FMO DATABASE

FMODB ID: J3ZZ9

Calculation Name: 5J9T-B-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9T

Chain ID: B

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-423136.676581
FMO2-HF: Nuclear repulsion	391345.151265
FMO2-HF: Total energy	-31791.525316
FMO2-MP2: Total energy	-31884.943689

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-2.87	1.564	0.17	-1.587	-3.016	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.018

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	B	3	ASP	-1	-0.907	-0.952	2.986	-1.976	0.306	0.017	-0.942	-1.357	0.002
4	B	4	GLU	-1	-0.961	-0.980	3.106	-1.032	0.953	0.154	-0.621	-1.517	-0.004
5	B	5	LEU	0	-0.008	0.000	4.694	0.183	0.350	-0.001	-0.024	-0.142	0.000
6	B	6	LYS	1	0.971	0.976	6.757	-0.234	-0.234	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.006	-0.001	7.913	0.051	0.051	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.034	0.018	9.049	0.034	0.034	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.930	-0.979	10.877	0.046	0.046	0.000	0.000	0.000	0.000
10	B	10	ALA	0	-0.038	-0.013	12.447	0.017	0.017	0.000	0.000	0.000	0.000
11	B	11	LEU	0	0.063	0.019	12.899	-0.002	-0.002	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.868	0.954	14.125	0.039	0.039	0.000	0.000	0.000	0.000
13	B	13	ALA	0	-0.052	-0.026	17.208	0.002	0.002	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.922	-0.959	18.017	0.034	0.034	0.000	0.000	0.000	0.000
15	B	15	LEU	0	-0.007	0.003	19.356	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.952	0.963	20.712	-0.017	-0.017	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.968	0.993	22.945	-0.052	-0.052	0.000	0.000	0.000	0.000
18	B	18	SER	0	0.014	0.008	23.058	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	19	LEU	0	-0.032	-0.022	24.525	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	20	GLN	0	0.000	0.033	27.135	-0.001	-0.001	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.848	-0.919	28.677	0.014	0.014	0.000	0.000	0.000	0.000
22	B	22	ARG	1	0.961	0.982	29.143	0.018	0.018	0.000	0.000	0.000	0.000
23	B	23	ARG	1	0.859	0.910	31.542	-0.010	-0.010	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.910	-0.948	33.287	0.021	0.021	0.000	0.000	0.000	0.000
25	B	25	GLN	0	-0.034	-0.037	33.269	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	26	GLU	-1	-0.976	-0.995	34.606	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.855	-0.924	37.604	0.004	0.004	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.085	-0.049	38.624	0.001	0.001	0.000	0.000	0.000	0.000
29	B	29	PHE	0	-0.070	-0.024	40.165	0.000	0.000	0.000	0.000	0.000	0.000
30	B	30	ASP	-1	-0.877	-0.945	41.857	-0.005	-0.005	0.000	0.000	0.000	0.000
31	B	31	ASN	0	-0.033	-0.019	43.252	0.000	0.000	0.000	0.000	0.000	0.000
32	B	32	LEU	0	0.013	0.018	43.075	0.000	0.000	0.000	0.000	0.000	0.000
33	B	33	GLN	0	0.009	0.026	45.319	0.000	0.000	0.000	0.000	0.000	0.000
34	B	34	GLN	0	-0.055	-0.027	47.985	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.921	-0.964	49.312	0.007	0.007	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.049	-0.036	48.622	0.000	0.000	0.000	0.000	0.000	0.000
37	B	37	TYR	0	-0.021	-0.005	52.148	0.000	0.000	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.820	-0.918	54.006	0.002	0.002	0.000	0.000	0.000	0.000
39	B	39	LYS	1	0.844	0.917	54.117	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	40	GLU	-1	-0.790	-0.881	55.986	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.027	-0.008	58.328	0.000	0.000	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.889	-0.920	58.864	0.005	0.005	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.042	-0.023	57.287	0.000	0.000	0.000	0.000	0.000	0.000
44	B	44	PHE	0	-0.041	-0.027	59.002	0.000	0.000	0.000	0.000	0.000	0.000
45	B	45	SER	0	-0.049	-0.024	63.875	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	66	SER	0	0.016	0.002	71.441	0.000	0.000	0.000	0.000	0.000	0.000
47	B	67	GLY	0	-0.009	-0.010	69.377	0.000	0.000	0.000	0.000	0.000	0.000
48	B	68	ASN	0	-0.094	-0.048	64.560	0.000	0.000	0.000	0.000	0.000	0.000
49	B	69	ILE	0	0.066	0.030	59.424	0.000	0.000	0.000	0.000	0.000	0.000
50	B	70	ILE	0	-0.014	0.004	60.033	0.000	0.000	0.000	0.000	0.000	0.000
51	B	71	LYS	1	0.946	0.965	63.298	0.000	0.000	0.000	0.000	0.000	0.000
52	B	72	GLY	0	0.022	0.031	66.276	0.000	0.000	0.000	0.000	0.000	0.000
53	B	73	PHE	0	-0.022	-0.030	62.817	0.000	0.000	0.000	0.000	0.000	0.000
54	B	74	ASP	-1	-0.954	-0.956	68.739	0.001	0.001	0.000	0.000	0.000	0.000
55	B	87	ALA	0	-0.048	-0.039	70.318	0.000	0.000	0.000	0.000	0.000	0.000
56	B	88	PHE	0	0.051	0.038	60.597	0.000	0.000	0.000	0.000	0.000	0.000
57	B	89	ASN	0	0.046	0.017	64.454	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	90	ASN	0	0.053	0.019	60.539	0.001	0.001	0.000	0.000	0.000	0.000
59	B	91	ASN	0	-0.086	-0.053	59.805	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	92	ASP	-1	-0.877	-0.937	61.264	-0.004	-0.004	0.000	0.000	0.000	0.000
61	B	93	ARG	1	0.772	0.918	57.066	0.003	0.003	0.000	0.000	0.000	0.000
62	B	94	ILE	0	0.002	-0.027	56.676	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	95	PHE	0	-0.019	0.002	53.095	0.000	0.000	0.000	0.000	0.000	0.000
64	B	96	SER	0	0.040	0.017	51.858	0.000	0.000	0.000	0.000	0.000	0.000
65	B	97	LEU	0	-0.061	-0.027	51.633	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	98	SER	0	-0.089	-0.049	50.328	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	99	SER	0	-0.016	-0.017	47.291	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	100	ALA	0	0.037	-0.004	46.342	0.000	0.000	0.000	0.000	0.000	0.000
69	B	101	THR	0	-0.032	-0.023	43.497	0.000	0.000	0.000	0.000	0.000	0.000
70	B	102	TYR	0	0.083	0.048	46.860	0.000	0.000	0.000	0.000	0.000	0.000
71	B	103	VAL	0	0.015	0.008	50.063	0.000	0.000	0.000	0.000	0.000	0.000
72	B	104	LYS	1	0.923	0.956	44.257	0.018	0.018	0.000	0.000	0.000	0.000
73	B	105	GLN	0	-0.022	-0.019	47.913	0.000	0.000	0.000	0.000	0.000	0.000
74	B	106	GLN	0	-0.014	0.003	50.866	0.001	0.001	0.000	0.000	0.000	0.000
75	B	107	HIS	0	-0.034	-0.024	53.373	0.000	0.000	0.000	0.000	0.000	0.000
76	B	108	GLY	0	-0.046	-0.001	53.055	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	109	GLN	0	-0.033	-0.005	52.729	0.000	0.000	0.000	0.000	0.000	0.000

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