FMO DATABASE

FMODB ID: ZYQMN

Calculation Name: 5J9U-F-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9U

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-397020.461796
FMO2-HF: Nuclear repulsion	365978.868268
FMO2-HF: Total energy	-31041.593528
FMO2-MP2: Total energy	-31132.708437

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:1:MET)

Summations of interaction energy for fragment #1(F:1: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.
-1.129	2.646	0.098	-1.266	-2.607	0

Interaction energy analysis for fragmet #1(F:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.073 / q_NPA : 0.017

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	3	ASP	-1	-0.904	-0.949	2.921	-2.397	-0.132	0.021	-0.884	-1.402	0.002
4	F	4	GLU	-1	-0.930	-0.958	3.161	0.560	2.070	0.077	-0.382	-1.205	-0.002
5	F	5	LEU	0	-0.010	-0.003	4.804	0.474	0.474	0.000	0.000	0.000	0.000
6	F	6	LYS	1	0.963	0.971	6.665	-0.043	-0.043	0.000	0.000	0.000	0.000
7	F	7	SER	0	0.014	0.005	7.778	0.120	0.120	0.000	0.000	0.000	0.000
8	F	8	TYR	0	0.027	0.018	9.094	0.068	0.068	0.000	0.000	0.000	0.000
9	F	9	GLU	-1	-0.907	-0.969	10.889	0.056	0.056	0.000	0.000	0.000	0.000
10	F	10	ALA	0	-0.042	-0.014	12.306	0.026	0.026	0.000	0.000	0.000	0.000
11	F	11	LEU	0	0.060	0.015	12.634	0.009	0.009	0.000	0.000	0.000	0.000
12	F	12	LYS	1	0.859	0.951	14.163	0.038	0.038	0.000	0.000	0.000	0.000
13	F	13	ALA	0	-0.047	-0.033	16.976	0.008	0.008	0.000	0.000	0.000	0.000
14	F	14	GLU	-1	-0.921	-0.963	18.074	-0.012	-0.012	0.000	0.000	0.000	0.000
15	F	15	LEU	0	-0.021	-0.009	19.421	0.000	0.000	0.000	0.000	0.000	0.000
16	F	16	LYS	1	0.900	0.951	19.391	-0.023	-0.023	0.000	0.000	0.000	0.000
17	F	17	LYS	1	0.961	0.988	22.889	-0.023	-0.023	0.000	0.000	0.000	0.000
18	F	18	SER	0	0.048	0.026	23.256	0.001	0.001	0.000	0.000	0.000	0.000
19	F	19	LEU	0	-0.028	-0.010	24.776	-0.001	-0.001	0.000	0.000	0.000	0.000
20	F	20	GLN	0	-0.056	-0.018	27.304	0.000	0.000	0.000	0.000	0.000	0.000
21	F	21	ASP	-1	-0.842	-0.923	28.604	0.001	0.001	0.000	0.000	0.000	0.000
22	F	22	ARG	1	0.919	0.964	29.300	0.018	0.018	0.000	0.000	0.000	0.000
23	F	23	ARG	1	0.860	0.951	31.463	0.003	0.003	0.000	0.000	0.000	0.000
24	F	24	GLU	-1	-0.855	-0.933	33.064	0.010	0.010	0.000	0.000	0.000	0.000
25	F	25	GLN	0	-0.069	-0.052	33.162	0.000	0.000	0.000	0.000	0.000	0.000
26	F	26	GLU	-1	-0.964	-0.999	34.088	-0.012	-0.012	0.000	0.000	0.000	0.000
27	F	27	ASP	-1	-0.823	-0.904	37.492	0.000	0.000	0.000	0.000	0.000	0.000
28	F	28	THR	0	-0.069	-0.032	38.654	0.001	0.001	0.000	0.000	0.000	0.000
29	F	29	PHE	0	-0.039	-0.018	40.153	0.000	0.000	0.000	0.000	0.000	0.000
30	F	30	ASP	-1	-0.906	-0.958	41.804	-0.006	-0.006	0.000	0.000	0.000	0.000
31	F	31	ASN	0	-0.100	-0.057	43.074	0.001	0.001	0.000	0.000	0.000	0.000
32	F	32	LEU	0	0.017	0.018	43.230	0.000	0.000	0.000	0.000	0.000	0.000
33	F	33	GLN	0	0.040	0.020	46.474	0.000	0.000	0.000	0.000	0.000	0.000
34	F	34	GLN	0	-0.015	0.006	48.453	-0.001	-0.001	0.000	0.000	0.000	0.000
35	F	35	GLU	-1	-0.872	-0.936	49.550	0.003	0.003	0.000	0.000	0.000	0.000
36	F	36	ILE	0	-0.087	-0.048	48.315	0.000	0.000	0.000	0.000	0.000	0.000
37	F	37	TYR	0	-0.028	-0.011	52.148	0.000	0.000	0.000	0.000	0.000	0.000
38	F	38	ASP	-1	-0.864	-0.954	54.032	0.000	0.000	0.000	0.000	0.000	0.000
39	F	39	LYS	1	0.863	0.930	54.200	-0.002	-0.002	0.000	0.000	0.000	0.000
40	F	40	GLU	-1	-0.805	-0.899	55.838	-0.004	-0.004	0.000	0.000	0.000	0.000
41	F	41	THR	0	-0.032	-0.005	58.344	0.000	0.000	0.000	0.000	0.000	0.000
42	F	42	GLU	-1	-0.921	-0.951	58.988	0.002	0.002	0.000	0.000	0.000	0.000
43	F	43	TYR	0	-0.033	-0.011	57.199	0.000	0.000	0.000	0.000	0.000	0.000
44	F	44	PHE	0	-0.036	-0.021	59.171	0.000	0.000	0.000	0.000	0.000	0.000
45	F	45	SER	0	-0.062	-0.026	63.974	0.000	0.000	0.000	0.000	0.000	0.000
46	F	65	TYR	0	-0.004	-0.015	68.391	0.000	0.000	0.000	0.000	0.000	0.000
47	F	66	SER	0	-0.018	-0.011	70.459	0.000	0.000	0.000	0.000	0.000	0.000
48	F	67	GLY	0	-0.008	0.009	68.596	0.000	0.000	0.000	0.000	0.000	0.000
49	F	68	ASN	0	-0.070	-0.030	63.897	0.001	0.001	0.000	0.000	0.000	0.000
50	F	69	ILE	0	0.050	0.017	58.577	0.000	0.000	0.000	0.000	0.000	0.000
51	F	70	ILE	0	-0.007	0.005	60.207	0.000	0.000	0.000	0.000	0.000	0.000
52	F	71	LYS	1	0.937	0.968	63.400	0.002	0.002	0.000	0.000	0.000	0.000
53	F	72	GLY	0	0.044	0.028	66.517	0.000	0.000	0.000	0.000	0.000	0.000
54	F	73	PHE	0	0.014	0.001	62.432	0.000	0.000	0.000	0.000	0.000	0.000
55	F	74	ASP	-1	-0.954	-0.971	68.393	-0.001	-0.001	0.000	0.000	0.000	0.000
56	F	75	THR	0	0.026	0.001	71.391	0.000	0.000	0.000	0.000	0.000	0.000
57	F	76	PHE	0	-0.051	-0.009	72.671	0.000	0.000	0.000	0.000	0.000	0.000
58	F	77	SER	0	-0.011	-0.007	76.948	0.000	0.000	0.000	0.000	0.000	0.000
59	F	86	SER	0	0.005	-0.006	70.308	0.000	0.000	0.000	0.000	0.000	0.000
60	F	87	ALA	0	-0.031	-0.021	70.045	0.000	0.000	0.000	0.000	0.000	0.000
61	F	88	PHE	0	0.040	0.024	60.452	0.000	0.000	0.000	0.000	0.000	0.000
62	F	89	ASN	0	0.013	0.004	65.163	0.000	0.000	0.000	0.000	0.000	0.000
63	F	90	ASN	0	0.064	0.019	60.249	0.000	0.000	0.000	0.000	0.000	0.000
64	F	91	ASN	0	-0.040	-0.029	59.894	0.000	0.000	0.000	0.000	0.000	0.000
65	F	92	ASP	-1	-0.884	-0.935	60.914	-0.005	-0.005	0.000	0.000	0.000	0.000
66	F	93	ARG	1	0.792	0.915	57.060	0.003	0.003	0.000	0.000	0.000	0.000
67	F	94	ILE	0	-0.009	-0.028	56.304	0.000	0.000	0.000	0.000	0.000	0.000
68	F	95	PHE	0	-0.009	0.003	52.974	0.000	0.000	0.000	0.000	0.000	0.000
69	F	96	SER	0	0.051	0.045	51.830	0.000	0.000	0.000	0.000	0.000	0.000
70	F	97	LEU	0	-0.097	-0.046	51.708	-0.001	-0.001	0.000	0.000	0.000	0.000
71	F	98	SER	0	-0.096	-0.063	50.207	-0.001	-0.001	0.000	0.000	0.000	0.000
72	F	99	SER	0	-0.019	-0.011	46.781	-0.001	-0.001	0.000	0.000	0.000	0.000
73	F	100	ALA	0	0.011	-0.009	46.459	0.000	0.000	0.000	0.000	0.000	0.000
74	F	101	THR	0	-0.042	-0.015	44.894	-0.001	-0.001	0.000	0.000	0.000	0.000
75	F	102	TYR	0	-0.019	0.004	47.183	0.000	0.000	0.000	0.000	0.000	0.000

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