	141	ALA	0	0.019	0.026	33.998	-0.001	-0.001	0.000	0.000	0.000	0.000

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