FMO DATABASE

FMODB ID: 8952Y

Calculation Name: 2O94-D-Xray372

Preferred Name: Histone deacetylase 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2O94

Chain ID: D

ChEMBL ID: CHEMBL3524

UniProt ID: P56524

Base Structure: X-ray

Registration Date: 2023-09-21

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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-325397.741716
FMO2-HF: Nuclear repulsion	296384.778604
FMO2-HF: Total energy	-29012.963112
FMO2-MP2: Total energy	-29098.033999

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(D:62:ALA)

Summations of interaction energy for fragment #1(D:62:ALA)

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.
2.739	2.183	7.671	-3.051	-4.066	-0.007

Interaction energy analysis for fragmet #1(D:62:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.010

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

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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	D	64	PRO	0	0.050	0.037	3.710	-0.722	1.504	-0.016	-1.199	-1.011	0.003
4	D	65	ALA	0	0.046	0.008	2.328	-0.402	0.007	0.820	-0.459	-0.770	-0.002
5	D	66	LEU	0	-0.009	-0.005	2.092	2.006	-1.259	6.868	-1.384	-2.220	-0.008
6	D	67	ARG	1	0.970	0.981	4.586	1.646	1.720	-0.001	-0.009	-0.065	0.000
7	D	68	GLU	-1	-0.984	-0.966	6.633	0.160	0.160	0.000	0.000	0.000	0.000
8	D	69	GLN	0	0.002	-0.013	6.705	-0.011	-0.011	0.000	0.000	0.000	0.000
9	D	70	GLN	0	-0.031	-0.007	8.590	-0.054	-0.054	0.000	0.000	0.000	0.000
10	D	71	LEU	0	0.047	0.036	10.580	0.086	0.086	0.000	0.000	0.000	0.000
11	D	72	GLN	0	-0.005	-0.005	10.554	0.018	0.018	0.000	0.000	0.000	0.000
12	D	73	GLN	0	-0.006	0.005	11.747	0.074	0.074	0.000	0.000	0.000	0.000
13	D	74	GLU	-1	-0.895	-0.982	14.321	-0.361	-0.361	0.000	0.000	0.000	0.000
14	D	75	LEU	0	0.006	0.013	16.447	0.029	0.029	0.000	0.000	0.000	0.000
15	D	76	LEU	0	-0.053	-0.032	16.807	0.017	0.017	0.000	0.000	0.000	0.000
16	D	77	ALA	0	0.020	0.009	18.740	0.015	0.015	0.000	0.000	0.000	0.000
17	D	78	LEU	0	-0.036	-0.018	20.556	0.009	0.009	0.000	0.000	0.000	0.000
18	D	79	LYS	1	0.979	0.982	22.439	0.026	0.026	0.000	0.000	0.000	0.000
19	D	80	GLN	0	-0.012	0.005	23.369	0.011	0.011	0.000	0.000	0.000	0.000
20	D	81	LYS	1	1.002	0.997	24.773	0.133	0.133	0.000	0.000	0.000	0.000
21	D	82	GLN	0	-0.017	-0.010	26.682	0.015	0.015	0.000	0.000	0.000	0.000
22	D	83	GLN	0	-0.072	-0.021	28.125	0.001	0.001	0.000	0.000	0.000	0.000
23	D	84	ILE	0	0.099	0.053	28.911	0.005	0.005	0.000	0.000	0.000	0.000
24	D	85	GLN	0	-0.001	-0.011	30.026	-0.005	-0.005	0.000	0.000	0.000	0.000
25	D	86	ARG	1	0.965	0.980	29.530	0.050	0.050	0.000	0.000	0.000	0.000
26	D	87	GLN	0	-0.002	-0.008	34.367	0.006	0.006	0.000	0.000	0.000	0.000
27	D	88	ILE	0	-0.021	-0.001	34.115	0.002	0.002	0.000	0.000	0.000	0.000
28	D	89	LEU	0	0.002	0.009	36.990	0.002	0.002	0.000	0.000	0.000	0.000
29	D	90	ILE	0	0.023	0.005	38.793	0.002	0.002	0.000	0.000	0.000	0.000
30	D	91	ALA	0	-0.013	0.003	40.195	0.002	0.002	0.000	0.000	0.000	0.000
31	D	92	GLU	-1	-0.957	-0.977	41.363	-0.047	-0.047	0.000	0.000	0.000	0.000
32	D	93	PHE	0	-0.002	-0.004	43.146	0.002	0.002	0.000	0.000	0.000	0.000
33	D	94	GLN	0	0.003	-0.011	44.600	0.001	0.001	0.000	0.000	0.000	0.000
34	D	95	ARG	1	1.019	1.006	46.057	0.035	0.035	0.000	0.000	0.000	0.000
35	D	96	GLN	0	-0.078	-0.053	46.329	0.000	0.000	0.000	0.000	0.000	0.000
36	D	97	PHE	0	-0.004	0.012	49.176	0.001	0.001	0.000	0.000	0.000	0.000
37	D	98	GLU	-1	-0.887	-0.946	50.772	-0.015	-0.015	0.000	0.000	0.000	0.000
38	D	99	GLN	0	-0.035	-0.017	52.098	0.000	0.000	0.000	0.000	0.000	0.000
39	D	100	LEU	0	-0.007	0.002	53.619	0.001	0.001	0.000	0.000	0.000	0.000
40	D	101	SER	0	0.035	0.008	54.591	0.001	0.001	0.000	0.000	0.000	0.000
41	D	102	ARG	1	0.943	0.976	55.501	0.017	0.017	0.000	0.000	0.000	0.000
42	D	103	GLN	0	-0.062	-0.021	56.656	0.001	0.001	0.000	0.000	0.000	0.000
43	D	104	HIS	0	0.031	0.003	58.511	0.001	0.001	0.000	0.000	0.000	0.000
44	D	105	GLU	-1	-0.950	-0.952	60.831	-0.013	-0.013	0.000	0.000	0.000	0.000
45	D	106	ALA	0	0.050	0.016	62.478	0.001	0.001	0.000	0.000	0.000	0.000
46	D	107	GLN	0	-0.010	0.004	63.497	0.000	0.000	0.000	0.000	0.000	0.000
47	D	108	LEU	0	0.043	0.012	64.479	0.001	0.001	0.000	0.000	0.000	0.000
48	D	109	HIS	0	-0.054	-0.026	66.366	0.001	0.001	0.000	0.000	0.000	0.000
49	D	110	GLU	-1	-0.951	-0.965	68.311	-0.015	-0.015	0.000	0.000	0.000	0.000
50	D	111	HIS	0	0.011	-0.017	69.959	0.000	0.000	0.000	0.000	0.000	0.000
51	D	112	ILE	0	-0.056	-0.031	70.779	0.001	0.001	0.000	0.000	0.000	0.000
52	D	113	LYS	1	0.924	0.956	72.190	0.013	0.013	0.000	0.000	0.000	0.000
53	D	114	GLN	0	0.069	0.042	73.022	0.001	0.001	0.000	0.000	0.000	0.000
54	D	115	GLN	0	-0.111	-0.065	75.941	0.000	0.000	0.000	0.000	0.000	0.000
55	D	116	GLN	0	-0.022	-0.001	77.198	0.001	0.001	0.000	0.000	0.000	0.000
56	D	117	GLU	-1	-0.871	-0.954	78.315	-0.011	-0.011	0.000	0.000	0.000	0.000
57	D	118	MET	0	0.019	0.036	80.758	0.000	0.000	0.000	0.000	0.000	0.000
58	D	119	LEU	0	-0.002	-0.035	81.366	0.000	0.000	0.000	0.000	0.000	0.000
59	D	120	ALA	0	-0.041	0.005	83.023	0.000	0.000	0.000	0.000	0.000	0.000
60	D	121	MET	0	0.106	0.020	84.891	0.000	0.000	0.000	0.000	0.000	0.000
61	D	122	LYS	1	0.841	0.950	86.173	0.009	0.009	0.000	0.000	0.000	0.000
62	D	123	HIS	0	-0.035	-0.096	88.388	0.000	0.000	0.000	0.000	0.000	0.000
63	D	124	GLN	0	-0.029	0.026	86.193	0.000	0.000	0.000	0.000	0.000	0.000
64	D	125	GLN	0	-0.003	-0.001	89.693	0.000	0.000	0.000	0.000	0.000	0.000
65	D	126	GLH	0	-0.070	-0.029	92.126	0.000	0.000	0.000	0.000	0.000	0.000
66	D	127	LEU	0	-0.038	-0.025	93.742	0.000	0.000	0.000	0.000	0.000	0.000
67	D	128	LEU	0	-0.123	-0.051	95.473	0.000	0.000	0.000	0.000	0.000	0.000
68	D	129	GLU	-1	-0.869	-0.876	94.112	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:62:ALA)