FMO DATABASE

FMODB ID: R9JL8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-955563.563707
FMO2-HF: Nuclear repulsion	908917.306479
FMO2-HF: Total energy	-46646.257229
FMO2-MP2: Total energy	-46780.606362

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.
6.492	-8.029	36.811	-2.438	-19.85	-0.003

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 : -0.091 / q_NPA : -0.046

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	-0.917	-0.945	1.749	2.697	1.270	6.747	-2.977	-2.343	0.022
4	A	730	PRO	0	0.009	-0.044	2.240	1.585	-1.269	15.771	-5.999	-6.918	-0.010
5	A	731	ASP	-1	-0.880	-0.933	3.150	10.310	2.080	-0.187	9.317	-0.899	-0.008
6	A	732	GLN	0	0.027	0.027	5.039	0.448	0.448	0.000	0.000	0.000	0.000
7	A	733	LEU	0	-0.043	0.003	2.208	-1.173	-2.413	6.225	-1.287	-3.698	0.006
8	A	734	TYR	0	-0.001	-0.008	4.565	-1.096	-0.977	-0.001	-0.029	-0.089	0.000
9	A	735	THR	0	-0.024	-0.030	6.936	-0.692	-0.692	0.000	0.000	0.000	0.000
10	A	736	THR	0	-0.003	-0.009	7.823	-0.347	-0.347	0.000	0.000	0.000	0.000
11	A	737	LEU	0	-0.025	-0.019	6.704	-0.323	-0.323	0.000	0.000	0.000	0.000
12	A	738	LYS	1	0.960	0.974	10.200	-1.153	-1.153	0.000	0.000	0.000	0.000
13	A	739	ASN	0	-0.003	-0.011	12.446	-0.213	-0.213	0.000	0.000	0.000	0.000
14	A	740	LEU	0	-0.014	0.029	12.561	-0.127	-0.127	0.000	0.000	0.000	0.000
15	A	741	LEU	0	0.016	-0.004	14.038	-0.100	-0.100	0.000	0.000	0.000	0.000
16	A	742	ALA	0	-0.025	-0.009	15.944	-0.091	-0.091	0.000	0.000	0.000	0.000
17	A	743	GLN	0	-0.018	-0.028	16.730	-0.110	-0.110	0.000	0.000	0.000	0.000
18	A	744	ILE	0	-0.014	-0.005	16.490	-0.048	-0.048	0.000	0.000	0.000	0.000
19	A	745	LYS	1	0.871	0.911	18.469	-0.509	-0.509	0.000	0.000	0.000	0.000
20	A	746	SER	0	-0.013	0.001	21.737	-0.039	-0.039	0.000	0.000	0.000	0.000
21	A	747	HIS	0	-0.006	0.017	23.922	-0.027	-0.027	0.000	0.000	0.000	0.000
22	A	748	PRO	0	0.056	0.018	25.650	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	749	SER	0	0.000	-0.011	27.200	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	750	ALA	0	0.013	-0.003	23.783	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	751	TRP	0	0.031	0.013	25.590	0.002	0.002	0.000	0.000	0.000	0.000
26	A	752	PRO	0	0.000	0.006	27.979	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	753	PHE	0	-0.015	-0.003	23.656	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	754	MET	0	-0.015	-0.011	23.183	0.043	0.043	0.000	0.000	0.000	0.000
29	A	755	GLU	-1	-0.939	-0.981	23.189	0.208	0.208	0.000	0.000	0.000	0.000
30	A	756	PRO	0	-0.011	0.010	22.824	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	757	VAL	0	0.088	0.061	25.126	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	758	LYS	1	0.923	1.018	28.150	-0.160	-0.160	0.000	0.000	0.000	0.000
33	A	759	LYS	1	1.011	0.990	30.203	-0.062	-0.062	0.000	0.000	0.000	0.000
34	A	760	SER	0	-0.019	-0.013	33.377	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	761	GLU	-1	-0.919	-0.926	33.942	0.121	0.121	0.000	0.000	0.000	0.000
36	A	762	ALA	0	0.039	0.021	32.527	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	763	PRO	0	-0.019	-0.018	33.316	0.001	0.001	0.000	0.000	0.000	0.000
38	A	764	ASP	-1	-0.825	-0.875	34.604	0.064	0.064	0.000	0.000	0.000	0.000
39	A	765	TYR	0	0.039	0.020	26.182	0.003	0.003	0.000	0.000	0.000	0.000
40	A	766	TYR	0	-0.129	-0.148	25.297	0.005	0.005	0.000	0.000	0.000	0.000
41	A	767	GLU	-1	-0.890	-0.905	28.771	0.018	0.018	0.000	0.000	0.000	0.000
42	A	768	VAL	0	0.008	0.011	30.784	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	769	ILE	0	-0.020	-0.005	25.200	0.001	0.001	0.000	0.000	0.000	0.000
44	A	770	ARG	1	0.829	0.893	25.406	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	771	PHE	0	-0.035	-0.017	19.845	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	772	PRO	0	0.039	0.042	21.705	0.030	0.030	0.000	0.000	0.000	0.000
47	A	773	ILE	0	-0.084	-0.052	16.352	0.011	0.011	0.000	0.000	0.000	0.000
48	A	774	ASP	-1	-0.698	-0.811	19.601	0.251	0.251	0.000	0.000	0.000	0.000
49	A	775	LEU	0	0.040	-0.010	18.742	0.052	0.052	0.000	0.000	0.000	0.000
50	A	776	LYS	1	0.881	0.988	18.412	-0.160	-0.160	0.000	0.000	0.000	0.000
51	A	777	THR	0	-0.007	-0.054	16.624	0.028	0.028	0.000	0.000	0.000	0.000
52	A	778	MET	0	-0.037	-0.007	14.121	0.019	0.019	0.000	0.000	0.000	0.000
53	A	779	THR	0	-0.021	-0.020	13.422	0.148	0.148	0.000	0.000	0.000	0.000
54	A	780	GLU	-1	-0.886	-0.946	13.902	0.335	0.335	0.000	0.000	0.000	0.000
55	A	781	ARG	1	0.900	0.960	11.227	-0.299	-0.299	0.000	0.000	0.000	0.000
56	A	782	LEU	0	-0.011	0.007	8.645	0.097	0.097	0.000	0.000	0.000	0.000
57	A	783	ARG	1	0.899	0.941	8.977	-0.302	-0.302	0.000	0.000	0.000	0.000
58	A	784	SER	0	-0.049	-0.020	10.257	-0.032	-0.032	0.000	0.000	0.000	0.000
59	A	785	ARG	1	0.938	0.973	4.730	-1.938	-1.849	-0.001	-0.005	-0.083	0.000
60	A	786	TYR	0	0.044	0.030	5.369	-0.314	-0.314	0.000	0.000	0.000	0.000
61	A	787	TYR	0	-0.074	-0.072	6.674	-0.249	-0.249	0.000	0.000	0.000	0.000
62	A	788	VAL	0	0.052	0.028	2.221	0.909	1.125	3.610	-0.813	-3.013	0.003
63	A	789	THR	0	0.033	0.007	3.124	0.609	-0.754	4.648	-0.627	-2.658	-0.016
64	A	790	ARG	1	1.015	1.003	4.823	-1.633	-1.464	-0.001	-0.018	-0.149	0.000
65	A	791	LYS	1	0.962	0.970	6.798	-0.159	-0.159	0.000	0.000	0.000	0.000
66	A	792	LEU	0	0.016	0.027	6.892	-0.056	-0.056	0.000	0.000	0.000	0.000
67	A	793	PHE	0	0.031	0.019	9.197	-0.072	-0.072	0.000	0.000	0.000	0.000
68	A	794	VAL	0	0.029	0.003	10.854	-0.114	-0.114	0.000	0.000	0.000	0.000
69	A	795	ALA	0	-0.021	-0.006	12.707	-0.080	-0.080	0.000	0.000	0.000	0.000
70	A	796	ASP	-1	-0.763	-0.866	14.072	0.351	0.351	0.000	0.000	0.000	0.000
71	A	797	LEU	0	0.046	0.019	15.139	-0.039	-0.039	0.000	0.000	0.000	0.000
72	A	798	GLN	0	-0.007	-0.008	16.538	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	799	ARG	1	0.844	0.933	16.473	-0.274	-0.274	0.000	0.000	0.000	0.000
74	A	800	VAL	0	0.008	0.012	19.423	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	801	ILE	0	-0.025	-0.003	21.551	-0.025	-0.025	0.000	0.000	0.000	0.000
76	A	802	ALA	0	-0.030	-0.021	22.813	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	803	ASN	0	0.036	0.002	22.847	-0.029	-0.029	0.000	0.000	0.000	0.000
78	A	804	CYS	0	-0.108	-0.020	25.903	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	805	ARG	1	0.846	0.876	25.235	-0.215	-0.215	0.000	0.000	0.000	0.000
80	A	806	GLU	-1	-0.953	-0.943	28.416	0.084	0.084	0.000	0.000	0.000	0.000
81	A	807	TYR	0	-0.071	-0.086	30.113	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	808	ASN	0	-0.020	-0.008	30.765	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	809	PRO	0	0.044	0.010	33.717	0.001	0.001	0.000	0.000	0.000	0.000
84	A	810	PRO	0	0.042	0.020	33.796	0.008	0.008	0.000	0.000	0.000	0.000
85	A	811	ASP	-1	-0.875	-0.942	34.301	0.129	0.129	0.000	0.000	0.000	0.000
86	A	812	SER	0	0.001	-0.006	34.489	0.000	0.000	0.000	0.000	0.000	0.000
87	A	813	GLU	-1	-0.853	-0.931	34.607	0.156	0.156	0.000	0.000	0.000	0.000
88	A	814	TYR	0	-0.033	-0.038	31.116	0.016	0.016	0.000	0.000	0.000	0.000
89	A	815	CYS	0	0.000	-0.002	30.247	0.018	0.018	0.000	0.000	0.000	0.000
90	A	816	ARG	1	0.834	0.936	30.543	-0.115	-0.115	0.000	0.000	0.000	0.000
91	A	817	CYS	0	-0.054	-0.021	29.058	0.013	0.013	0.000	0.000	0.000	0.000
92	A	818	ALA	0	0.022	0.007	26.332	0.021	0.021	0.000	0.000	0.000	0.000
93	A	819	SER	0	0.017	-0.005	25.760	0.024	0.024	0.000	0.000	0.000	0.000
94	A	820	ALA	0	-0.019	0.008	26.736	0.014	0.014	0.000	0.000	0.000	0.000
95	A	821	LEU	0	-0.013	-0.013	22.317	0.021	0.021	0.000	0.000	0.000	0.000
96	A	822	GLU	-1	-0.781	-0.887	21.883	0.288	0.288	0.000	0.000	0.000	0.000
97	A	823	LYS	1	0.954	0.987	21.775	-0.207	-0.207	0.000	0.000	0.000	0.000
98	A	824	PHE	0	-0.018	-0.011	21.414	0.021	0.021	0.000	0.000	0.000	0.000
99	A	825	PHE	0	0.047	0.007	17.847	0.037	0.037	0.000	0.000	0.000	0.000
100	A	826	TYR	0	0.006	-0.017	17.094	0.059	0.059	0.000	0.000	0.000	0.000
101	A	827	PHE	0	-0.046	-0.019	18.463	0.017	0.017	0.000	0.000	0.000	0.000
102	A	828	LYS	1	0.857	0.928	17.115	-0.424	-0.424	0.000	0.000	0.000	0.000
103	A	829	LEU	0	-0.019	-0.004	12.585	0.067	0.067	0.000	0.000	0.000	0.000
104	A	830	LYS	1	0.935	0.980	13.878	-0.297	-0.297	0.000	0.000	0.000	0.000
105	A	831	GLU	-1	-0.878	-0.927	16.127	0.511	0.511	0.000	0.000	0.000	0.000
106	A	832	GLY	0	-0.018	-0.009	13.077	0.001	0.001	0.000	0.000	0.000	0.000
107	A	833	GLY	0	-0.057	-0.029	11.441	0.110	0.110	0.000	0.000	0.000	0.000
108	A	834	LEU	0	-0.045	-0.022	8.168	0.129	0.129	0.000	0.000	0.000	0.000
109	A	835	ILE	0	-0.045	-0.024	10.652	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	836	ASP	-1	-0.866	-0.921	13.344	0.531	0.531	0.000	0.000	0.000	0.000
111	A	837	LYS	1	0.893	0.936	15.794	-0.618	-0.618	0.000	0.000	0.000	0.000

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