FMO DATABASE

FMODB ID: GNKK1

Calculation Name: 5J9T-F-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9T

Chain ID: F

ChEMBL ID:

UniProt ID: P47128

Base Structure: X-ray

Registration Date: 2023-06-20

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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-367992.877413
FMO2-HF: Nuclear repulsion	339873.671587
FMO2-HF: Total energy	-28119.205826
FMO2-MP2: Total energy	-28202.810408

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(F:7:SER)

Summations of interaction energy for fragment #1(F:7:SER)

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.
-4.32	-0.243	0.239	-1.737	-2.579	0.003

Interaction energy analysis for fragmet #1(F:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.003

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	F	9	GLU	-1	-0.898	-0.964	3.126	-3.039	-0.253	0.088	-1.330	-1.544	0.004
4	F	10	ALA	0	-0.021	-0.004	2.567	-1.086	-0.115	0.152	-0.336	-0.786	-0.001
5	F	11	LEU	0	0.060	0.027	4.275	0.407	0.727	-0.001	-0.071	-0.249	0.000
6	F	12	LYS	1	0.945	0.978	6.259	-0.458	-0.458	0.000	0.000	0.000	0.000
7	F	13	ALA	0	-0.037	-0.019	7.287	0.018	0.018	0.000	0.000	0.000	0.000
8	F	14	GLU	-1	-0.915	-0.966	8.127	0.021	0.021	0.000	0.000	0.000	0.000
9	F	15	LEU	0	0.008	0.016	10.254	0.030	0.030	0.000	0.000	0.000	0.000
10	F	16	LYS	1	0.935	0.951	12.043	-0.264	-0.264	0.000	0.000	0.000	0.000
11	F	17	LYS	1	0.968	0.999	13.062	0.074	0.074	0.000	0.000	0.000	0.000
12	F	18	SER	0	0.040	0.016	14.173	-0.004	-0.004	0.000	0.000	0.000	0.000
13	F	19	LEU	0	-0.040	-0.023	16.081	0.001	0.001	0.000	0.000	0.000	0.000
14	F	20	GLN	0	-0.034	-0.011	17.704	0.005	0.005	0.000	0.000	0.000	0.000
15	F	21	ASP	-1	-0.850	-0.923	18.947	0.029	0.029	0.000	0.000	0.000	0.000
16	F	22	ARG	1	0.938	0.975	20.297	-0.117	-0.117	0.000	0.000	0.000	0.000
17	F	23	ARG	1	0.956	0.983	22.168	-0.065	-0.065	0.000	0.000	0.000	0.000
18	F	24	GLU	-1	-0.923	-0.962	23.300	0.020	0.020	0.000	0.000	0.000	0.000
19	F	25	GLN	0	-0.060	-0.049	23.686	-0.005	-0.005	0.000	0.000	0.000	0.000
20	F	26	GLU	-1	-0.972	-0.996	25.987	0.075	0.075	0.000	0.000	0.000	0.000
21	F	27	ASP	-1	-0.874	-0.926	28.228	0.047	0.047	0.000	0.000	0.000	0.000
22	F	28	THR	0	-0.091	-0.043	28.840	-0.004	-0.004	0.000	0.000	0.000	0.000
23	F	29	PHE	0	-0.035	-0.016	30.739	-0.003	-0.003	0.000	0.000	0.000	0.000
24	F	30	ASP	-1	-0.884	-0.949	32.451	0.042	0.042	0.000	0.000	0.000	0.000
25	F	31	ASN	0	-0.038	-0.021	33.507	-0.001	-0.001	0.000	0.000	0.000	0.000
26	F	32	LEU	0	0.010	0.017	33.546	-0.002	-0.002	0.000	0.000	0.000	0.000
27	F	33	GLN	0	-0.001	0.000	36.329	0.001	0.001	0.000	0.000	0.000	0.000
28	F	34	GLN	0	-0.036	-0.015	38.768	0.000	0.000	0.000	0.000	0.000	0.000
29	F	35	GLU	-1	-0.906	-0.958	39.772	0.013	0.013	0.000	0.000	0.000	0.000
30	F	36	ILE	0	-0.054	-0.034	39.267	-0.002	-0.002	0.000	0.000	0.000	0.000
31	F	37	TYR	0	-0.032	-0.007	42.716	-0.001	-0.001	0.000	0.000	0.000	0.000
32	F	38	ASP	-1	-0.830	-0.925	44.464	0.019	0.019	0.000	0.000	0.000	0.000
33	F	39	LYS	1	0.885	0.945	44.618	-0.012	-0.012	0.000	0.000	0.000	0.000
34	F	40	GLU	-1	-0.791	-0.881	46.523	0.016	0.016	0.000	0.000	0.000	0.000
35	F	41	THR	0	-0.036	-0.012	48.851	-0.001	-0.001	0.000	0.000	0.000	0.000
36	F	42	GLU	-1	-0.930	-0.968	49.146	0.010	0.010	0.000	0.000	0.000	0.000
37	F	43	TYR	0	-0.022	-0.012	47.330	-0.001	-0.001	0.000	0.000	0.000	0.000
38	F	44	PHE	0	-0.024	-0.012	49.837	-0.001	-0.001	0.000	0.000	0.000	0.000
39	F	45	SER	0	-0.056	-0.015	54.395	0.001	0.001	0.000	0.000	0.000	0.000
40	F	66	SER	0	-0.021	-0.021	61.789	0.000	0.000	0.000	0.000	0.000	0.000
41	F	67	GLY	0	0.044	0.034	59.866	0.000	0.000	0.000	0.000	0.000	0.000
42	F	68	ASN	0	-0.026	-0.027	55.383	0.000	0.000	0.000	0.000	0.000	0.000
43	F	69	ILE	0	0.056	0.033	50.178	0.000	0.000	0.000	0.000	0.000	0.000
44	F	70	ILE	0	-0.011	-0.005	50.789	0.000	0.000	0.000	0.000	0.000	0.000
45	F	71	LYS	1	0.857	0.913	54.151	-0.010	-0.010	0.000	0.000	0.000	0.000
46	F	72	GLY	0	0.027	0.014	57.396	0.000	0.000	0.000	0.000	0.000	0.000
47	F	73	PHE	0	-0.089	-0.031	53.380	0.000	0.000	0.000	0.000	0.000	0.000
48	F	74	ASP	-1	-0.938	-0.947	59.284	0.003	0.003	0.000	0.000	0.000	0.000
49	F	88	PHE	0	0.051	0.021	51.932	0.000	0.000	0.000	0.000	0.000	0.000
50	F	89	ASN	0	-0.018	-0.029	55.661	0.000	0.000	0.000	0.000	0.000	0.000
51	F	90	ASN	0	0.065	0.029	51.536	-0.001	-0.001	0.000	0.000	0.000	0.000
52	F	91	ASN	0	-0.051	-0.031	51.174	0.001	0.001	0.000	0.000	0.000	0.000
53	F	92	ASP	-1	-0.891	-0.937	52.329	0.012	0.012	0.000	0.000	0.000	0.000
54	F	93	ARG	1	0.809	0.925	47.845	-0.018	-0.018	0.000	0.000	0.000	0.000
55	F	94	ILE	0	0.010	-0.010	47.448	0.001	0.001	0.000	0.000	0.000	0.000
56	F	95	PHE	0	0.001	0.010	43.964	0.000	0.000	0.000	0.000	0.000	0.000
57	F	96	SER	0	0.008	-0.030	42.818	0.002	0.002	0.000	0.000	0.000	0.000
58	F	97	LEU	0	-0.089	-0.044	42.836	0.002	0.002	0.000	0.000	0.000	0.000
59	F	98	SER	0	-0.040	-0.009	41.464	0.000	0.000	0.000	0.000	0.000	0.000
60	F	99	SER	0	-0.042	-0.004	37.889	0.002	0.002	0.000	0.000	0.000	0.000
61	F	100	ALA	0	0.036	-0.004	38.373	0.000	0.000	0.000	0.000	0.000	0.000
62	F	101	THR	0	0.008	-0.004	35.635	0.001	0.001	0.000	0.000	0.000	0.000
63	F	102	TYR	0	0.051	0.026	38.570	0.000	0.000	0.000	0.000	0.000	0.000
64	F	103	VAL	0	-0.017	-0.007	41.740	-0.001	-0.001	0.000	0.000	0.000	0.000
65	F	104	LYS	1	0.916	0.942	37.102	-0.046	-0.046	0.000	0.000	0.000	0.000
66	F	105	GLN	0	-0.002	0.014	41.332	-0.002	-0.002	0.000	0.000	0.000	0.000
67	F	106	GLN	0	-0.012	0.002	43.329	-0.002	-0.002	0.000	0.000	0.000	0.000
68	F	107	HIS	1	0.899	0.970	45.979	-0.027	-0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:7:SER)