FMO DATABASE

FMODB ID: 52NYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1158742.345866
FMO2-HF: Nuclear repulsion	1106797.6324
FMO2-HF: Total energy	-51944.713466
FMO2-MP2: Total energy	-52098.407005

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.
-5.203	-3.332	-0.009	-1.182	-0.68	0.004

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 : -0.048 / q_NPA : -0.039

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	A	58	ASP	-1	-0.877	-0.941	3.882	-6.405	-4.534	-0.009	-1.182	-0.680	0.004
4	A	59	SER	0	0.024	0.035	6.469	0.786	0.786	0.000	0.000	0.000	0.000
5	A	60	ALA	0	0.055	0.006	8.016	0.264	0.264	0.000	0.000	0.000	0.000
6	A	61	TRP	0	-0.040	-0.014	10.478	0.093	0.093	0.000	0.000	0.000	0.000
7	A	62	LEU	0	0.015	-0.013	6.321	0.143	0.143	0.000	0.000	0.000	0.000
8	A	63	GLU	-1	-0.773	-0.886	10.653	-1.179	-1.179	0.000	0.000	0.000	0.000
9	A	64	ALA	0	-0.026	-0.006	13.005	0.097	0.097	0.000	0.000	0.000	0.000
10	A	65	GLN	0	-0.053	-0.044	13.292	0.123	0.123	0.000	0.000	0.000	0.000
11	A	66	GLU	-1	-0.918	-0.949	13.495	0.034	0.034	0.000	0.000	0.000	0.000
12	A	67	GLU	-1	-0.964	-0.995	15.801	-0.293	-0.293	0.000	0.000	0.000	0.000
13	A	68	GLU	-1	-1.031	-1.018	18.651	0.160	0.160	0.000	0.000	0.000	0.000
14	A	69	GLU	-1	-0.939	-0.957	18.101	0.418	0.418	0.000	0.000	0.000	0.000
15	A	70	VAL	0	-0.071	-0.027	18.711	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	71	GLY	0	0.018	0.012	21.476	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	72	PHE	0	-0.066	-0.039	22.945	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	73	PRO	0	-0.012	-0.007	22.896	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	74	VAL	0	0.032	0.014	22.449	0.015	0.015	0.000	0.000	0.000	0.000
20	A	75	ARG	1	0.907	0.954	20.287	0.413	0.413	0.000	0.000	0.000	0.000
21	A	76	PRO	0	0.011	0.001	26.563	0.011	0.011	0.000	0.000	0.000	0.000
22	A	77	GLN	0	-0.004	0.002	27.234	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	78	VAL	0	-0.013	0.003	26.442	0.009	0.009	0.000	0.000	0.000	0.000
24	A	79	PRO	0	0.017	0.006	28.946	0.017	0.017	0.000	0.000	0.000	0.000
25	A	80	LEU	0	0.016	0.001	30.689	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	81	ARG	1	0.857	0.930	26.314	0.324	0.324	0.000	0.000	0.000	0.000
27	A	82	PRO	0	0.012	0.010	31.395	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	83	MET	0	0.045	0.037	25.833	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	84	THR	0	-0.043	-0.022	29.876	0.007	0.007	0.000	0.000	0.000	0.000
30	A	85	TYR	0	0.018	-0.012	29.440	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	86	LYS	1	0.870	0.918	27.085	0.365	0.365	0.000	0.000	0.000	0.000
32	A	87	ALA	0	0.021	0.028	26.497	-0.030	-0.030	0.000	0.000	0.000	0.000
33	A	88	ALA	0	0.108	0.045	24.791	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	89	LEU	0	-0.018	0.015	23.556	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	90	ASP	-1	-0.865	-0.937	22.466	-0.479	-0.479	0.000	0.000	0.000	0.000
36	A	91	ILE	0	-0.024	-0.010	19.892	-0.074	-0.074	0.000	0.000	0.000	0.000
37	A	92	SER	0	-0.019	-0.018	18.887	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	93	HIS	0	0.025	0.001	17.841	-0.080	-0.080	0.000	0.000	0.000	0.000
39	A	94	PHE	0	-0.015	0.001	15.743	-0.131	-0.131	0.000	0.000	0.000	0.000
40	A	95	LEU	0	0.024	-0.004	14.495	-0.164	-0.164	0.000	0.000	0.000	0.000
41	A	96	LYS	1	0.893	0.957	13.063	0.769	0.769	0.000	0.000	0.000	0.000
42	A	97	GLU	-1	-0.989	-0.991	12.058	-1.471	-1.471	0.000	0.000	0.000	0.000
43	A	98	LYS	1	0.766	0.911	10.533	1.384	1.384	0.000	0.000	0.000	0.000
44	A	99	GLY	0	0.040	0.024	8.188	-0.656	-0.656	0.000	0.000	0.000	0.000
45	A	100	GLY	0	-0.001	-0.013	8.510	0.047	0.047	0.000	0.000	0.000	0.000
46	A	101	LEU	0	-0.014	0.000	9.246	0.289	0.289	0.000	0.000	0.000	0.000
47	A	102	GLU	-1	-0.824	-0.922	11.836	-0.195	-0.195	0.000	0.000	0.000	0.000
48	A	103	GLY	0	-0.030	-0.015	11.688	0.024	0.024	0.000	0.000	0.000	0.000
49	A	104	LEU	0	-0.051	-0.001	12.031	0.173	0.173	0.000	0.000	0.000	0.000
50	A	105	ILE	0	0.045	0.018	13.838	-0.057	-0.057	0.000	0.000	0.000	0.000
51	A	106	TRP	0	-0.013	-0.019	16.861	0.029	0.029	0.000	0.000	0.000	0.000
52	A	107	SER	0	-0.017	-0.024	19.684	0.026	0.026	0.000	0.000	0.000	0.000
53	A	108	GLN	0	0.033	0.014	21.799	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	109	ARG	1	0.974	0.991	20.166	-0.270	-0.270	0.000	0.000	0.000	0.000
55	A	110	ARG	1	0.890	0.940	15.494	-0.507	-0.507	0.000	0.000	0.000	0.000
56	A	111	GLN	0	0.059	0.043	19.131	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	112	GLU	-1	-0.844	-0.920	21.179	0.016	0.016	0.000	0.000	0.000	0.000
58	A	113	ILE	0	-0.001	-0.001	17.473	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	114	LEU	0	-0.021	-0.013	14.925	-0.056	-0.056	0.000	0.000	0.000	0.000
60	A	115	ASP	-1	-0.824	-0.899	18.901	-0.185	-0.185	0.000	0.000	0.000	0.000
61	A	116	LEU	0	-0.040	-0.030	22.424	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	117	TRP	0	0.042	0.043	14.754	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	118	ILE	0	0.008	0.007	19.335	-0.048	-0.048	0.000	0.000	0.000	0.000
64	A	119	TYR	0	-0.024	-0.001	21.651	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	120	HIS	1	0.893	0.949	22.340	0.144	0.144	0.000	0.000	0.000	0.000
66	A	121	THR	0	-0.053	-0.029	19.508	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	122	GLN	0	-0.038	-0.039	21.120	0.019	0.019	0.000	0.000	0.000	0.000
68	A	123	GLY	0	0.033	0.038	24.745	0.009	0.009	0.000	0.000	0.000	0.000
69	A	124	TYR	0	-0.029	-0.024	25.109	0.006	0.006	0.000	0.000	0.000	0.000
70	A	125	PHE	0	0.028	0.002	27.275	0.003	0.003	0.000	0.000	0.000	0.000
71	A	126	PRO	0	-0.014	0.002	26.223	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	127	ASP	-1	-0.898	-0.952	27.782	-0.088	-0.088	0.000	0.000	0.000	0.000
73	A	128	TRP	0	0.037	0.028	22.188	0.003	0.003	0.000	0.000	0.000	0.000
74	A	129	GLN	0	0.000	0.030	21.152	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	130	ASN	0	-0.017	-0.002	26.129	0.033	0.033	0.000	0.000	0.000	0.000
76	A	131	TYR	0	-0.045	-0.057	22.198	-0.028	-0.028	0.000	0.000	0.000	0.000
77	A	132	THR	0	0.052	0.032	28.607	0.006	0.006	0.000	0.000	0.000	0.000
78	A	133	PRO	0	-0.001	0.000	30.162	0.009	0.009	0.000	0.000	0.000	0.000
79	A	134	GLY	0	-0.033	-0.008	31.168	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	135	PRO	0	-0.008	-0.016	31.476	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	136	GLY	0	0.027	0.011	29.478	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	137	ILE	0	-0.031	-0.020	25.791	0.003	0.003	0.000	0.000	0.000	0.000
83	A	138	ARG	1	0.835	0.924	26.234	-0.058	-0.058	0.000	0.000	0.000	0.000
84	A	139	TYR	0	0.021	-0.014	26.052	-0.023	-0.023	0.000	0.000	0.000	0.000
85	A	140	PRO	0	0.014	0.027	25.802	0.017	0.017	0.000	0.000	0.000	0.000
86	A	141	LEU	0	0.030	-0.006	27.752	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	142	THR	0	-0.068	-0.055	28.215	0.003	0.003	0.000	0.000	0.000	0.000
88	A	143	PHE	0	0.000	-0.006	28.531	-0.017	-0.017	0.000	0.000	0.000	0.000
89	A	144	GLY	0	0.058	0.009	27.726	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	145	TRP	0	-0.045	-0.026	19.135	-0.054	-0.054	0.000	0.000	0.000	0.000
91	A	146	CYS	0	-0.068	-0.035	21.685	0.026	0.026	0.000	0.000	0.000	0.000
92	A	147	PHE	0	0.028	0.001	15.767	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	148	LYS	1	0.856	0.921	21.325	0.155	0.155	0.000	0.000	0.000	0.000
94	A	149	LEU	0	-0.013	0.007	21.102	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	150	VAL	0	-0.051	-0.043	21.404	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	151	PRO	0	0.030	0.013	22.084	0.026	0.026	0.000	0.000	0.000	0.000
97	A	152	VAL	0	-0.065	-0.036	19.571	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	153	GLU	-1	-0.881	-0.942	22.686	0.201	0.201	0.000	0.000	0.000	0.000
99	A	154	PRO	0	-0.037	-0.019	22.304	0.033	0.033	0.000	0.000	0.000	0.000
100	A	155	GLU	-1	-1.009	-0.984	18.528	0.558	0.558	0.000	0.000	0.000	0.000
101	A	179	ASP	-1	-0.927	-0.955	27.523	0.318	0.318	0.000	0.000	0.000	0.000
102	A	180	ALA	0	-0.024	-0.007	27.434	0.017	0.017	0.000	0.000	0.000	0.000
103	A	181	GLU	-1	-1.006	-0.999	29.406	0.194	0.194	0.000	0.000	0.000	0.000
104	A	182	LYS	1	0.922	0.938	27.406	-0.182	-0.182	0.000	0.000	0.000	0.000
105	A	183	GLU	-1	-0.778	-0.885	26.479	0.113	0.113	0.000	0.000	0.000	0.000
106	A	184	VAL	0	0.041	0.030	20.679	0.000	0.000	0.000	0.000	0.000	0.000
107	A	185	LEU	0	-0.029	-0.020	21.879	-0.025	-0.025	0.000	0.000	0.000	0.000
108	A	186	VAL	0	-0.008	0.010	16.695	0.039	0.039	0.000	0.000	0.000	0.000
109	A	187	TRP	0	0.037	0.017	16.355	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	188	ARG	1	0.911	0.965	16.751	0.037	0.037	0.000	0.000	0.000	0.000
111	A	189	PHE	0	0.003	0.000	16.851	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	190	ASP	-1	-0.812	-0.902	18.630	-0.173	-0.173	0.000	0.000	0.000	0.000
113	A	191	SER	0	0.044	0.017	21.714	0.011	0.011	0.000	0.000	0.000	0.000
114	A	192	LYS	1	0.880	0.925	23.084	0.192	0.192	0.000	0.000	0.000	0.000
115	A	193	LEU	0	-0.006	0.002	23.726	0.020	0.020	0.000	0.000	0.000	0.000
116	A	194	ALA	0	0.006	0.022	25.683	0.005	0.005	0.000	0.000	0.000	0.000
117	A	195	PHE	0	-0.064	-0.033	27.180	0.002	0.002	0.000	0.000	0.000	0.000
118	A	196	HIS	0	-0.022	0.015	30.015	0.005	0.005	0.000	0.000	0.000	0.000
119	A	197	HIS	0	-0.007	0.006	30.435	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	198	MET	0	-0.001	-0.017	29.610	0.016	0.016	0.000	0.000	0.000	0.000
121	A	199	ALA	0	0.029	0.021	31.644	0.013	0.013	0.000	0.000	0.000	0.000
122	A	200	ARG	1	0.948	0.977	33.317	0.111	0.111	0.000	0.000	0.000	0.000
123	A	201	GLU	-1	-0.885	-0.968	34.857	-0.123	-0.123	0.000	0.000	0.000	0.000
124	A	202	LEU	0	-0.007	0.005	33.030	0.006	0.006	0.000	0.000	0.000	0.000
125	A	203	HIS	0	-0.014	-0.004	35.451	0.016	0.016	0.000	0.000	0.000	0.000
126	A	204	PRO	0	-0.108	-0.047	38.742	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	205	GLU	-1	-0.940	-0.959	36.175	-0.044	-0.044	0.000	0.000	0.000	0.000

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