FMO DATABASE

FMODB ID: NN91Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-325338.276126
FMO2-HF: Nuclear repulsion	296324.203188
FMO2-HF: Total energy	-29014.072938
FMO2-MP2: Total energy	-29099.023436

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.
0.505	3.757	1.757	-1.997	-3.009	-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 : 0.018 / q_NPA : 0.006

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	0.052	0.042	3.810	-0.980	1.340	-0.017	-1.269	-1.033	0.003
4	D	65	ALA	0	0.048	0.010	2.339	-0.285	-0.029	0.777	-0.316	-0.716	-0.002
5	D	66	LEU	0	-0.007	0.001	2.227	-0.421	0.184	0.998	-0.404	-1.199	-0.002
6	D	67	ARG	1	0.891	0.913	4.651	1.906	1.977	-0.001	-0.008	-0.061	0.000
7	D	68	GLU	-1	-0.988	-0.973	7.121	0.260	0.260	0.000	0.000	0.000	0.000
8	D	69	GLN	0	-0.006	-0.016	6.609	-0.021	-0.021	0.000	0.000	0.000	0.000
9	D	70	GLN	0	-0.065	-0.040	8.653	-0.088	-0.088	0.000	0.000	0.000	0.000
10	D	71	LEU	0	0.032	0.032	10.516	0.082	0.082	0.000	0.000	0.000	0.000
11	D	72	GLN	0	-0.014	-0.003	11.386	0.039	0.039	0.000	0.000	0.000	0.000
12	D	73	GLN	0	-0.007	0.001	11.220	0.078	0.078	0.000	0.000	0.000	0.000
13	D	74	GLU	-1	-0.854	-0.944	14.150	-0.353	-0.353	0.000	0.000	0.000	0.000
14	D	75	LEU	0	0.015	0.015	16.553	0.027	0.027	0.000	0.000	0.000	0.000
15	D	76	LEU	0	-0.053	-0.031	16.317	0.017	0.017	0.000	0.000	0.000	0.000
16	D	77	ALA	0	0.025	0.011	18.615	0.013	0.013	0.000	0.000	0.000	0.000
17	D	78	LEU	0	-0.040	-0.019	20.375	0.009	0.009	0.000	0.000	0.000	0.000
18	D	79	LYS	1	0.955	0.970	22.440	0.024	0.024	0.000	0.000	0.000	0.000
19	D	80	GLN	0	0.018	0.016	23.143	0.010	0.010	0.000	0.000	0.000	0.000
20	D	81	LYS	1	0.992	0.995	24.571	0.123	0.123	0.000	0.000	0.000	0.000
21	D	82	GLN	0	0.024	0.016	26.466	0.016	0.016	0.000	0.000	0.000	0.000
22	D	83	GLN	0	-0.086	-0.043	28.032	0.003	0.003	0.000	0.000	0.000	0.000
23	D	84	ILE	0	0.060	0.038	28.316	0.005	0.005	0.000	0.000	0.000	0.000
24	D	85	GLN	0	0.018	0.001	29.634	-0.004	-0.004	0.000	0.000	0.000	0.000
25	D	86	ARG	1	0.930	0.962	29.106	0.051	0.051	0.000	0.000	0.000	0.000
26	D	87	GLN	0	0.034	0.013	33.150	0.007	0.007	0.000	0.000	0.000	0.000
27	D	88	ILE	0	-0.019	-0.002	33.667	0.002	0.002	0.000	0.000	0.000	0.000
28	D	89	LEU	0	0.006	0.007	36.840	0.002	0.002	0.000	0.000	0.000	0.000
29	D	90	ILE	0	0.010	-0.002	38.672	0.002	0.002	0.000	0.000	0.000	0.000
30	D	91	ALA	0	-0.002	0.011	39.987	0.002	0.002	0.000	0.000	0.000	0.000
31	D	92	GLU	-1	-0.911	-0.945	41.141	-0.043	-0.043	0.000	0.000	0.000	0.000
32	D	93	PHE	0	-0.018	-0.011	42.937	0.002	0.002	0.000	0.000	0.000	0.000
33	D	94	GLN	0	0.019	-0.004	44.433	0.001	0.001	0.000	0.000	0.000	0.000
34	D	95	ARG	1	0.913	0.947	45.815	0.034	0.034	0.000	0.000	0.000	0.000
35	D	96	GLN	0	-0.064	-0.048	45.410	0.001	0.001	0.000	0.000	0.000	0.000
36	D	97	PHE	0	-0.002	0.006	49.008	0.001	0.001	0.000	0.000	0.000	0.000
37	D	98	GLU	-1	-0.807	-0.867	50.556	-0.015	-0.015	0.000	0.000	0.000	0.000
38	D	99	GLN	0	0.013	0.008	51.405	0.000	0.000	0.000	0.000	0.000	0.000
39	D	100	LEU	0	0.011	0.013	53.429	0.001	0.001	0.000	0.000	0.000	0.000
40	D	101	SER	0	0.011	-0.018	54.271	0.001	0.001	0.000	0.000	0.000	0.000
41	D	102	ARG	1	0.841	0.908	55.014	0.016	0.016	0.000	0.000	0.000	0.000
42	D	103	GLN	0	-0.063	-0.025	56.942	0.000	0.000	0.000	0.000	0.000	0.000
43	D	104	HIS	0	0.031	0.003	58.572	0.001	0.001	0.000	0.000	0.000	0.000
44	D	105	GLU	-1	-0.934	-0.947	60.643	-0.013	-0.013	0.000	0.000	0.000	0.000
45	D	106	ALA	0	0.052	0.017	62.234	0.001	0.001	0.000	0.000	0.000	0.000
46	D	107	GLN	0	0.007	0.012	63.030	0.000	0.000	0.000	0.000	0.000	0.000
47	D	108	LEU	0	0.027	0.005	64.039	0.001	0.001	0.000	0.000	0.000	0.000
48	D	109	HIS	0	-0.055	-0.022	65.073	0.001	0.001	0.000	0.000	0.000	0.000
49	D	110	GLU	-1	-0.929	-0.942	68.066	-0.015	-0.015	0.000	0.000	0.000	0.000
50	D	111	HIS	0	-0.010	-0.023	69.756	0.000	0.000	0.000	0.000	0.000	0.000
51	D	112	ILE	0	-0.033	-0.019	69.888	0.001	0.001	0.000	0.000	0.000	0.000
52	D	113	LYS	1	0.833	0.916	72.667	0.012	0.012	0.000	0.000	0.000	0.000
53	D	114	GLN	0	0.010	-0.016	72.899	0.001	0.001	0.000	0.000	0.000	0.000
54	D	115	GLN	0	-0.078	-0.039	75.751	0.000	0.000	0.000	0.000	0.000	0.000
55	D	116	GLN	0	-0.008	0.003	76.937	0.001	0.001	0.000	0.000	0.000	0.000
56	D	117	GLU	-1	-0.797	-0.913	78.022	-0.011	-0.011	0.000	0.000	0.000	0.000
57	D	118	MET	0	0.002	0.024	80.540	0.000	0.000	0.000	0.000	0.000	0.000
58	D	119	LEU	0	-0.006	-0.024	80.967	0.000	0.000	0.000	0.000	0.000	0.000
59	D	120	ALA	0	-0.025	0.004	82.854	0.000	0.000	0.000	0.000	0.000	0.000
60	D	121	MET	0	0.124	0.053	84.647	0.000	0.000	0.000	0.000	0.000	0.000
61	D	122	LYS	1	0.832	0.952	85.596	0.008	0.008	0.000	0.000	0.000	0.000
62	D	123	HIS	0	-0.017	-0.087	88.196	0.000	0.000	0.000	0.000	0.000	0.000
63	D	124	GLN	0	-0.046	-0.015	85.462	0.000	0.000	0.000	0.000	0.000	0.000
64	D	125	GLN	0	-0.019	-0.014	89.420	0.000	0.000	0.000	0.000	0.000	0.000
65	D	126	GLH	0	-0.054	-0.012	91.879	0.000	0.000	0.000	0.000	0.000	0.000
66	D	127	LEU	0	-0.022	-0.010	93.140	0.000	0.000	0.000	0.000	0.000	0.000
67	D	128	LEU	0	-0.113	-0.047	95.255	0.000	0.000	0.000	0.000	0.000	0.000
68	D	129	GLU	-1	-0.895	-0.901	94.128	-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)