FMO DATABASE

FMODB ID: 76YQK

Calculation Name: 4H7Y-A-Xray372

Preferred Name: Dual specificity protein kinase TTK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4H7Y

Chain ID: A

ChEMBL ID: CHEMBL3983

UniProt ID: P33981

Base Structure: X-ray

Registration Date: 2023-09-22

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1321183.617725
FMO2-HF: Nuclear repulsion	1265320.875013
FMO2-HF: Total energy	-55862.742712
FMO2-MP2: Total energy	-56027.792882

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(A:10:ALA)

Summations of interaction energy for fragment #1(A:10:ALA)

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.
-9.557	-2.746	1.153	-3.926	-4.038	-0.026

Interaction energy analysis for fragmet #1(A:10:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.010

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	A	12	ASN	0	-0.041	-0.019	2.409	-1.079	1.880	0.367	-1.493	-1.834	0.001
4	A	13	PRO	0	0.043	0.008	5.291	-0.786	-0.746	-0.001	-0.004	-0.034	0.000
5	A	14	GLU	-1	-0.841	-0.914	7.173	-0.758	-0.758	0.000	0.000	0.000	0.000
6	A	15	ASP	-1	-0.828	-0.916	2.666	-9.338	-5.616	0.788	-2.418	-2.092	-0.027
7	A	16	TRP	0	-0.034	-0.026	5.235	0.189	0.279	-0.001	-0.011	-0.078	0.000
8	A	17	LEU	0	-0.011	-0.004	7.226	0.287	0.287	0.000	0.000	0.000	0.000
9	A	18	SER	0	0.006	0.013	8.203	0.219	0.219	0.000	0.000	0.000	0.000
10	A	19	LEU	0	-0.030	-0.011	6.501	0.213	0.213	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.026	-0.019	9.518	0.177	0.177	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.025	0.011	12.313	0.098	0.098	0.000	0.000	0.000	0.000
13	A	22	LYS	1	0.940	0.982	11.383	0.685	0.685	0.000	0.000	0.000	0.000
14	A	23	LEU	0	-0.056	-0.029	13.320	0.069	0.069	0.000	0.000	0.000	0.000
15	A	24	GLU	-1	-0.879	-0.934	15.005	-0.213	-0.213	0.000	0.000	0.000	0.000
16	A	25	LYS	1	0.979	0.990	17.569	0.332	0.332	0.000	0.000	0.000	0.000
17	A	26	ASN	0	-0.097	-0.066	15.758	0.038	0.038	0.000	0.000	0.000	0.000
18	A	27	SER	0	-0.071	-0.040	18.522	0.025	0.025	0.000	0.000	0.000	0.000
19	A	28	VAL	0	-0.008	0.027	20.991	0.021	0.021	0.000	0.000	0.000	0.000
20	A	29	PRO	0	-0.023	-0.027	24.053	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	30	LEU	0	0.036	0.015	21.749	0.002	0.002	0.000	0.000	0.000	0.000
22	A	31	SER	0	0.028	0.014	25.410	0.012	0.012	0.000	0.000	0.000	0.000
23	A	32	ASP	-1	-0.836	-0.929	25.684	-0.089	-0.089	0.000	0.000	0.000	0.000
24	A	33	ALA	0	0.022	0.013	25.307	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	34	LEU	0	-0.072	-0.037	21.259	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	35	LEU	0	0.046	0.028	20.905	-0.022	-0.022	0.000	0.000	0.000	0.000
27	A	36	ASN	0	0.074	0.039	21.317	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	37	LYS	1	0.926	0.977	16.756	0.205	0.205	0.000	0.000	0.000	0.000
29	A	38	LEU	0	-0.045	-0.018	15.892	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	39	ILE	0	0.024	0.010	16.623	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	40	GLY	0	0.034	0.020	17.599	0.004	0.004	0.000	0.000	0.000	0.000
32	A	41	ARG	1	0.897	0.958	8.265	0.404	0.404	0.000	0.000	0.000	0.000
33	A	42	TYR	0	0.037	0.000	12.623	-0.062	-0.062	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.052	-0.027	14.073	0.013	0.013	0.000	0.000	0.000	0.000
35	A	44	GLN	0	0.049	0.014	11.360	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.006	0.010	9.699	0.033	0.033	0.000	0.000	0.000	0.000
37	A	46	ILE	0	-0.063	-0.043	10.724	0.055	0.055	0.000	0.000	0.000	0.000
38	A	47	GLU	-1	-0.934	-0.957	13.174	0.147	0.147	0.000	0.000	0.000	0.000
39	A	48	ALA	0	-0.056	-0.013	8.212	0.102	0.102	0.000	0.000	0.000	0.000
40	A	49	LEU	0	-0.058	-0.022	7.236	0.221	0.221	0.000	0.000	0.000	0.000
41	A	50	PRO	0	-0.011	-0.003	10.681	-0.053	-0.053	0.000	0.000	0.000	0.000
42	A	51	PRO	0	0.040	0.020	13.381	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	52	ASP	-1	-0.899	-0.950	15.383	0.297	0.297	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.945	0.974	9.111	-1.031	-1.031	0.000	0.000	0.000	0.000
45	A	54	TYR	0	-0.009	-0.016	7.536	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	55	GLY	0	0.079	0.049	13.932	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	56	GLN	0	-0.078	-0.058	16.681	-0.035	-0.035	0.000	0.000	0.000	0.000
48	A	57	ASN	0	-0.019	-0.016	10.570	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	58	GLU	-1	-0.885	-0.948	14.553	-0.252	-0.252	0.000	0.000	0.000	0.000
50	A	59	SER	0	0.064	0.012	11.051	0.031	0.031	0.000	0.000	0.000	0.000
51	A	60	PHE	0	0.008	0.003	12.113	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	61	ALA	0	0.058	0.016	13.268	0.031	0.031	0.000	0.000	0.000	0.000
53	A	62	ARG	1	0.902	0.953	14.888	0.276	0.276	0.000	0.000	0.000	0.000
54	A	63	ILE	0	-0.009	0.005	10.095	0.021	0.021	0.000	0.000	0.000	0.000
55	A	64	GLN	0	0.059	0.032	14.722	0.044	0.044	0.000	0.000	0.000	0.000
56	A	65	VAL	0	-0.008	0.002	17.610	0.019	0.019	0.000	0.000	0.000	0.000
57	A	66	ARG	1	0.897	0.953	16.961	0.240	0.240	0.000	0.000	0.000	0.000
58	A	67	PHE	0	-0.004	0.003	17.678	0.014	0.014	0.000	0.000	0.000	0.000
59	A	68	ALA	0	0.020	0.006	19.494	0.016	0.016	0.000	0.000	0.000	0.000
60	A	69	GLU	-1	-0.829	-0.907	22.516	-0.150	-0.150	0.000	0.000	0.000	0.000
61	A	70	LEU	0	-0.024	-0.018	19.137	0.007	0.007	0.000	0.000	0.000	0.000
62	A	71	LYS	1	0.895	0.948	22.393	0.081	0.081	0.000	0.000	0.000	0.000
63	A	72	ALA	0	-0.022	-0.009	24.849	0.011	0.011	0.000	0.000	0.000	0.000
64	A	73	ILE	0	-0.054	-0.017	25.426	0.005	0.005	0.000	0.000	0.000	0.000
65	A	74	GLN	0	-0.015	-0.022	23.887	0.008	0.008	0.000	0.000	0.000	0.000
66	A	75	GLU	-1	-0.908	-0.959	27.453	-0.044	-0.044	0.000	0.000	0.000	0.000
67	A	76	PRO	0	-0.007	0.008	29.532	0.003	0.003	0.000	0.000	0.000	0.000
68	A	77	ASP	-1	-0.938	-0.974	31.340	-0.036	-0.036	0.000	0.000	0.000	0.000
69	A	78	ASP	-1	-0.910	-0.942	29.385	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	79	ALA	0	-0.076	-0.042	27.184	0.000	0.000	0.000	0.000	0.000	0.000
71	A	80	ARG	1	0.861	0.892	27.270	0.030	0.030	0.000	0.000	0.000	0.000
72	A	81	ASP	-1	-0.859	-0.944	27.138	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	82	TYR	0	0.022	0.012	22.803	0.000	0.000	0.000	0.000	0.000	0.000
74	A	83	PHE	0	0.030	0.012	23.251	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	84	GLN	0	-0.109	-0.051	25.228	0.000	0.000	0.000	0.000	0.000	0.000
76	A	85	MET	0	-0.011	0.009	19.240	0.013	0.013	0.000	0.000	0.000	0.000
77	A	86	ALA	0	0.053	0.029	20.629	0.006	0.006	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.900	0.945	21.621	0.032	0.032	0.000	0.000	0.000	0.000
79	A	88	ALA	0	-0.073	-0.038	23.985	0.005	0.005	0.000	0.000	0.000	0.000
80	A	89	ASN	0	-0.019	-0.013	18.790	0.031	0.031	0.000	0.000	0.000	0.000
81	A	90	CYS	0	-0.050	0.000	17.857	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	91	LYS	1	1.012	1.003	20.649	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	92	LYS	1	0.958	0.999	20.206	0.084	0.084	0.000	0.000	0.000	0.000
84	A	93	PHE	0	0.029	0.018	18.156	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	94	ALA	0	0.050	0.026	23.450	0.003	0.003	0.000	0.000	0.000	0.000
86	A	95	PHE	0	0.055	0.000	18.605	0.006	0.006	0.000	0.000	0.000	0.000
87	A	96	VAL	0	-0.023	0.014	21.124	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	97	HIS	0	-0.074	-0.067	23.874	0.010	0.010	0.000	0.000	0.000	0.000
89	A	98	ILE	0	0.018	0.004	27.433	0.006	0.006	0.000	0.000	0.000	0.000
90	A	99	SER	0	-0.006	-0.002	24.752	0.007	0.007	0.000	0.000	0.000	0.000
91	A	100	PHE	0	-0.020	-0.009	26.768	0.007	0.007	0.000	0.000	0.000	0.000
92	A	101	ALA	0	-0.008	-0.018	28.453	0.006	0.006	0.000	0.000	0.000	0.000
93	A	102	GLN	0	0.055	0.041	29.374	0.006	0.006	0.000	0.000	0.000	0.000
94	A	103	PHE	0	0.040	0.029	29.009	0.002	0.002	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.781	-0.864	30.991	-0.034	-0.034	0.000	0.000	0.000	0.000
96	A	105	LEU	0	-0.046	-0.020	34.057	0.005	0.005	0.000	0.000	0.000	0.000
97	A	106	SER	0	-0.089	-0.042	33.177	0.002	0.002	0.000	0.000	0.000	0.000
98	A	107	GLN	0	0.002	0.005	33.918	0.004	0.004	0.000	0.000	0.000	0.000
99	A	108	GLY	0	0.022	0.022	36.700	0.004	0.004	0.000	0.000	0.000	0.000
100	A	109	ASN	0	-0.054	-0.027	36.389	0.006	0.006	0.000	0.000	0.000	0.000
101	A	110	VAL	0	0.056	0.010	38.097	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	111	LYS	1	0.954	0.963	39.694	0.025	0.025	0.000	0.000	0.000	0.000
103	A	112	LYS	1	0.969	0.997	34.463	0.026	0.026	0.000	0.000	0.000	0.000
104	A	113	SER	0	0.027	0.003	34.628	0.000	0.000	0.000	0.000	0.000	0.000
105	A	114	LYS	1	1.005	1.001	35.367	0.032	0.032	0.000	0.000	0.000	0.000
106	A	115	GLN	0	-0.064	-0.043	37.212	0.002	0.002	0.000	0.000	0.000	0.000
107	A	116	LEU	0	-0.054	-0.018	31.167	0.003	0.003	0.000	0.000	0.000	0.000
108	A	117	LEU	0	0.056	0.033	31.811	0.000	0.000	0.000	0.000	0.000	0.000
109	A	118	GLN	0	0.002	-0.005	33.941	0.000	0.000	0.000	0.000	0.000	0.000
110	A	119	LYS	1	0.934	0.963	33.702	0.018	0.018	0.000	0.000	0.000	0.000
111	A	120	ALA	0	0.003	0.015	30.025	0.003	0.003	0.000	0.000	0.000	0.000
112	A	121	VAL	0	0.025	0.011	31.621	0.000	0.000	0.000	0.000	0.000	0.000
113	A	122	GLU	-1	-0.999	-0.991	34.058	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	123	ARG	1	0.883	0.936	30.599	0.018	0.018	0.000	0.000	0.000	0.000
115	A	124	GLY	0	0.016	0.026	30.418	0.002	0.002	0.000	0.000	0.000	0.000
116	A	125	ALA	0	-0.057	-0.019	27.282	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	126	VAL	0	-0.024	0.003	24.834	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	127	PRO	0	0.021	-0.012	25.448	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	128	LEU	0	0.085	0.021	28.313	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	129	GLU	-1	-0.828	-0.921	31.823	-0.068	-0.068	0.000	0.000	0.000	0.000
121	A	130	MET	0	-0.014	0.005	25.324	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	131	LEU	0	-0.002	-0.016	29.864	0.001	0.001	0.000	0.000	0.000	0.000
123	A	132	GLU	-1	-0.932	-0.961	32.463	-0.050	-0.050	0.000	0.000	0.000	0.000
124	A	133	ILE	0	-0.008	0.004	32.677	0.004	0.004	0.000	0.000	0.000	0.000
125	A	134	ALA	0	0.003	0.011	32.256	0.002	0.002	0.000	0.000	0.000	0.000
126	A	135	LEU	0	-0.030	-0.036	34.373	0.004	0.004	0.000	0.000	0.000	0.000
127	A	136	ARG	1	0.931	0.976	37.458	0.065	0.065	0.000	0.000	0.000	0.000
128	A	137	ASN	0	-0.002	-0.025	35.197	0.007	0.007	0.000	0.000	0.000	0.000
129	A	138	LEU	0	0.001	0.010	37.313	0.002	0.002	0.000	0.000	0.000	0.000
130	A	139	ASN	0	-0.083	-0.039	39.072	0.005	0.005	0.000	0.000	0.000	0.000
131	A	140	LEU	0	-0.058	-0.024	41.352	0.002	0.002	0.000	0.000	0.000	0.000
132	A	141	GLN	0	-0.054	-0.019	41.716	0.000	0.000	0.000	0.000	0.000	0.000
133	A	142	LYS	1	0.944	0.987	38.482	0.067	0.067	0.000	0.000	0.000	0.000
134	A	143	LYS	1	0.963	0.968	37.234	0.065	0.065	0.000	0.000	0.000	0.000
135	A	144	GLN	0	0.011	0.010	32.558	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	145	LEU	0	-0.028	-0.019	32.016	0.003	0.003	0.000	0.000	0.000	0.000
137	A	146	LEU	0	-0.021	-0.008	28.010	0.003	0.003	0.000	0.000	0.000	0.000
138	A	147	SER	0	-0.051	-0.044	31.282	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	148	GLU	-1	-0.900	-0.956	28.454	-0.141	-0.141	0.000	0.000	0.000	0.000
140	A	149	GLU	-1	-0.965	-0.979	29.117	-0.127	-0.127	0.000	0.000	0.000	0.000
141	A	150	GLU	-1	-0.954	-0.944	28.266	-0.091	-0.091	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ALA)