FMO DATABASE

FMODB ID: JQL39

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	OptAll
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	-324905.905399
FMO2-HF: Nuclear repulsion	295891.161909
FMO2-HF: Total energy	-29014.74349
FMO2-MP2: Total energy	-29099.50435

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.
0.697	4.188	0.762	-1.654	-2.599	-0.001

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 : 0.028 / q_NPA : 0.012

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	D	64	PRO	0	0.012	0.011	3.885	-0.705	1.296	-0.010	-1.092	-0.900	0.002
4	D	65	ALA	0	0.081	0.021	2.576	-0.410	0.016	0.292	-0.187	-0.531	-0.001
5	D	66	LEU	0	-0.024	0.001	2.506	-0.532	0.431	0.480	-0.360	-1.083	-0.002
6	D	67	ARG	1	0.869	0.885	4.464	1.998	2.099	0.000	-0.015	-0.085	0.000
7	D	68	GLU	-1	-0.939	-0.955	7.013	0.263	0.263	0.000	0.000	0.000	0.000
8	D	69	GLN	0	-0.007	-0.010	6.870	-0.006	-0.006	0.000	0.000	0.000	0.000
9	D	70	GLN	0	-0.075	-0.041	8.531	-0.088	-0.088	0.000	0.000	0.000	0.000
10	D	71	LEU	0	0.042	0.019	10.433	0.090	0.090	0.000	0.000	0.000	0.000
11	D	72	GLN	0	-0.030	-0.007	10.896	0.073	0.073	0.000	0.000	0.000	0.000
12	D	73	GLN	0	0.000	-0.011	10.598	0.084	0.084	0.000	0.000	0.000	0.000
13	D	74	GLU	-1	-0.871	-0.925	14.332	-0.390	-0.390	0.000	0.000	0.000	0.000
14	D	75	LEU	0	-0.005	0.003	16.506	0.027	0.027	0.000	0.000	0.000	0.000
15	D	76	LEU	0	-0.023	-0.015	16.109	0.023	0.023	0.000	0.000	0.000	0.000
16	D	77	ALA	0	0.024	0.012	18.582	0.015	0.015	0.000	0.000	0.000	0.000
17	D	78	LEU	0	-0.018	-0.007	20.383	0.013	0.013	0.000	0.000	0.000	0.000
18	D	79	LYS	1	0.958	0.976	22.194	0.036	0.036	0.000	0.000	0.000	0.000
19	D	80	GLN	0	0.008	0.005	23.162	0.010	0.010	0.000	0.000	0.000	0.000
20	D	81	LYS	1	0.933	0.957	24.497	0.127	0.127	0.000	0.000	0.000	0.000
21	D	82	GLN	0	0.032	0.010	26.281	0.016	0.016	0.000	0.000	0.000	0.000
22	D	83	GLN	0	-0.085	-0.036	27.958	0.003	0.003	0.000	0.000	0.000	0.000
23	D	84	ILE	0	0.062	0.027	27.770	0.004	0.004	0.000	0.000	0.000	0.000
24	D	85	GLN	0	0.025	0.009	29.649	-0.005	-0.005	0.000	0.000	0.000	0.000
25	D	86	ARG	1	0.917	0.956	28.959	0.059	0.059	0.000	0.000	0.000	0.000
26	D	87	GLN	0	0.024	0.022	32.735	0.007	0.007	0.000	0.000	0.000	0.000
27	D	88	ILE	0	0.009	0.009	33.547	0.002	0.002	0.000	0.000	0.000	0.000
28	D	89	LEU	0	0.025	0.021	36.806	0.002	0.002	0.000	0.000	0.000	0.000
29	D	90	ILE	0	-0.002	0.000	38.643	0.002	0.002	0.000	0.000	0.000	0.000
30	D	91	ALA	0	0.007	0.004	39.885	0.003	0.003	0.000	0.000	0.000	0.000
31	D	92	GLU	-1	-0.919	-0.943	41.081	-0.047	-0.047	0.000	0.000	0.000	0.000
32	D	93	PHE	0	0.003	0.001	42.815	0.002	0.002	0.000	0.000	0.000	0.000
33	D	94	GLN	0	-0.006	-0.001	44.417	0.001	0.001	0.000	0.000	0.000	0.000
34	D	95	ARG	1	0.887	0.930	45.707	0.037	0.037	0.000	0.000	0.000	0.000
35	D	96	GLN	0	-0.011	-0.024	45.046	0.001	0.001	0.000	0.000	0.000	0.000
36	D	97	PHE	0	-0.006	0.005	48.772	0.001	0.001	0.000	0.000	0.000	0.000
37	D	98	GLU	-1	-0.818	-0.887	50.266	-0.018	-0.018	0.000	0.000	0.000	0.000
38	D	99	GLN	0	0.012	0.012	51.107	0.000	0.000	0.000	0.000	0.000	0.000
39	D	100	LEU	0	0.001	0.003	53.176	0.001	0.001	0.000	0.000	0.000	0.000
40	D	101	SER	0	-0.002	-0.013	54.126	0.001	0.001	0.000	0.000	0.000	0.000
41	D	102	ARG	1	0.781	0.868	55.123	0.018	0.018	0.000	0.000	0.000	0.000
42	D	103	GLN	0	-0.036	-0.009	56.870	0.000	0.000	0.000	0.000	0.000	0.000
43	D	104	HIS	0	0.034	0.008	58.374	0.001	0.001	0.000	0.000	0.000	0.000
44	D	105	GLU	-1	-0.868	-0.918	60.091	-0.015	-0.015	0.000	0.000	0.000	0.000
45	D	106	ALA	0	0.005	0.006	61.938	0.001	0.001	0.000	0.000	0.000	0.000
46	D	107	GLN	0	0.028	0.002	62.904	0.000	0.000	0.000	0.000	0.000	0.000
47	D	108	LEU	0	-0.007	0.005	63.866	0.001	0.001	0.000	0.000	0.000	0.000
48	D	109	HIS	0	-0.049	-0.036	64.651	0.001	0.001	0.000	0.000	0.000	0.000
49	D	110	GLU	-1	-0.904	-0.930	67.904	-0.016	-0.016	0.000	0.000	0.000	0.000
50	D	111	HIS	0	0.032	0.010	69.559	0.001	0.001	0.000	0.000	0.000	0.000
51	D	112	ILE	0	-0.027	-0.009	69.707	0.001	0.001	0.000	0.000	0.000	0.000
52	D	113	LYS	1	0.795	0.888	72.346	0.014	0.014	0.000	0.000	0.000	0.000
53	D	114	GLN	0	0.016	-0.007	72.357	0.001	0.001	0.000	0.000	0.000	0.000
54	D	115	GLN	0	-0.044	-0.031	75.502	0.000	0.000	0.000	0.000	0.000	0.000
55	D	116	GLN	0	-0.028	-0.008	76.236	0.001	0.001	0.000	0.000	0.000	0.000
56	D	117	GLU	-1	-0.813	-0.906	78.005	-0.012	-0.012	0.000	0.000	0.000	0.000
57	D	118	MET	0	-0.030	0.005	80.063	0.000	0.000	0.000	0.000	0.000	0.000
58	D	119	LEU	0	-0.013	-0.028	80.718	0.000	0.000	0.000	0.000	0.000	0.000
59	D	120	ALA	0	-0.022	0.004	82.737	0.000	0.000	0.000	0.000	0.000	0.000
60	D	121	MET	0	0.052	0.023	84.361	0.000	0.000	0.000	0.000	0.000	0.000
61	D	122	LYS	1	0.902	0.964	85.637	0.009	0.009	0.000	0.000	0.000	0.000
62	D	123	HIS	0	-0.016	-0.042	88.177	0.000	0.000	0.000	0.000	0.000	0.000
63	D	124	GLN	0	-0.022	-0.014	85.435	0.000	0.000	0.000	0.000	0.000	0.000
64	D	125	GLN	0	-0.017	-0.023	89.553	0.000	0.000	0.000	0.000	0.000	0.000
65	D	126	GLH	0	-0.023	-0.018	91.820	0.000	0.000	0.000	0.000	0.000	0.000
66	D	127	LEU	0	-0.041	-0.017	92.809	0.000	0.000	0.000	0.000	0.000	0.000
67	D	128	LEU	0	-0.087	-0.035	95.110	0.000	0.000	0.000	0.000	0.000	0.000
68	D	129	GLU	-1	-0.914	-0.905	94.261	-0.009	-0.009	0.000	0.000	0.000	0.000

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