FMO DATABASE

FMODB ID: V5KV1

Calculation Name: 3REA-A-Xray372

Preferred Name: Tyrosine-protein kinase HCK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3REA

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1163612.235711
FMO2-HF: Nuclear repulsion	1111665.943368
FMO2-HF: Total energy	-51946.292343
FMO2-MP2: Total energy	-52099.957066

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:56:ASN)

Summations of interaction energy for fragment #1(A:56:ASN)

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.
-2.577	-0.189	0.025	-1.214	-1.199	0.002

Interaction energy analysis for fragmet #1(A:56:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.020

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

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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	58	ASP	-1	-0.897	-0.941	3.347	-4.310	-1.922	0.025	-1.214	-1.199	0.002
4	A	59	SER	0	0.020	0.010	5.483	0.780	0.780	0.000	0.000	0.000	0.000
5	A	60	ALA	0	0.048	0.007	7.248	0.123	0.123	0.000	0.000	0.000	0.000
6	A	61	TRP	0	-0.042	-0.009	10.260	0.006	0.006	0.000	0.000	0.000	0.000
7	A	62	LEU	0	0.009	0.003	6.389	0.123	0.123	0.000	0.000	0.000	0.000
8	A	63	GLU	-1	-0.763	-0.873	10.514	-1.020	-1.020	0.000	0.000	0.000	0.000
9	A	64	ALA	0	-0.041	-0.016	12.819	0.036	0.036	0.000	0.000	0.000	0.000
10	A	65	GLN	0	-0.041	-0.032	13.783	0.125	0.125	0.000	0.000	0.000	0.000
11	A	66	GLU	-1	-0.907	-0.950	13.763	-0.192	-0.192	0.000	0.000	0.000	0.000
12	A	67	GLU	-1	-0.838	-0.926	15.692	-0.233	-0.233	0.000	0.000	0.000	0.000
13	A	68	GLU	-1	-0.849	-0.883	18.415	0.223	0.223	0.000	0.000	0.000	0.000
14	A	69	GLU	-1	-0.943	-0.974	17.306	0.386	0.386	0.000	0.000	0.000	0.000
15	A	70	VAL	0	-0.023	-0.009	18.358	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	71	GLY	0	-0.003	0.007	20.984	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	72	PHE	0	-0.083	-0.042	22.829	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	73	PRO	0	0.006	0.002	22.321	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	74	VAL	0	-0.004	0.000	21.782	0.013	0.013	0.000	0.000	0.000	0.000
20	A	75	ARG	1	0.826	0.891	19.674	0.317	0.317	0.000	0.000	0.000	0.000
21	A	76	PRO	0	0.009	-0.006	25.947	0.020	0.020	0.000	0.000	0.000	0.000
22	A	77	GLN	0	-0.011	0.003	26.459	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	78	VAL	0	-0.001	0.006	25.661	0.006	0.006	0.000	0.000	0.000	0.000
24	A	79	PRO	0	0.003	-0.011	28.281	0.018	0.018	0.000	0.000	0.000	0.000
25	A	80	LEU	0	0.018	0.017	30.085	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	81	ARG	1	0.820	0.906	25.495	0.220	0.220	0.000	0.000	0.000	0.000
27	A	82	PRO	0	0.009	0.011	30.755	0.004	0.004	0.000	0.000	0.000	0.000
28	A	83	MET	0	0.038	0.030	25.020	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	84	THR	0	-0.035	-0.029	29.105	0.004	0.004	0.000	0.000	0.000	0.000
30	A	85	TYR	0	0.018	-0.003	28.731	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	86	LYS	1	0.805	0.876	26.226	0.250	0.250	0.000	0.000	0.000	0.000
32	A	87	ALA	0	0.023	0.020	26.112	-0.021	-0.021	0.000	0.000	0.000	0.000
33	A	88	ALA	0	0.093	0.035	24.247	-0.022	-0.022	0.000	0.000	0.000	0.000
34	A	89	LEU	0	-0.005	0.027	23.100	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	90	ASP	-1	-0.829	-0.900	22.128	-0.306	-0.306	0.000	0.000	0.000	0.000
36	A	91	ILE	0	0.002	-0.002	19.421	-0.059	-0.059	0.000	0.000	0.000	0.000
37	A	92	SER	0	-0.015	-0.018	18.446	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	93	HIS	0	0.014	-0.005	17.467	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	94	PHE	0	-0.010	0.003	15.225	-0.093	-0.093	0.000	0.000	0.000	0.000
40	A	95	LEU	0	0.017	-0.002	13.950	-0.131	-0.131	0.000	0.000	0.000	0.000
41	A	96	LYS	1	0.770	0.877	12.952	0.533	0.533	0.000	0.000	0.000	0.000
42	A	97	GLU	-1	-0.854	-0.918	11.626	-0.750	-0.750	0.000	0.000	0.000	0.000
43	A	98	LYS	1	0.747	0.878	9.495	1.145	1.145	0.000	0.000	0.000	0.000
44	A	99	GLY	0	0.032	0.026	8.323	-0.445	-0.445	0.000	0.000	0.000	0.000
45	A	100	GLY	0	0.012	-0.010	8.601	-0.044	-0.044	0.000	0.000	0.000	0.000
46	A	101	LEU	0	-0.023	0.001	9.287	0.198	0.198	0.000	0.000	0.000	0.000
47	A	102	GLU	-1	-0.788	-0.890	11.955	0.452	0.452	0.000	0.000	0.000	0.000
48	A	103	GLY	0	-0.009	-0.003	11.954	0.184	0.184	0.000	0.000	0.000	0.000
49	A	104	LEU	0	-0.043	0.001	12.258	0.153	0.153	0.000	0.000	0.000	0.000
50	A	105	ILE	0	0.041	0.014	14.074	-0.148	-0.148	0.000	0.000	0.000	0.000
51	A	106	TRP	0	0.003	0.003	16.932	0.018	0.018	0.000	0.000	0.000	0.000
52	A	107	SER	0	-0.028	-0.032	19.683	0.013	0.013	0.000	0.000	0.000	0.000
53	A	108	GLN	0	-0.010	-0.010	21.445	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	109	ARG	1	0.831	0.872	21.127	-0.312	-0.312	0.000	0.000	0.000	0.000
55	A	110	ARG	1	0.885	0.940	15.116	-0.881	-0.881	0.000	0.000	0.000	0.000
56	A	111	GLN	0	0.024	0.022	18.806	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	112	GLU	-1	-0.840	-0.915	20.972	0.149	0.149	0.000	0.000	0.000	0.000
58	A	113	ILE	0	-0.004	0.007	17.142	-0.035	-0.035	0.000	0.000	0.000	0.000
59	A	114	LEU	0	-0.004	-0.002	14.744	-0.059	-0.059	0.000	0.000	0.000	0.000
60	A	115	ASP	-1	-0.790	-0.905	18.607	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	116	LEU	0	-0.024	-0.016	22.199	-0.043	-0.043	0.000	0.000	0.000	0.000
62	A	117	TRP	0	0.025	0.035	14.342	0.002	0.002	0.000	0.000	0.000	0.000
63	A	118	ILE	0	-0.004	-0.006	18.930	-0.065	-0.065	0.000	0.000	0.000	0.000
64	A	119	TYR	0	0.008	0.005	21.054	-0.030	-0.030	0.000	0.000	0.000	0.000
65	A	120	HIS	1	0.845	0.924	21.691	0.068	0.068	0.000	0.000	0.000	0.000
66	A	121	THR	0	0.012	0.022	18.428	-0.039	-0.039	0.000	0.000	0.000	0.000
67	A	122	GLN	0	-0.086	-0.042	21.378	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	123	GLY	0	0.057	0.047	23.958	0.006	0.006	0.000	0.000	0.000	0.000
69	A	124	TYR	0	-0.025	-0.023	24.558	0.005	0.005	0.000	0.000	0.000	0.000
70	A	125	PHE	0	0.029	0.010	26.673	0.004	0.004	0.000	0.000	0.000	0.000
71	A	126	PRO	0	-0.005	0.006	25.826	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	127	ASP	-1	-0.897	-0.957	27.287	0.011	0.011	0.000	0.000	0.000	0.000
73	A	128	TRP	0	-0.007	-0.003	21.975	0.003	0.003	0.000	0.000	0.000	0.000
74	A	129	GLN	0	-0.011	0.031	20.853	0.033	0.033	0.000	0.000	0.000	0.000
75	A	130	ASN	0	-0.003	-0.004	25.917	0.039	0.039	0.000	0.000	0.000	0.000
76	A	131	TYR	0	-0.026	-0.040	22.074	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	132	THR	0	0.016	0.021	28.503	0.000	0.000	0.000	0.000	0.000	0.000
78	A	133	PRO	0	0.001	0.000	30.247	0.019	0.019	0.000	0.000	0.000	0.000
79	A	134	GLY	0	-0.017	0.006	31.356	0.004	0.004	0.000	0.000	0.000	0.000
80	A	135	PRO	0	-0.032	-0.023	31.464	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	136	GLY	0	0.012	-0.008	29.643	-0.018	-0.018	0.000	0.000	0.000	0.000
82	A	137	ILE	0	-0.056	-0.048	25.562	0.013	0.013	0.000	0.000	0.000	0.000
83	A	138	ARG	1	0.825	0.926	26.123	-0.254	-0.254	0.000	0.000	0.000	0.000
84	A	139	TYR	0	0.064	0.016	26.114	0.002	0.002	0.000	0.000	0.000	0.000
85	A	140	PRO	0	0.017	0.019	25.724	0.004	0.004	0.000	0.000	0.000	0.000
86	A	141	LEU	0	0.013	-0.012	27.722	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	142	THR	0	-0.074	-0.047	27.927	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	143	PHE	0	-0.010	-0.008	28.129	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	144	GLY	0	0.053	0.014	27.547	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	145	TRP	0	-0.009	-0.005	18.719	-0.043	-0.043	0.000	0.000	0.000	0.000
91	A	146	CYS	0	-0.088	-0.047	21.649	0.021	0.021	0.000	0.000	0.000	0.000
92	A	147	PHE	0	0.016	-0.007	15.522	0.002	0.002	0.000	0.000	0.000	0.000
93	A	148	LYS	1	0.849	0.928	21.365	-0.152	-0.152	0.000	0.000	0.000	0.000
94	A	149	LEU	0	0.005	0.019	21.164	0.035	0.035	0.000	0.000	0.000	0.000
95	A	150	VAL	0	-0.046	-0.036	21.409	-0.042	-0.042	0.000	0.000	0.000	0.000
96	A	151	PRO	0	0.026	0.014	22.067	0.051	0.051	0.000	0.000	0.000	0.000
97	A	152	VAL	0	-0.056	-0.026	19.101	0.002	0.002	0.000	0.000	0.000	0.000
98	A	153	GLU	-1	-0.862	-0.933	22.337	0.394	0.394	0.000	0.000	0.000	0.000
99	A	154	PRO	0	-0.030	-0.004	21.413	0.066	0.066	0.000	0.000	0.000	0.000
100	A	155	GLU	-1	-1.048	-1.013	17.910	0.849	0.849	0.000	0.000	0.000	0.000
101	A	179	ASP	-1	-0.891	-0.951	26.990	0.403	0.403	0.000	0.000	0.000	0.000
102	A	180	ALA	0	-0.061	-0.029	26.682	0.029	0.029	0.000	0.000	0.000	0.000
103	A	181	GLU	-1	-0.968	-0.980	28.742	0.322	0.322	0.000	0.000	0.000	0.000
104	A	182	LYS	1	0.922	0.933	27.158	-0.351	-0.351	0.000	0.000	0.000	0.000
105	A	183	GLU	-1	-0.753	-0.863	26.439	0.297	0.297	0.000	0.000	0.000	0.000
106	A	184	VAL	0	0.029	0.032	20.611	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	185	LEU	0	-0.020	-0.007	22.109	-0.018	-0.018	0.000	0.000	0.000	0.000
108	A	186	VAL	0	-0.007	-0.001	16.903	0.067	0.067	0.000	0.000	0.000	0.000
109	A	187	TRP	0	0.019	0.008	16.446	-0.065	-0.065	0.000	0.000	0.000	0.000
110	A	188	ARG	1	0.824	0.900	15.746	-0.430	-0.430	0.000	0.000	0.000	0.000
111	A	189	PHE	0	0.024	0.010	16.788	-0.060	-0.060	0.000	0.000	0.000	0.000
112	A	190	ASP	-1	-0.805	-0.892	18.665	0.091	0.091	0.000	0.000	0.000	0.000
113	A	191	SER	0	0.048	0.020	21.821	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	192	LYS	1	0.869	0.912	23.188	-0.063	-0.063	0.000	0.000	0.000	0.000
115	A	193	LEU	0	0.000	0.014	23.704	0.001	0.001	0.000	0.000	0.000	0.000
116	A	194	ALA	0	0.026	0.018	25.657	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	195	PHE	0	-0.085	-0.043	26.948	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	196	HIS	0	-0.045	-0.019	30.042	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	197	HIS	0	-0.014	0.004	30.371	0.005	0.005	0.000	0.000	0.000	0.000
120	A	198	MET	0	0.003	-0.020	29.262	0.011	0.011	0.000	0.000	0.000	0.000
121	A	199	ALA	0	0.037	0.040	31.564	0.009	0.009	0.000	0.000	0.000	0.000
122	A	200	ARG	1	0.952	0.966	33.238	0.003	0.003	0.000	0.000	0.000	0.000
123	A	201	GLU	-1	-0.859	-0.926	34.679	0.009	0.009	0.000	0.000	0.000	0.000
124	A	202	LEU	0	-0.024	0.000	33.014	0.005	0.005	0.000	0.000	0.000	0.000
125	A	203	HIS	0	-0.056	-0.025	35.321	0.016	0.016	0.000	0.000	0.000	0.000
126	A	204	PRO	0	-0.017	-0.007	38.484	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	205	GLU	-1	-0.957	-0.976	35.822	0.060	0.060	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:56:ASN)