FMO DATABASE

FMODB ID: 6NZ5Z

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	OptHSide
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	-1235567.498175
FMO2-HF: Nuclear repulsion	1181401.226828
FMO2-HF: Total energy	-54166.271347
FMO2-MP2: Total energy	-54326.594881

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.
-213.69	-207	12.528	-10.679	-8.538	-0.112

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 : 0.895 / q_NPA : 0.939

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	0.876	0.955	2.720	24.314	27.861	0.469	-2.043	-1.973	-0.005
4	A	106	VAL	0	0.005	0.011	4.333	4.936	5.144	-0.001	-0.010	-0.197	0.000
5	A	107	PRO	0	-0.022	-0.026	6.735	1.050	1.050	0.000	0.000	0.000	0.000
6	A	108	LEU	0	-0.001	-0.003	9.609	-1.361	-1.361	0.000	0.000	0.000	0.000
7	A	109	ARG	1	0.830	0.922	7.248	34.013	34.013	0.000	0.000	0.000	0.000
8	A	110	THR	0	0.047	0.026	13.139	-0.711	-0.711	0.000	0.000	0.000	0.000
9	A	111	MET	0	0.012	0.023	13.355	-0.518	-0.518	0.000	0.000	0.000	0.000
10	A	112	SER	0	0.012	0.003	15.025	1.214	1.214	0.000	0.000	0.000	0.000
11	A	113	TYR	0	0.121	0.041	16.610	-0.646	-0.646	0.000	0.000	0.000	0.000
12	A	114	LYS	1	0.925	0.963	16.851	14.801	14.801	0.000	0.000	0.000	0.000
13	A	115	LEU	0	0.004	0.019	10.732	-0.195	-0.195	0.000	0.000	0.000	0.000
14	A	116	ALA	0	0.058	0.034	13.843	-0.714	-0.714	0.000	0.000	0.000	0.000
15	A	117	ILE	0	-0.009	0.017	16.057	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	118	ASP	-1	-0.955	-0.978	12.253	-22.622	-22.622	0.000	0.000	0.000	0.000
17	A	119	MET	0	0.017	-0.007	8.382	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	120	SER	0	-0.017	-0.008	12.838	0.014	0.014	0.000	0.000	0.000	0.000
19	A	121	HIS	0	0.041	0.014	16.187	0.396	0.396	0.000	0.000	0.000	0.000
20	A	122	PHE	0	0.036	0.038	9.669	0.024	0.024	0.000	0.000	0.000	0.000
21	A	123	ILE	0	0.014	-0.012	11.885	-0.058	-0.058	0.000	0.000	0.000	0.000
22	A	124	LYS	1	0.821	0.913	14.120	14.605	14.605	0.000	0.000	0.000	0.000
23	A	125	GLU	-1	-0.927	-0.969	16.064	-18.151	-18.151	0.000	0.000	0.000	0.000
24	A	126	LYS	1	0.727	0.873	12.149	21.866	21.866	0.000	0.000	0.000	0.000
25	A	127	GLY	0	-0.006	0.005	15.407	-0.171	-0.171	0.000	0.000	0.000	0.000
26	A	128	GLY	0	0.001	0.012	15.651	0.113	0.113	0.000	0.000	0.000	0.000
27	A	129	LEU	0	0.015	-0.009	15.981	0.498	0.498	0.000	0.000	0.000	0.000
28	A	130	GLU	-1	-0.814	-0.910	18.807	-12.414	-12.414	0.000	0.000	0.000	0.000
29	A	131	GLY	0	-0.017	-0.006	21.908	0.040	0.040	0.000	0.000	0.000	0.000
30	A	132	ILE	0	-0.064	-0.015	19.114	0.329	0.329	0.000	0.000	0.000	0.000
31	A	133	TYR	0	0.029	0.009	23.256	0.029	0.029	0.000	0.000	0.000	0.000
32	A	134	TYR	0	-0.010	-0.026	22.081	-0.391	-0.391	0.000	0.000	0.000	0.000
33	A	135	SER	0	0.018	-0.012	23.095	0.265	0.265	0.000	0.000	0.000	0.000
34	A	136	ALA	0	0.080	0.041	22.632	-0.680	-0.680	0.000	0.000	0.000	0.000
35	A	137	ARG	1	0.757	0.847	21.346	11.309	11.309	0.000	0.000	0.000	0.000
36	A	138	ARG	1	0.897	0.943	18.862	12.763	12.763	0.000	0.000	0.000	0.000
37	A	139	HIS	0	0.061	0.073	17.791	-0.707	-0.707	0.000	0.000	0.000	0.000
38	A	140	ARG	1	0.966	0.979	17.434	12.954	12.954	0.000	0.000	0.000	0.000
39	A	141	ILE	0	-0.033	-0.020	14.408	-1.152	-1.152	0.000	0.000	0.000	0.000
40	A	142	LEU	0	-0.015	0.005	12.903	-2.045	-2.045	0.000	0.000	0.000	0.000
41	A	143	ASP	-1	-0.825	-0.911	12.560	-19.649	-19.649	0.000	0.000	0.000	0.000
42	A	144	ILE	0	-0.060	-0.040	11.792	-1.829	-1.829	0.000	0.000	0.000	0.000
43	A	145	TYR	0	-0.015	-0.008	6.962	-2.704	-2.704	0.000	0.000	0.000	0.000
44	A	146	LEU	0	0.084	0.029	7.581	-4.504	-4.504	0.000	0.000	0.000	0.000
45	A	147	GLU	-1	-0.811	-0.866	8.085	-29.375	-29.375	0.000	0.000	0.000	0.000
46	A	148	LYS	1	0.759	0.842	7.363	24.221	24.221	0.000	0.000	0.000	0.000
47	A	149	GLU	-1	-0.855	-0.915	1.726	-128.207	-126.085	12.039	-8.250	-5.911	-0.104
48	A	150	GLU	-1	-0.933	-0.956	3.418	-58.260	-57.447	0.021	-0.376	-0.457	-0.003
49	A	151	GLY	0	-0.048	-0.014	5.709	3.724	3.724	0.000	0.000	0.000	0.000
50	A	152	ILE	0	-0.033	-0.013	8.196	3.331	3.331	0.000	0.000	0.000	0.000
51	A	153	ILE	0	0.015	-0.005	10.975	-0.102	-0.102	0.000	0.000	0.000	0.000
52	A	154	PRO	0	-0.016	0.002	14.094	0.236	0.236	0.000	0.000	0.000	0.000
53	A	155	ASP	-1	-0.909	-0.970	15.891	-16.254	-16.254	0.000	0.000	0.000	0.000
54	A	156	TRP	0	0.046	0.023	13.929	0.889	0.889	0.000	0.000	0.000	0.000
55	A	157	GLN	0	-0.022	-0.003	17.206	1.128	1.128	0.000	0.000	0.000	0.000
56	A	158	ASP	-1	-0.805	-0.904	19.456	-11.795	-11.795	0.000	0.000	0.000	0.000
57	A	159	TYR	0	-0.077	-0.066	20.140	-0.251	-0.251	0.000	0.000	0.000	0.000
58	A	160	THR	0	-0.003	0.002	25.885	0.090	0.090	0.000	0.000	0.000	0.000
59	A	161	SER	0	-0.039	-0.062	29.596	0.060	0.060	0.000	0.000	0.000	0.000
60	A	162	GLY	0	-0.045	0.011	32.130	0.040	0.040	0.000	0.000	0.000	0.000
61	A	163	PRO	0	0.024	-0.001	33.799	-0.212	-0.212	0.000	0.000	0.000	0.000
62	A	164	GLY	0	-0.015	-0.003	34.565	0.055	0.055	0.000	0.000	0.000	0.000
63	A	165	ILE	0	-0.069	-0.058	29.426	-0.278	-0.278	0.000	0.000	0.000	0.000
64	A	166	ARG	1	0.734	0.852	27.431	10.109	10.109	0.000	0.000	0.000	0.000
65	A	167	TYR	0	-0.048	-0.058	27.074	-0.415	-0.415	0.000	0.000	0.000	0.000
66	A	168	PRO	0	0.009	-0.001	22.138	0.081	0.081	0.000	0.000	0.000	0.000
67	A	169	LYS	1	0.864	0.941	24.291	11.388	11.388	0.000	0.000	0.000	0.000
68	A	170	THR	0	-0.020	-0.003	18.763	0.309	0.309	0.000	0.000	0.000	0.000
69	A	171	PHE	0	-0.003	-0.009	21.948	-0.283	-0.283	0.000	0.000	0.000	0.000
70	A	172	GLY	0	-0.009	-0.019	20.384	-0.582	-0.582	0.000	0.000	0.000	0.000
71	A	173	TRP	0	0.031	0.005	14.028	-0.864	-0.864	0.000	0.000	0.000	0.000
72	A	174	LEU	0	-0.048	-0.029	19.241	0.769	0.769	0.000	0.000	0.000	0.000
73	A	175	TRP	0	0.000	0.007	16.722	0.745	0.745	0.000	0.000	0.000	0.000
74	A	176	LYS	1	0.879	0.936	21.343	10.818	10.818	0.000	0.000	0.000	0.000
75	A	177	LEU	0	-0.006	0.008	23.159	-0.264	-0.264	0.000	0.000	0.000	0.000
76	A	178	VAL	0	-0.037	-0.032	26.431	0.425	0.425	0.000	0.000	0.000	0.000
77	A	179	PRO	0	0.052	0.036	29.476	-0.218	-0.218	0.000	0.000	0.000	0.000
78	A	180	VAL	0	-0.051	-0.025	30.038	0.058	0.058	0.000	0.000	0.000	0.000
79	A	181	ASN	0	-0.020	-0.011	33.006	0.108	0.108	0.000	0.000	0.000	0.000
80	A	182	VAL	0	0.007	-0.006	33.646	-0.100	-0.100	0.000	0.000	0.000	0.000
81	A	183	SER	0	-0.062	-0.055	36.995	0.228	0.228	0.000	0.000	0.000	0.000
82	A	184	ASP	-1	-0.888	-0.917	38.624	-7.745	-7.745	0.000	0.000	0.000	0.000
83	A	185	GLU	-1	-0.893	-0.951	38.643	-7.682	-7.682	0.000	0.000	0.000	0.000
84	A	186	ALA	0	-0.063	-0.023	40.089	0.051	0.051	0.000	0.000	0.000	0.000
85	A	187	GLN	0	-0.107	-0.055	35.181	-0.069	-0.069	0.000	0.000	0.000	0.000
86	A	188	GLU	-1	-0.856	-0.941	33.434	-9.754	-9.754	0.000	0.000	0.000	0.000
87	A	189	ASP	-1	-0.823	-0.891	37.637	-8.007	-8.007	0.000	0.000	0.000	0.000
88	A	190	GLU	-1	-0.907	-0.971	37.223	-8.406	-8.406	0.000	0.000	0.000	0.000
89	A	191	GLU	-1	-0.974	-0.983	36.868	-7.899	-7.899	0.000	0.000	0.000	0.000
90	A	192	HIS	0	-0.087	-0.061	33.119	-0.200	-0.200	0.000	0.000	0.000	0.000
91	A	193	TYR	0	-0.034	-0.034	29.536	-0.338	-0.338	0.000	0.000	0.000	0.000
92	A	194	LEU	0	-0.066	-0.022	32.250	-0.330	-0.330	0.000	0.000	0.000	0.000
93	A	195	MET	0	-0.059	-0.021	32.623	-0.278	-0.278	0.000	0.000	0.000	0.000
94	A	196	HIS	0	-0.018	-0.016	31.656	-0.111	-0.111	0.000	0.000	0.000	0.000
95	A	197	PRO	0	-0.034	-0.002	26.359	-0.143	-0.143	0.000	0.000	0.000	0.000
96	A	198	ALA	0	0.027	0.020	27.654	-0.379	-0.379	0.000	0.000	0.000	0.000
97	A	199	GLN	0	-0.031	-0.019	22.780	-0.192	-0.192	0.000	0.000	0.000	0.000
98	A	200	THR	0	0.003	-0.006	26.956	-0.065	-0.065	0.000	0.000	0.000	0.000
99	A	201	SER	0	0.019	-0.003	27.600	-0.071	-0.071	0.000	0.000	0.000	0.000
100	A	202	GLN	0	0.004	0.017	29.150	0.289	0.289	0.000	0.000	0.000	0.000
101	A	203	TRP	0	0.072	0.022	32.147	0.191	0.191	0.000	0.000	0.000	0.000
102	A	204	ASP	-1	-0.819	-0.847	27.054	-11.671	-11.671	0.000	0.000	0.000	0.000
103	A	205	ASP	-1	-0.763	-0.865	29.911	-10.015	-10.015	0.000	0.000	0.000	0.000
104	A	206	PRO	0	-0.023	-0.009	30.944	0.285	0.285	0.000	0.000	0.000	0.000
105	A	207	TRP	0	-0.054	-0.033	33.603	0.509	0.509	0.000	0.000	0.000	0.000
106	A	208	GLY	0	0.032	0.025	34.801	0.193	0.193	0.000	0.000	0.000	0.000
107	A	209	GLU	-1	-0.815	-0.872	33.197	-9.153	-9.153	0.000	0.000	0.000	0.000
108	A	210	VAL	0	-0.003	0.006	30.326	-0.373	-0.373	0.000	0.000	0.000	0.000
109	A	211	LEU	0	0.004	0.005	27.563	0.021	0.021	0.000	0.000	0.000	0.000
110	A	212	ALA	0	0.013	-0.003	25.890	-0.293	-0.293	0.000	0.000	0.000	0.000
111	A	213	TRP	0	-0.014	0.001	19.450	0.032	0.032	0.000	0.000	0.000	0.000
112	A	214	LYS	1	0.934	0.971	23.538	11.044	11.044	0.000	0.000	0.000	0.000
113	A	215	PHE	0	0.009	0.001	19.463	-0.021	-0.021	0.000	0.000	0.000	0.000
114	A	216	ASP	-1	-0.853	-0.903	23.179	-10.517	-10.517	0.000	0.000	0.000	0.000
115	A	217	PRO	0	0.048	0.013	23.675	-0.245	-0.245	0.000	0.000	0.000	0.000
116	A	218	THR	0	-0.040	-0.038	24.688	0.057	0.057	0.000	0.000	0.000	0.000
117	A	219	LEU	0	0.020	0.022	24.052	0.277	0.277	0.000	0.000	0.000	0.000
118	A	220	ALA	0	-0.033	-0.014	22.717	-0.230	-0.230	0.000	0.000	0.000	0.000
119	A	221	TYR	0	-0.117	-0.062	24.255	0.116	0.116	0.000	0.000	0.000	0.000
120	A	222	THR	0	0.012	-0.003	27.969	0.317	0.317	0.000	0.000	0.000	0.000
121	A	223	TYR	0	-0.026	-0.012	25.650	-0.232	-0.232	0.000	0.000	0.000	0.000
122	A	224	GLU	-1	-0.778	-0.883	28.534	-9.393	-9.393	0.000	0.000	0.000	0.000
123	A	225	ALA	0	0.051	0.033	27.842	0.290	0.290	0.000	0.000	0.000	0.000
124	A	226	TYR	0	-0.027	-0.003	29.401	0.354	0.354	0.000	0.000	0.000	0.000
125	A	227	VAL	0	-0.043	-0.023	31.097	0.292	0.292	0.000	0.000	0.000	0.000
126	A	228	ARG	1	0.806	0.888	32.995	9.566	9.566	0.000	0.000	0.000	0.000
127	A	229	TYR	0	0.006	0.006	32.451	0.186	0.186	0.000	0.000	0.000	0.000
128	A	230	PRO	0	0.020	0.011	33.332	-0.238	-0.238	0.000	0.000	0.000	0.000
129	A	231	GLU	-1	-0.881	-0.955	34.238	-8.829	-8.829	0.000	0.000	0.000	0.000
130	A	232	GLU	-1	-0.840	-0.887	31.136	-10.081	-10.081	0.000	0.000	0.000	0.000
131	A	233	PHE	0	-0.082	-0.038	27.010	-0.422	-0.422	0.000	0.000	0.000	0.000

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