FMO DATABASE

FMODB ID: K9283

Calculation Name: 3REA-C-Xray372

Preferred Name: Tyrosine-protein kinase HCK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3REA

Chain ID: C

ChEMBL ID: CHEMBL3234

UniProt ID: P08631

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1141774.822743
FMO2-HF: Nuclear repulsion	1090196.190621
FMO2-HF: Total energy	-51578.632122
FMO2-MP2: Total energy	-51731.487265

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:59:SER)

Summations of interaction energy for fragment #1(C:59: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.
-27.195	-23.263	23.154	-10.394	-16.692	0.022

Interaction energy analysis for fragmet #1(C:59:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.011

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

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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	61	TRP	0	-0.002	-0.006	2.274	-9.426	-5.728	8.574	-4.362	-7.910	0.014
4	C	62	LEU	0	-0.018	-0.030	2.025	-7.445	-10.109	10.634	-3.456	-4.514	0.022
5	C	63	GLU	-1	-0.747	-0.856	3.623	-0.840	-0.454	0.028	0.130	-0.543	0.001
6	C	64	ALA	0	-0.074	-0.015	5.554	-0.882	-0.882	0.000	0.000	0.000	0.000
7	C	65	GLN	0	-0.044	-0.035	6.773	-0.653	-0.653	0.000	0.000	0.000	0.000
8	C	66	GLU	-1	-0.964	-0.967	7.310	1.592	1.592	0.000	0.000	0.000	0.000
9	C	67	GLU	-1	-0.821	-0.894	9.089	0.356	0.356	0.000	0.000	0.000	0.000
10	C	68	GLU	-1	-0.931	-0.957	11.361	0.460	0.460	0.000	0.000	0.000	0.000
11	C	69	GLU	-1	-0.880	-0.948	11.239	0.870	0.870	0.000	0.000	0.000	0.000
12	C	70	VAL	0	-0.016	0.001	14.849	-0.099	-0.099	0.000	0.000	0.000	0.000
13	C	71	GLY	0	-0.002	-0.003	16.934	0.003	0.003	0.000	0.000	0.000	0.000
14	C	72	PHE	0	-0.065	-0.038	19.831	-0.041	-0.041	0.000	0.000	0.000	0.000
15	C	73	PRO	0	0.009	0.011	18.841	0.000	0.000	0.000	0.000	0.000	0.000
16	C	74	VAL	0	0.023	0.013	19.459	-0.026	-0.026	0.000	0.000	0.000	0.000
17	C	75	ARG	1	0.923	0.963	15.509	-0.316	-0.316	0.000	0.000	0.000	0.000
18	C	76	PRO	0	0.027	0.001	21.846	0.015	0.015	0.000	0.000	0.000	0.000
19	C	77	GLN	0	-0.014	0.002	19.670	0.037	0.037	0.000	0.000	0.000	0.000
20	C	78	VAL	0	-0.005	0.006	19.006	-0.021	-0.021	0.000	0.000	0.000	0.000
21	C	79	PRO	0	0.012	-0.012	21.878	0.009	0.009	0.000	0.000	0.000	0.000
22	C	80	LEU	0	0.010	0.016	23.145	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	81	ARG	1	0.843	0.918	18.424	-0.048	-0.048	0.000	0.000	0.000	0.000
24	C	82	PRO	0	0.012	0.013	23.199	0.009	0.009	0.000	0.000	0.000	0.000
25	C	83	MET	0	0.025	0.017	17.750	-0.019	-0.019	0.000	0.000	0.000	0.000
26	C	84	THR	0	-0.003	-0.006	21.894	-0.008	-0.008	0.000	0.000	0.000	0.000
27	C	85	TYR	0	-0.002	-0.012	21.552	-0.006	-0.006	0.000	0.000	0.000	0.000
28	C	86	LYS	1	0.849	0.893	19.795	0.116	0.116	0.000	0.000	0.000	0.000
29	C	87	ALA	0	0.014	0.020	18.702	-0.020	-0.020	0.000	0.000	0.000	0.000
30	C	88	ALA	0	0.100	0.036	16.967	-0.019	-0.019	0.000	0.000	0.000	0.000
31	C	89	LEU	0	-0.009	0.019	16.170	-0.031	-0.031	0.000	0.000	0.000	0.000
32	C	90	ASP	-1	-0.839	-0.903	15.582	-0.201	-0.201	0.000	0.000	0.000	0.000
33	C	91	ILE	0	0.009	0.012	12.048	-0.067	-0.067	0.000	0.000	0.000	0.000
34	C	92	SER	0	-0.052	-0.034	11.301	-0.083	-0.083	0.000	0.000	0.000	0.000
35	C	93	HIS	0	0.031	-0.005	11.305	-0.135	-0.135	0.000	0.000	0.000	0.000
36	C	94	PHE	0	-0.010	0.011	7.783	-0.198	-0.198	0.000	0.000	0.000	0.000
37	C	95	LEU	0	0.012	-0.006	6.809	-0.321	-0.321	0.000	0.000	0.000	0.000
38	C	96	LYS	1	0.789	0.896	6.504	0.269	0.269	0.000	0.000	0.000	0.000
39	C	97	GLU	-1	-0.897	-0.949	7.740	-1.004	-1.004	0.000	0.000	0.000	0.000
40	C	98	LYS	1	0.796	0.911	2.447	-1.488	-0.286	0.342	-0.552	-0.993	0.002
41	C	99	GLY	0	0.033	0.027	2.964	-4.588	-2.881	0.173	-0.948	-0.933	-0.009
42	C	100	GLY	0	-0.031	-0.035	2.288	-3.417	-2.491	3.229	-2.581	-1.573	-0.008
43	C	101	LEU	0	0.002	0.003	2.914	2.217	0.894	0.174	1.375	-0.226	0.000
44	C	102	GLU	-1	-0.770	-0.866	6.521	-0.121	-0.121	0.000	0.000	0.000	0.000
45	C	103	GLY	0	-0.029	-0.019	7.517	0.050	0.050	0.000	0.000	0.000	0.000
46	C	104	LEU	0	-0.033	0.006	6.545	-0.051	-0.051	0.000	0.000	0.000	0.000
47	C	105	ILE	0	0.024	-0.002	9.226	-0.129	-0.129	0.000	0.000	0.000	0.000
48	C	106	TRP	0	0.013	0.012	11.807	0.150	0.150	0.000	0.000	0.000	0.000
49	C	107	SER	0	-0.034	-0.031	14.064	-0.013	-0.013	0.000	0.000	0.000	0.000
50	C	108	GLN	0	0.013	-0.009	15.526	0.022	0.022	0.000	0.000	0.000	0.000
51	C	109	ARG	1	0.876	0.925	14.758	-0.529	-0.529	0.000	0.000	0.000	0.000
52	C	110	ARG	1	0.933	0.954	9.970	-0.837	-0.837	0.000	0.000	0.000	0.000
53	C	111	GLN	0	0.001	0.013	12.427	0.049	0.049	0.000	0.000	0.000	0.000
54	C	112	GLU	-1	-0.825	-0.902	14.701	0.298	0.298	0.000	0.000	0.000	0.000
55	C	113	ILE	0	-0.043	-0.008	10.723	-0.017	-0.017	0.000	0.000	0.000	0.000
56	C	114	LEU	0	-0.014	0.001	9.584	-0.010	-0.010	0.000	0.000	0.000	0.000
57	C	115	ASP	-1	-0.828	-0.927	12.087	0.164	0.164	0.000	0.000	0.000	0.000
58	C	116	LEU	0	-0.013	-0.009	15.623	-0.055	-0.055	0.000	0.000	0.000	0.000
59	C	117	TRP	0	-0.001	0.026	6.378	-0.183	-0.183	0.000	0.000	0.000	0.000
60	C	118	ILE	0	-0.008	-0.011	11.790	-0.084	-0.084	0.000	0.000	0.000	0.000
61	C	119	TYR	0	-0.009	0.003	13.982	-0.041	-0.041	0.000	0.000	0.000	0.000
62	C	120	HIS	1	0.798	0.871	15.250	-0.467	-0.467	0.000	0.000	0.000	0.000
63	C	121	THR	0	-0.026	-0.001	12.108	-0.010	-0.010	0.000	0.000	0.000	0.000
64	C	122	GLN	0	-0.070	-0.043	13.950	-0.056	-0.056	0.000	0.000	0.000	0.000
65	C	123	GLY	0	0.059	0.045	16.880	-0.028	-0.028	0.000	0.000	0.000	0.000
66	C	124	TYR	0	-0.023	-0.025	17.191	-0.017	-0.017	0.000	0.000	0.000	0.000
67	C	125	PHE	0	0.010	0.009	19.549	0.027	0.027	0.000	0.000	0.000	0.000
68	C	126	PRO	0	0.008	0.007	19.089	-0.015	-0.015	0.000	0.000	0.000	0.000
69	C	127	ASP	-1	-0.895	-0.951	20.600	0.106	0.106	0.000	0.000	0.000	0.000
70	C	128	TRP	0	0.024	0.015	14.666	-0.029	-0.029	0.000	0.000	0.000	0.000
71	C	129	GLN	0	0.013	0.034	14.406	-0.027	-0.027	0.000	0.000	0.000	0.000
72	C	130	ASN	0	-0.011	0.004	19.049	0.035	0.035	0.000	0.000	0.000	0.000
73	C	131	TYR	0	-0.008	-0.040	15.333	-0.033	-0.033	0.000	0.000	0.000	0.000
74	C	132	THR	0	0.045	0.022	21.983	0.003	0.003	0.000	0.000	0.000	0.000
75	C	133	PRO	0	-0.013	-0.002	24.293	0.011	0.011	0.000	0.000	0.000	0.000
76	C	134	GLY	0	-0.010	0.024	25.753	-0.007	-0.007	0.000	0.000	0.000	0.000
77	C	135	PRO	0	0.012	0.007	26.365	-0.003	-0.003	0.000	0.000	0.000	0.000
78	C	136	GLY	0	0.021	-0.003	25.025	-0.010	-0.010	0.000	0.000	0.000	0.000
79	C	137	ILE	0	-0.050	-0.038	20.709	0.009	0.009	0.000	0.000	0.000	0.000
80	C	138	ARG	1	0.864	0.943	20.537	-0.121	-0.121	0.000	0.000	0.000	0.000
81	C	139	TYR	0	0.048	0.009	20.239	-0.003	-0.003	0.000	0.000	0.000	0.000
82	C	140	PRO	0	0.039	0.040	19.006	0.018	0.018	0.000	0.000	0.000	0.000
83	C	141	LEU	0	0.009	-0.018	21.044	-0.014	-0.014	0.000	0.000	0.000	0.000
84	C	142	THR	0	-0.059	-0.041	21.081	-0.008	-0.008	0.000	0.000	0.000	0.000
85	C	143	PHE	0	-0.032	-0.016	21.552	-0.010	-0.010	0.000	0.000	0.000	0.000
86	C	144	GLY	0	0.083	0.021	20.778	0.004	0.004	0.000	0.000	0.000	0.000
87	C	145	TRP	0	-0.022	-0.007	11.636	-0.045	-0.045	0.000	0.000	0.000	0.000
88	C	146	CYS	0	-0.081	-0.040	15.871	0.013	0.013	0.000	0.000	0.000	0.000
89	C	147	PHE	0	0.028	0.012	9.675	-0.022	-0.022	0.000	0.000	0.000	0.000
90	C	148	LYS	1	0.854	0.917	15.058	0.111	0.111	0.000	0.000	0.000	0.000
91	C	149	LEU	0	-0.020	0.000	15.282	0.007	0.007	0.000	0.000	0.000	0.000
92	C	150	VAL	0	-0.038	-0.036	16.864	-0.022	-0.022	0.000	0.000	0.000	0.000
93	C	151	PRO	0	0.038	0.016	17.990	0.016	0.016	0.000	0.000	0.000	0.000
94	C	152	VAL	0	-0.043	-0.020	16.254	-0.022	-0.022	0.000	0.000	0.000	0.000
95	C	153	GLU	-1	-0.960	-0.964	19.600	0.021	0.021	0.000	0.000	0.000	0.000
96	C	181	GLU	-1	-0.785	-0.874	22.257	0.122	0.122	0.000	0.000	0.000	0.000
97	C	182	LYS	1	0.773	0.864	21.334	-0.154	-0.154	0.000	0.000	0.000	0.000
98	C	183	GLU	-1	-0.885	-0.954	22.354	0.077	0.077	0.000	0.000	0.000	0.000
99	C	184	VAL	0	0.021	0.013	16.966	0.027	0.027	0.000	0.000	0.000	0.000
100	C	185	LEU	0	0.005	0.011	17.725	-0.026	-0.026	0.000	0.000	0.000	0.000
101	C	186	VAL	0	0.004	0.000	12.904	0.056	0.056	0.000	0.000	0.000	0.000
102	C	187	TRP	0	0.003	0.003	10.736	-0.014	-0.014	0.000	0.000	0.000	0.000
103	C	188	ARG	1	0.820	0.888	11.840	0.091	0.091	0.000	0.000	0.000	0.000
104	C	189	PHE	0	0.030	0.011	11.921	0.013	0.013	0.000	0.000	0.000	0.000
105	C	190	ASP	-1	-0.806	-0.881	13.804	-0.111	-0.111	0.000	0.000	0.000	0.000
106	C	191	SER	0	0.059	0.018	17.535	0.017	0.017	0.000	0.000	0.000	0.000
107	C	192	LYS	1	0.888	0.923	18.937	0.119	0.119	0.000	0.000	0.000	0.000
108	C	193	LEU	0	-0.010	0.004	18.669	0.016	0.016	0.000	0.000	0.000	0.000
109	C	194	ALA	0	0.034	0.018	19.865	0.010	0.010	0.000	0.000	0.000	0.000
110	C	195	PHE	0	-0.072	-0.023	21.600	0.010	0.010	0.000	0.000	0.000	0.000
111	C	196	HIS	0	-0.040	-0.027	24.782	0.005	0.005	0.000	0.000	0.000	0.000
112	C	197	HIS	0	-0.003	0.008	24.747	-0.005	-0.005	0.000	0.000	0.000	0.000
113	C	198	MET	0	0.036	0.013	24.457	0.008	0.008	0.000	0.000	0.000	0.000
114	C	199	ALA	0	-0.047	-0.019	24.994	0.005	0.005	0.000	0.000	0.000	0.000
115	C	200	ARG	1	0.907	0.954	26.851	0.007	0.007	0.000	0.000	0.000	0.000
116	C	201	GLU	-1	-0.829	-0.877	29.831	-0.026	-0.026	0.000	0.000	0.000	0.000
117	C	202	LEU	0	-0.013	-0.007	31.786	0.004	0.004	0.000	0.000	0.000	0.000
118	C	203	HIS	1	0.822	0.883	34.246	0.011	0.011	0.000	0.000	0.000	0.000
119	C	204	PRO	0	0.069	0.019	28.793	-0.005	-0.005	0.000	0.000	0.000	0.000
120	C	205	GLU	-1	-0.815	-0.893	30.148	-0.020	-0.020	0.000	0.000	0.000	0.000
121	C	206	TYR	0	-0.010	0.004	31.951	-0.003	-0.003	0.000	0.000	0.000	0.000
122	C	207	TYR	0	-0.067	-0.049	28.752	-0.006	-0.006	0.000	0.000	0.000	0.000
123	C	208	LYS	1	0.822	0.914	26.525	0.012	0.012	0.000	0.000	0.000	0.000
124	C	209	ASP	-1	-0.874	-0.903	27.647	-0.063	-0.063	0.000	0.000	0.000	0.000
125	C	210	ALA	0	-0.064	-0.051	28.695	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:59:SER)