FMO DATABASE

FMODB ID: R9YM8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-902441.125179
FMO2-HF: Nuclear repulsion	858450.538721
FMO2-HF: Total energy	-43990.586459
FMO2-MP2: Total energy	-44120.952804

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.
0.437	2.407	-0.02	-1.026	-0.924	0.002

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 : 0.012 / q_NPA : -0.009

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	0.018	0.010	3.872	0.867	2.837	-0.020	-1.026	-0.924	0.002
4	A	77	GLN	0	-0.045	-0.017	7.207	-0.057	-0.057	0.000	0.000	0.000	0.000
5	A	78	VAL	0	-0.023	0.003	9.697	-0.147	-0.147	0.000	0.000	0.000	0.000
6	A	79	PRO	0	0.015	-0.003	12.100	0.027	0.027	0.000	0.000	0.000	0.000
7	A	80	LEU	0	0.010	0.021	15.773	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	81	ARG	1	0.842	0.911	16.555	-0.146	-0.146	0.000	0.000	0.000	0.000
9	A	82	PRO	0	0.012	0.013	20.791	0.008	0.008	0.000	0.000	0.000	0.000
10	A	83	MET	0	0.020	0.021	21.192	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	84	THR	0	-0.020	-0.020	24.153	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	85	TYR	0	0.014	-0.004	26.346	0.000	0.000	0.000	0.000	0.000	0.000
13	A	86	LYS	1	0.833	0.892	25.117	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	87	ALA	0	0.035	0.024	22.019	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	88	ALA	0	0.080	0.028	22.629	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	89	LEU	0	0.017	0.040	24.652	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	90	ASP	-1	-0.819	-0.891	21.735	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	91	ILE	0	-0.019	-0.013	18.799	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	92	SER	0	-0.019	-0.024	21.050	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	93	HIS	0	-0.042	-0.016	23.768	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	94	PHE	0	0.003	-0.004	14.175	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	95	LEU	0	-0.010	-0.014	17.494	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	96	LYS	1	0.822	0.904	20.772	0.022	0.022	0.000	0.000	0.000	0.000
24	A	97	GLU	-1	-0.868	-0.922	21.481	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	98	LYS	1	0.856	0.950	14.080	0.013	0.013	0.000	0.000	0.000	0.000
26	A	99	GLY	0	0.024	0.025	19.637	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	100	GLY	0	-0.035	-0.028	20.619	0.004	0.004	0.000	0.000	0.000	0.000
28	A	101	LEU	0	-0.019	-0.017	21.442	0.012	0.012	0.000	0.000	0.000	0.000
29	A	102	GLU	-1	-0.801	-0.909	23.744	0.014	0.014	0.000	0.000	0.000	0.000
30	A	103	GLY	0	0.003	0.010	27.211	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	104	LEU	0	-0.070	-0.017	22.547	0.000	0.000	0.000	0.000	0.000	0.000
32	A	105	ILE	0	0.021	0.003	26.762	0.006	0.006	0.000	0.000	0.000	0.000
33	A	106	TRP	0	0.025	0.008	26.145	0.002	0.002	0.000	0.000	0.000	0.000
34	A	107	SER	0	-0.041	-0.038	24.807	0.001	0.001	0.000	0.000	0.000	0.000
35	A	108	GLN	0	0.030	0.008	24.336	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	109	ARG	1	1.008	1.009	17.447	-0.157	-0.157	0.000	0.000	0.000	0.000
37	A	110	ARG	1	0.847	0.916	20.119	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	111	GLN	0	0.027	0.026	19.954	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	112	GLU	-1	-0.827	-0.903	19.271	0.192	0.192	0.000	0.000	0.000	0.000
40	A	113	ILE	0	-0.047	-0.028	14.736	0.035	0.035	0.000	0.000	0.000	0.000
41	A	114	LEU	0	-0.030	-0.003	15.228	0.028	0.028	0.000	0.000	0.000	0.000
42	A	115	ASP	-1	-0.740	-0.880	16.414	0.163	0.163	0.000	0.000	0.000	0.000
43	A	116	LEU	0	-0.007	-0.003	13.916	0.029	0.029	0.000	0.000	0.000	0.000
44	A	117	TRP	0	-0.007	0.005	10.437	0.046	0.046	0.000	0.000	0.000	0.000
45	A	118	ILE	0	0.005	0.007	12.204	0.018	0.018	0.000	0.000	0.000	0.000
46	A	119	TYR	0	0.043	0.027	14.357	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	120	HIS	0	-0.007	0.000	5.923	-0.280	-0.280	0.000	0.000	0.000	0.000
48	A	121	THR	0	-0.068	-0.049	9.413	0.041	0.041	0.000	0.000	0.000	0.000
49	A	122	GLN	0	-0.045	-0.031	10.810	-0.086	-0.086	0.000	0.000	0.000	0.000
50	A	123	GLY	0	0.060	0.050	14.082	-0.043	-0.043	0.000	0.000	0.000	0.000
51	A	124	TYR	0	-0.011	-0.017	15.749	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	125	PHE	0	0.035	0.013	17.938	0.027	0.027	0.000	0.000	0.000	0.000
53	A	126	PRO	0	-0.030	-0.009	17.859	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	127	ASP	-1	-0.883	-0.953	19.944	0.161	0.161	0.000	0.000	0.000	0.000
55	A	128	TRP	0	0.066	0.040	20.158	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	129	GLN	0	-0.022	0.022	21.838	-0.030	-0.030	0.000	0.000	0.000	0.000
57	A	130	ASN	0	-0.001	-0.005	25.220	0.001	0.001	0.000	0.000	0.000	0.000
58	A	131	TYR	0	-0.027	-0.037	25.959	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	132	THR	0	0.018	0.015	31.457	0.002	0.002	0.000	0.000	0.000	0.000
60	A	133	PRO	0	0.013	0.004	34.773	0.001	0.001	0.000	0.000	0.000	0.000
61	A	134	GLY	0	-0.006	0.007	36.992	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	135	PRO	0	-0.030	-0.019	38.962	0.001	0.001	0.000	0.000	0.000	0.000
63	A	136	GLY	0	0.035	0.007	39.590	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	137	ILE	0	-0.055	-0.050	35.590	0.003	0.003	0.000	0.000	0.000	0.000
65	A	138	ARG	1	0.856	0.933	32.775	-0.051	-0.051	0.000	0.000	0.000	0.000
66	A	139	TYR	0	0.065	0.023	33.161	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	140	PRO	0	0.008	0.012	29.808	0.005	0.005	0.000	0.000	0.000	0.000
68	A	141	LEU	0	0.030	0.004	30.847	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	142	THR	0	-0.032	-0.025	26.623	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	143	PHE	0	0.025	0.009	29.603	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	144	GLY	0	0.051	0.013	29.137	0.003	0.003	0.000	0.000	0.000	0.000
72	A	145	TRP	0	-0.031	-0.016	22.827	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	146	CYS	0	-0.080	-0.050	27.349	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	147	PHE	0	0.009	-0.009	24.551	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	148	LYS	1	0.857	0.925	28.931	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	149	LEU	0	0.003	0.013	27.807	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	150	VAL	0	-0.032	-0.015	31.702	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	151	PRO	0	0.029	0.016	34.280	0.000	0.000	0.000	0.000	0.000	0.000
79	A	152	VAL	0	-0.044	-0.032	35.031	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	153	GLU	-1	-0.877	-0.934	37.861	0.017	0.017	0.000	0.000	0.000	0.000
81	A	154	PRO	0	-0.053	-0.019	37.854	0.000	0.000	0.000	0.000	0.000	0.000
82	A	183	GLU	-1	-0.822	-0.906	37.215	0.039	0.039	0.000	0.000	0.000	0.000
83	A	184	VAL	0	0.012	0.016	32.687	0.005	0.005	0.000	0.000	0.000	0.000
84	A	185	LEU	0	0.014	0.004	31.518	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	186	VAL	0	-0.005	-0.002	29.832	0.001	0.001	0.000	0.000	0.000	0.000
86	A	187	TRP	0	0.006	0.001	23.248	0.001	0.001	0.000	0.000	0.000	0.000
87	A	188	ARG	1	0.894	0.954	28.549	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	189	PHE	0	0.027	0.010	27.511	0.003	0.003	0.000	0.000	0.000	0.000
89	A	190	ASP	-1	-0.820	-0.897	30.082	0.013	0.013	0.000	0.000	0.000	0.000
90	A	191	SER	0	0.047	0.022	32.330	0.003	0.003	0.000	0.000	0.000	0.000
91	A	192	LYS	1	0.901	0.929	33.306	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	193	LEU	0	-0.020	0.005	31.673	0.001	0.001	0.000	0.000	0.000	0.000
93	A	194	ALA	0	0.022	0.015	31.740	0.004	0.004	0.000	0.000	0.000	0.000
94	A	195	PHE	0	-0.054	-0.027	32.991	0.000	0.000	0.000	0.000	0.000	0.000
95	A	196	HIS	0	-0.048	-0.019	36.700	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	197	HIS	0	-0.040	-0.006	34.140	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	198	MET	0	0.034	0.015	37.208	0.002	0.002	0.000	0.000	0.000	0.000
98	A	199	ALA	0	0.028	0.020	35.154	0.000	0.000	0.000	0.000	0.000	0.000
99	A	200	ARG	1	0.875	0.938	37.161	-0.040	-0.040	0.000	0.000	0.000	0.000
100	A	201	GLU	-1	-0.850	-0.936	39.215	0.031	0.031	0.000	0.000	0.000	0.000
101	A	202	LEU	0	-0.084	-0.034	40.423	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	203	HIS	1	0.867	0.923	40.023	-0.049	-0.049	0.000	0.000	0.000	0.000
103	A	204	PRO	0	0.018	-0.015	40.145	0.003	0.003	0.000	0.000	0.000	0.000
104	A	205	GLU	-1	-0.861	-0.891	36.674	0.062	0.062	0.000	0.000	0.000	0.000
105	A	206	TYR	0	-0.061	-0.037	33.699	0.003	0.003	0.000	0.000	0.000	0.000
106	A	207	TYR	0	0.018	0.017	38.626	-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)