FMO DATABASE

FMODB ID: 974M2

Calculation Name: 3D7C-A-Xray547

Preferred Name: Histone acetyltransferase GCN5

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 3D7C

Chain ID: A

ChEMBL ID: CHEMBL5501

UniProt ID: Q92830

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	111
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-955223.606281
FMO2-HF: Nuclear repulsion	908576.789884
FMO2-HF: Total energy	-46646.816397
FMO2-MP2: Total energy	-46781.137637

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:727:MET)

Summations of interaction energy for fragment #1(A:727:MET)

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.
61.676	58.479	19.615	-1.456	-14.964	-0.045

Interaction energy analysis for fragmet #1(A:727:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.780 / q_NPA : 0.913

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	729	ASP	-1	-0.733	-0.855	3.673	-30.774	-28.367	-0.013	-0.992	-1.403	-0.004
4	A	730	PRO	0	-0.003	-0.049	2.214	-8.321	-9.726	13.897	-6.522	-5.970	-0.017
5	A	731	ASP	-1	-0.846	-0.918	3.177	-16.890	-24.286	-0.100	8.171	-0.674	-0.008
7	A	733	LEU	0	-0.030	0.000	2.547	0.142	0.540	2.978	-0.689	-2.688	-0.002
8	A	734	TYR	0	-0.009	-0.010	4.835	3.591	3.708	-0.001	-0.015	-0.100	0.000
62	A	788	VAL	0	0.051	0.022	2.866	-3.084	-1.877	0.995	-0.513	-1.689	0.001
63	A	789	THR	0	-0.017	-0.030	2.922	-12.161	-10.782	1.860	-0.883	-2.357	-0.015
64	A	790	ARG	1	1.016	1.015	4.486	40.860	40.956	-0.001	-0.013	-0.083	0.000
6	A	732	GLN	0	-0.002	0.018	5.610	4.139	4.139	0.000	0.000	0.000	0.000
9	A	735	THR	0	-0.023	-0.042	6.910	2.390	2.390	0.000	0.000	0.000	0.000
10	A	736	THR	0	-0.004	-0.007	8.219	2.556	2.556	0.000	0.000	0.000	0.000
11	A	737	LEU	0	-0.010	-0.016	6.889	1.657	1.657	0.000	0.000	0.000	0.000
12	A	738	LYS	1	0.926	0.967	10.289	18.732	18.732	0.000	0.000	0.000	0.000
13	A	739	ASN	0	-0.005	-0.016	12.566	2.086	2.086	0.000	0.000	0.000	0.000
14	A	740	LEU	0	-0.006	0.026	12.610	1.087	1.087	0.000	0.000	0.000	0.000
15	A	741	LEU	0	0.021	-0.003	14.105	0.968	0.968	0.000	0.000	0.000	0.000
16	A	742	ALA	0	-0.016	-0.003	15.886	0.890	0.890	0.000	0.000	0.000	0.000
17	A	743	GLN	0	-0.004	0.000	17.185	1.263	1.263	0.000	0.000	0.000	0.000
18	A	744	ILE	0	-0.015	-0.011	16.636	0.580	0.580	0.000	0.000	0.000	0.000
19	A	745	LYS	1	0.874	0.914	18.661	14.242	14.242	0.000	0.000	0.000	0.000
20	A	746	SER	0	-0.021	-0.009	21.734	0.550	0.550	0.000	0.000	0.000	0.000
21	A	747	HIS	0	-0.005	0.015	23.946	0.436	0.436	0.000	0.000	0.000	0.000
22	A	748	PRO	0	0.036	0.018	25.737	0.025	0.025	0.000	0.000	0.000	0.000
23	A	749	SER	0	0.000	-0.012	27.673	0.215	0.215	0.000	0.000	0.000	0.000
24	A	750	ALA	0	0.017	-0.002	23.981	-0.127	-0.127	0.000	0.000	0.000	0.000
25	A	751	TRP	0	0.004	0.003	25.788	-0.178	-0.178	0.000	0.000	0.000	0.000
26	A	752	PRO	0	0.000	0.008	28.172	0.005	0.005	0.000	0.000	0.000	0.000
27	A	753	PHE	0	0.001	-0.004	23.656	-0.158	-0.158	0.000	0.000	0.000	0.000
28	A	754	MET	0	-0.024	-0.015	23.203	-0.837	-0.837	0.000	0.000	0.000	0.000
29	A	755	GLU	-1	-0.904	-0.942	23.532	-10.589	-10.589	0.000	0.000	0.000	0.000
30	A	756	PRO	0	-0.023	0.003	23.275	0.100	0.100	0.000	0.000	0.000	0.000
31	A	757	VAL	0	0.075	0.048	25.651	0.361	0.361	0.000	0.000	0.000	0.000
32	A	758	LYS	1	0.885	0.943	28.614	9.925	9.925	0.000	0.000	0.000	0.000
33	A	759	LYS	1	0.978	0.982	31.107	9.379	9.379	0.000	0.000	0.000	0.000
34	A	760	SER	0	-0.005	-0.007	34.116	0.090	0.090	0.000	0.000	0.000	0.000
35	A	761	GLU	-1	-0.928	-0.922	33.991	-8.672	-8.672	0.000	0.000	0.000	0.000
36	A	762	ALA	0	0.045	0.017	33.068	0.114	0.114	0.000	0.000	0.000	0.000
37	A	763	PRO	0	-0.021	-0.010	33.861	-0.257	-0.257	0.000	0.000	0.000	0.000
38	A	764	ASP	-1	-0.836	-0.906	35.009	-8.706	-8.706	0.000	0.000	0.000	0.000
39	A	765	TYR	0	0.042	0.024	26.865	-0.410	-0.410	0.000	0.000	0.000	0.000
40	A	766	TYR	0	-0.077	-0.077	25.990	-0.390	-0.390	0.000	0.000	0.000	0.000
41	A	767	GLU	-1	-0.880	-0.898	29.315	-9.636	-9.636	0.000	0.000	0.000	0.000
42	A	768	VAL	0	0.021	0.009	31.188	-0.161	-0.161	0.000	0.000	0.000	0.000
43	A	769	ILE	0	-0.038	-0.011	25.757	-0.358	-0.358	0.000	0.000	0.000	0.000
44	A	770	ARG	1	0.830	0.887	26.331	9.912	9.912	0.000	0.000	0.000	0.000
45	A	771	PHE	0	-0.031	-0.010	20.865	-0.409	-0.409	0.000	0.000	0.000	0.000
46	A	772	PRO	0	0.047	0.042	22.303	-0.395	-0.395	0.000	0.000	0.000	0.000
47	A	773	ILE	0	-0.070	-0.047	16.747	-0.660	-0.660	0.000	0.000	0.000	0.000
48	A	774	ASP	-1	-0.689	-0.811	20.018	-12.594	-12.594	0.000	0.000	0.000	0.000
49	A	775	LEU	0	0.067	0.008	18.755	-0.842	-0.842	0.000	0.000	0.000	0.000
50	A	776	LYS	1	0.848	0.942	18.637	11.537	11.537	0.000	0.000	0.000	0.000
51	A	777	THR	0	-0.018	-0.047	17.448	-0.579	-0.579	0.000	0.000	0.000	0.000
52	A	778	MET	0	-0.038	-0.016	13.892	-0.594	-0.594	0.000	0.000	0.000	0.000
53	A	779	THR	0	-0.020	-0.021	13.866	-0.979	-0.979	0.000	0.000	0.000	0.000
54	A	780	GLU	-1	-0.853	-0.905	14.557	-13.795	-13.795	0.000	0.000	0.000	0.000
55	A	781	ARG	1	0.886	0.956	11.996	16.937	16.937	0.000	0.000	0.000	0.000
56	A	782	LEU	0	-0.013	-0.005	8.959	-1.432	-1.432	0.000	0.000	0.000	0.000
57	A	783	ARG	1	0.903	0.949	9.620	13.995	13.995	0.000	0.000	0.000	0.000
58	A	784	SER	0	-0.035	-0.030	10.891	-0.391	-0.391	0.000	0.000	0.000	0.000
59	A	785	ARG	1	0.898	0.953	5.324	24.804	24.804	0.000	0.000	0.000	0.000
60	A	786	TYR	0	0.048	0.033	5.889	-2.289	-2.289	0.000	0.000	0.000	0.000
61	A	787	TYR	0	-0.079	-0.069	7.133	-1.520	-1.520	0.000	0.000	0.000	0.000
65	A	791	LYS	1	0.976	0.985	6.959	31.632	31.632	0.000	0.000	0.000	0.000
66	A	792	LEU	0	0.010	0.022	7.449	2.534	2.534	0.000	0.000	0.000	0.000
67	A	793	PHE	0	0.044	0.018	9.126	2.093	2.093	0.000	0.000	0.000	0.000
68	A	794	VAL	0	0.019	-0.003	10.808	1.744	1.744	0.000	0.000	0.000	0.000
69	A	795	ALA	0	-0.007	0.003	12.499	1.518	1.518	0.000	0.000	0.000	0.000
70	A	796	ASP	-1	-0.742	-0.826	13.813	-17.376	-17.376	0.000	0.000	0.000	0.000
71	A	797	LEU	0	0.008	0.000	15.000	0.985	0.985	0.000	0.000	0.000	0.000
72	A	798	GLN	0	0.003	0.010	16.153	1.177	1.177	0.000	0.000	0.000	0.000
73	A	799	ARG	1	0.839	0.919	16.604	16.668	16.668	0.000	0.000	0.000	0.000
74	A	800	VAL	0	-0.006	0.008	19.337	0.644	0.644	0.000	0.000	0.000	0.000
75	A	801	ILE	0	-0.027	-0.006	21.506	0.626	0.626	0.000	0.000	0.000	0.000
76	A	802	ALA	0	-0.011	-0.005	22.711	0.513	0.513	0.000	0.000	0.000	0.000
77	A	803	ASN	0	0.012	-0.013	22.901	0.466	0.466	0.000	0.000	0.000	0.000
78	A	804	CYS	0	-0.124	-0.023	25.713	0.604	0.604	0.000	0.000	0.000	0.000
79	A	805	ARG	1	0.835	0.847	25.534	11.827	11.827	0.000	0.000	0.000	0.000
80	A	806	GLU	-1	-0.941	-0.946	28.076	-10.189	-10.189	0.000	0.000	0.000	0.000
81	A	807	TYR	0	-0.067	-0.060	29.998	0.254	0.254	0.000	0.000	0.000	0.000
82	A	808	ASN	0	-0.040	-0.029	30.574	0.547	0.547	0.000	0.000	0.000	0.000
83	A	809	PRO	0	0.066	0.023	33.370	-0.100	-0.100	0.000	0.000	0.000	0.000
84	A	810	PRO	0	0.033	0.021	33.544	-0.136	-0.136	0.000	0.000	0.000	0.000
85	A	811	ASP	-1	-0.821	-0.884	34.013	-8.389	-8.389	0.000	0.000	0.000	0.000
86	A	812	SER	0	-0.006	-0.006	34.199	0.151	0.151	0.000	0.000	0.000	0.000
87	A	813	GLU	-1	-0.827	-0.921	34.458	-8.845	-8.845	0.000	0.000	0.000	0.000
88	A	814	TYR	0	-0.021	-0.037	30.775	-0.284	-0.284	0.000	0.000	0.000	0.000
89	A	815	CYS	0	0.001	0.007	29.997	-0.511	-0.511	0.000	0.000	0.000	0.000
90	A	816	ARG	1	0.782	0.880	30.400	7.932	7.932	0.000	0.000	0.000	0.000
91	A	817	CYS	0	-0.051	-0.019	29.385	-0.260	-0.260	0.000	0.000	0.000	0.000
92	A	818	ALA	0	0.033	0.006	26.247	-0.401	-0.401	0.000	0.000	0.000	0.000
93	A	819	SER	0	0.018	-0.005	25.735	-0.522	-0.522	0.000	0.000	0.000	0.000
94	A	820	ALA	0	-0.044	-0.014	27.040	-0.235	-0.235	0.000	0.000	0.000	0.000
95	A	821	LEU	0	-0.027	-0.012	22.433	-0.323	-0.323	0.000	0.000	0.000	0.000
96	A	822	GLU	-1	-0.778	-0.862	22.041	-12.914	-12.914	0.000	0.000	0.000	0.000
97	A	823	LYS	1	0.946	0.979	22.174	10.001	10.001	0.000	0.000	0.000	0.000
98	A	824	PHE	0	-0.009	-0.005	21.525	-0.275	-0.275	0.000	0.000	0.000	0.000
99	A	825	PHE	0	0.051	0.007	18.110	-0.518	-0.518	0.000	0.000	0.000	0.000
100	A	826	TYR	0	0.002	-0.026	17.892	-0.754	-0.754	0.000	0.000	0.000	0.000
101	A	827	PHE	0	-0.028	-0.007	19.431	-0.293	-0.293	0.000	0.000	0.000	0.000
102	A	828	LYS	1	0.836	0.909	17.547	13.484	13.484	0.000	0.000	0.000	0.000
103	A	829	LEU	0	-0.035	-0.018	13.218	-1.050	-1.050	0.000	0.000	0.000	0.000
104	A	830	LYS	1	0.830	0.903	15.262	13.323	13.323	0.000	0.000	0.000	0.000
105	A	831	GLU	-1	-0.926	-0.930	17.949	-14.595	-14.595	0.000	0.000	0.000	0.000
106	A	832	GLY	0	-0.021	-0.015	13.982	-0.094	-0.094	0.000	0.000	0.000	0.000
107	A	833	GLY	0	0.016	0.017	12.776	-1.546	-1.546	0.000	0.000	0.000	0.000
108	A	834	LEU	0	-0.098	-0.050	9.414	-2.523	-2.523	0.000	0.000	0.000	0.000
109	A	835	ILE	0	-0.075	-0.051	11.487	-1.556	-1.556	0.000	0.000	0.000	0.000
110	A	836	ASP	-1	-0.865	-0.920	14.205	-18.930	-18.930	0.000	0.000	0.000	0.000
111	A	837	LYS	0	0.129	0.074	16.886	0.192	0.192	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:727:MET)