FMO DATABASE

FMODB ID: Z679N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1234227.387283
FMO2-HF: Nuclear repulsion	1180060.729599
FMO2-HF: Total energy	-54166.657684
FMO2-MP2: Total energy	-54326.956581

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.
-231.309	-232.12	26.099	-13.575	-11.711	-0.153

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 : 0.862 / q_NPA : 0.916

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	0.844	0.945	2.672	26.272	29.382	0.639	-1.802	-1.946	-0.009
4	A	106	VAL	0	0.002	0.008	3.938	6.250	6.593	0.000	-0.031	-0.311	0.000
5	A	107	PRO	0	-0.012	-0.023	6.151	1.408	1.408	0.000	0.000	0.000	0.000
6	A	108	LEU	0	-0.008	0.003	8.974	-1.635	-1.635	0.000	0.000	0.000	0.000
7	A	109	ARG	1	0.797	0.886	6.164	37.416	37.416	0.000	0.000	0.000	0.000
8	A	110	THR	0	0.050	0.035	12.444	-0.902	-0.902	0.000	0.000	0.000	0.000
9	A	111	MET	0	0.012	0.028	13.064	-0.467	-0.467	0.000	0.000	0.000	0.000
10	A	112	SER	0	-0.009	0.001	14.618	1.313	1.313	0.000	0.000	0.000	0.000
11	A	113	TYR	0	0.106	0.028	16.035	-0.744	-0.744	0.000	0.000	0.000	0.000
12	A	114	LYS	1	0.915	0.959	16.507	15.013	15.013	0.000	0.000	0.000	0.000
13	A	115	LEU	0	0.018	0.017	10.397	-0.214	-0.214	0.000	0.000	0.000	0.000
14	A	116	ALA	0	0.047	0.023	13.295	-0.841	-0.841	0.000	0.000	0.000	0.000
15	A	117	ILE	0	-0.003	0.027	15.665	-0.071	-0.071	0.000	0.000	0.000	0.000
16	A	118	ASP	-1	-0.960	-0.973	11.704	-23.431	-23.431	0.000	0.000	0.000	0.000
17	A	119	MET	0	0.033	0.008	7.860	0.130	0.130	0.000	0.000	0.000	0.000
18	A	120	SER	0	-0.019	-0.012	12.375	0.182	0.182	0.000	0.000	0.000	0.000
19	A	121	HIS	0	0.046	0.008	15.868	0.472	0.472	0.000	0.000	0.000	0.000
20	A	122	PHE	0	0.034	0.025	9.584	0.147	0.147	0.000	0.000	0.000	0.000
21	A	123	ILE	0	0.013	-0.009	11.801	-0.173	-0.173	0.000	0.000	0.000	0.000
22	A	124	LYS	1	0.824	0.924	14.058	14.624	14.624	0.000	0.000	0.000	0.000
23	A	125	GLU	-1	-0.921	-0.965	15.875	-18.443	-18.443	0.000	0.000	0.000	0.000
24	A	126	LYS	1	0.765	0.883	12.043	22.259	22.259	0.000	0.000	0.000	0.000
25	A	127	GLY	0	-0.020	0.008	15.311	-0.125	-0.125	0.000	0.000	0.000	0.000
26	A	128	GLY	0	0.012	0.009	15.589	0.312	0.312	0.000	0.000	0.000	0.000
27	A	129	LEU	0	0.004	-0.014	15.957	0.555	0.555	0.000	0.000	0.000	0.000
28	A	130	GLU	-1	-0.812	-0.904	18.781	-12.455	-12.455	0.000	0.000	0.000	0.000
29	A	131	GLY	0	-0.009	0.006	22.038	0.108	0.108	0.000	0.000	0.000	0.000
30	A	132	ILE	0	-0.066	-0.019	19.030	0.295	0.295	0.000	0.000	0.000	0.000
31	A	133	TYR	0	0.035	0.011	23.157	-0.104	-0.104	0.000	0.000	0.000	0.000
32	A	134	TYR	0	-0.014	-0.029	21.931	-0.387	-0.387	0.000	0.000	0.000	0.000
33	A	135	SER	0	0.023	-0.008	22.987	0.230	0.230	0.000	0.000	0.000	0.000
34	A	136	ALA	0	0.056	0.029	22.338	-0.744	-0.744	0.000	0.000	0.000	0.000
35	A	137	ARG	1	0.728	0.841	21.442	11.618	11.618	0.000	0.000	0.000	0.000
36	A	138	ARG	1	0.883	0.925	18.624	12.835	12.835	0.000	0.000	0.000	0.000
37	A	139	HIS	0	0.046	0.066	17.448	-0.748	-0.748	0.000	0.000	0.000	0.000
38	A	140	ARG	1	0.962	0.967	16.958	13.211	13.211	0.000	0.000	0.000	0.000
39	A	141	ILE	0	-0.029	-0.008	14.293	-1.190	-1.190	0.000	0.000	0.000	0.000
40	A	142	LEU	0	0.001	0.010	12.627	-2.148	-2.148	0.000	0.000	0.000	0.000
41	A	143	ASP	-1	-0.826	-0.907	12.067	-20.317	-20.317	0.000	0.000	0.000	0.000
42	A	144	ILE	0	-0.046	-0.029	11.592	-2.117	-2.117	0.000	0.000	0.000	0.000
43	A	145	TYR	0	-0.003	-0.003	6.236	-1.758	-1.758	0.000	0.000	0.000	0.000
44	A	146	LEU	0	0.045	0.016	7.160	-5.214	-5.214	0.000	0.000	0.000	0.000
45	A	147	GLU	-1	-0.792	-0.869	7.654	-31.353	-31.353	0.000	0.000	0.000	0.000
46	A	148	LYS	1	0.785	0.864	6.801	25.946	25.946	0.000	0.000	0.000	0.000
47	A	149	GLU	-1	-0.838	-0.894	1.739	-137.189	-143.199	24.103	-10.454	-7.638	-0.128
48	A	150	GLU	-1	-0.867	-0.923	2.630	-72.715	-71.003	1.358	-1.287	-1.783	-0.016
49	A	151	GLY	0	-0.017	-0.003	4.911	4.739	4.773	-0.001	-0.001	-0.033	0.000
50	A	152	ILE	0	-0.048	-0.022	7.634	3.748	3.748	0.000	0.000	0.000	0.000
51	A	153	ILE	0	0.012	-0.003	10.312	0.064	0.064	0.000	0.000	0.000	0.000
52	A	154	PRO	0	-0.007	-0.004	13.577	0.107	0.107	0.000	0.000	0.000	0.000
53	A	155	ASP	-1	-0.898	-0.971	15.494	-17.101	-17.101	0.000	0.000	0.000	0.000
54	A	156	TRP	0	0.035	0.021	13.589	1.075	1.075	0.000	0.000	0.000	0.000
55	A	157	GLN	0	-0.020	-0.005	16.774	1.181	1.181	0.000	0.000	0.000	0.000
56	A	158	ASP	-1	-0.802	-0.900	19.165	-11.819	-11.819	0.000	0.000	0.000	0.000
57	A	159	TYR	0	-0.059	-0.058	19.727	-0.327	-0.327	0.000	0.000	0.000	0.000
58	A	160	THR	0	-0.018	0.002	25.537	0.145	0.145	0.000	0.000	0.000	0.000
59	A	161	SER	0	-0.027	-0.046	29.320	0.101	0.101	0.000	0.000	0.000	0.000
60	A	162	GLY	0	-0.011	0.008	31.324	0.090	0.090	0.000	0.000	0.000	0.000
61	A	163	PRO	0	0.000	-0.003	33.227	-0.222	-0.222	0.000	0.000	0.000	0.000
62	A	164	GLY	0	-0.016	-0.004	34.235	0.130	0.130	0.000	0.000	0.000	0.000
63	A	165	ILE	0	-0.067	-0.057	29.224	-0.282	-0.282	0.000	0.000	0.000	0.000
64	A	166	ARG	1	0.771	0.874	27.131	10.151	10.151	0.000	0.000	0.000	0.000
65	A	167	TYR	0	-0.016	-0.053	26.499	-0.538	-0.538	0.000	0.000	0.000	0.000
66	A	168	PRO	0	-0.025	-0.007	21.708	0.094	0.094	0.000	0.000	0.000	0.000
67	A	169	LYS	1	0.821	0.913	23.846	11.500	11.500	0.000	0.000	0.000	0.000
68	A	170	THR	0	-0.026	-0.008	18.248	0.314	0.314	0.000	0.000	0.000	0.000
69	A	171	PHE	0	-0.010	-0.011	21.560	-0.238	-0.238	0.000	0.000	0.000	0.000
70	A	172	GLY	0	-0.003	-0.015	20.108	-0.683	-0.683	0.000	0.000	0.000	0.000
71	A	173	TRP	0	0.035	0.012	13.655	-0.868	-0.868	0.000	0.000	0.000	0.000
72	A	174	LEU	0	-0.049	-0.025	19.026	0.803	0.803	0.000	0.000	0.000	0.000
73	A	175	TRP	0	-0.017	-0.015	16.727	0.660	0.660	0.000	0.000	0.000	0.000
74	A	176	LYS	1	0.869	0.938	21.057	10.766	10.766	0.000	0.000	0.000	0.000
75	A	177	LEU	0	0.004	0.016	22.745	-0.196	-0.196	0.000	0.000	0.000	0.000
76	A	178	VAL	0	-0.052	-0.037	25.995	0.399	0.399	0.000	0.000	0.000	0.000
77	A	179	PRO	0	0.033	0.025	29.286	-0.217	-0.217	0.000	0.000	0.000	0.000
78	A	180	VAL	0	-0.046	-0.022	29.973	0.006	0.006	0.000	0.000	0.000	0.000
79	A	181	ASN	0	0.000	-0.001	33.028	0.063	0.063	0.000	0.000	0.000	0.000
80	A	182	VAL	0	-0.004	-0.007	33.622	-0.120	-0.120	0.000	0.000	0.000	0.000
81	A	183	SER	0	-0.059	-0.045	37.014	0.254	0.254	0.000	0.000	0.000	0.000
82	A	184	ASP	-1	-0.888	-0.928	38.277	-7.838	-7.838	0.000	0.000	0.000	0.000
83	A	185	GLU	-1	-0.888	-0.947	38.285	-7.762	-7.762	0.000	0.000	0.000	0.000
84	A	186	ALA	0	-0.055	-0.018	39.635	0.061	0.061	0.000	0.000	0.000	0.000
85	A	187	GLN	0	-0.118	-0.060	35.190	-0.037	-0.037	0.000	0.000	0.000	0.000
86	A	188	GLU	-1	-0.867	-0.936	33.112	-9.849	-9.849	0.000	0.000	0.000	0.000
87	A	189	ASP	-1	-0.806	-0.885	37.428	-8.076	-8.076	0.000	0.000	0.000	0.000
88	A	190	GLU	-1	-0.905	-0.967	36.968	-8.443	-8.443	0.000	0.000	0.000	0.000
89	A	191	GLU	-1	-0.976	-0.981	36.672	-7.934	-7.934	0.000	0.000	0.000	0.000
90	A	192	HIS	0	-0.095	-0.071	33.208	-0.198	-0.198	0.000	0.000	0.000	0.000
91	A	193	TYR	0	-0.011	-0.032	29.170	-0.332	-0.332	0.000	0.000	0.000	0.000
92	A	194	LEU	0	-0.054	-0.024	32.036	-0.341	-0.341	0.000	0.000	0.000	0.000
93	A	195	MET	0	-0.064	-0.019	32.990	-0.206	-0.206	0.000	0.000	0.000	0.000
94	A	196	HIS	0	-0.044	-0.018	31.405	-0.054	-0.054	0.000	0.000	0.000	0.000
95	A	197	PRO	0	-0.024	0.009	25.992	-0.133	-0.133	0.000	0.000	0.000	0.000
96	A	198	ALA	0	0.055	0.029	26.952	-0.496	-0.496	0.000	0.000	0.000	0.000
97	A	199	GLN	0	-0.081	-0.051	23.714	-0.698	-0.698	0.000	0.000	0.000	0.000
98	A	200	THR	0	0.045	0.016	26.617	-0.097	-0.097	0.000	0.000	0.000	0.000
99	A	201	SER	0	0.003	-0.021	27.228	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	202	GLN	0	0.003	0.010	28.826	0.301	0.301	0.000	0.000	0.000	0.000
101	A	203	TRP	0	0.067	0.028	31.621	0.242	0.242	0.000	0.000	0.000	0.000
102	A	204	ASP	-1	-0.814	-0.847	26.871	-11.793	-11.793	0.000	0.000	0.000	0.000
103	A	205	ASP	-1	-0.750	-0.866	29.589	-10.075	-10.075	0.000	0.000	0.000	0.000
104	A	206	PRO	0	-0.039	-0.022	30.848	0.282	0.282	0.000	0.000	0.000	0.000
105	A	207	TRP	0	-0.075	-0.046	33.435	0.512	0.512	0.000	0.000	0.000	0.000
106	A	208	GLY	0	0.048	0.040	34.546	0.205	0.205	0.000	0.000	0.000	0.000
107	A	209	GLU	-1	-0.805	-0.882	32.595	-9.341	-9.341	0.000	0.000	0.000	0.000
108	A	210	VAL	0	0.006	0.024	30.431	-0.446	-0.446	0.000	0.000	0.000	0.000
109	A	211	LEU	0	0.007	0.007	27.587	0.064	0.064	0.000	0.000	0.000	0.000
110	A	212	ALA	0	-0.001	-0.006	25.542	-0.257	-0.257	0.000	0.000	0.000	0.000
111	A	213	TRP	0	-0.015	-0.002	19.299	0.113	0.113	0.000	0.000	0.000	0.000
112	A	214	LYS	1	0.881	0.943	23.267	11.676	11.676	0.000	0.000	0.000	0.000
113	A	215	PHE	0	-0.007	-0.007	19.415	0.158	0.158	0.000	0.000	0.000	0.000
114	A	216	ASP	-1	-0.859	-0.925	23.240	-10.509	-10.509	0.000	0.000	0.000	0.000
115	A	217	PRO	0	0.052	0.020	23.385	-0.245	-0.245	0.000	0.000	0.000	0.000
116	A	218	THR	0	-0.040	-0.040	24.398	0.069	0.069	0.000	0.000	0.000	0.000
117	A	219	LEU	0	0.038	0.023	23.564	0.250	0.250	0.000	0.000	0.000	0.000
118	A	220	ALA	0	-0.016	-0.006	22.534	-0.369	-0.369	0.000	0.000	0.000	0.000
119	A	221	TYR	0	-0.106	-0.054	23.827	0.073	0.073	0.000	0.000	0.000	0.000
120	A	222	THR	0	0.017	0.006	27.537	0.337	0.337	0.000	0.000	0.000	0.000
121	A	223	TYR	0	-0.028	-0.025	25.135	-0.250	-0.250	0.000	0.000	0.000	0.000
122	A	224	GLU	-1	-0.781	-0.867	28.251	-9.629	-9.629	0.000	0.000	0.000	0.000
123	A	225	ALA	0	0.028	0.018	27.340	0.306	0.306	0.000	0.000	0.000	0.000
124	A	226	TYR	0	-0.011	0.000	28.955	0.346	0.346	0.000	0.000	0.000	0.000
125	A	227	VAL	0	-0.061	-0.035	30.661	0.302	0.302	0.000	0.000	0.000	0.000
126	A	228	ARG	1	0.802	0.882	32.536	9.719	9.719	0.000	0.000	0.000	0.000
127	A	229	TYR	0	0.031	0.030	32.128	0.163	0.163	0.000	0.000	0.000	0.000
128	A	230	PRO	0	0.015	0.003	33.050	-0.234	-0.234	0.000	0.000	0.000	0.000
129	A	231	GLU	-1	-0.888	-0.957	33.862	-8.962	-8.962	0.000	0.000	0.000	0.000
130	A	232	GLU	-1	-0.791	-0.856	30.396	-10.319	-10.319	0.000	0.000	0.000	0.000
131	A	233	PHE	0	-0.086	-0.033	26.726	-0.416	-0.416	0.000	0.000	0.000	0.000

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