FMO DATABASE

FMODB ID: Z6NLN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-902597.278644
FMO2-HF: Nuclear repulsion	858607.256075
FMO2-HF: Total energy	-43990.022568
FMO2-MP2: Total energy	-44120.463502

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.
-0.136	2.261	-0.036	-1.231	-1.13	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 : 0.006 / q_NPA : -0.012

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	0.016	0.010	3.788	0.095	2.492	-0.036	-1.231	-1.130	0.001
4	A	77	GLN	0	-0.038	-0.010	6.856	0.051	0.051	0.000	0.000	0.000	0.000
5	A	78	VAL	0	-0.033	0.000	9.766	-0.158	-0.158	0.000	0.000	0.000	0.000
6	A	79	PRO	0	0.027	0.007	12.291	0.026	0.026	0.000	0.000	0.000	0.000
7	A	80	LEU	0	0.022	0.016	15.748	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	81	ARG	1	0.844	0.903	16.637	-0.156	-0.156	0.000	0.000	0.000	0.000
9	A	82	PRO	0	-0.005	0.020	20.970	0.006	0.006	0.000	0.000	0.000	0.000
10	A	83	MET	0	0.038	0.025	21.849	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	84	THR	0	-0.004	-0.023	24.361	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	85	TYR	0	-0.009	-0.001	26.587	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	86	LYS	1	0.860	0.900	25.286	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	87	ALA	0	0.051	0.041	22.480	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	88	ALA	0	0.085	0.039	23.353	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	89	LEU	0	0.007	0.017	24.848	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	90	ASP	-1	-0.828	-0.899	21.992	0.003	0.003	0.000	0.000	0.000	0.000
18	A	91	ILE	0	-0.055	-0.039	19.263	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	92	SER	0	-0.022	-0.023	21.432	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	93	HIS	0	-0.078	-0.041	23.794	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	94	PHE	0	-0.012	-0.007	14.500	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	95	LEU	0	0.004	-0.001	17.865	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	96	LYS	1	0.863	0.928	20.939	0.014	0.014	0.000	0.000	0.000	0.000
24	A	97	GLU	-1	-0.896	-0.940	21.810	-0.039	-0.039	0.000	0.000	0.000	0.000
25	A	98	LYS	1	0.891	0.969	14.175	0.013	0.013	0.000	0.000	0.000	0.000
26	A	99	GLY	0	0.017	0.023	20.156	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	100	GLY	0	-0.043	-0.030	21.206	0.005	0.005	0.000	0.000	0.000	0.000
28	A	101	LEU	0	-0.017	-0.018	21.738	0.011	0.011	0.000	0.000	0.000	0.000
29	A	102	GLU	-1	-0.809	-0.903	24.290	0.020	0.020	0.000	0.000	0.000	0.000
30	A	103	GLY	0	-0.015	-0.006	27.804	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	104	LEU	0	-0.070	-0.016	22.768	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	105	ILE	0	0.005	-0.007	27.160	0.004	0.004	0.000	0.000	0.000	0.000
33	A	106	TRP	0	0.004	-0.030	26.654	0.002	0.002	0.000	0.000	0.000	0.000
34	A	107	SER	0	-0.056	-0.043	24.407	0.002	0.002	0.000	0.000	0.000	0.000
35	A	108	GLN	0	0.052	0.018	24.672	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	109	ARG	1	1.016	1.010	17.839	-0.169	-0.169	0.000	0.000	0.000	0.000
37	A	110	ARG	1	0.860	0.917	20.600	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	111	GLN	0	0.019	0.027	20.280	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	112	GLU	-1	-0.771	-0.869	19.526	0.206	0.206	0.000	0.000	0.000	0.000
40	A	113	ILE	0	-0.085	-0.041	14.980	0.035	0.035	0.000	0.000	0.000	0.000
41	A	114	LEU	0	-0.033	-0.014	15.649	0.033	0.033	0.000	0.000	0.000	0.000
42	A	115	ASP	-1	-0.755	-0.891	16.466	0.188	0.188	0.000	0.000	0.000	0.000
43	A	116	LEU	0	-0.024	-0.001	14.075	0.031	0.031	0.000	0.000	0.000	0.000
44	A	117	TRP	0	-0.012	-0.009	10.466	0.024	0.024	0.000	0.000	0.000	0.000
45	A	118	ILE	0	0.044	0.031	12.266	0.013	0.013	0.000	0.000	0.000	0.000
46	A	119	TYR	0	0.049	0.040	14.524	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	120	HIS	0	-0.017	-0.005	6.583	-0.170	-0.170	0.000	0.000	0.000	0.000
48	A	121	THR	0	-0.084	-0.054	9.949	0.037	0.037	0.000	0.000	0.000	0.000
49	A	122	GLN	0	-0.043	-0.041	11.046	-0.061	-0.061	0.000	0.000	0.000	0.000
50	A	123	GLY	0	0.070	0.057	14.367	-0.048	-0.048	0.000	0.000	0.000	0.000
51	A	124	TYR	0	-0.037	-0.017	15.976	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	125	PHE	0	0.041	0.005	18.181	0.030	0.030	0.000	0.000	0.000	0.000
53	A	126	PRO	0	-0.035	-0.016	18.326	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	127	ASP	-1	-0.861	-0.925	20.547	0.173	0.173	0.000	0.000	0.000	0.000
55	A	128	TRP	0	0.042	0.023	20.328	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	129	GLN	0	-0.018	0.023	22.157	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	130	ASN	0	-0.025	-0.013	25.526	0.004	0.004	0.000	0.000	0.000	0.000
58	A	131	TYR	0	-0.007	-0.049	26.273	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	132	THR	0	0.028	0.018	31.853	0.002	0.002	0.000	0.000	0.000	0.000
60	A	133	PRO	0	0.003	-0.002	35.158	0.001	0.001	0.000	0.000	0.000	0.000
61	A	134	GLY	0	-0.027	0.010	36.996	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	135	PRO	0	-0.014	-0.011	38.925	0.000	0.000	0.000	0.000	0.000	0.000
63	A	136	GLY	0	0.070	0.020	39.550	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	137	ILE	0	-0.054	-0.048	35.728	0.003	0.003	0.000	0.000	0.000	0.000
65	A	138	ARG	1	0.851	0.941	32.938	-0.057	-0.057	0.000	0.000	0.000	0.000
66	A	139	TYR	0	0.054	0.009	33.416	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	140	PRO	0	0.015	0.022	29.979	0.004	0.004	0.000	0.000	0.000	0.000
68	A	141	LEU	0	0.036	0.016	31.046	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	142	THR	0	-0.028	-0.027	26.901	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	143	PHE	0	-0.006	-0.002	29.888	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	144	GLY	0	0.091	0.024	29.230	0.002	0.002	0.000	0.000	0.000	0.000
72	A	145	TRP	0	-0.013	0.004	22.891	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	146	CYS	0	-0.099	-0.045	27.618	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	147	PHE	0	0.010	-0.013	24.833	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	148	LYS	1	0.866	0.940	29.117	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	149	LEU	0	-0.011	0.002	28.070	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	150	VAL	0	-0.010	-0.024	31.911	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	151	PRO	0	0.025	0.034	34.329	0.001	0.001	0.000	0.000	0.000	0.000
79	A	152	VAL	0	-0.036	-0.025	35.361	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	153	GLU	-1	-0.888	-0.944	38.102	0.021	0.021	0.000	0.000	0.000	0.000
81	A	154	PRO	0	-0.043	-0.018	38.110	0.000	0.000	0.000	0.000	0.000	0.000
82	A	183	GLU	-1	-0.879	-0.944	37.537	0.043	0.043	0.000	0.000	0.000	0.000
83	A	184	VAL	0	0.004	0.009	32.659	0.005	0.005	0.000	0.000	0.000	0.000
84	A	185	LEU	0	0.026	0.005	31.622	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	186	VAL	0	0.017	0.013	30.098	0.002	0.002	0.000	0.000	0.000	0.000
86	A	187	TRP	0	0.006	0.014	23.529	0.000	0.000	0.000	0.000	0.000	0.000
87	A	188	ARG	1	0.920	0.972	28.710	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	189	PHE	0	0.012	0.010	27.737	0.003	0.003	0.000	0.000	0.000	0.000
89	A	190	ASP	-1	-0.807	-0.890	30.543	0.016	0.016	0.000	0.000	0.000	0.000
90	A	191	SER	0	0.077	0.045	32.657	0.003	0.003	0.000	0.000	0.000	0.000
91	A	192	LYS	1	0.890	0.931	33.629	-0.014	-0.014	0.000	0.000	0.000	0.000
92	A	193	LEU	0	-0.007	-0.006	32.384	0.001	0.001	0.000	0.000	0.000	0.000
93	A	194	ALA	0	-0.012	-0.009	32.307	0.003	0.003	0.000	0.000	0.000	0.000
94	A	195	PHE	0	-0.030	-0.016	33.310	0.002	0.002	0.000	0.000	0.000	0.000
95	A	196	HIS	0	-0.059	-0.012	36.791	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	197	HIS	0	-0.044	-0.019	34.782	0.000	0.000	0.000	0.000	0.000	0.000
97	A	198	MET	0	0.066	0.032	37.276	0.001	0.001	0.000	0.000	0.000	0.000
98	A	199	ALA	0	0.002	0.025	35.560	0.000	0.000	0.000	0.000	0.000	0.000
99	A	200	ARG	1	0.927	0.958	37.598	-0.044	-0.044	0.000	0.000	0.000	0.000
100	A	201	GLU	-1	-0.876	-0.945	39.470	0.034	0.034	0.000	0.000	0.000	0.000
101	A	202	LEU	0	-0.066	-0.044	40.206	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	203	HIS	1	0.853	0.902	40.212	-0.054	-0.054	0.000	0.000	0.000	0.000
103	A	204	PRO	0	0.012	-0.005	40.448	0.003	0.003	0.000	0.000	0.000	0.000
104	A	205	GLU	-1	-0.883	-0.891	37.002	0.066	0.066	0.000	0.000	0.000	0.000
105	A	206	TYR	0	-0.046	-0.044	34.206	0.003	0.003	0.000	0.000	0.000	0.000
106	A	207	TYR	0	0.004	0.014	39.095	-0.005	-0.005	0.000	0.000	0.000	0.000

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