FMO DATABASE

FMODB ID: 6NG7Z

Calculation Name: 3REB-A-Xray372

Preferred Name: Tyrosine-protein kinase HCK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3REB

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-904038.198428
FMO2-HF: Nuclear repulsion	860049.255553
FMO2-HF: Total energy	-43988.942875
FMO2-MP2: Total energy	-44119.532189

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:74:VAL)

Summations of interaction energy for fragment #1(A:74:VAL)

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.
-0.128	2.308	-0.036	-1.247	-1.153	0.001

Interaction energy analysis for fragmet #1(A:74:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.007

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	76	PRO	0	0.000	0.005	3.788	-0.071	2.365	-0.036	-1.247	-1.153	0.001
4	A	77	GLN	0	-0.015	0.021	6.877	0.056	0.056	0.000	0.000	0.000	0.000
5	A	78	VAL	0	-0.053	-0.004	9.766	-0.152	-0.152	0.000	0.000	0.000	0.000
6	A	79	PRO	0	0.026	-0.001	12.291	0.025	0.025	0.000	0.000	0.000	0.000
7	A	80	LEU	0	0.044	0.017	15.748	-0.023	-0.023	0.000	0.000	0.000	0.000
8	A	81	ARG	1	0.853	0.904	16.573	-0.143	-0.143	0.000	0.000	0.000	0.000
9	A	82	PRO	0	-0.007	0.033	20.969	0.007	0.007	0.000	0.000	0.000	0.000
10	A	83	MET	0	0.077	0.026	22.246	-0.016	-0.016	0.000	0.000	0.000	0.000
11	A	84	THR	0	-0.054	-0.040	24.359	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	85	TYR	0	0.010	-0.012	26.585	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	86	LYS	1	0.925	0.954	25.267	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	87	ALA	0	0.034	0.040	22.546	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	88	ALA	0	0.094	0.052	23.352	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	89	LEU	0	0.020	0.076	24.897	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	90	ASP	-1	-0.868	-0.948	21.883	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	91	ILE	0	-0.063	-0.040	19.310	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	92	SER	0	-0.076	-0.117	21.477	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	93	HIS	0	-0.050	-0.022	23.522	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	94	PHE	0	-0.024	-0.017	14.755	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	95	LEU	0	0.010	0.000	17.909	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	96	LYS	1	0.922	0.981	21.014	0.019	0.019	0.000	0.000	0.000	0.000
24	A	97	GLU	-1	-0.966	-0.987	21.812	-0.057	-0.057	0.000	0.000	0.000	0.000
25	A	98	LYS	1	0.865	0.955	13.515	0.065	0.065	0.000	0.000	0.000	0.000
26	A	99	GLY	0	0.016	0.021	20.249	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	100	GLY	0	-0.045	-0.031	21.080	0.004	0.004	0.000	0.000	0.000	0.000
28	A	101	LEU	0	-0.007	-0.020	21.499	0.011	0.011	0.000	0.000	0.000	0.000
29	A	102	GLU	-1	-0.778	-0.887	24.094	0.015	0.015	0.000	0.000	0.000	0.000
30	A	103	GLY	0	-0.033	-0.014	27.620	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	104	LEU	0	-0.060	-0.013	22.960	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	105	ILE	0	-0.008	-0.012	27.117	0.004	0.004	0.000	0.000	0.000	0.000
33	A	106	TRP	0	0.003	-0.017	26.260	0.001	0.001	0.000	0.000	0.000	0.000
34	A	107	SER	0	-0.028	-0.025	24.184	0.000	0.000	0.000	0.000	0.000	0.000
35	A	108	GLN	0	0.003	0.001	24.095	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	109	ARG	1	1.023	1.013	17.627	-0.157	-0.157	0.000	0.000	0.000	0.000
37	A	110	ARG	1	0.849	0.907	20.612	-0.043	-0.043	0.000	0.000	0.000	0.000
38	A	111	GLN	0	-0.001	0.005	20.277	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	112	GLU	-1	-0.743	-0.868	19.532	0.198	0.198	0.000	0.000	0.000	0.000
40	A	113	ILE	0	-0.072	-0.036	14.907	0.033	0.033	0.000	0.000	0.000	0.000
41	A	114	LEU	0	-0.025	-0.015	15.646	0.030	0.030	0.000	0.000	0.000	0.000
42	A	115	ASP	-1	-0.774	-0.880	16.463	0.175	0.175	0.000	0.000	0.000	0.000
43	A	116	LEU	0	-0.010	0.007	14.124	0.032	0.032	0.000	0.000	0.000	0.000
44	A	117	TRP	0	-0.001	-0.004	10.407	0.028	0.028	0.000	0.000	0.000	0.000
45	A	118	ILE	0	0.051	0.028	12.263	0.009	0.009	0.000	0.000	0.000	0.000
46	A	119	TYR	0	0.049	0.039	14.522	0.001	0.001	0.000	0.000	0.000	0.000
47	A	120	HIS	0	-0.040	-0.025	7.219	-0.052	-0.052	0.000	0.000	0.000	0.000
48	A	121	THR	0	-0.064	-0.046	10.028	0.037	0.037	0.000	0.000	0.000	0.000
49	A	122	GLN	0	-0.029	-0.033	11.044	-0.059	-0.059	0.000	0.000	0.000	0.000
50	A	123	GLY	0	0.032	0.046	14.340	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	124	TYR	0	-0.050	-0.021	15.973	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	125	PHE	0	0.078	0.010	18.178	0.031	0.031	0.000	0.000	0.000	0.000
53	A	126	PRO	0	-0.057	-0.022	17.713	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	127	ASP	-1	-0.883	-0.927	20.544	0.168	0.168	0.000	0.000	0.000	0.000
55	A	128	TRP	0	0.038	0.022	20.401	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	129	GLN	0	0.004	-0.005	22.306	-0.030	-0.030	0.000	0.000	0.000	0.000
57	A	130	ASN	0	-0.024	-0.024	25.523	0.005	0.005	0.000	0.000	0.000	0.000
58	A	131	TYR	0	-0.017	-0.036	26.336	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	132	THR	0	0.029	0.022	31.850	0.002	0.002	0.000	0.000	0.000	0.000
60	A	133	PRO	0	0.011	-0.007	35.156	0.000	0.000	0.000	0.000	0.000	0.000
61	A	134	GLY	0	-0.036	0.012	36.993	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	135	PRO	0	-0.005	-0.006	38.922	0.001	0.001	0.000	0.000	0.000	0.000
63	A	136	GLY	0	0.098	0.031	39.543	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	137	ILE	0	-0.060	-0.050	35.749	0.003	0.003	0.000	0.000	0.000	0.000
65	A	138	ARG	1	0.909	0.981	32.930	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	139	TYR	0	0.037	0.007	33.414	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	140	PRO	0	0.021	0.032	30.013	0.004	0.004	0.000	0.000	0.000	0.000
68	A	141	LEU	0	0.021	0.005	31.059	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	142	THR	0	-0.009	-0.010	26.996	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	143	PHE	0	-0.026	-0.015	29.886	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	144	GLY	0	0.092	0.019	29.275	0.001	0.001	0.000	0.000	0.000	0.000
72	A	145	TRP	0	0.008	0.022	22.867	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	146	CYS	0	-0.101	-0.049	27.638	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	147	PHE	0	0.005	-0.009	24.398	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	148	LYS	1	0.931	0.981	29.115	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	149	LEU	0	-0.014	-0.006	28.216	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	150	VAL	0	-0.012	-0.026	31.908	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	151	PRO	0	0.035	0.032	34.327	0.001	0.001	0.000	0.000	0.000	0.000
79	A	152	VAL	0	-0.041	-0.020	35.535	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	153	GLU	-1	-0.890	-0.943	38.100	0.018	0.018	0.000	0.000	0.000	0.000
81	A	154	PRO	0	-0.043	-0.024	38.108	0.000	0.000	0.000	0.000	0.000	0.000
82	A	183	GLU	-1	-0.952	-0.990	37.951	0.036	0.036	0.000	0.000	0.000	0.000
83	A	184	VAL	0	-0.009	0.010	32.522	0.005	0.005	0.000	0.000	0.000	0.000
84	A	185	LEU	0	0.022	0.001	31.515	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	186	VAL	0	0.006	0.013	30.103	0.002	0.002	0.000	0.000	0.000	0.000
86	A	187	TRP	0	0.008	0.020	23.475	0.000	0.000	0.000	0.000	0.000	0.000
87	A	188	ARG	1	0.934	0.977	28.708	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	189	PHE	0	0.021	0.006	27.589	0.004	0.004	0.000	0.000	0.000	0.000
89	A	190	ASP	-1	-0.888	-0.965	30.516	0.012	0.012	0.000	0.000	0.000	0.000
90	A	191	SER	0	0.095	0.042	32.734	0.002	0.002	0.000	0.000	0.000	0.000
91	A	192	LYS	1	0.899	0.963	33.712	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	193	LEU	0	-0.013	-0.008	32.380	0.002	0.002	0.000	0.000	0.000	0.000
93	A	194	ALA	0	-0.001	-0.002	32.400	0.003	0.003	0.000	0.000	0.000	0.000
94	A	195	PHE	0	-0.025	0.008	33.349	0.002	0.002	0.000	0.000	0.000	0.000
95	A	196	HIS	0	-0.022	0.002	36.815	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	197	HIS	0	-0.053	-0.026	34.648	0.000	0.000	0.000	0.000	0.000	0.000
97	A	198	MET	0	0.063	0.025	37.177	0.001	0.001	0.000	0.000	0.000	0.000
98	A	199	ALA	0	-0.011	0.025	35.556	0.000	0.000	0.000	0.000	0.000	0.000
99	A	200	ARG	1	0.934	0.962	37.595	-0.041	-0.041	0.000	0.000	0.000	0.000
100	A	201	GLU	-1	-0.884	-0.941	39.467	0.030	0.030	0.000	0.000	0.000	0.000
101	A	202	LEU	0	-0.077	-0.049	40.270	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	203	HIS	1	0.931	0.965	40.424	-0.051	-0.051	0.000	0.000	0.000	0.000
103	A	204	PRO	0	0.019	-0.007	40.445	0.003	0.003	0.000	0.000	0.000	0.000
104	A	205	GLU	-1	-0.948	-0.954	37.049	0.064	0.064	0.000	0.000	0.000	0.000
105	A	206	TYR	0	-0.054	-0.032	34.531	0.003	0.003	0.000	0.000	0.000	0.000
106	A	207	TYR	0	0.001	0.012	39.093	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:74:VAL)