FMO DATABASE

FMODB ID: 6YZKZ

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:

Apendix: None

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1326859.606194
FMO2-HF: Nuclear repulsion	1270995.877821
FMO2-HF: Total energy	-55863.728373
FMO2-MP2: Total energy	-56028.797595

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.
-14.427	-12.412	9.529	-6.164	-5.38	-0.053

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 : -0.005 / 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	A	12	ASN	0	-0.019	-0.005	2.310	-1.397	1.467	0.853	-1.861	-1.857	0.000
4	A	13	PRO	0	0.062	0.010	5.099	-1.030	-1.032	-0.001	-0.004	0.007	0.000
5	A	14	GLU	-1	-0.773	-0.840	6.445	-0.461	-0.461	0.000	0.000	0.000	0.000
6	A	15	ASP	-1	-0.813	-0.900	1.908	-14.260	-15.206	8.678	-4.288	-3.444	-0.053
7	A	16	TRP	0	-0.027	-0.016	5.251	0.155	0.254	-0.001	-0.011	-0.086	0.000
8	A	17	LEU	0	0.003	0.004	7.201	0.256	0.256	0.000	0.000	0.000	0.000
9	A	18	SER	0	-0.021	0.001	7.814	0.219	0.219	0.000	0.000	0.000	0.000
10	A	19	LEU	0	-0.010	-0.014	7.185	0.228	0.228	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.025	-0.007	9.305	0.185	0.185	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.050	0.025	12.264	0.105	0.105	0.000	0.000	0.000	0.000
13	A	22	LYS	1	0.947	0.982	11.230	0.845	0.845	0.000	0.000	0.000	0.000
14	A	23	LEU	0	-0.024	-0.017	13.362	0.075	0.075	0.000	0.000	0.000	0.000
15	A	24	GLU	-1	-0.784	-0.871	15.034	-0.271	-0.271	0.000	0.000	0.000	0.000
16	A	25	LYS	1	0.922	0.951	17.373	0.378	0.378	0.000	0.000	0.000	0.000
17	A	26	ASN	0	-0.057	-0.032	16.738	0.047	0.047	0.000	0.000	0.000	0.000
18	A	27	SER	0	-0.029	-0.015	18.676	0.021	0.021	0.000	0.000	0.000	0.000
19	A	28	VAL	0	0.000	0.024	21.093	0.022	0.022	0.000	0.000	0.000	0.000
20	A	29	PRO	0	0.003	-0.018	24.066	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	30	LEU	0	0.010	0.009	22.065	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	31	SER	0	0.020	0.004	25.751	0.013	0.013	0.000	0.000	0.000	0.000
23	A	32	ASP	-1	-0.794	-0.903	25.986	-0.141	-0.141	0.000	0.000	0.000	0.000
24	A	33	ALA	0	0.050	0.028	25.655	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	34	LEU	0	-0.073	-0.032	22.217	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	35	LEU	0	0.073	0.033	21.231	-0.035	-0.035	0.000	0.000	0.000	0.000
27	A	36	ASN	0	0.024	0.018	21.486	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	37	LYS	1	0.817	0.912	17.801	0.291	0.291	0.000	0.000	0.000	0.000
29	A	38	LEU	0	-0.048	-0.008	16.074	-0.036	-0.036	0.000	0.000	0.000	0.000
30	A	39	ILE	0	0.033	0.013	16.862	-0.043	-0.043	0.000	0.000	0.000	0.000
31	A	40	GLY	0	0.046	0.030	18.004	0.000	0.000	0.000	0.000	0.000	0.000
32	A	41	ARG	1	0.844	0.938	7.908	0.817	0.817	0.000	0.000	0.000	0.000
33	A	42	TYR	0	0.023	-0.037	13.022	-0.086	-0.086	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.044	-0.023	14.375	0.010	0.010	0.000	0.000	0.000	0.000
35	A	44	GLN	0	0.025	0.003	11.745	-0.054	-0.054	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.017	0.009	10.093	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	46	ILE	0	-0.051	-0.032	11.004	0.059	0.059	0.000	0.000	0.000	0.000
38	A	47	GLU	-1	-0.931	-0.957	13.591	0.028	0.028	0.000	0.000	0.000	0.000
39	A	48	ALA	0	-0.041	-0.005	8.383	0.081	0.081	0.000	0.000	0.000	0.000
40	A	49	LEU	0	-0.081	-0.030	7.165	0.246	0.246	0.000	0.000	0.000	0.000
41	A	50	PRO	0	0.016	0.003	10.849	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	51	PRO	0	0.040	0.013	13.419	0.032	0.032	0.000	0.000	0.000	0.000
43	A	52	ASP	-1	-0.879	-0.935	15.677	0.338	0.338	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.888	0.937	9.204	-1.036	-1.036	0.000	0.000	0.000	0.000
45	A	54	TYR	0	-0.020	-0.013	7.472	0.148	0.148	0.000	0.000	0.000	0.000
46	A	55	GLY	0	0.082	0.046	13.680	-0.068	-0.068	0.000	0.000	0.000	0.000
47	A	56	GLN	0	-0.006	-0.017	16.629	-0.049	-0.049	0.000	0.000	0.000	0.000
48	A	57	ASN	0	-0.036	-0.036	10.402	-0.069	-0.069	0.000	0.000	0.000	0.000
49	A	58	GLU	-1	-0.824	-0.918	14.339	-0.190	-0.190	0.000	0.000	0.000	0.000
50	A	59	SER	0	-0.004	-0.040	10.633	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	60	PHE	0	0.020	0.013	11.861	-0.041	-0.041	0.000	0.000	0.000	0.000
52	A	61	ALA	0	0.064	0.016	13.081	0.000	0.000	0.000	0.000	0.000	0.000
53	A	62	ARG	1	0.827	0.916	14.737	0.232	0.232	0.000	0.000	0.000	0.000
54	A	63	ILE	0	0.002	0.007	10.257	0.006	0.006	0.000	0.000	0.000	0.000
55	A	64	GLN	0	0.042	0.025	14.883	0.028	0.028	0.000	0.000	0.000	0.000
56	A	65	VAL	0	-0.022	-0.006	17.784	0.017	0.017	0.000	0.000	0.000	0.000
57	A	66	ARG	1	0.793	0.895	17.120	0.278	0.278	0.000	0.000	0.000	0.000
58	A	67	PHE	0	0.006	0.001	17.437	0.009	0.009	0.000	0.000	0.000	0.000
59	A	68	ALA	0	0.023	0.009	19.292	0.015	0.015	0.000	0.000	0.000	0.000
60	A	69	GLU	-1	-0.796	-0.890	22.429	-0.179	-0.179	0.000	0.000	0.000	0.000
61	A	70	LEU	0	-0.029	-0.020	19.252	0.010	0.010	0.000	0.000	0.000	0.000
62	A	71	LYS	1	0.794	0.880	22.364	0.129	0.129	0.000	0.000	0.000	0.000
63	A	72	ALA	0	-0.017	-0.019	24.757	0.012	0.012	0.000	0.000	0.000	0.000
64	A	73	ILE	0	-0.061	-0.025	25.301	0.007	0.007	0.000	0.000	0.000	0.000
65	A	74	GLN	0	-0.018	-0.010	24.244	0.006	0.006	0.000	0.000	0.000	0.000
66	A	75	GLU	-1	-0.827	-0.908	27.740	-0.089	-0.089	0.000	0.000	0.000	0.000
67	A	76	PRO	0	-0.013	0.004	29.822	0.001	0.001	0.000	0.000	0.000	0.000
68	A	77	ASP	-1	-0.942	-0.971	31.343	-0.057	-0.057	0.000	0.000	0.000	0.000
69	A	78	ASP	-1	-0.898	-0.952	29.693	-0.052	-0.052	0.000	0.000	0.000	0.000
70	A	79	ALA	0	-0.074	-0.029	27.353	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	80	ARG	1	0.854	0.889	27.115	0.046	0.046	0.000	0.000	0.000	0.000
72	A	81	ASP	-1	-0.817	-0.918	27.341	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	82	TYR	0	0.021	0.023	22.543	0.001	0.001	0.000	0.000	0.000	0.000
74	A	83	PHE	0	0.040	0.016	23.084	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	84	GLN	0	-0.116	-0.061	25.124	0.009	0.009	0.000	0.000	0.000	0.000
76	A	85	MET	0	-0.007	0.004	19.488	0.015	0.015	0.000	0.000	0.000	0.000
77	A	86	ALA	0	0.039	0.023	20.396	0.011	0.011	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.887	0.939	21.435	0.036	0.036	0.000	0.000	0.000	0.000
79	A	88	ALA	0	-0.055	-0.028	23.861	0.010	0.010	0.000	0.000	0.000	0.000
80	A	89	ASN	0	-0.024	-0.022	18.432	0.039	0.039	0.000	0.000	0.000	0.000
81	A	90	CYS	0	-0.036	0.008	17.438	0.011	0.011	0.000	0.000	0.000	0.000
82	A	91	LYS	1	0.986	0.995	20.253	-0.055	-0.055	0.000	0.000	0.000	0.000
83	A	92	LYS	1	0.870	0.954	18.771	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	93	PHE	0	0.030	0.020	17.541	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	94	ALA	0	0.022	0.008	22.896	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	95	PHE	0	0.081	0.011	18.564	0.002	0.002	0.000	0.000	0.000	0.000
87	A	96	VAL	0	-0.032	0.012	20.924	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	97	HIS	0	-0.044	-0.039	23.760	0.001	0.001	0.000	0.000	0.000	0.000
89	A	98	ILE	0	0.009	0.004	27.313	0.003	0.003	0.000	0.000	0.000	0.000
90	A	99	SER	0	-0.004	-0.008	24.490	0.005	0.005	0.000	0.000	0.000	0.000
91	A	100	PHE	0	0.018	0.004	26.722	0.004	0.004	0.000	0.000	0.000	0.000
92	A	101	ALA	0	-0.003	-0.006	28.343	0.004	0.004	0.000	0.000	0.000	0.000
93	A	102	GLN	0	0.040	0.041	29.389	0.006	0.006	0.000	0.000	0.000	0.000
94	A	103	PHE	0	0.038	0.030	28.949	0.001	0.001	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.752	-0.845	30.950	-0.044	-0.044	0.000	0.000	0.000	0.000
96	A	105	LEU	0	-0.082	-0.037	34.086	0.004	0.004	0.000	0.000	0.000	0.000
97	A	106	SER	0	-0.092	-0.058	33.036	0.001	0.001	0.000	0.000	0.000	0.000
98	A	107	GLN	0	-0.006	0.001	33.598	0.004	0.004	0.000	0.000	0.000	0.000
99	A	108	GLY	0	0.034	0.028	36.632	0.004	0.004	0.000	0.000	0.000	0.000
100	A	109	ASN	0	-0.035	-0.010	36.604	0.007	0.007	0.000	0.000	0.000	0.000
101	A	110	VAL	0	0.028	-0.004	38.130	0.001	0.001	0.000	0.000	0.000	0.000
102	A	111	LYS	1	0.957	0.965	39.264	0.028	0.028	0.000	0.000	0.000	0.000
103	A	112	LYS	1	0.916	0.963	35.243	0.027	0.027	0.000	0.000	0.000	0.000
104	A	113	SER	0	0.027	-0.003	34.475	0.001	0.001	0.000	0.000	0.000	0.000
105	A	114	LYS	1	0.948	0.968	35.031	0.031	0.031	0.000	0.000	0.000	0.000
106	A	115	GLN	0	-0.005	-0.003	36.953	0.002	0.002	0.000	0.000	0.000	0.000
107	A	116	LEU	0	-0.037	-0.003	30.691	0.005	0.005	0.000	0.000	0.000	0.000
108	A	117	LEU	0	0.043	0.027	31.472	0.002	0.002	0.000	0.000	0.000	0.000
109	A	118	GLN	0	0.010	-0.006	33.530	0.001	0.001	0.000	0.000	0.000	0.000
110	A	119	LYS	1	0.808	0.880	33.731	0.010	0.010	0.000	0.000	0.000	0.000
111	A	120	ALA	0	0.014	0.018	29.603	0.005	0.005	0.000	0.000	0.000	0.000
112	A	121	VAL	0	0.018	0.007	31.041	0.003	0.003	0.000	0.000	0.000	0.000
113	A	122	GLU	-1	-0.820	-0.882	33.540	0.001	0.001	0.000	0.000	0.000	0.000
114	A	123	ARG	1	0.799	0.888	30.273	0.002	0.002	0.000	0.000	0.000	0.000
115	A	124	GLY	0	0.014	0.025	29.653	0.004	0.004	0.000	0.000	0.000	0.000
116	A	125	ALA	0	-0.028	0.000	26.613	0.001	0.001	0.000	0.000	0.000	0.000
117	A	126	VAL	0	-0.025	0.000	24.056	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	127	PRO	0	0.021	-0.006	24.684	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	128	LEU	0	0.068	0.017	27.515	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	129	GLU	-1	-0.696	-0.819	31.025	-0.052	-0.052	0.000	0.000	0.000	0.000
121	A	130	MET	0	-0.015	0.006	24.729	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	131	LEU	0	0.001	-0.004	29.001	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	132	GLU	-1	-0.932	-0.962	31.898	-0.033	-0.033	0.000	0.000	0.000	0.000
124	A	133	ILE	0	-0.012	0.003	32.139	0.002	0.002	0.000	0.000	0.000	0.000
125	A	134	ALA	0	0.019	0.024	31.967	0.001	0.001	0.000	0.000	0.000	0.000
126	A	135	LEU	0	-0.044	-0.036	34.105	0.002	0.002	0.000	0.000	0.000	0.000
127	A	136	ARG	1	0.798	0.855	36.511	0.050	0.050	0.000	0.000	0.000	0.000
128	A	137	ASN	0	-0.043	-0.043	34.695	0.005	0.005	0.000	0.000	0.000	0.000
129	A	138	LEU	0	0.005	0.009	36.686	0.001	0.001	0.000	0.000	0.000	0.000
130	A	139	ASN	0	-0.072	-0.044	38.918	0.004	0.004	0.000	0.000	0.000	0.000
131	A	140	LEU	0	-0.023	-0.006	41.234	0.003	0.003	0.000	0.000	0.000	0.000
132	A	141	GLN	0	-0.076	-0.031	41.358	0.000	0.000	0.000	0.000	0.000	0.000
133	A	142	LYS	1	0.877	0.947	36.436	0.069	0.069	0.000	0.000	0.000	0.000
134	A	143	LYS	1	0.940	0.955	37.396	0.070	0.070	0.000	0.000	0.000	0.000
135	A	144	GLN	0	0.023	0.023	32.064	0.001	0.001	0.000	0.000	0.000	0.000
136	A	145	LEU	0	-0.025	-0.024	31.547	0.004	0.004	0.000	0.000	0.000	0.000
137	A	146	LEU	0	-0.011	-0.004	28.095	0.005	0.005	0.000	0.000	0.000	0.000
138	A	147	SER	0	-0.046	-0.049	31.424	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	148	GLU	-1	-0.887	-0.957	28.178	-0.132	-0.132	0.000	0.000	0.000	0.000
140	A	149	GLU	-1	-0.955	-0.962	29.091	-0.120	-0.120	0.000	0.000	0.000	0.000
141	A	150	GLU	-1	-0.859	-0.883	28.556	-0.076	-0.076	0.000	0.000	0.000	0.000

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