FMO DATABASE

FMODB ID: LJ259

Calculation Name: 5J9U-J-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9U

Chain ID: J

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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-408136.421775
FMO2-HF: Nuclear repulsion	376625.456102
FMO2-HF: Total energy	-31510.965673
FMO2-MP2: Total energy	-31603.530674

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(J:1:MET)

Summations of interaction energy for fragment #1(J: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.
-1.158	3.054	0.16	-1.436	-2.936	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.010

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	J	3	ASP	-1	-0.904	-0.955	2.849	-2.562	-0.131	0.045	-0.988	-1.488	0.001
4	J	4	GLU	-1	-0.920	-0.952	3.000	0.743	2.376	0.116	-0.428	-1.322	-0.002
5	J	5	LEU	0	-0.005	-0.004	4.707	0.282	0.430	-0.001	-0.020	-0.126	0.000
6	J	6	LYS	1	0.971	0.986	6.561	0.098	0.098	0.000	0.000	0.000	0.000
7	J	7	SER	0	0.019	0.010	7.663	0.122	0.122	0.000	0.000	0.000	0.000
8	J	8	TYR	0	0.026	0.015	8.918	0.063	0.063	0.000	0.000	0.000	0.000
9	J	9	GLU	-1	-0.918	-0.978	10.553	0.014	0.014	0.000	0.000	0.000	0.000
10	J	10	ALA	0	-0.036	-0.013	11.986	0.030	0.030	0.000	0.000	0.000	0.000
11	J	11	LEU	0	0.040	0.014	12.580	0.011	0.011	0.000	0.000	0.000	0.000
12	J	12	LYS	1	0.826	0.934	14.016	0.065	0.065	0.000	0.000	0.000	0.000
13	J	13	ALA	0	-0.043	-0.021	16.775	0.007	0.007	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.923	-0.969	17.297	-0.015	-0.015	0.000	0.000	0.000	0.000
15	J	15	LEU	0	0.008	0.006	19.137	0.001	0.001	0.000	0.000	0.000	0.000
16	J	16	LYS	1	0.937	0.960	20.966	0.006	0.006	0.000	0.000	0.000	0.000
17	J	17	LYS	1	0.976	0.995	22.721	-0.014	-0.014	0.000	0.000	0.000	0.000
18	J	18	SER	0	0.024	0.014	23.455	0.001	0.001	0.000	0.000	0.000	0.000
19	J	19	LEU	0	-0.055	-0.034	24.652	-0.001	-0.001	0.000	0.000	0.000	0.000
20	J	20	GLN	0	-0.051	-0.021	26.899	0.000	0.000	0.000	0.000	0.000	0.000
21	J	21	ASP	-1	-0.834	-0.915	28.368	-0.005	-0.005	0.000	0.000	0.000	0.000
22	J	22	ARG	1	0.892	0.957	28.763	0.022	0.022	0.000	0.000	0.000	0.000
23	J	23	ARG	1	0.880	0.945	31.007	0.008	0.008	0.000	0.000	0.000	0.000
24	J	24	GLU	-1	-0.872	-0.943	32.764	0.004	0.004	0.000	0.000	0.000	0.000
25	J	25	GLN	0	-0.023	-0.020	33.666	0.002	0.002	0.000	0.000	0.000	0.000
26	J	26	GLU	-1	-0.967	-1.002	34.192	-0.015	-0.015	0.000	0.000	0.000	0.000
27	J	27	ASP	-1	-0.860	-0.915	37.380	-0.004	-0.004	0.000	0.000	0.000	0.000
28	J	28	THR	0	-0.104	-0.048	38.462	0.001	0.001	0.000	0.000	0.000	0.000
29	J	29	PHE	0	-0.004	-0.002	40.119	0.000	0.000	0.000	0.000	0.000	0.000
30	J	30	ASP	-1	-0.901	-0.954	41.529	-0.009	-0.009	0.000	0.000	0.000	0.000
31	J	31	ASN	0	-0.033	-0.012	43.739	0.000	0.000	0.000	0.000	0.000	0.000
32	J	32	LEU	0	-0.020	-0.014	43.097	0.000	0.000	0.000	0.000	0.000	0.000
33	J	33	GLN	0	0.000	0.012	45.834	0.000	0.000	0.000	0.000	0.000	0.000
34	J	34	GLN	0	-0.061	-0.028	47.663	-0.001	-0.001	0.000	0.000	0.000	0.000
35	J	35	GLU	-1	-0.898	-0.952	49.376	-0.001	-0.001	0.000	0.000	0.000	0.000
36	J	36	ILE	0	-0.036	-0.025	48.399	0.000	0.000	0.000	0.000	0.000	0.000
37	J	37	TYR	0	-0.014	0.006	52.071	0.000	0.000	0.000	0.000	0.000	0.000
38	J	38	ASP	-1	-0.805	-0.923	53.906	-0.003	-0.003	0.000	0.000	0.000	0.000
39	J	39	LYS	1	0.902	0.974	54.489	0.001	0.001	0.000	0.000	0.000	0.000
40	J	40	GLU	-1	-0.793	-0.901	55.759	-0.006	-0.006	0.000	0.000	0.000	0.000
41	J	41	THR	0	-0.163	-0.099	58.186	0.000	0.000	0.000	0.000	0.000	0.000
42	J	42	GLU	-1	-0.895	-0.957	58.777	0.000	0.000	0.000	0.000	0.000	0.000
43	J	43	TYR	0	-0.060	-0.025	57.406	0.000	0.000	0.000	0.000	0.000	0.000
44	J	44	PHE	0	-0.054	-0.037	58.996	0.000	0.000	0.000	0.000	0.000	0.000
45	J	45	SER	0	0.001	0.025	63.718	0.000	0.000	0.000	0.000	0.000	0.000
46	J	46	HIS	0	-0.029	-0.017	65.507	0.000	0.000	0.000	0.000	0.000	0.000
47	J	65	TYR	0	-0.042	-0.063	68.549	0.000	0.000	0.000	0.000	0.000	0.000
48	J	66	SER	0	-0.012	-0.003	70.250	0.000	0.000	0.000	0.000	0.000	0.000
49	J	67	GLY	0	0.024	0.040	68.485	0.000	0.000	0.000	0.000	0.000	0.000
50	J	68	ASN	0	-0.115	-0.075	63.649	0.000	0.000	0.000	0.000	0.000	0.000
51	J	69	ILE	0	0.056	0.018	58.659	0.000	0.000	0.000	0.000	0.000	0.000
52	J	70	ILE	0	-0.021	0.002	59.786	0.000	0.000	0.000	0.000	0.000	0.000
53	J	71	LYS	1	0.878	0.939	63.009	0.005	0.005	0.000	0.000	0.000	0.000
54	J	72	GLY	0	0.043	0.029	66.258	0.000	0.000	0.000	0.000	0.000	0.000
55	J	73	PHE	0	0.031	0.012	62.286	0.000	0.000	0.000	0.000	0.000	0.000
56	J	74	ASP	-1	-0.936	-0.945	68.241	-0.003	-0.003	0.000	0.000	0.000	0.000
57	J	75	THR	0	-0.014	-0.010	71.719	0.000	0.000	0.000	0.000	0.000	0.000
58	J	76	PHE	0	-0.037	-0.020	72.479	0.000	0.000	0.000	0.000	0.000	0.000
59	J	77	SER	0	0.019	0.022	76.822	0.000	0.000	0.000	0.000	0.000	0.000
60	J	86	SER	0	-0.006	-0.018	70.345	0.000	0.000	0.000	0.000	0.000	0.000
61	J	87	ALA	0	0.045	0.027	69.930	0.000	0.000	0.000	0.000	0.000	0.000
62	J	88	PHE	0	0.032	0.020	60.327	0.000	0.000	0.000	0.000	0.000	0.000
63	J	89	ASN	0	0.017	0.010	64.779	0.000	0.000	0.000	0.000	0.000	0.000
64	J	90	ASN	0	0.065	0.016	59.987	0.000	0.000	0.000	0.000	0.000	0.000
65	J	91	ASN	0	-0.043	-0.029	59.554	0.000	0.000	0.000	0.000	0.000	0.000
66	J	92	ASP	-1	-0.888	-0.937	60.571	-0.007	-0.007	0.000	0.000	0.000	0.000
67	J	93	ARG	1	0.819	0.938	56.768	0.006	0.006	0.000	0.000	0.000	0.000
68	J	94	ILE	0	-0.011	-0.028	56.045	0.000	0.000	0.000	0.000	0.000	0.000
69	J	95	PHE	0	-0.012	0.005	52.822	0.000	0.000	0.000	0.000	0.000	0.000
70	J	96	SER	0	0.048	0.046	51.592	-0.001	-0.001	0.000	0.000	0.000	0.000
71	J	97	LEU	0	-0.075	-0.039	51.277	-0.001	-0.001	0.000	0.000	0.000	0.000
72	J	98	SER	0	-0.090	-0.060	49.831	-0.001	-0.001	0.000	0.000	0.000	0.000
73	J	99	SER	0	-0.020	-0.003	46.276	-0.001	-0.001	0.000	0.000	0.000	0.000
74	J	100	ALA	0	0.019	-0.010	45.759	0.000	0.000	0.000	0.000	0.000	0.000
75	J	101	THR	0	-0.047	-0.019	43.598	0.000	0.000	0.000	0.000	0.000	0.000
76	J	102	TYR	0	-0.018	0.008	46.576	0.000	0.000	0.000	0.000	0.000	0.000

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