FMO DATABASE

FMODB ID: QY3LY

Calculation Name: 3D7C-A-Xray372

Preferred Name: Histone acetyltransferase GCN5

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7C

Chain ID: A

ChEMBL ID: CHEMBL5501

UniProt ID: Q92830

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	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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-955615.688006
FMO2-HF: Nuclear repulsion	908968.885066
FMO2-HF: Total energy	-46646.80294
FMO2-MP2: Total energy	-46781.170621

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.
7.478	-8.671	37.163	-1.083	-19.929	-0.006

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 : 0 / q_Mulliken : -0.100 / q_NPA : -0.047

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	-0.893	-0.924	1.757	2.942	1.733	6.499	-2.866	-2.425	0.024
4	A	730	PRO	0	0.028	-0.028	2.065	1.239	-1.888	17.464	-7.350	-6.986	-0.007
5	A	731	ASP	-1	-0.800	-0.899	2.880	12.599	2.258	-0.276	11.578	-0.961	-0.010
6	A	732	GLN	0	-0.021	-0.001	4.926	0.265	0.265	0.000	0.000	0.000	0.000
7	A	733	LEU	0	-0.027	0.007	2.359	-1.895	-2.095	4.724	-1.107	-3.417	0.004
8	A	734	TYR	0	-0.004	-0.003	4.684	-1.115	-0.992	-0.001	-0.033	-0.088	0.000
9	A	735	THR	0	-0.019	-0.024	6.801	-0.746	-0.746	0.000	0.000	0.000	0.000
10	A	736	THR	0	0.000	-0.012	7.824	-0.362	-0.362	0.000	0.000	0.000	0.000
11	A	737	LEU	0	-0.018	-0.018	6.769	-0.323	-0.323	0.000	0.000	0.000	0.000
12	A	738	LYS	1	0.959	0.980	10.009	-1.133	-1.133	0.000	0.000	0.000	0.000
13	A	739	ASN	0	-0.016	-0.020	12.343	-0.190	-0.190	0.000	0.000	0.000	0.000
14	A	740	LEU	0	-0.008	0.013	12.134	-0.123	-0.123	0.000	0.000	0.000	0.000
15	A	741	LEU	0	0.014	-0.001	13.908	-0.095	-0.095	0.000	0.000	0.000	0.000
16	A	742	ALA	0	-0.019	-0.005	15.794	-0.086	-0.086	0.000	0.000	0.000	0.000
17	A	743	GLN	0	-0.002	-0.003	16.960	-0.106	-0.106	0.000	0.000	0.000	0.000
18	A	744	ILE	0	-0.014	-0.005	16.232	-0.045	-0.045	0.000	0.000	0.000	0.000
19	A	745	LYS	1	0.867	0.911	18.509	-0.446	-0.446	0.000	0.000	0.000	0.000
20	A	746	SER	0	-0.028	-0.010	21.594	-0.034	-0.034	0.000	0.000	0.000	0.000
21	A	747	HIS	0	0.001	0.024	23.606	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	748	PRO	0	0.057	0.018	25.337	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	749	SER	0	-0.006	-0.014	27.019	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	750	ALA	0	0.005	-0.007	23.631	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	751	TRP	0	0.022	0.012	25.450	0.001	0.001	0.000	0.000	0.000	0.000
26	A	752	PRO	0	0.002	0.008	27.912	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	753	PHE	0	-0.008	0.001	23.504	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	754	MET	0	-0.010	-0.012	23.017	0.039	0.039	0.000	0.000	0.000	0.000
29	A	755	GLU	-1	-0.894	-0.941	23.001	0.173	0.173	0.000	0.000	0.000	0.000
30	A	756	PRO	0	-0.026	-0.001	22.579	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	757	VAL	0	0.067	0.046	24.943	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	758	LYS	1	0.888	0.950	27.891	-0.138	-0.138	0.000	0.000	0.000	0.000
33	A	759	LYS	1	1.004	0.993	30.067	-0.040	-0.040	0.000	0.000	0.000	0.000
34	A	760	SER	0	-0.020	-0.014	33.203	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	761	GLU	-1	-0.927	-0.930	33.231	0.103	0.103	0.000	0.000	0.000	0.000
36	A	762	ALA	0	0.044	0.022	32.336	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	763	PRO	0	-0.017	-0.013	33.127	0.000	0.000	0.000	0.000	0.000	0.000
38	A	764	ASP	-1	-0.836	-0.899	34.419	0.045	0.045	0.000	0.000	0.000	0.000
39	A	765	TYR	0	0.042	0.018	26.005	0.001	0.001	0.000	0.000	0.000	0.000
40	A	766	TYR	0	-0.100	-0.091	25.086	0.001	0.001	0.000	0.000	0.000	0.000
41	A	767	GLU	-1	-0.883	-0.891	28.600	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	768	VAL	0	0.003	0.010	30.603	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	769	ILE	0	-0.016	-0.003	25.036	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	770	ARG	1	0.824	0.877	25.287	0.001	0.001	0.000	0.000	0.000	0.000
45	A	771	PHE	0	-0.034	-0.015	20.032	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	772	PRO	0	0.045	0.047	21.498	0.026	0.026	0.000	0.000	0.000	0.000
47	A	773	ILE	0	-0.078	-0.047	16.221	0.007	0.007	0.000	0.000	0.000	0.000
48	A	774	ASP	-1	-0.702	-0.820	19.393	0.215	0.215	0.000	0.000	0.000	0.000
49	A	775	LEU	0	0.050	-0.004	18.545	0.045	0.045	0.000	0.000	0.000	0.000
50	A	776	LYS	1	0.867	0.951	18.221	-0.139	-0.139	0.000	0.000	0.000	0.000
51	A	777	THR	0	-0.012	-0.045	16.430	0.026	0.026	0.000	0.000	0.000	0.000
52	A	778	MET	0	-0.044	-0.008	13.829	0.016	0.016	0.000	0.000	0.000	0.000
53	A	779	THR	0	-0.014	-0.018	13.232	0.134	0.134	0.000	0.000	0.000	0.000
54	A	780	GLU	-1	-0.873	-0.914	13.761	0.298	0.298	0.000	0.000	0.000	0.000
55	A	781	ARG	1	0.892	0.952	11.069	-0.223	-0.223	0.000	0.000	0.000	0.000
56	A	782	LEU	0	-0.013	-0.002	8.619	0.085	0.085	0.000	0.000	0.000	0.000
57	A	783	ARG	1	0.895	0.942	8.857	-0.250	-0.250	0.000	0.000	0.000	0.000
58	A	784	SER	0	-0.045	-0.028	10.207	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	785	ARG	1	0.837	0.917	4.741	-2.484	-2.354	-0.001	-0.012	-0.117	0.000
60	A	786	TYR	0	0.040	0.026	5.286	-0.375	-0.375	0.000	0.000	0.000	0.000
61	A	787	TYR	0	-0.075	-0.079	6.446	-0.289	-0.289	0.000	0.000	0.000	0.000
62	A	788	VAL	0	0.057	0.028	2.175	1.051	1.187	3.918	-0.941	-3.112	0.002
63	A	789	THR	0	0.037	0.005	2.820	-0.061	-1.722	4.836	-0.352	-2.823	-0.019
64	A	790	ARG	1	0.998	0.999	4.826	-0.948	-0.948	0.000	0.000	0.000	0.000
65	A	791	LYS	1	0.974	0.979	6.802	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	792	LEU	0	0.008	0.023	6.649	-0.030	-0.030	0.000	0.000	0.000	0.000
67	A	793	PHE	0	0.034	0.014	9.285	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	794	VAL	0	0.024	0.000	10.881	-0.092	-0.092	0.000	0.000	0.000	0.000
69	A	795	ALA	0	-0.016	0.000	12.835	-0.060	-0.060	0.000	0.000	0.000	0.000
70	A	796	ASP	-1	-0.739	-0.819	13.785	0.255	0.255	0.000	0.000	0.000	0.000
71	A	797	LEU	0	0.045	0.020	15.148	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	798	GLN	0	-0.013	-0.009	16.721	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	799	ARG	1	0.827	0.908	16.321	-0.193	-0.193	0.000	0.000	0.000	0.000
74	A	800	VAL	0	0.001	0.010	19.381	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	801	ILE	0	-0.022	-0.001	21.538	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	802	ALA	0	-0.028	-0.018	22.867	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	803	ASN	0	0.027	-0.002	22.523	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	804	CYS	0	-0.067	-0.010	25.822	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	805	ARG	1	0.814	0.849	25.477	-0.175	-0.175	0.000	0.000	0.000	0.000
80	A	806	GLU	-1	-0.954	-0.945	28.479	0.058	0.058	0.000	0.000	0.000	0.000
81	A	807	TYR	0	-0.059	-0.066	30.051	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	808	ASN	0	-0.054	-0.026	30.604	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	809	PRO	0	0.067	0.021	33.735	0.000	0.000	0.000	0.000	0.000	0.000
84	A	810	PRO	0	0.033	0.021	33.806	0.007	0.007	0.000	0.000	0.000	0.000
85	A	811	ASP	-1	-0.845	-0.904	34.270	0.109	0.109	0.000	0.000	0.000	0.000
86	A	812	SER	0	0.014	0.004	34.505	0.001	0.001	0.000	0.000	0.000	0.000
87	A	813	GLU	-1	-0.841	-0.925	34.649	0.131	0.131	0.000	0.000	0.000	0.000
88	A	814	TYR	0	-0.036	-0.037	31.017	0.014	0.014	0.000	0.000	0.000	0.000
89	A	815	CYS	0	0.013	0.005	30.162	0.015	0.015	0.000	0.000	0.000	0.000
90	A	816	ARG	1	0.788	0.876	30.458	-0.096	-0.096	0.000	0.000	0.000	0.000
91	A	817	CYS	0	-0.051	-0.022	28.925	0.012	0.012	0.000	0.000	0.000	0.000
92	A	818	ALA	0	0.025	0.009	26.225	0.019	0.019	0.000	0.000	0.000	0.000
93	A	819	SER	0	0.006	-0.006	25.646	0.018	0.018	0.000	0.000	0.000	0.000
94	A	820	ALA	0	-0.030	0.003	26.759	0.012	0.012	0.000	0.000	0.000	0.000
95	A	821	LEU	0	-0.015	-0.013	22.176	0.019	0.019	0.000	0.000	0.000	0.000
96	A	822	GLU	-1	-0.770	-0.858	21.877	0.235	0.235	0.000	0.000	0.000	0.000
97	A	823	LYS	1	0.956	0.986	21.790	-0.176	-0.176	0.000	0.000	0.000	0.000
98	A	824	PHE	0	-0.016	-0.008	21.119	0.019	0.019	0.000	0.000	0.000	0.000
99	A	825	PHE	0	0.052	0.003	17.782	0.034	0.034	0.000	0.000	0.000	0.000
100	A	826	TYR	0	-0.004	-0.024	17.424	0.049	0.049	0.000	0.000	0.000	0.000
101	A	827	PHE	0	-0.033	-0.013	18.442	0.015	0.015	0.000	0.000	0.000	0.000
102	A	828	LYS	1	0.806	0.907	16.984	-0.416	-0.416	0.000	0.000	0.000	0.000
103	A	829	LEU	0	-0.006	-0.004	12.618	0.059	0.059	0.000	0.000	0.000	0.000
104	A	830	LYS	1	0.931	0.979	13.839	-0.260	-0.260	0.000	0.000	0.000	0.000
105	A	831	GLU	-1	-0.856	-0.910	16.063	0.469	0.469	0.000	0.000	0.000	0.000
106	A	832	GLY	0	-0.009	-0.004	13.022	0.004	0.004	0.000	0.000	0.000	0.000
107	A	833	GLY	0	-0.058	-0.032	11.369	0.090	0.090	0.000	0.000	0.000	0.000
108	A	834	LEU	0	-0.049	-0.021	8.411	0.098	0.098	0.000	0.000	0.000	0.000
109	A	835	ILE	0	-0.037	-0.025	10.615	-0.024	-0.024	0.000	0.000	0.000	0.000
110	A	836	ASP	-1	-0.867	-0.919	13.317	0.446	0.446	0.000	0.000	0.000	0.000
111	A	837	LYS	1	0.901	0.937	15.540	-0.543	-0.543	0.000	0.000	0.000	0.000

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