FMO DATABASE

FMODB ID: 2J4GR

Calculation Name: 5NUH-A-Xray372

Preferred Name: Tyrosine-protein kinase HCK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5NUH

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1235394.288974
FMO2-HF: Nuclear repulsion	1181228.904734
FMO2-HF: Total energy	-54165.38424
FMO2-MP2: Total energy	-54325.685936

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:103:ARG)

Summations of interaction energy for fragment #1(A:103:ARG)

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.
-171.52	-163.51	0.659	-4.465	-4.204	-0.044

Interaction energy analysis for fragmet #1(A:103:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.920 / q_NPA : 0.949

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	105	LYS	1	0.871	0.949	2.703	23.146	25.779	0.500	-1.469	-1.664	-0.010
4	A	106	VAL	0	0.004	0.007	4.373	4.625	4.817	-0.001	-0.008	-0.183	0.000
5	A	107	PRO	0	-0.026	-0.027	6.817	1.161	1.161	0.000	0.000	0.000	0.000
6	A	108	LEU	0	0.020	0.003	10.006	-1.455	-1.455	0.000	0.000	0.000	0.000
7	A	109	ARG	1	0.938	0.974	8.638	29.144	29.144	0.000	0.000	0.000	0.000
8	A	110	THR	0	0.056	0.035	13.480	-0.668	-0.668	0.000	0.000	0.000	0.000
9	A	111	MET	0	0.031	0.023	13.159	-0.559	-0.559	0.000	0.000	0.000	0.000
10	A	112	SER	0	0.005	0.003	15.291	1.113	1.113	0.000	0.000	0.000	0.000
11	A	113	TYR	0	0.126	0.042	16.849	-0.609	-0.609	0.000	0.000	0.000	0.000
12	A	114	LYS	1	0.933	0.963	16.889	15.082	15.082	0.000	0.000	0.000	0.000
13	A	115	LEU	0	-0.012	0.013	10.885	-0.322	-0.322	0.000	0.000	0.000	0.000
14	A	116	ALA	0	0.053	0.039	13.993	-0.729	-0.729	0.000	0.000	0.000	0.000
15	A	117	ILE	0	-0.005	0.019	16.209	-0.036	-0.036	0.000	0.000	0.000	0.000
16	A	118	ASP	-1	-0.928	-0.972	13.354	-21.714	-21.714	0.000	0.000	0.000	0.000
17	A	119	MET	0	-0.006	-0.012	8.862	-0.411	-0.411	0.000	0.000	0.000	0.000
18	A	120	SER	0	-0.022	-0.011	12.883	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	121	HIS	0	0.040	0.012	16.187	0.331	0.331	0.000	0.000	0.000	0.000
20	A	122	PHE	0	0.050	0.044	9.404	-0.163	-0.163	0.000	0.000	0.000	0.000
21	A	123	ILE	0	-0.002	-0.015	12.228	-0.087	-0.087	0.000	0.000	0.000	0.000
22	A	124	LYS	1	0.885	0.962	14.137	14.733	14.733	0.000	0.000	0.000	0.000
23	A	125	GLU	-1	-0.966	-0.997	16.103	-17.725	-17.725	0.000	0.000	0.000	0.000
24	A	126	LYS	1	0.809	0.914	11.966	24.283	24.283	0.000	0.000	0.000	0.000
25	A	127	GLY	0	-0.013	0.000	15.212	-0.174	-0.174	0.000	0.000	0.000	0.000
26	A	128	GLY	0	0.004	0.014	15.587	0.133	0.133	0.000	0.000	0.000	0.000
27	A	129	LEU	0	0.016	-0.013	16.273	0.513	0.513	0.000	0.000	0.000	0.000
28	A	130	GLU	-1	-0.847	-0.933	18.820	-12.312	-12.312	0.000	0.000	0.000	0.000
29	A	131	GLY	0	-0.030	-0.011	21.900	0.044	0.044	0.000	0.000	0.000	0.000
30	A	132	ILE	0	-0.065	-0.013	19.199	0.334	0.334	0.000	0.000	0.000	0.000
31	A	133	TYR	0	0.017	0.004	23.248	0.039	0.039	0.000	0.000	0.000	0.000
32	A	134	TYR	0	-0.014	-0.049	22.161	-0.383	-0.383	0.000	0.000	0.000	0.000
33	A	135	SER	0	0.028	0.009	23.268	0.273	0.273	0.000	0.000	0.000	0.000
34	A	136	ALA	0	0.077	0.040	22.833	-0.638	-0.638	0.000	0.000	0.000	0.000
35	A	137	ARG	1	0.779	0.848	21.586	11.099	11.099	0.000	0.000	0.000	0.000
36	A	138	ARG	1	0.903	0.949	18.989	12.855	12.855	0.000	0.000	0.000	0.000
37	A	139	HIS	0	0.090	0.102	17.978	-0.697	-0.697	0.000	0.000	0.000	0.000
38	A	140	ARG	1	0.985	0.992	17.726	12.683	12.683	0.000	0.000	0.000	0.000
39	A	141	ILE	0	-0.036	-0.021	14.467	-1.095	-1.095	0.000	0.000	0.000	0.000
40	A	142	LEU	0	-0.016	0.005	13.231	-1.920	-1.920	0.000	0.000	0.000	0.000
41	A	143	ASP	-1	-0.832	-0.911	12.865	-19.214	-19.214	0.000	0.000	0.000	0.000
42	A	144	ILE	0	-0.066	-0.040	11.877	-1.746	-1.746	0.000	0.000	0.000	0.000
43	A	145	TYR	0	-0.008	-0.007	7.451	-2.652	-2.652	0.000	0.000	0.000	0.000
44	A	146	LEU	0	0.098	0.033	7.892	-3.983	-3.983	0.000	0.000	0.000	0.000
45	A	147	GLU	-1	-0.821	-0.864	8.446	-24.921	-24.921	0.000	0.000	0.000	0.000
46	A	148	LYS	1	0.731	0.823	7.631	22.871	22.871	0.000	0.000	0.000	0.000
47	A	149	GLU	-1	-0.918	-0.951	2.752	-86.243	-81.568	0.156	-2.769	-2.062	-0.032
48	A	150	GLU	-1	-0.960	-0.980	3.554	-59.823	-59.313	0.004	-0.219	-0.295	-0.002
49	A	151	GLY	0	-0.119	-0.052	5.930	3.224	3.224	0.000	0.000	0.000	0.000
50	A	152	ILE	0	-0.040	-0.015	8.488	3.133	3.133	0.000	0.000	0.000	0.000
51	A	153	ILE	0	0.023	-0.003	11.217	-0.082	-0.082	0.000	0.000	0.000	0.000
52	A	154	PRO	0	-0.018	0.001	14.404	0.232	0.232	0.000	0.000	0.000	0.000
53	A	155	ASP	-1	-0.932	-0.971	16.256	-15.502	-15.502	0.000	0.000	0.000	0.000
54	A	156	TRP	0	0.031	0.019	14.345	0.872	0.872	0.000	0.000	0.000	0.000
55	A	157	GLN	0	-0.024	-0.014	17.608	1.036	1.036	0.000	0.000	0.000	0.000
56	A	158	ASP	-1	-0.841	-0.930	19.790	-11.743	-11.743	0.000	0.000	0.000	0.000
57	A	159	TYR	0	-0.075	-0.063	20.685	-0.234	-0.234	0.000	0.000	0.000	0.000
58	A	160	THR	0	-0.006	-0.010	26.222	0.095	0.095	0.000	0.000	0.000	0.000
59	A	161	SER	0	-0.030	-0.029	29.895	0.044	0.044	0.000	0.000	0.000	0.000
60	A	162	GLY	0	-0.022	0.025	32.497	0.029	0.029	0.000	0.000	0.000	0.000
61	A	163	PRO	0	0.023	0.003	34.108	-0.214	-0.214	0.000	0.000	0.000	0.000
62	A	164	GLY	0	-0.029	-0.012	34.808	0.045	0.045	0.000	0.000	0.000	0.000
63	A	165	ILE	0	-0.051	-0.048	29.604	-0.276	-0.276	0.000	0.000	0.000	0.000
64	A	166	ARG	1	0.786	0.912	27.593	10.062	10.062	0.000	0.000	0.000	0.000
65	A	167	TYR	0	-0.021	-0.026	27.281	-0.327	-0.327	0.000	0.000	0.000	0.000
66	A	168	PRO	0	0.024	0.005	22.341	0.086	0.086	0.000	0.000	0.000	0.000
67	A	169	LYS	1	0.902	0.959	24.442	11.172	11.172	0.000	0.000	0.000	0.000
68	A	170	THR	0	-0.013	0.028	18.987	0.283	0.283	0.000	0.000	0.000	0.000
69	A	171	PHE	0	0.010	-0.004	22.093	-0.318	-0.318	0.000	0.000	0.000	0.000
70	A	172	GLY	0	-0.008	-0.017	20.549	-0.583	-0.583	0.000	0.000	0.000	0.000
71	A	173	TRP	0	0.022	0.003	14.430	-0.856	-0.856	0.000	0.000	0.000	0.000
72	A	174	LEU	0	-0.043	-0.024	19.289	0.737	0.737	0.000	0.000	0.000	0.000
73	A	175	TRP	0	-0.009	0.006	16.981	0.711	0.711	0.000	0.000	0.000	0.000
74	A	176	LYS	1	0.909	0.962	21.561	10.934	10.934	0.000	0.000	0.000	0.000
75	A	177	LEU	0	0.002	0.007	23.621	-0.275	-0.275	0.000	0.000	0.000	0.000
76	A	178	VAL	0	-0.049	-0.039	26.642	0.427	0.427	0.000	0.000	0.000	0.000
77	A	179	PRO	0	0.052	0.033	29.638	-0.221	-0.221	0.000	0.000	0.000	0.000
78	A	180	VAL	0	-0.053	-0.024	30.173	0.035	0.035	0.000	0.000	0.000	0.000
79	A	181	ASN	0	0.006	0.000	33.089	0.083	0.083	0.000	0.000	0.000	0.000
80	A	182	VAL	0	-0.019	-0.017	33.676	-0.095	-0.095	0.000	0.000	0.000	0.000
81	A	183	SER	0	-0.057	-0.053	37.033	0.229	0.229	0.000	0.000	0.000	0.000
82	A	184	ASP	-1	-0.889	-0.920	38.771	-7.732	-7.732	0.000	0.000	0.000	0.000
83	A	185	GLU	-1	-0.886	-0.944	38.813	-7.593	-7.593	0.000	0.000	0.000	0.000
84	A	186	ALA	0	-0.060	-0.021	40.501	0.085	0.085	0.000	0.000	0.000	0.000
85	A	187	GLN	0	-0.112	-0.061	35.405	-0.078	-0.078	0.000	0.000	0.000	0.000
86	A	188	GLU	-1	-0.855	-0.956	33.745	-9.620	-9.620	0.000	0.000	0.000	0.000
87	A	189	ASP	-1	-0.823	-0.885	37.699	-7.863	-7.863	0.000	0.000	0.000	0.000
88	A	190	GLU	-1	-0.903	-0.972	37.340	-8.354	-8.354	0.000	0.000	0.000	0.000
89	A	191	GLU	-1	-0.981	-0.984	37.004	-7.816	-7.816	0.000	0.000	0.000	0.000
90	A	192	HIS	0	-0.074	-0.047	33.094	-0.186	-0.186	0.000	0.000	0.000	0.000
91	A	193	TYR	0	-0.038	-0.036	29.932	-0.333	-0.333	0.000	0.000	0.000	0.000
92	A	194	LEU	0	-0.058	-0.023	32.364	-0.318	-0.318	0.000	0.000	0.000	0.000
93	A	195	MET	0	-0.073	-0.027	32.733	-0.261	-0.261	0.000	0.000	0.000	0.000
94	A	196	HIS	0	-0.018	-0.013	31.653	-0.132	-0.132	0.000	0.000	0.000	0.000
95	A	197	PRO	0	-0.018	0.008	26.411	-0.150	-0.150	0.000	0.000	0.000	0.000
96	A	198	ALA	0	0.032	0.019	27.670	-0.379	-0.379	0.000	0.000	0.000	0.000
97	A	199	GLN	0	-0.070	-0.054	22.370	-0.163	-0.163	0.000	0.000	0.000	0.000
98	A	200	THR	0	-0.004	-0.005	26.998	-0.055	-0.055	0.000	0.000	0.000	0.000
99	A	201	SER	0	0.016	-0.004	27.805	-0.072	-0.072	0.000	0.000	0.000	0.000
100	A	202	GLN	0	0.003	0.022	29.311	0.305	0.305	0.000	0.000	0.000	0.000
101	A	203	TRP	0	0.070	0.025	32.327	0.171	0.171	0.000	0.000	0.000	0.000
102	A	204	ASP	-1	-0.842	-0.862	27.194	-11.496	-11.496	0.000	0.000	0.000	0.000
103	A	205	ASP	-1	-0.793	-0.903	30.143	-9.881	-9.881	0.000	0.000	0.000	0.000
104	A	206	PRO	0	-0.023	-0.009	31.233	0.281	0.281	0.000	0.000	0.000	0.000
105	A	207	TRP	0	-0.065	-0.038	33.645	0.500	0.500	0.000	0.000	0.000	0.000
106	A	208	GLY	0	0.035	0.028	35.036	0.191	0.191	0.000	0.000	0.000	0.000
107	A	209	GLU	-1	-0.833	-0.898	33.555	-8.980	-8.980	0.000	0.000	0.000	0.000
108	A	210	VAL	0	0.007	0.013	30.440	-0.360	-0.360	0.000	0.000	0.000	0.000
109	A	211	LEU	0	-0.014	-0.006	27.858	0.024	0.024	0.000	0.000	0.000	0.000
110	A	212	ALA	0	0.010	-0.003	25.988	-0.282	-0.282	0.000	0.000	0.000	0.000
111	A	213	TRP	0	-0.010	0.002	19.349	0.017	0.017	0.000	0.000	0.000	0.000
112	A	214	LYS	1	0.900	0.962	23.656	10.855	10.855	0.000	0.000	0.000	0.000
113	A	215	PHE	0	0.002	-0.017	19.418	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	216	ASP	-1	-0.867	-0.942	23.291	-10.557	-10.557	0.000	0.000	0.000	0.000
115	A	217	PRO	0	0.044	0.013	23.681	-0.258	-0.258	0.000	0.000	0.000	0.000
116	A	218	THR	0	-0.040	-0.020	24.699	0.038	0.038	0.000	0.000	0.000	0.000
117	A	219	LEU	0	0.038	0.029	24.168	0.236	0.236	0.000	0.000	0.000	0.000
118	A	220	ALA	0	-0.043	-0.017	22.745	-0.221	-0.221	0.000	0.000	0.000	0.000
119	A	221	TYR	0	-0.119	-0.061	24.365	0.118	0.118	0.000	0.000	0.000	0.000
120	A	222	THR	0	0.021	-0.002	28.090	0.295	0.295	0.000	0.000	0.000	0.000
121	A	223	TYR	0	-0.057	-0.045	25.958	-0.250	-0.250	0.000	0.000	0.000	0.000
122	A	224	GLU	-1	-0.880	-0.982	28.683	-9.480	-9.480	0.000	0.000	0.000	0.000
123	A	225	ALA	0	0.027	0.024	28.000	0.288	0.288	0.000	0.000	0.000	0.000
124	A	226	TYR	0	-0.038	-0.011	29.607	0.344	0.344	0.000	0.000	0.000	0.000
125	A	227	VAL	0	-0.043	-0.009	31.267	0.291	0.291	0.000	0.000	0.000	0.000
126	A	228	ARG	1	0.891	0.945	33.237	9.352	9.352	0.000	0.000	0.000	0.000
127	A	229	TYR	0	0.007	0.010	32.785	0.179	0.179	0.000	0.000	0.000	0.000
128	A	230	PRO	0	0.005	0.008	33.488	-0.237	-0.237	0.000	0.000	0.000	0.000
129	A	231	GLU	-1	-0.859	-0.949	34.430	-8.691	-8.691	0.000	0.000	0.000	0.000
130	A	232	GLU	-1	-0.880	-0.927	31.744	-9.809	-9.809	0.000	0.000	0.000	0.000
131	A	233	PHE	0	-0.060	-0.020	27.124	-0.397	-0.397	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:103:ARG)