FMO DATABASE

FMODB ID: YZN92

Calculation Name: 3REA-A-Xray372

Preferred Name: Tyrosine-protein kinase HCK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3REA

Chain ID: A

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1160460.283884
FMO2-HF: Nuclear repulsion	1108514.555435
FMO2-HF: Total energy	-51945.728449
FMO2-MP2: Total energy	-52099.433011

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:56:ASN)

Summations of interaction energy for fragment #1(A:56:ASN)

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.
-4.581	-2.795	-0.007	-1.132	-0.646	0.003

Interaction energy analysis for fragmet #1(A:56:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.033

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	58	ASP	-1	-0.867	-0.932	3.882	-6.212	-4.426	-0.007	-1.132	-0.646	0.003
4	A	59	SER	0	0.036	0.045	6.327	0.765	0.765	0.000	0.000	0.000	0.000
5	A	60	ALA	0	0.035	-0.003	7.878	0.139	0.139	0.000	0.000	0.000	0.000
6	A	61	TRP	0	-0.031	-0.008	10.402	0.031	0.031	0.000	0.000	0.000	0.000
7	A	62	LEU	0	0.007	-0.016	6.381	0.103	0.103	0.000	0.000	0.000	0.000
8	A	63	GLU	-1	-0.746	-0.862	10.490	-1.175	-1.175	0.000	0.000	0.000	0.000
9	A	64	ALA	0	-0.029	-0.009	12.787	0.068	0.068	0.000	0.000	0.000	0.000
10	A	65	GLN	0	-0.026	-0.023	13.639	0.138	0.138	0.000	0.000	0.000	0.000
11	A	66	GLU	-1	-0.922	-0.954	13.667	-0.302	-0.302	0.000	0.000	0.000	0.000
12	A	67	GLU	-1	-0.948	-0.993	15.580	-0.273	-0.273	0.000	0.000	0.000	0.000
13	A	68	GLU	-1	-0.855	-0.887	18.422	0.180	0.180	0.000	0.000	0.000	0.000
14	A	69	GLU	-1	-0.978	-0.978	17.798	0.287	0.287	0.000	0.000	0.000	0.000
15	A	70	VAL	0	-0.050	-0.021	18.754	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	71	GLY	0	0.015	0.015	21.398	0.002	0.002	0.000	0.000	0.000	0.000
17	A	72	PHE	0	-0.056	-0.037	22.894	0.002	0.002	0.000	0.000	0.000	0.000
18	A	73	PRO	0	-0.018	-0.009	22.939	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	74	VAL	0	0.031	0.014	22.389	0.017	0.017	0.000	0.000	0.000	0.000
20	A	75	ARG	1	0.903	0.956	19.961	0.430	0.430	0.000	0.000	0.000	0.000
21	A	76	PRO	0	0.011	0.000	26.674	0.013	0.013	0.000	0.000	0.000	0.000
22	A	77	GLN	0	0.006	0.013	26.855	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	78	VAL	0	-0.013	0.002	26.204	0.008	0.008	0.000	0.000	0.000	0.000
24	A	79	PRO	0	0.020	0.003	28.722	0.018	0.018	0.000	0.000	0.000	0.000
25	A	80	LEU	0	0.008	-0.002	30.459	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	81	ARG	1	0.826	0.911	26.034	0.260	0.260	0.000	0.000	0.000	0.000
27	A	82	PRO	0	0.009	0.010	31.269	0.002	0.002	0.000	0.000	0.000	0.000
28	A	83	MET	0	0.041	0.031	25.697	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	84	THR	0	-0.026	-0.017	29.821	0.006	0.006	0.000	0.000	0.000	0.000
30	A	85	TYR	0	0.026	-0.001	29.463	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	86	LYS	1	0.811	0.873	26.592	0.274	0.274	0.000	0.000	0.000	0.000
32	A	87	ALA	0	0.014	0.024	26.530	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	88	ALA	0	0.112	0.045	24.821	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	89	LEU	0	-0.010	0.023	23.584	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	90	ASP	-1	-0.830	-0.902	22.496	-0.334	-0.334	0.000	0.000	0.000	0.000
36	A	91	ILE	0	-0.016	-0.009	19.929	-0.059	-0.059	0.000	0.000	0.000	0.000
37	A	92	SER	0	-0.011	-0.016	18.915	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	93	HIS	0	0.026	0.003	17.870	-0.031	-0.031	0.000	0.000	0.000	0.000
39	A	94	PHE	0	-0.018	0.000	15.784	-0.096	-0.096	0.000	0.000	0.000	0.000
40	A	95	LEU	0	0.022	-0.003	14.525	-0.140	-0.140	0.000	0.000	0.000	0.000
41	A	96	LYS	1	0.786	0.893	13.090	0.554	0.554	0.000	0.000	0.000	0.000
42	A	97	GLU	-1	-0.907	-0.942	12.087	-0.855	-0.855	0.000	0.000	0.000	0.000
43	A	98	LYS	1	0.741	0.877	10.416	1.288	1.288	0.000	0.000	0.000	0.000
44	A	99	GLY	0	0.038	0.026	8.215	-0.553	-0.553	0.000	0.000	0.000	0.000
45	A	100	GLY	0	0.002	-0.013	8.554	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	101	LEU	0	-0.011	0.004	9.274	0.239	0.239	0.000	0.000	0.000	0.000
47	A	102	GLU	-1	-0.775	-0.888	11.854	0.382	0.382	0.000	0.000	0.000	0.000
48	A	103	GLY	0	-0.033	-0.018	11.857	0.155	0.155	0.000	0.000	0.000	0.000
49	A	104	LEU	0	-0.051	-0.001	12.261	0.163	0.163	0.000	0.000	0.000	0.000
50	A	105	ILE	0	0.057	0.022	13.974	-0.117	-0.117	0.000	0.000	0.000	0.000
51	A	106	TRP	0	-0.018	-0.014	17.007	0.003	0.003	0.000	0.000	0.000	0.000
52	A	107	SER	0	-0.027	-0.030	19.788	0.013	0.013	0.000	0.000	0.000	0.000
53	A	108	GLN	0	0.017	-0.003	21.836	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	109	ARG	1	0.820	0.876	20.638	-0.266	-0.266	0.000	0.000	0.000	0.000
55	A	110	ARG	1	0.883	0.946	15.473	-0.784	-0.784	0.000	0.000	0.000	0.000
56	A	111	GLN	0	0.030	0.019	19.100	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	112	GLU	-1	-0.821	-0.904	21.173	0.095	0.095	0.000	0.000	0.000	0.000
58	A	113	ILE	0	0.008	0.008	17.296	-0.031	-0.031	0.000	0.000	0.000	0.000
59	A	114	LEU	0	-0.030	-0.020	14.913	-0.064	-0.064	0.000	0.000	0.000	0.000
60	A	115	ASP	-1	-0.816	-0.907	18.821	-0.062	-0.062	0.000	0.000	0.000	0.000
61	A	116	LEU	0	-0.034	-0.024	22.304	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	117	TRP	0	0.044	0.044	14.498	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	118	ILE	0	-0.007	-0.007	19.197	-0.058	-0.058	0.000	0.000	0.000	0.000
64	A	119	TYR	0	-0.011	0.004	21.513	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	120	HIS	1	0.870	0.934	22.227	0.124	0.124	0.000	0.000	0.000	0.000
66	A	121	THR	0	-0.052	-0.015	19.341	-0.034	-0.034	0.000	0.000	0.000	0.000
67	A	122	GLN	0	-0.046	-0.038	21.199	0.010	0.010	0.000	0.000	0.000	0.000
68	A	123	GLY	0	0.061	0.052	24.570	0.008	0.008	0.000	0.000	0.000	0.000
69	A	124	TYR	0	-0.026	-0.024	24.999	0.006	0.006	0.000	0.000	0.000	0.000
70	A	125	PHE	0	0.022	0.004	27.152	0.003	0.003	0.000	0.000	0.000	0.000
71	A	126	PRO	0	-0.002	0.008	26.086	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	127	ASP	-1	-0.896	-0.952	27.693	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	128	TRP	0	0.031	0.017	22.112	0.006	0.006	0.000	0.000	0.000	0.000
74	A	129	GLN	0	-0.001	0.022	21.066	0.029	0.029	0.000	0.000	0.000	0.000
75	A	130	ASN	0	-0.010	0.002	26.127	0.035	0.035	0.000	0.000	0.000	0.000
76	A	131	TYR	0	-0.036	-0.048	22.228	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	132	THR	0	0.050	0.035	28.686	0.001	0.001	0.000	0.000	0.000	0.000
78	A	133	PRO	0	-0.011	0.001	30.278	0.018	0.018	0.000	0.000	0.000	0.000
79	A	134	GLY	0	-0.034	-0.004	31.319	0.002	0.002	0.000	0.000	0.000	0.000
80	A	135	PRO	0	-0.010	-0.018	31.660	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	136	GLY	0	0.016	0.003	29.680	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	137	ILE	0	-0.039	-0.030	25.785	0.009	0.009	0.000	0.000	0.000	0.000
83	A	138	ARG	1	0.851	0.940	26.356	-0.224	-0.224	0.000	0.000	0.000	0.000
84	A	139	TYR	0	0.024	-0.013	26.186	0.001	0.001	0.000	0.000	0.000	0.000
85	A	140	PRO	0	0.017	0.022	25.826	0.006	0.006	0.000	0.000	0.000	0.000
86	A	141	LEU	0	0.023	-0.010	27.830	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	142	THR	0	-0.065	-0.042	28.227	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	143	PHE	0	-0.007	-0.004	28.566	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	144	GLY	0	0.065	0.009	27.753	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	145	TRP	0	-0.037	-0.013	18.951	-0.045	-0.045	0.000	0.000	0.000	0.000
91	A	146	CYS	0	-0.072	-0.043	21.777	0.020	0.020	0.000	0.000	0.000	0.000
92	A	147	PHE	0	0.023	0.004	15.796	0.001	0.001	0.000	0.000	0.000	0.000
93	A	148	LYS	1	0.870	0.932	21.344	-0.116	-0.116	0.000	0.000	0.000	0.000
94	A	149	LEU	0	-0.014	0.009	21.227	0.028	0.028	0.000	0.000	0.000	0.000
95	A	150	VAL	0	-0.045	-0.038	21.508	-0.032	-0.032	0.000	0.000	0.000	0.000
96	A	151	PRO	0	0.029	0.014	22.291	0.047	0.047	0.000	0.000	0.000	0.000
97	A	152	VAL	0	-0.055	-0.029	19.324	0.001	0.001	0.000	0.000	0.000	0.000
98	A	153	GLU	-1	-0.879	-0.944	22.601	0.370	0.370	0.000	0.000	0.000	0.000
99	A	154	PRO	0	-0.019	-0.006	21.791	0.062	0.062	0.000	0.000	0.000	0.000
100	A	155	GLU	-1	-1.043	-1.005	17.774	0.880	0.880	0.000	0.000	0.000	0.000
101	A	179	ASP	-1	-0.929	-0.960	26.796	0.414	0.414	0.000	0.000	0.000	0.000
102	A	180	ALA	0	-0.019	-0.025	26.791	0.028	0.028	0.000	0.000	0.000	0.000
103	A	181	GLU	-1	-1.009	-0.982	28.868	0.315	0.315	0.000	0.000	0.000	0.000
104	A	182	LYS	1	0.918	0.942	27.131	-0.318	-0.318	0.000	0.000	0.000	0.000
105	A	183	GLU	-1	-0.752	-0.877	26.514	0.275	0.275	0.000	0.000	0.000	0.000
106	A	184	VAL	0	0.026	0.024	20.498	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	185	LEU	0	-0.023	-0.014	22.058	-0.017	-0.017	0.000	0.000	0.000	0.000
108	A	186	VAL	0	-0.008	0.008	16.950	0.055	0.055	0.000	0.000	0.000	0.000
109	A	187	TRP	0	0.031	0.015	16.464	-0.060	-0.060	0.000	0.000	0.000	0.000
110	A	188	ARG	1	0.844	0.920	16.085	-0.350	-0.350	0.000	0.000	0.000	0.000
111	A	189	PHE	0	0.001	-0.006	16.831	-0.051	-0.051	0.000	0.000	0.000	0.000
112	A	190	ASP	-1	-0.793	-0.884	18.649	0.063	0.063	0.000	0.000	0.000	0.000
113	A	191	SER	0	0.052	0.024	21.792	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	192	LYS	1	0.853	0.897	23.108	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	193	LEU	0	-0.006	0.004	23.685	0.007	0.007	0.000	0.000	0.000	0.000
116	A	194	ALA	0	0.008	0.011	25.683	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	195	PHE	0	-0.073	-0.039	27.022	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	196	HIS	0	-0.026	0.002	30.039	0.001	0.001	0.000	0.000	0.000	0.000
119	A	197	HIS	0	-0.009	0.003	30.457	0.004	0.004	0.000	0.000	0.000	0.000
120	A	198	MET	0	0.004	-0.009	29.689	0.011	0.011	0.000	0.000	0.000	0.000
121	A	199	ALA	0	0.026	0.017	31.682	0.008	0.008	0.000	0.000	0.000	0.000
122	A	200	ARG	1	0.947	0.977	33.368	0.022	0.022	0.000	0.000	0.000	0.000
123	A	201	GLU	-1	-0.876	-0.947	34.956	-0.010	-0.010	0.000	0.000	0.000	0.000
124	A	202	LEU	0	-0.014	0.003	33.033	0.006	0.006	0.000	0.000	0.000	0.000
125	A	203	HIS	0	-0.020	-0.013	35.531	0.015	0.015	0.000	0.000	0.000	0.000
126	A	204	PRO	0	-0.098	-0.035	38.858	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	205	GLU	-1	-0.922	-0.957	36.478	0.041	0.041	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:56:ASN)