FMO DATABASE

FMODB ID: 39Y3L

Calculation Name: 1E6I-A-Xray372

Preferred Name: Histone acetyltransferase GCN5

Target Type: SINGLE PROTEIN

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 1E6I

Chain ID: A

ChEMBL ID: CHEMBL4669

UniProt ID: Q03330

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptH
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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-958520.075111
FMO2-HF: Nuclear repulsion	911898.426999
FMO2-HF: Total energy	-46621.648113
FMO2-MP2: Total energy	-46756.590634

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:329:ARG)

Summations of interaction energy for fragment #1(A:329:ARG)

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.
-135.487	-127.937	2.236	-3.091	-6.694	-0.009

Interaction energy analysis for fragmet #1(A:329:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.948 / q_NPA : 0.951

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	331	PRO	0	-0.041	-0.034	3.128	-6.237	-4.371	0.094	-0.904	-1.056	-0.003
4	A	332	HIS	0	0.087	0.089	5.737	1.159	1.159	0.000	0.000	0.000	0.000
5	A	333	ASP	-1	-0.848	-0.908	2.699	-64.687	-61.658	1.357	-1.513	-2.873	-0.006
6	A	334	ALA	0	-0.065	-0.037	2.726	-6.056	-4.323	0.691	-0.693	-1.732	0.001
7	A	335	ALA	0	0.042	0.025	3.681	3.835	3.833	0.056	0.247	-0.301	0.001
8	A	336	ILE	0	0.027	0.005	6.360	3.133	3.133	0.000	0.000	0.000	0.000
9	A	337	GLN	0	0.023	0.010	2.940	7.297	8.070	0.040	-0.220	-0.593	-0.002
10	A	338	ASN	0	-0.028	-0.009	5.060	6.143	6.187	-0.001	-0.002	-0.040	0.000
11	A	339	ILE	0	0.028	0.012	7.249	3.656	3.656	0.000	0.000	0.000	0.000
12	A	340	LEU	0	-0.003	0.005	7.952	2.784	2.784	0.000	0.000	0.000	0.000
13	A	341	THR	0	0.027	0.016	7.639	2.358	2.358	0.000	0.000	0.000	0.000
14	A	342	GLU	-1	-0.936	-0.983	10.182	-18.302	-18.302	0.000	0.000	0.000	0.000
15	A	343	LEU	0	-0.089	-0.051	12.866	1.951	1.951	0.000	0.000	0.000	0.000
16	A	344	GLN	0	-0.030	-0.031	11.053	0.606	0.606	0.000	0.000	0.000	0.000
17	A	345	ASN	0	-0.017	0.006	14.530	1.351	1.351	0.000	0.000	0.000	0.000
18	A	346	HIS	0	-0.005	0.023	16.280	1.459	1.459	0.000	0.000	0.000	0.000
19	A	347	ALA	0	0.018	0.000	18.818	0.330	0.330	0.000	0.000	0.000	0.000
20	A	348	ALA	0	-0.093	-0.072	21.878	0.527	0.527	0.000	0.000	0.000	0.000
21	A	349	ALA	0	0.051	0.022	17.991	0.247	0.247	0.000	0.000	0.000	0.000
22	A	350	TRP	0	0.029	0.010	20.082	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	351	PRO	0	-0.061	-0.033	22.067	0.039	0.039	0.000	0.000	0.000	0.000
24	A	352	PHE	0	-0.007	-0.013	19.495	0.306	0.306	0.000	0.000	0.000	0.000
25	A	353	LEU	0	0.008	0.019	16.655	-0.776	-0.776	0.000	0.000	0.000	0.000
26	A	354	GLN	0	-0.008	-0.001	17.436	-1.041	-1.041	0.000	0.000	0.000	0.000
27	A	355	PRO	0	-0.011	0.007	19.227	0.441	0.441	0.000	0.000	0.000	0.000
28	A	356	VAL	0	0.034	0.029	21.988	0.321	0.321	0.000	0.000	0.000	0.000
29	A	357	ASN	0	0.045	0.035	25.504	0.213	0.213	0.000	0.000	0.000	0.000
30	A	358	LYS	1	0.993	0.975	27.825	9.970	9.970	0.000	0.000	0.000	0.000
31	A	359	GLU	-1	-0.971	-0.984	30.679	-8.972	-8.972	0.000	0.000	0.000	0.000
32	A	360	GLU	-1	-0.950	-0.968	30.678	-9.049	-9.049	0.000	0.000	0.000	0.000
33	A	361	VAL	0	-0.083	-0.033	30.211	0.153	0.153	0.000	0.000	0.000	0.000
34	A	362	PRO	0	-0.011	-0.012	32.316	-0.179	-0.179	0.000	0.000	0.000	0.000
35	A	363	ASP	-1	-0.783	-0.852	34.648	-8.899	-8.899	0.000	0.000	0.000	0.000
36	A	364	TYR	0	0.051	0.028	25.169	-0.133	-0.133	0.000	0.000	0.000	0.000
37	A	365	TYR	0	-0.052	-0.055	25.450	-0.195	-0.195	0.000	0.000	0.000	0.000
38	A	366	ASP	-1	-0.933	-0.956	30.541	-8.820	-8.820	0.000	0.000	0.000	0.000
39	A	367	PHE	0	-0.099	-0.050	32.508	0.121	0.121	0.000	0.000	0.000	0.000
40	A	368	ILE	0	-0.057	-0.010	26.202	-0.131	-0.131	0.000	0.000	0.000	0.000
41	A	369	LYS	1	0.869	0.910	28.395	9.680	9.680	0.000	0.000	0.000	0.000
42	A	370	GLU	-1	-0.878	-0.915	23.344	-12.936	-12.936	0.000	0.000	0.000	0.000
43	A	371	PRO	0	-0.007	0.010	23.066	-0.277	-0.277	0.000	0.000	0.000	0.000
44	A	372	MET	0	-0.034	-0.010	16.997	-0.948	-0.948	0.000	0.000	0.000	0.000
45	A	373	ASP	-1	-0.738	-0.827	17.746	-15.967	-15.967	0.000	0.000	0.000	0.000
46	A	374	LEU	0	0.042	-0.020	14.048	-0.916	-0.916	0.000	0.000	0.000	0.000
47	A	375	SER	0	-0.055	-0.020	13.038	-1.578	-1.578	0.000	0.000	0.000	0.000
48	A	376	THR	0	-0.020	-0.048	13.536	-1.120	-1.120	0.000	0.000	0.000	0.000
49	A	377	MET	0	-0.045	-0.022	11.874	-0.557	-0.557	0.000	0.000	0.000	0.000
50	A	378	GLU	-1	-0.868	-0.926	8.565	-27.813	-27.813	0.000	0.000	0.000	0.000
51	A	379	ILE	0	0.033	0.018	8.914	-2.469	-2.469	0.000	0.000	0.000	0.000
52	A	380	LYS	1	0.802	0.876	10.439	19.096	19.096	0.000	0.000	0.000	0.000
53	A	381	LEU	0	-0.030	-0.013	4.300	-1.273	-1.166	-0.001	-0.006	-0.099	0.000
54	A	382	GLU	-1	-0.945	-0.971	5.793	-36.262	-36.262	0.000	0.000	0.000	0.000
55	A	383	SER	0	-0.094	-0.038	6.829	1.175	1.175	0.000	0.000	0.000	0.000
56	A	384	ASN	0	-0.054	-0.030	6.800	-0.817	-0.817	0.000	0.000	0.000	0.000
57	A	385	LYS	1	0.895	0.943	8.607	22.424	22.424	0.000	0.000	0.000	0.000
58	A	386	TYR	0	-0.051	-0.040	8.461	1.560	1.560	0.000	0.000	0.000	0.000
59	A	387	GLN	0	0.018	0.015	9.234	-1.103	-1.103	0.000	0.000	0.000	0.000
60	A	388	LYS	1	0.942	0.967	10.491	17.189	17.189	0.000	0.000	0.000	0.000
61	A	389	MET	0	0.038	0.038	11.275	-0.837	-0.837	0.000	0.000	0.000	0.000
62	A	390	GLU	-1	-0.881	-0.966	12.822	-18.774	-18.774	0.000	0.000	0.000	0.000
63	A	391	ASP	-1	-0.896	-0.945	13.933	-18.380	-18.380	0.000	0.000	0.000	0.000
64	A	392	PHE	0	-0.005	-0.003	10.750	0.198	0.198	0.000	0.000	0.000	0.000
65	A	393	ILE	0	-0.019	-0.018	13.332	0.961	0.961	0.000	0.000	0.000	0.000
66	A	394	TYR	0	-0.103	-0.058	16.149	1.017	1.017	0.000	0.000	0.000	0.000
67	A	395	ASP	-1	-0.683	-0.826	15.087	-18.346	-18.346	0.000	0.000	0.000	0.000
68	A	396	ALA	0	0.037	0.008	15.352	0.677	0.677	0.000	0.000	0.000	0.000
69	A	397	ARG	1	0.907	0.947	17.083	15.860	15.860	0.000	0.000	0.000	0.000
70	A	398	LEU	0	-0.001	0.040	19.734	0.843	0.843	0.000	0.000	0.000	0.000
71	A	399	VAL	0	-0.004	0.019	17.772	0.648	0.648	0.000	0.000	0.000	0.000
72	A	400	PHE	0	-0.007	-0.017	18.116	0.640	0.640	0.000	0.000	0.000	0.000
73	A	401	ASN	0	-0.035	-0.056	23.089	1.079	1.079	0.000	0.000	0.000	0.000
74	A	402	ASN	0	0.036	0.017	23.330	0.890	0.890	0.000	0.000	0.000	0.000
75	A	403	CYS	0	-0.097	-0.014	25.042	0.628	0.628	0.000	0.000	0.000	0.000
76	A	404	ARG	1	0.797	0.861	25.449	12.203	12.203	0.000	0.000	0.000	0.000
77	A	405	MET	0	-0.028	0.008	29.019	0.268	0.268	0.000	0.000	0.000	0.000
78	A	406	TYR	0	-0.080	-0.080	29.998	0.227	0.227	0.000	0.000	0.000	0.000
79	A	407	ASN	0	-0.048	-0.020	29.024	0.491	0.491	0.000	0.000	0.000	0.000
80	A	408	GLY	0	0.060	0.024	32.566	0.041	0.041	0.000	0.000	0.000	0.000
81	A	409	GLU	-1	-0.895	-0.960	34.044	-8.548	-8.548	0.000	0.000	0.000	0.000
82	A	410	ASN	0	-0.042	-0.020	34.828	-0.138	-0.138	0.000	0.000	0.000	0.000
83	A	411	THR	0	-0.042	-0.025	32.807	-0.055	-0.055	0.000	0.000	0.000	0.000
84	A	412	SER	0	0.006	-0.021	30.785	-0.088	-0.088	0.000	0.000	0.000	0.000
85	A	413	TYR	0	0.061	0.037	27.451	-0.363	-0.363	0.000	0.000	0.000	0.000
86	A	414	TYR	0	0.063	0.059	27.616	-0.548	-0.548	0.000	0.000	0.000	0.000
87	A	415	LYS	1	0.941	0.967	28.624	9.266	9.266	0.000	0.000	0.000	0.000
88	A	416	TYR	0	-0.010	-0.006	24.721	-0.244	-0.244	0.000	0.000	0.000	0.000
89	A	417	ALA	0	0.067	0.038	23.908	-0.519	-0.519	0.000	0.000	0.000	0.000
90	A	418	ASN	0	0.019	0.017	24.038	-0.621	-0.621	0.000	0.000	0.000	0.000
91	A	419	ARG	1	0.855	0.940	23.958	11.445	11.445	0.000	0.000	0.000	0.000
92	A	420	LEU	0	0.045	0.015	18.125	-0.275	-0.275	0.000	0.000	0.000	0.000
93	A	421	GLU	-1	-0.782	-0.864	20.046	-13.855	-13.855	0.000	0.000	0.000	0.000
94	A	422	LYS	1	0.898	0.949	21.284	11.165	11.165	0.000	0.000	0.000	0.000
95	A	423	PHE	0	-0.069	-0.035	15.838	0.130	0.130	0.000	0.000	0.000	0.000
96	A	424	PHE	0	0.086	0.037	13.905	-0.494	-0.494	0.000	0.000	0.000	0.000
97	A	425	ASN	0	0.019	-0.011	17.444	-1.007	-1.007	0.000	0.000	0.000	0.000
98	A	426	ASN	0	-0.055	-0.034	19.434	0.067	0.067	0.000	0.000	0.000	0.000
99	A	427	LYS	1	0.943	0.988	14.205	18.751	18.751	0.000	0.000	0.000	0.000
100	A	428	VAL	0	0.027	0.021	14.201	-0.989	-0.989	0.000	0.000	0.000	0.000
101	A	429	LYS	1	0.817	0.904	15.700	13.899	13.899	0.000	0.000	0.000	0.000
102	A	430	GLU	-1	-0.979	-0.982	15.854	-17.533	-17.533	0.000	0.000	0.000	0.000
103	A	431	ILE	0	0.010	0.019	11.675	-0.369	-0.369	0.000	0.000	0.000	0.000
104	A	432	PRO	0	0.023	0.000	15.498	0.331	0.331	0.000	0.000	0.000	0.000
105	A	433	GLU	-1	-0.892	-0.943	12.881	-20.480	-20.480	0.000	0.000	0.000	0.000
106	A	434	TYR	0	-0.034	-0.081	9.657	-0.289	-0.289	0.000	0.000	0.000	0.000
107	A	435	SER	0	-0.043	-0.014	16.206	1.031	1.031	0.000	0.000	0.000	0.000
108	A	436	HIS	0	-0.043	-0.032	16.668	1.491	1.491	0.000	0.000	0.000	0.000
109	A	437	LEU	0	0.009	0.021	16.133	0.519	0.519	0.000	0.000	0.000	0.000
110	A	438	ILE	0	-0.047	-0.012	18.273	0.514	0.514	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:329:ARG)