FMO DATABASE

FMODB ID: 49L6N

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	OptAll
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	-1144495.971309
FMO2-HF: Nuclear repulsion	1092916.926148
FMO2-HF: Total energy	-51579.045161
FMO2-MP2: Total energy	-51731.882852

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.
-36.774	-29.757	23.643	-12.848	-17.81	-0.015

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 : 0.030 / q_NPA : 0.005

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	-0.001	-0.002	2.354	-7.181	-3.483	5.878	-3.128	-6.448	0.006
4	C	62	LEU	0	-0.019	-0.002	2.122	-7.975	-7.601	5.709	-2.487	-3.596	0.016
5	C	63	GLU	-1	-0.742	-0.879	3.905	1.076	1.670	0.017	-0.167	-0.443	0.001
6	C	64	ALA	0	-0.065	-0.019	5.704	-0.809	-0.809	0.000	0.000	0.000	0.000
7	C	65	GLN	0	-0.082	-0.040	7.243	-0.575	-0.575	0.000	0.000	0.000	0.000
8	C	66	GLU	-1	-0.926	-0.964	7.569	1.534	1.534	0.000	0.000	0.000	0.000
9	C	67	GLU	-1	-0.848	-0.915	9.650	0.508	0.508	0.000	0.000	0.000	0.000
10	C	68	GLU	-1	-0.914	-0.939	11.861	0.437	0.437	0.000	0.000	0.000	0.000
11	C	69	GLU	-1	-0.886	-0.935	11.429	0.656	0.656	0.000	0.000	0.000	0.000
12	C	70	VAL	0	-0.017	-0.011	14.691	-0.093	-0.093	0.000	0.000	0.000	0.000
13	C	71	GLY	0	-0.003	-0.001	16.672	0.000	0.000	0.000	0.000	0.000	0.000
14	C	72	PHE	0	-0.058	-0.031	19.603	-0.041	-0.041	0.000	0.000	0.000	0.000
15	C	73	PRO	0	0.018	0.011	18.735	0.002	0.002	0.000	0.000	0.000	0.000
16	C	74	VAL	0	-0.004	0.001	19.121	-0.032	-0.032	0.000	0.000	0.000	0.000
17	C	75	ARG	1	0.933	0.961	15.295	-0.456	-0.456	0.000	0.000	0.000	0.000
18	C	76	PRO	0	0.010	0.000	22.033	0.013	0.013	0.000	0.000	0.000	0.000
19	C	77	GLN	0	-0.010	-0.005	19.538	0.044	0.044	0.000	0.000	0.000	0.000
20	C	78	VAL	0	0.001	0.006	18.496	-0.031	-0.031	0.000	0.000	0.000	0.000
21	C	79	PRO	0	0.004	-0.013	21.612	0.004	0.004	0.000	0.000	0.000	0.000
22	C	80	LEU	0	0.014	0.020	22.895	0.007	0.007	0.000	0.000	0.000	0.000
23	C	81	ARG	1	0.837	0.917	18.112	-0.189	-0.189	0.000	0.000	0.000	0.000
24	C	82	PRO	0	0.028	0.018	23.000	0.014	0.014	0.000	0.000	0.000	0.000
25	C	83	MET	0	0.025	0.024	17.134	-0.014	-0.014	0.000	0.000	0.000	0.000
26	C	84	THR	0	-0.023	-0.023	21.153	-0.017	-0.017	0.000	0.000	0.000	0.000
27	C	85	TYR	0	0.011	-0.005	20.894	0.004	0.004	0.000	0.000	0.000	0.000
28	C	86	LYS	1	0.828	0.887	19.190	0.013	0.013	0.000	0.000	0.000	0.000
29	C	87	ALA	0	0.029	0.024	18.194	-0.012	-0.012	0.000	0.000	0.000	0.000
30	C	88	ALA	0	0.089	0.032	16.365	0.002	0.002	0.000	0.000	0.000	0.000
31	C	89	LEU	0	-0.005	0.029	15.558	-0.017	-0.017	0.000	0.000	0.000	0.000
32	C	90	ASP	-1	-0.828	-0.898	15.038	-0.063	-0.063	0.000	0.000	0.000	0.000
33	C	91	ILE	0	0.009	0.002	11.512	-0.046	-0.046	0.000	0.000	0.000	0.000
34	C	92	SER	0	-0.028	-0.024	10.764	-0.033	-0.033	0.000	0.000	0.000	0.000
35	C	93	HIS	0	0.009	-0.007	10.744	-0.122	-0.122	0.000	0.000	0.000	0.000
36	C	94	PHE	0	-0.004	0.007	7.439	-0.219	-0.219	0.000	0.000	0.000	0.000
37	C	95	LEU	0	0.018	0.001	6.250	-0.283	-0.283	0.000	0.000	0.000	0.000
38	C	96	LYS	1	0.804	0.894	6.139	0.245	0.245	0.000	0.000	0.000	0.000
39	C	97	GLU	-1	-0.889	-0.929	7.036	-0.997	-0.997	0.000	0.000	0.000	0.000
40	C	98	LYS	1	0.779	0.893	2.109	-9.790	-8.122	2.150	-1.482	-2.336	0.011
41	C	99	GLY	0	0.060	0.034	2.034	-9.670	-9.253	5.117	-2.869	-2.664	-0.039
42	C	100	GLY	0	-0.012	-0.026	2.221	-2.665	-1.655	4.740	-3.536	-2.214	-0.010
43	C	101	LEU	0	0.012	0.014	3.099	1.475	0.731	0.032	0.821	-0.109	0.000
44	C	102	GLU	-1	-0.790	-0.884	6.257	-0.163	-0.163	0.000	0.000	0.000	0.000
45	C	103	GLY	0	-0.013	-0.010	7.665	-0.014	-0.014	0.000	0.000	0.000	0.000
46	C	104	LEU	0	-0.038	0.001	6.610	-0.050	-0.050	0.000	0.000	0.000	0.000
47	C	105	ILE	0	0.023	0.001	9.187	-0.090	-0.090	0.000	0.000	0.000	0.000
48	C	106	TRP	0	-0.005	-0.002	11.922	0.114	0.114	0.000	0.000	0.000	0.000
49	C	107	SER	0	-0.017	-0.025	14.113	-0.018	-0.018	0.000	0.000	0.000	0.000
50	C	108	GLN	0	0.008	-0.001	15.222	0.037	0.037	0.000	0.000	0.000	0.000
51	C	109	ARG	1	0.845	0.906	14.845	-0.478	-0.478	0.000	0.000	0.000	0.000
52	C	110	ARG	1	0.922	0.949	10.146	-0.612	-0.612	0.000	0.000	0.000	0.000
53	C	111	GLN	0	-0.002	0.015	12.150	0.078	0.078	0.000	0.000	0.000	0.000
54	C	112	GLU	-1	-0.808	-0.895	14.543	0.351	0.351	0.000	0.000	0.000	0.000
55	C	113	ILE	0	-0.019	0.010	10.366	-0.009	-0.009	0.000	0.000	0.000	0.000
56	C	114	LEU	0	-0.005	0.002	9.328	0.029	0.029	0.000	0.000	0.000	0.000
57	C	115	ASP	-1	-0.785	-0.907	11.799	0.297	0.297	0.000	0.000	0.000	0.000
58	C	116	LEU	0	-0.038	-0.018	15.338	-0.048	-0.048	0.000	0.000	0.000	0.000
59	C	117	TRP	0	-0.003	0.016	6.158	-0.140	-0.140	0.000	0.000	0.000	0.000
60	C	118	ILE	0	-0.009	-0.006	11.764	-0.053	-0.053	0.000	0.000	0.000	0.000
61	C	119	TYR	0	-0.011	0.000	13.783	-0.049	-0.049	0.000	0.000	0.000	0.000
62	C	120	HIS	1	0.807	0.880	15.157	-0.570	-0.570	0.000	0.000	0.000	0.000
63	C	121	THR	0	-0.026	-0.005	11.509	-0.016	-0.016	0.000	0.000	0.000	0.000
64	C	122	GLN	0	-0.085	-0.048	14.031	-0.099	-0.099	0.000	0.000	0.000	0.000
65	C	123	GLY	0	0.050	0.044	16.644	-0.043	-0.043	0.000	0.000	0.000	0.000
66	C	124	TYR	0	-0.020	-0.027	16.787	-0.030	-0.030	0.000	0.000	0.000	0.000
67	C	125	PHE	0	0.021	0.013	19.281	0.032	0.032	0.000	0.000	0.000	0.000
68	C	126	PRO	0	0.011	0.014	19.074	-0.006	-0.006	0.000	0.000	0.000	0.000
69	C	127	ASP	-1	-0.892	-0.958	20.367	0.160	0.160	0.000	0.000	0.000	0.000
70	C	128	TRP	0	-0.020	-0.014	14.454	-0.039	-0.039	0.000	0.000	0.000	0.000
71	C	129	GLN	0	0.018	0.047	14.046	-0.031	-0.031	0.000	0.000	0.000	0.000
72	C	130	ASN	0	-0.010	-0.008	18.834	0.017	0.017	0.000	0.000	0.000	0.000
73	C	131	TYR	0	-0.001	-0.029	15.103	-0.031	-0.031	0.000	0.000	0.000	0.000
74	C	132	THR	0	0.018	0.016	21.731	0.004	0.004	0.000	0.000	0.000	0.000
75	C	133	PRO	0	0.005	0.012	24.106	0.011	0.011	0.000	0.000	0.000	0.000
76	C	134	GLY	0	0.016	0.032	25.724	-0.004	-0.004	0.000	0.000	0.000	0.000
77	C	135	PRO	0	-0.010	-0.011	26.265	-0.002	-0.002	0.000	0.000	0.000	0.000
78	C	136	GLY	0	-0.003	-0.017	24.639	-0.007	-0.007	0.000	0.000	0.000	0.000
79	C	137	ILE	0	-0.062	-0.047	20.399	0.010	0.010	0.000	0.000	0.000	0.000
80	C	138	ARG	1	0.852	0.938	20.357	-0.141	-0.141	0.000	0.000	0.000	0.000
81	C	139	TYR	0	0.062	0.022	20.009	0.002	0.002	0.000	0.000	0.000	0.000
82	C	140	PRO	0	0.042	0.035	18.814	0.013	0.013	0.000	0.000	0.000	0.000
83	C	141	LEU	0	0.002	-0.021	20.887	-0.016	-0.016	0.000	0.000	0.000	0.000
84	C	142	THR	0	-0.062	-0.041	20.769	-0.012	-0.012	0.000	0.000	0.000	0.000
85	C	143	PHE	0	-0.012	-0.007	20.977	-0.002	-0.002	0.000	0.000	0.000	0.000
86	C	144	GLY	0	0.064	0.022	20.245	0.008	0.008	0.000	0.000	0.000	0.000
87	C	145	TRP	0	0.008	0.005	11.360	-0.032	-0.032	0.000	0.000	0.000	0.000
88	C	146	CYS	0	-0.097	-0.050	15.317	-0.001	-0.001	0.000	0.000	0.000	0.000
89	C	147	PHE	0	0.010	-0.007	9.231	-0.026	-0.026	0.000	0.000	0.000	0.000
90	C	148	LYS	1	0.856	0.923	14.883	0.076	0.076	0.000	0.000	0.000	0.000
91	C	149	LEU	0	-0.017	0.008	15.012	0.012	0.012	0.000	0.000	0.000	0.000
92	C	150	VAL	0	-0.033	-0.028	16.670	-0.025	-0.025	0.000	0.000	0.000	0.000
93	C	151	PRO	0	0.035	0.014	17.769	0.015	0.015	0.000	0.000	0.000	0.000
94	C	152	VAL	0	-0.051	-0.019	16.102	-0.019	-0.019	0.000	0.000	0.000	0.000
95	C	153	GLU	-1	-0.947	-0.959	19.484	-0.008	-0.008	0.000	0.000	0.000	0.000
96	C	181	GLU	-1	-0.768	-0.864	22.419	0.082	0.082	0.000	0.000	0.000	0.000
97	C	182	LYS	1	0.747	0.852	21.118	-0.110	-0.110	0.000	0.000	0.000	0.000
98	C	183	GLU	-1	-0.825	-0.919	22.296	0.064	0.064	0.000	0.000	0.000	0.000
99	C	184	VAL	0	0.009	0.005	17.178	0.023	0.023	0.000	0.000	0.000	0.000
100	C	185	LEU	0	0.006	0.005	17.660	-0.020	-0.020	0.000	0.000	0.000	0.000
101	C	186	VAL	0	-0.011	-0.008	12.787	0.042	0.042	0.000	0.000	0.000	0.000
102	C	187	TRP	0	0.033	0.018	10.524	-0.009	-0.009	0.000	0.000	0.000	0.000
103	C	188	ARG	1	0.817	0.892	11.390	0.090	0.090	0.000	0.000	0.000	0.000
104	C	189	PHE	0	0.053	0.016	11.812	0.017	0.017	0.000	0.000	0.000	0.000
105	C	190	ASP	-1	-0.829	-0.901	13.638	-0.072	-0.072	0.000	0.000	0.000	0.000
106	C	191	SER	0	0.056	0.026	17.340	0.017	0.017	0.000	0.000	0.000	0.000
107	C	192	LYS	1	0.903	0.932	18.820	0.080	0.080	0.000	0.000	0.000	0.000
108	C	193	LEU	0	-0.010	0.008	18.138	0.011	0.011	0.000	0.000	0.000	0.000
109	C	194	ALA	0	0.040	0.021	19.448	0.013	0.013	0.000	0.000	0.000	0.000
110	C	195	PHE	0	-0.071	-0.031	21.177	0.007	0.007	0.000	0.000	0.000	0.000
111	C	196	HIS	0	-0.026	-0.018	24.523	0.002	0.002	0.000	0.000	0.000	0.000
112	C	197	HIS	0	-0.029	-0.004	24.179	-0.005	-0.005	0.000	0.000	0.000	0.000
113	C	198	MET	0	0.023	0.005	24.077	0.006	0.006	0.000	0.000	0.000	0.000
114	C	199	ALA	0	-0.031	-0.013	24.397	0.001	0.001	0.000	0.000	0.000	0.000
115	C	200	ARG	1	0.879	0.934	26.361	-0.028	-0.028	0.000	0.000	0.000	0.000
116	C	201	GLU	-1	-0.831	-0.877	29.453	-0.001	-0.001	0.000	0.000	0.000	0.000
117	C	202	LEU	0	-0.012	-0.007	31.390	0.002	0.002	0.000	0.000	0.000	0.000
118	C	203	HIS	1	0.832	0.886	33.541	-0.003	-0.003	0.000	0.000	0.000	0.000
119	C	204	PRO	0	0.077	0.036	28.381	-0.005	-0.005	0.000	0.000	0.000	0.000
120	C	205	GLU	-1	-0.817	-0.902	29.429	-0.007	-0.007	0.000	0.000	0.000	0.000
121	C	206	TYR	0	-0.041	-0.013	31.638	-0.004	-0.004	0.000	0.000	0.000	0.000
122	C	207	TYR	0	-0.042	-0.032	28.293	-0.005	-0.005	0.000	0.000	0.000	0.000
123	C	208	LYS	1	0.806	0.895	26.262	0.000	0.000	0.000	0.000	0.000	0.000
124	C	209	ASP	-1	-0.859	-0.889	27.657	-0.053	-0.053	0.000	0.000	0.000	0.000
125	C	210	ALA	0	-0.071	-0.051	28.682	0.005	0.005	0.000	0.000	0.000	0.000

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