FMO DATABASE

FMODB ID: 2JLRR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-979935.289682
FMO2-HF: Nuclear repulsion	932782.160656
FMO2-HF: Total energy	-47153.129026
FMO2-MP2: Total energy	-47292.891436

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.
-28.43	-28.177	0.057	1.211	-1.521	0.01

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 : -0.892 / q_NPA : -0.956

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	-0.003	-0.010	3.299	-8.351	-8.098	0.057	1.211	-1.521	0.010
4	C	72	PHE	0	-0.095	-0.035	6.032	-3.439	-3.439	0.000	0.000	0.000	0.000
5	C	73	PRO	0	0.030	0.032	8.485	0.357	0.357	0.000	0.000	0.000	0.000
6	C	74	VAL	0	0.015	-0.010	10.947	-0.847	-0.847	0.000	0.000	0.000	0.000
7	C	75	ARG	1	0.951	0.951	13.201	-16.696	-16.696	0.000	0.000	0.000	0.000
8	C	76	PRO	0	0.037	0.023	11.283	-0.765	-0.765	0.000	0.000	0.000	0.000
9	C	77	GLN	0	-0.012	0.005	13.783	-1.116	-1.116	0.000	0.000	0.000	0.000
10	C	78	VAL	0	-0.019	0.005	16.758	0.800	0.800	0.000	0.000	0.000	0.000
11	C	79	PRO	0	0.017	-0.003	17.380	-0.592	-0.592	0.000	0.000	0.000	0.000
12	C	80	LEU	0	0.006	0.019	20.065	-0.459	-0.459	0.000	0.000	0.000	0.000
13	C	81	ARG	1	0.842	0.911	23.673	-12.671	-12.671	0.000	0.000	0.000	0.000
14	C	82	PRO	0	0.008	0.011	26.358	-0.162	-0.162	0.000	0.000	0.000	0.000
15	C	83	MET	0	0.024	0.023	30.216	0.091	0.091	0.000	0.000	0.000	0.000
16	C	84	THR	0	-0.022	-0.021	32.303	-0.246	-0.246	0.000	0.000	0.000	0.000
17	C	85	TYR	0	0.028	0.002	34.836	0.169	0.169	0.000	0.000	0.000	0.000
18	C	86	LYS	1	0.806	0.884	34.037	-9.358	-9.358	0.000	0.000	0.000	0.000
19	C	87	ALA	0	0.046	0.027	31.139	0.037	0.037	0.000	0.000	0.000	0.000
20	C	88	ALA	0	0.075	0.027	32.812	0.095	0.095	0.000	0.000	0.000	0.000
21	C	89	LEU	0	0.015	0.038	35.354	-0.072	-0.072	0.000	0.000	0.000	0.000
22	C	90	ASP	-1	-0.818	-0.891	32.228	9.583	9.583	0.000	0.000	0.000	0.000
23	C	91	ILE	0	-0.022	-0.013	30.077	0.080	0.080	0.000	0.000	0.000	0.000
24	C	92	SER	0	-0.024	-0.026	33.273	-0.136	-0.136	0.000	0.000	0.000	0.000
25	C	93	HIS	0	-0.037	-0.013	35.967	-0.147	-0.147	0.000	0.000	0.000	0.000
26	C	94	PHE	0	0.000	-0.004	28.588	0.023	0.023	0.000	0.000	0.000	0.000
27	C	95	LEU	0	-0.015	-0.021	31.727	0.054	0.054	0.000	0.000	0.000	0.000
28	C	96	LYS	1	0.805	0.913	35.286	-7.664	-7.664	0.000	0.000	0.000	0.000
29	C	97	GLU	-1	-0.916	-0.964	35.617	8.198	8.198	0.000	0.000	0.000	0.000
30	C	98	LYS	1	0.847	0.944	29.469	-10.508	-10.508	0.000	0.000	0.000	0.000
31	C	99	GLY	0	0.027	0.028	35.197	-0.057	-0.057	0.000	0.000	0.000	0.000
32	C	100	GLY	0	-0.033	-0.026	36.238	0.213	0.213	0.000	0.000	0.000	0.000
33	C	101	LEU	0	-0.012	-0.012	36.311	0.126	0.126	0.000	0.000	0.000	0.000
34	C	102	GLU	-1	-0.776	-0.895	38.908	7.167	7.167	0.000	0.000	0.000	0.000
35	C	103	GLY	0	0.005	0.010	42.489	-0.031	-0.031	0.000	0.000	0.000	0.000
36	C	104	LEU	0	-0.059	-0.011	37.531	-0.078	-0.078	0.000	0.000	0.000	0.000
37	C	105	ILE	0	0.040	0.012	41.986	0.013	0.013	0.000	0.000	0.000	0.000
38	C	106	TRP	0	0.017	0.003	39.517	0.112	0.112	0.000	0.000	0.000	0.000
39	C	107	SER	0	-0.026	-0.030	38.947	-0.058	-0.058	0.000	0.000	0.000	0.000
40	C	108	GLN	0	0.029	0.005	36.102	-0.007	-0.007	0.000	0.000	0.000	0.000
41	C	109	ARG	1	0.913	0.944	28.663	-9.665	-9.665	0.000	0.000	0.000	0.000
42	C	110	ARG	1	0.890	0.936	33.746	-7.671	-7.671	0.000	0.000	0.000	0.000
43	C	111	GLN	0	0.027	0.027	34.031	0.021	0.021	0.000	0.000	0.000	0.000
44	C	112	GLU	-1	-0.798	-0.872	31.537	9.375	9.375	0.000	0.000	0.000	0.000
45	C	113	ILE	0	-0.055	-0.024	29.112	0.401	0.401	0.000	0.000	0.000	0.000
46	C	114	LEU	0	-0.008	0.005	29.006	0.439	0.439	0.000	0.000	0.000	0.000
47	C	115	ASP	-1	-0.747	-0.883	29.740	9.771	9.771	0.000	0.000	0.000	0.000
48	C	116	LEU	0	-0.018	-0.011	25.922	0.382	0.382	0.000	0.000	0.000	0.000
49	C	117	TRP	0	-0.006	0.007	24.644	0.334	0.334	0.000	0.000	0.000	0.000
50	C	118	ILE	0	0.011	0.011	25.070	0.558	0.558	0.000	0.000	0.000	0.000
51	C	119	TYR	0	0.035	0.023	22.900	0.466	0.466	0.000	0.000	0.000	0.000
52	C	120	HIS	0	-0.057	-0.037	17.770	0.788	0.788	0.000	0.000	0.000	0.000
53	C	121	THR	0	-0.066	-0.046	20.583	0.918	0.918	0.000	0.000	0.000	0.000
54	C	122	GLN	0	-0.047	-0.030	22.236	0.202	0.202	0.000	0.000	0.000	0.000
55	C	123	GLY	0	0.058	0.051	23.504	-0.206	-0.206	0.000	0.000	0.000	0.000
56	C	124	TYR	0	-0.007	-0.016	24.087	-0.110	-0.110	0.000	0.000	0.000	0.000
57	C	125	PHE	0	0.038	0.014	26.487	0.135	0.135	0.000	0.000	0.000	0.000
58	C	126	PRO	0	-0.032	-0.010	27.470	-0.248	-0.248	0.000	0.000	0.000	0.000
59	C	127	ASP	-1	-0.893	-0.957	30.423	9.535	9.535	0.000	0.000	0.000	0.000
60	C	128	TRP	0	0.069	0.043	31.087	-0.472	-0.472	0.000	0.000	0.000	0.000
61	C	129	GLN	0	-0.017	0.025	34.510	-0.552	-0.552	0.000	0.000	0.000	0.000
62	C	130	ASN	0	-0.007	-0.009	36.915	-0.137	-0.137	0.000	0.000	0.000	0.000
63	C	131	TYR	0	-0.029	-0.041	39.059	-0.079	-0.079	0.000	0.000	0.000	0.000
64	C	132	THR	0	0.029	0.023	43.446	0.002	0.002	0.000	0.000	0.000	0.000
65	C	133	PRO	0	0.014	0.000	47.014	0.043	0.043	0.000	0.000	0.000	0.000
66	C	134	GLY	0	-0.010	0.005	48.958	0.015	0.015	0.000	0.000	0.000	0.000
67	C	135	PRO	0	-0.031	-0.019	51.726	-0.036	-0.036	0.000	0.000	0.000	0.000
68	C	136	GLY	0	0.006	-0.005	52.971	-0.063	-0.063	0.000	0.000	0.000	0.000
69	C	137	ILE	0	-0.052	-0.045	49.164	0.113	0.113	0.000	0.000	0.000	0.000
70	C	138	ARG	1	0.827	0.924	45.851	-6.592	-6.592	0.000	0.000	0.000	0.000
71	C	139	TYR	0	0.074	0.026	46.106	0.158	0.158	0.000	0.000	0.000	0.000
72	C	140	PRO	0	0.013	0.014	41.829	0.004	0.004	0.000	0.000	0.000	0.000
73	C	141	LEU	0	0.005	-0.004	41.710	-0.074	-0.074	0.000	0.000	0.000	0.000
74	C	142	THR	0	-0.053	-0.038	36.887	-0.038	-0.038	0.000	0.000	0.000	0.000
75	C	143	PHE	0	0.012	0.004	40.349	0.072	0.072	0.000	0.000	0.000	0.000
76	C	144	GLY	0	0.046	0.010	39.415	0.196	0.196	0.000	0.000	0.000	0.000
77	C	145	TRP	0	-0.031	-0.015	36.051	0.202	0.202	0.000	0.000	0.000	0.000
78	C	146	CYS	0	-0.079	-0.044	39.422	-0.243	-0.243	0.000	0.000	0.000	0.000
79	C	147	PHE	0	0.000	-0.007	38.428	-0.124	-0.124	0.000	0.000	0.000	0.000
80	C	148	LYS	1	0.850	0.923	42.341	-6.537	-6.537	0.000	0.000	0.000	0.000
81	C	149	LEU	0	-0.001	0.011	41.421	0.015	0.015	0.000	0.000	0.000	0.000
82	C	150	VAL	0	-0.044	-0.025	45.445	-0.156	-0.156	0.000	0.000	0.000	0.000
83	C	151	PRO	0	0.030	0.013	48.761	0.078	0.078	0.000	0.000	0.000	0.000
84	C	152	VAL	0	-0.047	-0.034	50.082	-0.012	-0.012	0.000	0.000	0.000	0.000
85	C	153	GLU	-1	-0.886	-0.942	52.762	5.844	5.844	0.000	0.000	0.000	0.000
86	C	154	PRO	0	-0.045	-0.027	52.613	0.102	0.102	0.000	0.000	0.000	0.000
87	C	155	GLU	-1	-0.978	-0.975	53.201	5.808	5.808	0.000	0.000	0.000	0.000
88	C	181	GLU	-1	-0.926	-0.968	55.036	5.711	5.711	0.000	0.000	0.000	0.000
89	C	182	LYS	1	0.905	0.936	48.053	-6.423	-6.423	0.000	0.000	0.000	0.000
90	C	183	GLU	-1	-0.769	-0.869	50.594	6.204	6.204	0.000	0.000	0.000	0.000
91	C	184	VAL	0	0.031	0.039	47.218	0.161	0.161	0.000	0.000	0.000	0.000
92	C	185	LEU	0	-0.007	-0.012	45.536	-0.066	-0.066	0.000	0.000	0.000	0.000
93	C	186	VAL	0	0.002	0.005	44.468	0.106	0.106	0.000	0.000	0.000	0.000
94	C	187	TRP	0	0.015	0.010	37.206	-0.081	-0.081	0.000	0.000	0.000	0.000
95	C	188	ARG	1	0.904	0.959	42.925	-6.602	-6.602	0.000	0.000	0.000	0.000
96	C	189	PHE	0	0.029	0.008	40.698	-0.003	-0.003	0.000	0.000	0.000	0.000
97	C	190	ASP	-1	-0.822	-0.897	44.464	6.337	6.337	0.000	0.000	0.000	0.000
98	C	191	SER	0	0.050	0.025	45.253	0.054	0.054	0.000	0.000	0.000	0.000
99	C	192	LYS	1	0.897	0.927	46.331	-6.327	-6.327	0.000	0.000	0.000	0.000
100	C	193	LEU	0	-0.009	0.004	44.729	-0.041	-0.041	0.000	0.000	0.000	0.000
101	C	194	ALA	0	0.035	0.022	43.187	0.145	0.145	0.000	0.000	0.000	0.000
102	C	195	PHE	0	-0.069	-0.035	44.149	0.067	0.067	0.000	0.000	0.000	0.000
103	C	196	HIS	0	-0.022	-0.013	47.288	0.031	0.031	0.000	0.000	0.000	0.000
104	C	197	HIS	0	-0.029	-0.026	44.543	0.059	0.059	0.000	0.000	0.000	0.000
105	C	198	MET	0	0.014	0.002	47.834	-0.049	-0.049	0.000	0.000	0.000	0.000
106	C	199	ALA	0	0.002	0.020	46.526	-0.112	-0.112	0.000	0.000	0.000	0.000
107	C	200	ARG	1	0.949	0.980	46.115	-6.905	-6.905	0.000	0.000	0.000	0.000
108	C	201	GLU	-1	-0.947	-0.960	49.477	5.888	5.888	0.000	0.000	0.000	0.000
109	C	202	LEU	0	-0.024	-0.024	52.034	-0.118	-0.118	0.000	0.000	0.000	0.000
110	C	203	HIS	0	0.033	0.011	50.804	-0.154	-0.154	0.000	0.000	0.000	0.000
111	C	204	PRO	0	0.007	0.009	50.369	0.168	0.168	0.000	0.000	0.000	0.000
112	C	205	GLU	-1	-0.875	-0.922	46.509	6.897	6.897	0.000	0.000	0.000	0.000
113	C	206	TYR	0	-0.069	-0.041	43.825	0.220	0.220	0.000	0.000	0.000	0.000
114	C	207	TYR	0	-0.050	-0.025	43.047	-0.217	-0.217	0.000	0.000	0.000	0.000

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