FMO DATABASE

FMODB ID: 72MNK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-981548.66802
FMO2-HF: Nuclear repulsion	934396.675083
FMO2-HF: Total energy	-47151.992937
FMO2-MP2: Total energy	-47291.898701

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.
-25.552	-22.934	-0.011	-0.736	-1.872	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 : -0.918 / q_NPA : -0.971

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	0.010	-0.006	3.512	-5.234	-2.616	-0.011	-0.736	-1.872	0.009
4	C	72	PHE	0	-0.094	-0.046	6.415	-3.249	-3.249	0.000	0.000	0.000	0.000
5	C	73	PRO	0	-0.017	0.006	8.962	0.219	0.219	0.000	0.000	0.000	0.000
6	C	74	VAL	0	0.001	-0.046	11.750	-0.195	-0.195	0.000	0.000	0.000	0.000
7	C	75	ARG	1	1.031	1.062	13.163	-17.635	-17.635	0.000	0.000	0.000	0.000
8	C	76	PRO	0	-0.008	-0.014	11.490	-0.806	-0.806	0.000	0.000	0.000	0.000
9	C	77	GLN	0	-0.016	-0.001	14.199	-1.130	-1.130	0.000	0.000	0.000	0.000
10	C	78	VAL	0	-0.030	0.005	17.335	0.608	0.608	0.000	0.000	0.000	0.000
11	C	79	PRO	0	0.028	0.007	17.755	-0.562	-0.562	0.000	0.000	0.000	0.000
12	C	80	LEU	0	0.015	0.014	20.320	-0.409	-0.409	0.000	0.000	0.000	0.000
13	C	81	ARG	1	0.849	0.905	23.963	-12.600	-12.600	0.000	0.000	0.000	0.000
14	C	82	PRO	0	0.000	0.022	26.598	-0.179	-0.179	0.000	0.000	0.000	0.000
15	C	83	MET	0	0.034	0.025	30.346	0.124	0.124	0.000	0.000	0.000	0.000
16	C	84	THR	0	0.008	-0.021	32.354	-0.230	-0.230	0.000	0.000	0.000	0.000
17	C	85	TYR	0	0.001	0.017	35.001	0.189	0.189	0.000	0.000	0.000	0.000
18	C	86	LYS	1	0.864	0.912	34.023	-9.400	-9.400	0.000	0.000	0.000	0.000
19	C	87	ALA	0	0.061	0.045	31.603	0.050	0.050	0.000	0.000	0.000	0.000
20	C	88	ALA	0	0.077	0.029	33.147	0.027	0.027	0.000	0.000	0.000	0.000
21	C	89	LEU	0	0.002	0.012	35.758	-0.030	-0.030	0.000	0.000	0.000	0.000
22	C	90	ASP	-1	-0.854	-0.919	32.444	9.585	9.585	0.000	0.000	0.000	0.000
23	C	91	ILE	0	-0.066	-0.044	30.407	0.107	0.107	0.000	0.000	0.000	0.000
24	C	92	SER	0	-0.012	-0.024	33.468	-0.113	-0.113	0.000	0.000	0.000	0.000
25	C	93	HIS	0	-0.078	-0.037	35.971	-0.174	-0.174	0.000	0.000	0.000	0.000
26	C	94	PHE	0	-0.017	-0.003	28.800	0.006	0.006	0.000	0.000	0.000	0.000
27	C	95	LEU	0	0.016	-0.005	32.042	0.096	0.096	0.000	0.000	0.000	0.000
28	C	96	LYS	1	0.825	0.926	35.384	-7.620	-7.620	0.000	0.000	0.000	0.000
29	C	97	GLU	-1	-0.939	-0.970	35.891	8.210	8.210	0.000	0.000	0.000	0.000
30	C	98	LYS	1	0.874	0.953	29.627	-10.562	-10.562	0.000	0.000	0.000	0.000
31	C	99	GLY	0	0.031	0.030	35.436	-0.050	-0.050	0.000	0.000	0.000	0.000
32	C	100	GLY	0	-0.056	-0.037	36.785	0.193	0.193	0.000	0.000	0.000	0.000
33	C	101	LEU	0	-0.002	-0.009	36.867	0.192	0.192	0.000	0.000	0.000	0.000
34	C	102	GLU	-1	-0.807	-0.901	39.426	7.055	7.055	0.000	0.000	0.000	0.000
35	C	103	GLY	0	0.006	0.000	42.902	-0.033	-0.033	0.000	0.000	0.000	0.000
36	C	104	LEU	0	-0.050	-0.003	38.062	-0.044	-0.044	0.000	0.000	0.000	0.000
37	C	105	ILE	0	0.019	0.003	42.485	-0.023	-0.023	0.000	0.000	0.000	0.000
38	C	106	TRP	0	-0.014	-0.034	40.061	0.103	0.103	0.000	0.000	0.000	0.000
39	C	107	SER	0	-0.041	-0.036	38.773	-0.034	-0.034	0.000	0.000	0.000	0.000
40	C	108	GLN	0	0.041	0.015	36.676	-0.097	-0.097	0.000	0.000	0.000	0.000
41	C	109	ARG	1	0.916	0.940	29.254	-9.567	-9.567	0.000	0.000	0.000	0.000
42	C	110	ARG	1	0.917	0.942	34.466	-7.668	-7.668	0.000	0.000	0.000	0.000
43	C	111	GLN	0	0.011	0.023	34.647	-0.020	-0.020	0.000	0.000	0.000	0.000
44	C	112	GLU	-1	-0.743	-0.839	31.974	9.250	9.250	0.000	0.000	0.000	0.000
45	C	113	ILE	0	-0.088	-0.035	29.499	0.388	0.388	0.000	0.000	0.000	0.000
46	C	114	LEU	0	-0.005	-0.002	29.610	0.402	0.402	0.000	0.000	0.000	0.000
47	C	115	ASP	-1	-0.779	-0.904	30.029	9.643	9.643	0.000	0.000	0.000	0.000
48	C	116	LEU	0	-0.038	-0.015	26.319	0.310	0.310	0.000	0.000	0.000	0.000
49	C	117	TRP	0	0.000	-0.003	24.765	0.297	0.297	0.000	0.000	0.000	0.000
50	C	118	ILE	0	0.048	0.037	25.380	0.486	0.486	0.000	0.000	0.000	0.000
51	C	119	TYR	0	0.042	0.041	23.749	0.506	0.506	0.000	0.000	0.000	0.000
52	C	120	HIS	0	-0.057	-0.033	18.821	0.855	0.855	0.000	0.000	0.000	0.000
53	C	121	THR	0	-0.056	-0.042	21.042	0.865	0.865	0.000	0.000	0.000	0.000
54	C	122	GLN	0	-0.055	-0.046	22.062	0.557	0.557	0.000	0.000	0.000	0.000
55	C	123	GLY	0	0.060	0.052	23.724	-0.187	-0.187	0.000	0.000	0.000	0.000
56	C	124	TYR	0	-0.020	-0.017	24.371	-0.126	-0.126	0.000	0.000	0.000	0.000
57	C	125	PHE	0	0.030	0.003	27.043	0.110	0.110	0.000	0.000	0.000	0.000
58	C	126	PRO	0	-0.037	-0.015	27.922	-0.192	-0.192	0.000	0.000	0.000	0.000
59	C	127	ASP	-1	-0.873	-0.936	30.928	9.407	9.407	0.000	0.000	0.000	0.000
60	C	128	TRP	0	0.048	0.031	31.449	-0.403	-0.403	0.000	0.000	0.000	0.000
61	C	129	GLN	0	-0.006	0.031	35.011	-0.546	-0.546	0.000	0.000	0.000	0.000
62	C	130	ASN	0	-0.021	-0.011	37.358	-0.062	-0.062	0.000	0.000	0.000	0.000
63	C	131	TYR	0	-0.013	-0.047	39.555	-0.060	-0.060	0.000	0.000	0.000	0.000
64	C	132	THR	0	0.047	0.028	43.861	-0.003	-0.003	0.000	0.000	0.000	0.000
65	C	133	PRO	0	-0.005	-0.004	47.415	0.037	0.037	0.000	0.000	0.000	0.000
66	C	134	GLY	0	-0.030	0.005	49.003	-0.031	-0.031	0.000	0.000	0.000	0.000
67	C	135	PRO	0	-0.040	-0.025	51.591	-0.035	-0.035	0.000	0.000	0.000	0.000
68	C	136	GLY	0	0.057	0.010	53.090	-0.087	-0.087	0.000	0.000	0.000	0.000
69	C	137	ILE	0	-0.064	-0.057	49.464	0.120	0.120	0.000	0.000	0.000	0.000
70	C	138	ARG	1	0.832	0.933	46.099	-6.568	-6.568	0.000	0.000	0.000	0.000
71	C	139	TYR	0	0.056	0.013	46.537	0.150	0.150	0.000	0.000	0.000	0.000
72	C	140	PRO	0	-0.001	0.019	42.172	0.015	0.015	0.000	0.000	0.000	0.000
73	C	141	LEU	0	0.034	0.012	42.053	-0.067	-0.067	0.000	0.000	0.000	0.000
74	C	142	THR	0	-0.050	-0.040	37.130	-0.060	-0.060	0.000	0.000	0.000	0.000
75	C	143	PHE	0	-0.013	0.001	40.596	0.099	0.099	0.000	0.000	0.000	0.000
76	C	144	GLY	0	0.078	0.015	39.410	0.175	0.175	0.000	0.000	0.000	0.000
77	C	145	TRP	0	-0.012	-0.001	36.178	0.214	0.214	0.000	0.000	0.000	0.000
78	C	146	CYS	0	-0.101	-0.046	39.505	-0.239	-0.239	0.000	0.000	0.000	0.000
79	C	147	PHE	0	0.006	-0.011	38.635	-0.117	-0.117	0.000	0.000	0.000	0.000
80	C	148	LYS	1	0.871	0.936	42.632	-6.490	-6.490	0.000	0.000	0.000	0.000
81	C	149	LEU	0	-0.015	-0.003	41.838	0.039	0.039	0.000	0.000	0.000	0.000
82	C	150	VAL	0	-0.022	-0.024	45.829	-0.151	-0.151	0.000	0.000	0.000	0.000
83	C	151	PRO	0	0.019	0.025	48.916	0.095	0.095	0.000	0.000	0.000	0.000
84	C	152	VAL	0	-0.043	-0.028	50.344	-0.040	-0.040	0.000	0.000	0.000	0.000
85	C	153	GLU	-1	-0.896	-0.949	53.017	5.804	5.804	0.000	0.000	0.000	0.000
86	C	154	PRO	0	-0.052	-0.027	53.196	0.103	0.103	0.000	0.000	0.000	0.000
87	C	155	GLU	-1	-0.955	-0.973	53.505	5.919	5.919	0.000	0.000	0.000	0.000
88	C	181	GLU	-1	-0.941	-0.979	55.231	5.688	5.688	0.000	0.000	0.000	0.000
89	C	182	LYS	1	0.906	0.945	48.586	-6.354	-6.354	0.000	0.000	0.000	0.000
90	C	183	GLU	-1	-0.770	-0.870	50.989	6.157	6.157	0.000	0.000	0.000	0.000
91	C	184	VAL	0	0.030	0.030	47.449	0.133	0.133	0.000	0.000	0.000	0.000
92	C	185	LEU	0	-0.004	-0.014	45.783	-0.054	-0.054	0.000	0.000	0.000	0.000
93	C	186	VAL	0	0.024	0.017	44.924	0.131	0.131	0.000	0.000	0.000	0.000
94	C	187	TRP	0	0.014	0.015	37.792	-0.080	-0.080	0.000	0.000	0.000	0.000
95	C	188	ARG	1	0.920	0.974	43.298	-6.571	-6.571	0.000	0.000	0.000	0.000
96	C	189	PHE	0	0.028	0.015	40.805	-0.009	-0.009	0.000	0.000	0.000	0.000
97	C	190	ASP	-1	-0.810	-0.889	44.710	6.323	6.323	0.000	0.000	0.000	0.000
98	C	191	SER	0	0.074	0.042	45.353	0.057	0.057	0.000	0.000	0.000	0.000
99	C	192	LYS	1	0.902	0.932	46.421	-6.293	-6.293	0.000	0.000	0.000	0.000
100	C	193	LEU	0	-0.013	-0.003	45.186	-0.035	-0.035	0.000	0.000	0.000	0.000
101	C	194	ALA	0	0.008	0.003	43.617	0.103	0.103	0.000	0.000	0.000	0.000
102	C	195	PHE	0	-0.044	-0.022	44.592	0.094	0.094	0.000	0.000	0.000	0.000
103	C	196	HIS	0	-0.024	-0.002	47.429	0.052	0.052	0.000	0.000	0.000	0.000
104	C	197	HIS	0	-0.018	-0.023	44.808	0.038	0.038	0.000	0.000	0.000	0.000
105	C	198	MET	0	0.030	0.007	48.128	-0.058	-0.058	0.000	0.000	0.000	0.000
106	C	199	ALA	0	0.004	0.032	46.813	-0.108	-0.108	0.000	0.000	0.000	0.000
107	C	200	ARG	1	0.962	0.980	46.594	-6.832	-6.832	0.000	0.000	0.000	0.000
108	C	201	GLU	-1	-0.951	-0.975	49.751	5.828	5.828	0.000	0.000	0.000	0.000
109	C	202	LEU	0	-0.070	-0.067	52.352	-0.101	-0.101	0.000	0.000	0.000	0.000
110	C	203	HIS	0	0.043	0.031	51.627	-0.069	-0.069	0.000	0.000	0.000	0.000
111	C	204	PRO	0	-0.038	-0.027	50.473	0.158	0.158	0.000	0.000	0.000	0.000
112	C	205	GLU	-1	-0.870	-0.903	46.547	6.815	6.815	0.000	0.000	0.000	0.000
113	C	206	TYR	0	-0.055	-0.031	44.105	0.215	0.215	0.000	0.000	0.000	0.000
114	C	207	TYR	0	-0.054	-0.028	43.240	-0.262	-0.262	0.000	0.000	0.000	0.000

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