FMO DATABASE

FMODB ID: MV98Z

Calculation Name: 3REB-C-Xray372

Preferred Name: Tyrosine-protein kinase HCK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3REB

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	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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-982762.798427
FMO2-HF: Nuclear repulsion	935611.901057
FMO2-HF: Total energy	-47150.897369
FMO2-MP2: Total energy	-47290.918555

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:69:GLU)

Summations of interaction energy for fragment #1(C:69:GLU)

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.
-26.034	-23.498	-0.002	-0.667	-1.868	0.009

Interaction energy analysis for fragmet #1(C:69:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.917 / q_NPA : -0.974

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	C	71	GLY	0	0.017	-0.004	3.471	-5.843	-3.307	-0.002	-0.667	-1.868	0.009
4	C	72	PHE	0	-0.096	-0.047	6.402	-3.247	-3.247	0.000	0.000	0.000	0.000
5	C	73	PRO	0	-0.011	0.010	8.959	0.191	0.191	0.000	0.000	0.000	0.000
6	C	74	VAL	0	0.024	-0.046	11.753	-0.139	-0.139	0.000	0.000	0.000	0.000
7	C	75	ARG	1	1.028	1.066	13.203	-17.876	-17.876	0.000	0.000	0.000	0.000
8	C	76	PRO	0	-0.035	-0.027	11.543	-0.826	-0.826	0.000	0.000	0.000	0.000
9	C	77	GLN	0	-0.022	0.013	14.189	-0.983	-0.983	0.000	0.000	0.000	0.000
10	C	78	VAL	0	-0.050	0.000	17.317	0.583	0.583	0.000	0.000	0.000	0.000
11	C	79	PRO	0	0.022	-0.005	17.787	-0.558	-0.558	0.000	0.000	0.000	0.000
12	C	80	LEU	0	0.045	0.019	20.451	-0.396	-0.396	0.000	0.000	0.000	0.000
13	C	81	ARG	1	0.853	0.903	24.046	-12.495	-12.495	0.000	0.000	0.000	0.000
14	C	82	PRO	0	-0.007	0.034	26.729	-0.176	-0.176	0.000	0.000	0.000	0.000
15	C	83	MET	0	0.085	0.030	30.478	0.103	0.103	0.000	0.000	0.000	0.000
16	C	84	THR	0	-0.045	-0.039	32.469	-0.221	-0.221	0.000	0.000	0.000	0.000
17	C	85	TYR	0	0.010	-0.022	35.110	0.173	0.173	0.000	0.000	0.000	0.000
18	C	86	LYS	1	0.911	0.951	33.724	-9.433	-9.433	0.000	0.000	0.000	0.000
19	C	87	ALA	0	0.051	0.047	31.734	0.059	0.059	0.000	0.000	0.000	0.000
20	C	88	ALA	0	0.100	0.046	33.232	0.028	0.028	0.000	0.000	0.000	0.000
21	C	89	LEU	0	0.034	0.089	35.841	-0.035	-0.035	0.000	0.000	0.000	0.000
22	C	90	ASP	-1	-0.887	-0.952	32.511	9.566	9.566	0.000	0.000	0.000	0.000
23	C	91	ILE	0	-0.071	-0.045	30.566	0.115	0.115	0.000	0.000	0.000	0.000
24	C	92	SER	0	-0.109	-0.152	33.525	-0.069	-0.069	0.000	0.000	0.000	0.000
25	C	93	HIS	0	-0.044	-0.012	35.807	-0.233	-0.233	0.000	0.000	0.000	0.000
26	C	94	PHE	0	-0.031	-0.015	29.046	0.006	0.006	0.000	0.000	0.000	0.000
27	C	95	LEU	0	0.016	-0.005	32.085	0.101	0.101	0.000	0.000	0.000	0.000
28	C	96	LYS	1	0.846	0.960	35.411	-7.621	-7.621	0.000	0.000	0.000	0.000
29	C	97	GLU	-1	-0.923	-0.961	35.894	8.234	8.234	0.000	0.000	0.000	0.000
30	C	98	LYS	1	0.844	0.939	29.306	-10.735	-10.735	0.000	0.000	0.000	0.000
31	C	99	GLY	0	0.030	0.028	35.436	-0.049	-0.049	0.000	0.000	0.000	0.000
32	C	100	GLY	0	-0.058	-0.037	36.782	0.192	0.192	0.000	0.000	0.000	0.000
33	C	101	LEU	0	0.005	-0.011	36.595	0.193	0.193	0.000	0.000	0.000	0.000
34	C	102	GLU	-1	-0.788	-0.904	39.423	7.045	7.045	0.000	0.000	0.000	0.000
35	C	103	GLY	0	-0.017	-0.008	42.899	-0.036	-0.036	0.000	0.000	0.000	0.000
36	C	104	LEU	0	-0.042	0.000	38.194	-0.044	-0.044	0.000	0.000	0.000	0.000
37	C	105	ILE	0	0.011	-0.001	42.486	-0.022	-0.022	0.000	0.000	0.000	0.000
38	C	106	TRP	0	-0.023	-0.024	39.748	0.095	0.095	0.000	0.000	0.000	0.000
39	C	107	SER	0	0.004	-0.017	38.274	-0.067	-0.067	0.000	0.000	0.000	0.000
40	C	108	GLN	0	-0.031	-0.009	36.485	-0.070	-0.070	0.000	0.000	0.000	0.000
41	C	109	ARG	1	0.927	0.940	29.655	-9.472	-9.472	0.000	0.000	0.000	0.000
42	C	110	ARG	1	0.904	0.933	34.468	-7.699	-7.699	0.000	0.000	0.000	0.000
43	C	111	GLN	0	-0.013	0.003	34.648	-0.023	-0.023	0.000	0.000	0.000	0.000
44	C	112	GLU	-1	-0.703	-0.835	32.029	9.133	9.133	0.000	0.000	0.000	0.000
45	C	113	ILE	0	-0.070	-0.022	29.425	0.386	0.386	0.000	0.000	0.000	0.000
46	C	114	LEU	0	0.000	-0.003	29.609	0.409	0.409	0.000	0.000	0.000	0.000
47	C	115	ASP	-1	-0.793	-0.894	30.024	9.587	9.587	0.000	0.000	0.000	0.000
48	C	116	LEU	0	-0.024	-0.007	26.445	0.305	0.305	0.000	0.000	0.000	0.000
49	C	117	TRP	0	0.001	0.001	24.713	0.326	0.326	0.000	0.000	0.000	0.000
50	C	118	ILE	0	0.048	0.026	25.373	0.482	0.482	0.000	0.000	0.000	0.000
51	C	119	TYR	0	0.044	0.041	23.860	0.534	0.534	0.000	0.000	0.000	0.000
52	C	120	HIS	0	-0.049	-0.032	19.374	1.053	1.053	0.000	0.000	0.000	0.000
53	C	121	THR	0	-0.041	-0.030	21.031	0.873	0.873	0.000	0.000	0.000	0.000
54	C	122	GLN	0	-0.045	-0.037	22.128	0.675	0.675	0.000	0.000	0.000	0.000
55	C	123	GLY	0	0.032	0.044	23.704	-0.198	-0.198	0.000	0.000	0.000	0.000
56	C	124	TYR	0	-0.036	-0.021	24.403	-0.127	-0.127	0.000	0.000	0.000	0.000
57	C	125	PHE	0	0.066	0.008	27.616	0.125	0.125	0.000	0.000	0.000	0.000
58	C	126	PRO	0	-0.061	-0.020	27.985	-0.197	-0.197	0.000	0.000	0.000	0.000
59	C	127	ASP	-1	-0.881	-0.933	30.918	9.403	9.403	0.000	0.000	0.000	0.000
60	C	128	TRP	0	0.040	0.032	31.650	-0.397	-0.397	0.000	0.000	0.000	0.000
61	C	129	GLN	0	0.007	0.005	35.165	-0.513	-0.513	0.000	0.000	0.000	0.000
62	C	130	ASN	0	-0.025	-0.027	37.347	-0.038	-0.038	0.000	0.000	0.000	0.000
63	C	131	TYR	0	-0.027	-0.045	39.525	-0.044	-0.044	0.000	0.000	0.000	0.000
64	C	132	THR	0	0.045	0.027	43.852	-0.003	-0.003	0.000	0.000	0.000	0.000
65	C	133	PRO	0	0.006	-0.005	47.388	0.029	0.029	0.000	0.000	0.000	0.000
66	C	134	GLY	0	-0.038	0.011	48.995	-0.026	-0.026	0.000	0.000	0.000	0.000
67	C	135	PRO	0	-0.040	-0.023	51.585	-0.028	-0.028	0.000	0.000	0.000	0.000
68	C	136	GLY	0	0.085	0.024	53.065	-0.089	-0.089	0.000	0.000	0.000	0.000
69	C	137	ILE	0	-0.067	-0.055	49.316	0.124	0.124	0.000	0.000	0.000	0.000
70	C	138	ARG	1	0.891	0.971	46.080	-6.592	-6.592	0.000	0.000	0.000	0.000
71	C	139	TYR	0	0.039	0.013	46.528	0.144	0.144	0.000	0.000	0.000	0.000
72	C	140	PRO	0	0.007	0.030	42.221	0.022	0.022	0.000	0.000	0.000	0.000
73	C	141	LEU	0	0.048	0.012	42.080	-0.065	-0.065	0.000	0.000	0.000	0.000
74	C	142	THR	0	-0.023	-0.011	37.336	-0.064	-0.064	0.000	0.000	0.000	0.000
75	C	143	PHE	0	-0.023	-0.007	40.644	0.096	0.096	0.000	0.000	0.000	0.000
76	C	144	GLY	0	0.077	0.011	39.514	0.172	0.172	0.000	0.000	0.000	0.000
77	C	145	TRP	0	0.012	0.023	35.961	0.208	0.208	0.000	0.000	0.000	0.000
78	C	146	CYS	0	-0.094	-0.043	39.584	-0.231	-0.231	0.000	0.000	0.000	0.000
79	C	147	PHE	0	0.004	-0.008	38.490	-0.107	-0.107	0.000	0.000	0.000	0.000
80	C	148	LYS	1	0.933	0.977	42.623	-6.476	-6.476	0.000	0.000	0.000	0.000
81	C	149	LEU	0	-0.014	-0.008	41.908	0.040	0.040	0.000	0.000	0.000	0.000
82	C	150	VAL	0	-0.022	-0.025	45.823	-0.154	-0.154	0.000	0.000	0.000	0.000
83	C	151	PRO	0	0.033	0.022	48.913	0.100	0.100	0.000	0.000	0.000	0.000
84	C	152	VAL	0	-0.051	-0.026	50.450	-0.044	-0.044	0.000	0.000	0.000	0.000
85	C	153	GLU	-1	-0.912	-0.950	53.017	5.802	5.802	0.000	0.000	0.000	0.000
86	C	154	PRO	0	-0.046	-0.024	53.199	0.111	0.111	0.000	0.000	0.000	0.000
87	C	155	GLU	-1	-0.952	-0.980	53.510	5.953	5.953	0.000	0.000	0.000	0.000
88	C	181	GLU	-1	-0.933	-0.972	55.277	5.684	5.684	0.000	0.000	0.000	0.000
89	C	182	LYS	1	0.896	0.937	48.596	-6.361	-6.361	0.000	0.000	0.000	0.000
90	C	183	GLU	-1	-0.834	-0.918	51.246	6.107	6.107	0.000	0.000	0.000	0.000
91	C	184	VAL	0	0.034	0.032	47.290	0.135	0.135	0.000	0.000	0.000	0.000
92	C	185	LEU	0	-0.025	-0.021	45.697	-0.055	-0.055	0.000	0.000	0.000	0.000
93	C	186	VAL	0	0.011	0.018	44.935	0.140	0.140	0.000	0.000	0.000	0.000
94	C	187	TRP	0	0.015	0.018	37.649	-0.091	-0.091	0.000	0.000	0.000	0.000
95	C	188	ARG	1	0.946	0.983	43.295	-6.541	-6.541	0.000	0.000	0.000	0.000
96	C	189	PHE	0	0.001	-0.009	40.918	0.013	0.013	0.000	0.000	0.000	0.000
97	C	190	ASP	-1	-0.888	-0.965	44.728	6.368	6.368	0.000	0.000	0.000	0.000
98	C	191	SER	0	0.074	0.035	45.404	0.063	0.063	0.000	0.000	0.000	0.000
99	C	192	LYS	1	0.944	0.981	46.471	-6.215	-6.215	0.000	0.000	0.000	0.000
100	C	193	LEU	0	-0.024	-0.010	45.254	-0.031	-0.031	0.000	0.000	0.000	0.000
101	C	194	ALA	0	0.019	0.014	43.674	0.097	0.097	0.000	0.000	0.000	0.000
102	C	195	PHE	0	-0.036	0.022	44.662	0.101	0.101	0.000	0.000	0.000	0.000
103	C	196	HIS	0	-0.022	0.002	47.507	0.052	0.052	0.000	0.000	0.000	0.000
104	C	197	HIS	0	-0.011	-0.017	44.783	0.052	0.052	0.000	0.000	0.000	0.000
105	C	198	MET	0	0.029	0.002	48.223	-0.058	-0.058	0.000	0.000	0.000	0.000
106	C	199	ALA	0	0.001	0.027	46.833	-0.105	-0.105	0.000	0.000	0.000	0.000
107	C	200	ARG	1	0.965	0.981	47.153	-6.792	-6.792	0.000	0.000	0.000	0.000
108	C	201	GLU	-1	-0.946	-0.976	49.809	5.821	5.821	0.000	0.000	0.000	0.000
109	C	202	LEU	0	-0.077	-0.070	52.348	-0.100	-0.100	0.000	0.000	0.000	0.000
110	C	203	HIS	0	0.042	0.030	51.565	-0.077	-0.077	0.000	0.000	0.000	0.000
111	C	204	PRO	0	-0.044	-0.025	50.457	0.152	0.152	0.000	0.000	0.000	0.000
112	C	205	GLU	-1	-0.929	-0.938	46.302	6.653	6.653	0.000	0.000	0.000	0.000
113	C	206	TYR	0	-0.080	-0.046	44.020	0.142	0.142	0.000	0.000	0.000	0.000
114	C	207	TYR	0	-0.014	0.001	43.046	-0.203	-0.203	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:69:GLU)