FMO DATABASE

FMODB ID: QYNMY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1141214.834796
FMO2-HF: Nuclear repulsion	1089636.955287
FMO2-HF: Total energy	-51577.879509
FMO2-MP2: Total energy	-51730.72618

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.
-22.179	-23.111	28.801	-10.862	-17.009	0.027

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 : 0.052 / 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

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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	-0.024	-0.020	2.349	-8.984	-4.656	7.167	-4.099	-7.396	0.016
4	C	62	LEU	0	-0.022	-0.041	1.916	-5.029	-12.434	17.695	-4.865	-5.426	0.020
5	C	63	GLU	-1	-0.832	-0.913	3.490	-1.238	-0.958	0.038	0.350	-0.669	0.002
6	C	64	ALA	0	-0.091	-0.019	5.523	-0.731	-0.731	0.000	0.000	0.000	0.000
7	C	65	GLN	0	-0.048	-0.046	6.731	-0.651	-0.651	0.000	0.000	0.000	0.000
8	C	66	GLU	-1	-0.994	-0.960	6.990	1.338	1.338	0.000	0.000	0.000	0.000
9	C	67	GLU	-1	-0.808	-0.895	8.843	0.194	0.194	0.000	0.000	0.000	0.000
10	C	68	GLU	-1	-0.930	-0.953	11.126	0.392	0.392	0.000	0.000	0.000	0.000
11	C	69	GLU	-1	-0.886	-0.950	10.832	0.722	0.722	0.000	0.000	0.000	0.000
12	C	70	VAL	0	-0.021	0.001	14.625	-0.081	-0.081	0.000	0.000	0.000	0.000
13	C	71	GLY	0	0.000	-0.004	16.670	-0.003	-0.003	0.000	0.000	0.000	0.000
14	C	72	PHE	0	-0.076	-0.041	19.556	-0.033	-0.033	0.000	0.000	0.000	0.000
15	C	73	PRO	0	0.030	0.018	18.708	0.000	0.000	0.000	0.000	0.000	0.000
16	C	74	VAL	0	0.017	0.016	19.054	-0.018	-0.018	0.000	0.000	0.000	0.000
17	C	75	ARG	1	0.919	0.956	15.626	-0.177	-0.177	0.000	0.000	0.000	0.000
18	C	76	PRO	0	0.024	0.001	21.641	0.012	0.012	0.000	0.000	0.000	0.000
19	C	77	GLN	0	-0.002	0.011	19.391	0.030	0.030	0.000	0.000	0.000	0.000
20	C	78	VAL	0	-0.009	0.007	18.896	-0.012	-0.012	0.000	0.000	0.000	0.000
21	C	79	PRO	0	0.012	-0.013	21.710	0.009	0.009	0.000	0.000	0.000	0.000
22	C	80	LEU	0	0.016	0.020	23.001	-0.006	-0.006	0.000	0.000	0.000	0.000
23	C	81	ARG	1	0.860	0.931	18.393	0.035	0.035	0.000	0.000	0.000	0.000
24	C	82	PRO	0	0.025	0.021	23.089	0.005	0.005	0.000	0.000	0.000	0.000
25	C	83	MET	0	0.029	0.015	17.876	-0.019	-0.019	0.000	0.000	0.000	0.000
26	C	84	THR	0	-0.004	-0.002	21.844	-0.002	-0.002	0.000	0.000	0.000	0.000
27	C	85	TYR	0	-0.008	-0.025	21.527	-0.012	-0.012	0.000	0.000	0.000	0.000
28	C	86	LYS	1	0.898	0.938	20.080	0.143	0.143	0.000	0.000	0.000	0.000
29	C	87	ALA	0	0.017	0.021	18.669	-0.022	-0.022	0.000	0.000	0.000	0.000
30	C	88	ALA	0	0.108	0.039	16.943	-0.026	-0.026	0.000	0.000	0.000	0.000
31	C	89	LEU	0	-0.024	0.010	16.180	-0.032	-0.032	0.000	0.000	0.000	0.000
32	C	90	ASP	-1	-0.875	-0.942	15.623	-0.242	-0.242	0.000	0.000	0.000	0.000
33	C	91	ILE	0	-0.003	0.004	11.852	-0.074	-0.074	0.000	0.000	0.000	0.000
34	C	92	SER	0	-0.054	-0.028	11.307	-0.093	-0.093	0.000	0.000	0.000	0.000
35	C	93	HIS	0	0.036	-0.005	11.373	-0.122	-0.122	0.000	0.000	0.000	0.000
36	C	94	PHE	0	-0.008	0.013	7.482	-0.164	-0.164	0.000	0.000	0.000	0.000
37	C	95	LEU	0	0.003	-0.013	6.833	-0.332	-0.332	0.000	0.000	0.000	0.000
38	C	96	LYS	1	0.872	0.952	6.599	0.199	0.199	0.000	0.000	0.000	0.000
39	C	97	GLU	-1	-0.969	-0.999	7.904	-0.900	-0.900	0.000	0.000	0.000	0.000
40	C	98	LYS	1	0.899	0.986	2.305	0.430	1.240	0.672	-0.474	-1.008	0.000
41	C	99	GLY	0	0.019	0.021	3.148	-4.053	-2.548	0.146	-0.798	-0.852	-0.006
42	C	100	GLY	0	-0.020	-0.033	2.308	-3.020	-2.164	2.918	-2.319	-1.456	-0.005
43	C	101	LEU	0	0.007	0.005	2.923	2.098	0.792	0.165	1.343	-0.202	0.000
44	C	102	GLU	-1	-0.808	-0.906	6.546	-0.078	-0.078	0.000	0.000	0.000	0.000
45	C	103	GLY	0	-0.048	-0.037	7.506	0.101	0.101	0.000	0.000	0.000	0.000
46	C	104	LEU	0	-0.030	0.009	6.418	-0.055	-0.055	0.000	0.000	0.000	0.000
47	C	105	ILE	0	0.026	-0.002	9.314	-0.152	-0.152	0.000	0.000	0.000	0.000
48	C	106	TRP	0	0.004	-0.002	11.879	0.144	0.144	0.000	0.000	0.000	0.000
49	C	107	SER	0	-0.021	-0.021	14.134	-0.014	-0.014	0.000	0.000	0.000	0.000
50	C	108	GLN	0	0.019	0.008	15.574	0.021	0.021	0.000	0.000	0.000	0.000
51	C	109	ARG	1	0.833	0.901	14.729	-0.485	-0.485	0.000	0.000	0.000	0.000
52	C	110	ARG	1	0.941	0.950	9.873	-0.888	-0.888	0.000	0.000	0.000	0.000
53	C	111	GLN	0	0.040	0.045	12.451	0.040	0.040	0.000	0.000	0.000	0.000
54	C	112	GLU	-1	-0.832	-0.922	14.734	0.216	0.216	0.000	0.000	0.000	0.000
55	C	113	ILE	0	-0.034	-0.008	10.518	-0.025	-0.025	0.000	0.000	0.000	0.000
56	C	114	LEU	0	-0.015	-0.005	9.435	-0.033	-0.033	0.000	0.000	0.000	0.000
57	C	115	ASP	-1	-0.859	-0.915	12.087	0.088	0.088	0.000	0.000	0.000	0.000
58	C	116	LEU	0	-0.018	-0.017	15.623	-0.053	-0.053	0.000	0.000	0.000	0.000
59	C	117	TRP	0	0.069	0.060	6.172	-0.166	-0.166	0.000	0.000	0.000	0.000
60	C	118	ILE	0	-0.009	-0.009	11.958	-0.084	-0.084	0.000	0.000	0.000	0.000
61	C	119	TYR	0	-0.015	0.002	13.841	-0.031	-0.031	0.000	0.000	0.000	0.000
62	C	120	HIS	1	0.817	0.877	15.176	-0.307	-0.307	0.000	0.000	0.000	0.000
63	C	121	THR	0	-0.032	-0.006	12.098	-0.005	-0.005	0.000	0.000	0.000	0.000
64	C	122	GLN	0	-0.060	-0.041	13.366	-0.018	-0.018	0.000	0.000	0.000	0.000
65	C	123	GLY	0	0.027	0.022	16.741	-0.015	-0.015	0.000	0.000	0.000	0.000
66	C	124	TYR	0	-0.028	-0.027	17.107	-0.011	-0.011	0.000	0.000	0.000	0.000
67	C	125	PHE	0	0.016	0.006	19.420	0.020	0.020	0.000	0.000	0.000	0.000
68	C	126	PRO	0	0.006	0.005	18.967	-0.015	-0.015	0.000	0.000	0.000	0.000
69	C	127	ASP	-1	-0.891	-0.940	20.482	0.066	0.066	0.000	0.000	0.000	0.000
70	C	128	TRP	0	0.039	0.025	14.645	-0.016	-0.016	0.000	0.000	0.000	0.000
71	C	129	GLN	0	-0.008	0.008	14.905	-0.012	-0.012	0.000	0.000	0.000	0.000
72	C	130	ASN	0	-0.016	0.000	19.097	0.036	0.036	0.000	0.000	0.000	0.000
73	C	131	TYR	0	0.001	-0.014	15.509	-0.031	-0.031	0.000	0.000	0.000	0.000
74	C	132	THR	0	0.037	0.019	22.014	0.003	0.003	0.000	0.000	0.000	0.000
75	C	133	PRO	0	-0.014	0.008	24.310	0.012	0.012	0.000	0.000	0.000	0.000
76	C	134	GLY	0	-0.004	0.022	25.755	-0.005	-0.005	0.000	0.000	0.000	0.000
77	C	135	PRO	0	0.012	0.005	26.353	-0.004	-0.004	0.000	0.000	0.000	0.000
78	C	136	GLY	0	0.030	0.004	25.002	-0.010	-0.010	0.000	0.000	0.000	0.000
79	C	137	ILE	0	-0.058	-0.042	20.731	0.008	0.008	0.000	0.000	0.000	0.000
80	C	138	ARG	1	0.866	0.936	20.576	-0.117	-0.117	0.000	0.000	0.000	0.000
81	C	139	TYR	0	0.037	0.000	20.264	-0.002	-0.002	0.000	0.000	0.000	0.000
82	C	140	PRO	0	0.033	0.036	19.080	0.017	0.017	0.000	0.000	0.000	0.000
83	C	141	LEU	0	0.005	-0.016	21.092	-0.011	-0.011	0.000	0.000	0.000	0.000
84	C	142	THR	0	-0.053	-0.050	21.029	-0.005	-0.005	0.000	0.000	0.000	0.000
85	C	143	PHE	0	-0.034	-0.019	21.583	-0.011	-0.011	0.000	0.000	0.000	0.000
86	C	144	GLY	0	0.088	0.021	20.809	0.002	0.002	0.000	0.000	0.000	0.000
87	C	145	TRP	0	-0.033	-0.021	11.890	-0.048	-0.048	0.000	0.000	0.000	0.000
88	C	146	CYS	0	-0.075	-0.034	15.945	0.019	0.019	0.000	0.000	0.000	0.000
89	C	147	PHE	0	0.031	0.014	9.657	-0.013	-0.013	0.000	0.000	0.000	0.000
90	C	148	LYS	1	0.843	0.910	15.109	0.075	0.075	0.000	0.000	0.000	0.000
91	C	149	LEU	0	-0.019	0.004	15.352	0.012	0.012	0.000	0.000	0.000	0.000
92	C	150	VAL	0	-0.039	-0.038	16.860	-0.024	-0.024	0.000	0.000	0.000	0.000
93	C	151	PRO	0	0.040	0.020	17.975	0.022	0.022	0.000	0.000	0.000	0.000
94	C	152	VAL	0	-0.040	-0.027	16.455	-0.018	-0.018	0.000	0.000	0.000	0.000
95	C	153	GLU	-1	-0.956	-0.962	19.759	0.056	0.056	0.000	0.000	0.000	0.000
96	C	181	GLU	-1	-0.791	-0.883	22.127	0.144	0.144	0.000	0.000	0.000	0.000
97	C	182	LYS	1	0.775	0.874	21.104	-0.176	-0.176	0.000	0.000	0.000	0.000
98	C	183	GLU	-1	-0.887	-0.957	22.379	0.094	0.094	0.000	0.000	0.000	0.000
99	C	184	VAL	0	0.028	0.017	17.037	0.025	0.025	0.000	0.000	0.000	0.000
100	C	185	LEU	0	-0.004	0.003	17.836	-0.022	-0.022	0.000	0.000	0.000	0.000
101	C	186	VAL	0	0.000	0.003	12.723	0.057	0.057	0.000	0.000	0.000	0.000
102	C	187	TRP	0	0.007	0.007	10.743	-0.026	-0.026	0.000	0.000	0.000	0.000
103	C	188	ARG	1	0.862	0.941	11.735	0.005	0.005	0.000	0.000	0.000	0.000
104	C	189	PHE	0	0.022	0.008	12.012	0.004	0.004	0.000	0.000	0.000	0.000
105	C	190	ASP	-1	-0.816	-0.908	13.853	-0.088	-0.088	0.000	0.000	0.000	0.000
106	C	191	SER	0	0.043	0.008	17.588	0.010	0.010	0.000	0.000	0.000	0.000
107	C	192	LYS	1	0.935	0.970	19.005	0.092	0.092	0.000	0.000	0.000	0.000
108	C	193	LEU	0	-0.024	-0.005	18.597	0.014	0.014	0.000	0.000	0.000	0.000
109	C	194	ALA	0	0.037	0.026	19.957	0.006	0.006	0.000	0.000	0.000	0.000
110	C	195	PHE	0	-0.063	-0.007	21.685	0.007	0.007	0.000	0.000	0.000	0.000
111	C	196	HIS	0	-0.049	-0.050	24.860	0.004	0.004	0.000	0.000	0.000	0.000
112	C	197	HIS	0	-0.015	-0.005	24.905	-0.004	-0.004	0.000	0.000	0.000	0.000
113	C	198	MET	0	0.044	0.020	24.526	0.008	0.008	0.000	0.000	0.000	0.000
114	C	199	ALA	0	-0.053	-0.022	25.099	0.006	0.006	0.000	0.000	0.000	0.000
115	C	200	ARG	1	0.919	0.959	26.897	0.015	0.015	0.000	0.000	0.000	0.000
116	C	201	GLU	-1	-0.849	-0.889	29.879	-0.026	-0.026	0.000	0.000	0.000	0.000
117	C	202	LEU	0	-0.016	-0.011	31.833	0.004	0.004	0.000	0.000	0.000	0.000
118	C	203	HIS	1	0.821	0.903	34.282	0.009	0.009	0.000	0.000	0.000	0.000
119	C	204	PRO	0	0.077	0.017	28.957	-0.005	-0.005	0.000	0.000	0.000	0.000
120	C	205	GLU	-1	-0.845	-0.919	30.181	-0.013	-0.013	0.000	0.000	0.000	0.000
121	C	206	TYR	0	-0.013	0.006	31.978	-0.002	-0.002	0.000	0.000	0.000	0.000
122	C	207	TYR	0	-0.018	-0.009	28.753	-0.005	-0.005	0.000	0.000	0.000	0.000
123	C	208	LYS	1	0.829	0.914	26.041	0.001	0.001	0.000	0.000	0.000	0.000
124	C	209	ASP	-1	-0.920	-0.951	27.671	-0.048	-0.048	0.000	0.000	0.000	0.000
125	C	210	ALA	0	-0.007	0.002	28.712	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)