FMO DATABASE

FMODB ID: 2N49R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1321920.608713
FMO2-HF: Nuclear repulsion	1266057.231549
FMO2-HF: Total energy	-55863.377164
FMO2-MP2: Total energy	-56028.453115

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.
-8.929	-2.527	1.721	-4.05	-4.072	-0.03

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 : 0.032 / q_NPA : 0.007

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	-0.050	-0.037	2.459	-0.679	2.359	0.289	-1.528	-1.800	-0.001
4	A	13	PRO	0	0.062	0.018	5.086	-0.609	-0.567	-0.001	-0.005	-0.036	0.000
5	A	14	GLU	-1	-0.775	-0.847	7.051	-0.943	-0.943	0.000	0.000	0.000	0.000
6	A	15	ASP	-1	-0.828	-0.909	2.508	-9.737	-6.506	1.434	-2.506	-2.158	-0.029
7	A	16	TRP	0	-0.036	-0.026	5.253	0.367	0.458	-0.001	-0.011	-0.078	0.000
8	A	17	LEU	0	-0.009	-0.001	7.249	0.336	0.336	0.000	0.000	0.000	0.000
9	A	18	SER	0	0.002	0.012	8.180	0.253	0.253	0.000	0.000	0.000	0.000
10	A	19	LEU	0	-0.013	-0.008	6.724	0.243	0.243	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.021	-0.013	9.599	0.183	0.183	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.037	0.016	12.394	0.103	0.103	0.000	0.000	0.000	0.000
13	A	22	LYS	1	0.939	0.980	11.267	0.658	0.658	0.000	0.000	0.000	0.000
14	A	23	LEU	0	-0.037	-0.021	13.327	0.076	0.076	0.000	0.000	0.000	0.000
15	A	24	GLU	-1	-0.824	-0.919	15.076	-0.250	-0.250	0.000	0.000	0.000	0.000
16	A	25	LYS	1	0.950	0.976	17.646	0.323	0.323	0.000	0.000	0.000	0.000
17	A	26	ASN	0	-0.078	-0.055	16.243	0.033	0.033	0.000	0.000	0.000	0.000
18	A	27	SER	0	-0.024	-0.019	18.596	0.028	0.028	0.000	0.000	0.000	0.000
19	A	28	VAL	0	-0.014	0.025	21.058	0.020	0.020	0.000	0.000	0.000	0.000
20	A	29	PRO	0	-0.011	-0.021	24.125	0.000	0.000	0.000	0.000	0.000	0.000
21	A	30	LEU	0	0.026	0.012	21.865	0.002	0.002	0.000	0.000	0.000	0.000
22	A	31	SER	0	0.027	0.011	25.487	0.010	0.010	0.000	0.000	0.000	0.000
23	A	32	ASP	-1	-0.795	-0.910	25.747	-0.091	-0.091	0.000	0.000	0.000	0.000
24	A	33	ALA	0	0.026	0.017	25.431	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	34	LEU	0	-0.062	-0.037	21.570	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	35	LEU	0	0.054	0.028	20.966	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	36	ASN	0	0.049	0.031	21.379	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	37	LYS	1	0.848	0.950	17.157	0.195	0.195	0.000	0.000	0.000	0.000
29	A	38	LEU	0	-0.054	-0.022	15.986	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	39	ILE	0	0.029	0.013	16.686	-0.035	-0.035	0.000	0.000	0.000	0.000
31	A	40	GLY	0	0.043	0.025	17.645	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	41	ARG	1	0.860	0.938	7.840	0.397	0.397	0.000	0.000	0.000	0.000
33	A	42	TYR	0	0.037	-0.007	12.677	-0.072	-0.072	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.042	-0.017	14.129	0.001	0.001	0.000	0.000	0.000	0.000
35	A	44	GLN	0	0.035	0.014	11.433	-0.022	-0.022	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.011	0.005	9.747	0.028	0.028	0.000	0.000	0.000	0.000
37	A	46	ILE	0	-0.062	-0.042	10.774	0.021	0.021	0.000	0.000	0.000	0.000
38	A	47	GLU	-1	-0.935	-0.957	13.300	0.112	0.112	0.000	0.000	0.000	0.000
39	A	48	ALA	0	-0.059	-0.012	8.220	0.108	0.108	0.000	0.000	0.000	0.000
40	A	49	LEU	0	-0.057	-0.019	7.067	0.141	0.141	0.000	0.000	0.000	0.000
41	A	50	PRO	0	-0.011	-0.003	10.498	-0.032	-0.032	0.000	0.000	0.000	0.000
42	A	51	PRO	0	0.035	0.014	13.117	-0.038	-0.038	0.000	0.000	0.000	0.000
43	A	52	ASP	-1	-0.892	-0.945	14.970	0.167	0.167	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.916	0.958	8.340	-0.676	-0.676	0.000	0.000	0.000	0.000
45	A	54	TYR	0	-0.004	-0.013	7.085	0.032	0.032	0.000	0.000	0.000	0.000
46	A	55	GLY	0	0.093	0.056	13.710	-0.051	-0.051	0.000	0.000	0.000	0.000
47	A	56	GLN	0	-0.048	-0.037	16.487	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	57	ASN	0	-0.022	-0.026	10.553	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	58	GLU	-1	-0.867	-0.943	14.397	-0.310	-0.310	0.000	0.000	0.000	0.000
50	A	59	SER	0	0.008	-0.033	11.026	0.041	0.041	0.000	0.000	0.000	0.000
51	A	60	PHE	0	0.003	-0.005	11.993	0.001	0.001	0.000	0.000	0.000	0.000
52	A	61	ALA	0	0.046	0.014	13.291	0.048	0.048	0.000	0.000	0.000	0.000
53	A	62	ARG	1	0.898	0.956	14.894	0.346	0.346	0.000	0.000	0.000	0.000
54	A	63	ILE	0	-0.014	0.000	10.103	0.031	0.031	0.000	0.000	0.000	0.000
55	A	64	GLN	0	0.056	0.033	14.746	0.061	0.061	0.000	0.000	0.000	0.000
56	A	65	VAL	0	-0.028	-0.006	17.634	0.029	0.029	0.000	0.000	0.000	0.000
57	A	66	ARG	1	0.843	0.931	16.931	0.289	0.289	0.000	0.000	0.000	0.000
58	A	67	PHE	0	-0.001	0.004	17.701	0.021	0.021	0.000	0.000	0.000	0.000
59	A	68	ALA	0	0.020	0.004	19.548	0.022	0.022	0.000	0.000	0.000	0.000
60	A	69	GLU	-1	-0.807	-0.903	22.525	-0.195	-0.195	0.000	0.000	0.000	0.000
61	A	70	LEU	0	-0.014	-0.015	19.271	0.012	0.012	0.000	0.000	0.000	0.000
62	A	71	LYS	1	0.873	0.939	22.476	0.099	0.099	0.000	0.000	0.000	0.000
63	A	72	ALA	0	-0.025	-0.011	24.915	0.013	0.013	0.000	0.000	0.000	0.000
64	A	73	ILE	0	-0.058	-0.020	25.508	0.007	0.007	0.000	0.000	0.000	0.000
65	A	74	GLN	0	-0.013	-0.023	23.760	0.006	0.006	0.000	0.000	0.000	0.000
66	A	75	GLU	-1	-0.910	-0.961	27.296	-0.054	-0.054	0.000	0.000	0.000	0.000
67	A	76	PRO	0	0.015	0.015	29.593	0.002	0.002	0.000	0.000	0.000	0.000
68	A	77	ASP	-1	-0.950	-0.978	31.405	-0.049	-0.049	0.000	0.000	0.000	0.000
69	A	78	ASP	-1	-0.925	-0.957	29.412	-0.036	-0.036	0.000	0.000	0.000	0.000
70	A	79	ALA	0	-0.074	-0.036	27.375	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	80	ARG	1	0.849	0.882	27.295	0.048	0.048	0.000	0.000	0.000	0.000
72	A	81	ASP	-1	-0.804	-0.906	27.175	-0.040	-0.040	0.000	0.000	0.000	0.000
73	A	82	TYR	0	0.014	0.015	22.849	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	83	PHE	0	0.023	0.009	23.276	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	84	GLN	0	-0.141	-0.073	25.252	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	85	MET	0	-0.017	0.002	19.411	0.010	0.010	0.000	0.000	0.000	0.000
77	A	86	ALA	0	0.050	0.028	20.641	0.000	0.000	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.900	0.947	21.644	0.062	0.062	0.000	0.000	0.000	0.000
79	A	88	ALA	0	-0.066	-0.032	23.934	0.004	0.004	0.000	0.000	0.000	0.000
80	A	89	ASN	0	-0.024	-0.018	18.569	0.031	0.031	0.000	0.000	0.000	0.000
81	A	90	CYS	0	-0.048	0.000	17.656	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	91	LYS	1	1.015	1.005	20.445	0.031	0.031	0.000	0.000	0.000	0.000
83	A	92	LYS	1	0.910	0.966	19.881	0.160	0.160	0.000	0.000	0.000	0.000
84	A	93	PHE	0	0.020	0.017	17.849	0.004	0.004	0.000	0.000	0.000	0.000
85	A	94	ALA	0	0.037	0.017	23.408	0.005	0.005	0.000	0.000	0.000	0.000
86	A	95	PHE	0	0.061	0.003	18.574	0.011	0.011	0.000	0.000	0.000	0.000
87	A	96	VAL	0	-0.028	0.008	21.085	0.000	0.000	0.000	0.000	0.000	0.000
88	A	97	HIS	0	-0.044	-0.047	23.897	0.015	0.015	0.000	0.000	0.000	0.000
89	A	98	ILE	0	0.009	0.001	27.445	0.009	0.009	0.000	0.000	0.000	0.000
90	A	99	SER	0	0.008	0.005	24.601	0.011	0.011	0.000	0.000	0.000	0.000
91	A	100	PHE	0	0.000	-0.001	26.792	0.009	0.009	0.000	0.000	0.000	0.000
92	A	101	ALA	0	-0.005	-0.013	28.477	0.008	0.008	0.000	0.000	0.000	0.000
93	A	102	GLN	0	0.052	0.043	29.393	0.007	0.007	0.000	0.000	0.000	0.000
94	A	103	PHE	0	0.046	0.029	29.020	0.005	0.005	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.763	-0.848	31.015	-0.052	-0.052	0.000	0.000	0.000	0.000
96	A	105	LEU	0	-0.050	-0.021	34.082	0.006	0.006	0.000	0.000	0.000	0.000
97	A	106	SER	0	-0.093	-0.048	33.209	0.004	0.004	0.000	0.000	0.000	0.000
98	A	107	GLN	0	-0.003	0.001	33.695	0.006	0.006	0.000	0.000	0.000	0.000
99	A	108	GLY	0	0.021	0.022	36.725	0.005	0.005	0.000	0.000	0.000	0.000
100	A	109	ASN	0	-0.054	-0.028	36.517	0.007	0.007	0.000	0.000	0.000	0.000
101	A	110	VAL	0	0.045	0.005	38.121	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	111	LYS	1	0.957	0.966	39.717	0.037	0.037	0.000	0.000	0.000	0.000
103	A	112	LYS	1	0.942	0.984	34.800	0.045	0.045	0.000	0.000	0.000	0.000
104	A	113	SER	0	0.026	0.002	34.633	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	114	LYS	1	0.981	0.988	35.390	0.049	0.049	0.000	0.000	0.000	0.000
106	A	115	GLN	0	-0.020	-0.017	37.329	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	116	LEU	0	-0.047	-0.013	31.197	0.002	0.002	0.000	0.000	0.000	0.000
108	A	117	LEU	0	0.036	0.026	31.869	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	118	GLN	0	0.006	-0.007	33.963	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	119	LYS	1	0.850	0.911	33.739	0.041	0.041	0.000	0.000	0.000	0.000
111	A	120	ALA	0	0.004	0.014	30.063	0.002	0.002	0.000	0.000	0.000	0.000
112	A	121	VAL	0	0.029	0.013	31.478	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	122	GLU	-1	-0.812	-0.874	33.919	-0.039	-0.039	0.000	0.000	0.000	0.000
114	A	123	ARG	1	0.775	0.868	30.364	0.046	0.046	0.000	0.000	0.000	0.000
115	A	124	GLY	0	0.009	0.025	30.240	0.000	0.000	0.000	0.000	0.000	0.000
116	A	125	ALA	0	-0.054	-0.019	27.166	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	126	VAL	0	-0.017	0.006	24.680	0.002	0.002	0.000	0.000	0.000	0.000
118	A	127	PRO	0	0.016	-0.010	25.469	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	128	LEU	0	0.074	0.015	28.301	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	129	GLU	-1	-0.760	-0.875	31.803	-0.089	-0.089	0.000	0.000	0.000	0.000
121	A	130	MET	0	-0.004	0.007	25.130	0.000	0.000	0.000	0.000	0.000	0.000
122	A	131	LEU	0	0.010	-0.004	29.631	0.002	0.002	0.000	0.000	0.000	0.000
123	A	132	GLU	-1	-0.915	-0.958	32.483	-0.071	-0.071	0.000	0.000	0.000	0.000
124	A	133	ILE	0	-0.019	0.003	32.556	0.006	0.006	0.000	0.000	0.000	0.000
125	A	134	ALA	0	0.004	0.011	32.259	0.004	0.004	0.000	0.000	0.000	0.000
126	A	135	LEU	0	-0.031	-0.032	34.394	0.006	0.006	0.000	0.000	0.000	0.000
127	A	136	ARG	1	0.853	0.918	36.960	0.088	0.088	0.000	0.000	0.000	0.000
128	A	137	ASN	0	0.010	0.002	35.158	0.010	0.010	0.000	0.000	0.000	0.000
129	A	138	LEU	0	0.013	0.015	36.993	0.003	0.003	0.000	0.000	0.000	0.000
130	A	139	ASN	0	-0.072	-0.038	39.094	0.005	0.005	0.000	0.000	0.000	0.000
131	A	140	LEU	0	-0.050	-0.022	41.447	0.003	0.003	0.000	0.000	0.000	0.000
132	A	141	GLN	0	-0.070	-0.025	41.696	0.002	0.002	0.000	0.000	0.000	0.000
133	A	142	LYS	1	0.922	0.962	38.370	0.085	0.085	0.000	0.000	0.000	0.000
134	A	143	LYS	1	0.965	0.966	37.267	0.075	0.075	0.000	0.000	0.000	0.000
135	A	144	GLN	0	0.014	0.012	32.582	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	145	LEU	0	-0.034	-0.022	31.838	0.003	0.003	0.000	0.000	0.000	0.000
137	A	146	LEU	0	-0.023	-0.009	28.185	0.002	0.002	0.000	0.000	0.000	0.000
138	A	147	SER	0	-0.064	-0.067	31.302	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	148	GLU	-1	-0.903	-0.960	28.526	-0.163	-0.163	0.000	0.000	0.000	0.000
140	A	149	GLU	-1	-0.964	-0.976	29.135	-0.143	-0.143	0.000	0.000	0.000	0.000
141	A	150	GLU	-1	-0.933	-0.921	28.399	-0.111	-0.111	0.000	0.000	0.000	0.000

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