FMO DATABASE

FMODB ID: K3613

Calculation Name: 5J9U-B-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9U

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-442989.247473
FMO2-HF: Nuclear repulsion	410151.138806
FMO2-HF: Total energy	-32838.108667
FMO2-MP2: Total energy	-32934.708956

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.
-2.84	1.434	0.08	-1.561	-2.79	-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 : 0.073 / q_NPA : 0.016

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	-0.887	-0.946	2.878	-4.100	-1.026	0.056	-1.337	-1.792	-0.002
4	B	4	GLU	-1	-0.912	-0.945	3.340	0.808	1.887	0.025	-0.213	-0.890	0.000
5	B	5	LEU	0	-0.015	-0.006	5.054	0.346	0.467	-0.001	-0.011	-0.108	0.000
6	B	6	LYS	1	0.940	0.957	6.959	-0.224	-0.224	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.026	0.012	7.980	0.135	0.135	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.008	0.011	9.226	0.080	0.080	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.916	-0.974	11.140	0.023	0.023	0.000	0.000	0.000	0.000
10	B	10	ALA	0	-0.008	0.007	12.685	0.026	0.026	0.000	0.000	0.000	0.000
11	B	11	LEU	0	0.053	0.019	12.603	0.012	0.012	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.855	0.948	14.226	0.064	0.064	0.000	0.000	0.000	0.000
13	B	13	ALA	0	-0.019	-0.009	17.086	0.009	0.009	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.930	-0.975	18.065	-0.024	-0.024	0.000	0.000	0.000	0.000
15	B	15	LEU	0	-0.003	0.004	19.428	0.002	0.002	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.882	0.933	21.015	0.012	0.012	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.997	0.999	23.182	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	18	SER	0	0.029	0.020	23.740	0.001	0.001	0.000	0.000	0.000	0.000
19	B	19	LEU	0	-0.056	-0.032	24.481	0.000	0.000	0.000	0.000	0.000	0.000
20	B	20	GLN	0	-0.061	-0.022	27.050	0.000	0.000	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.851	-0.932	28.676	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	22	ARG	1	0.915	0.973	28.543	0.022	0.022	0.000	0.000	0.000	0.000
23	B	23	ARG	1	0.888	0.948	31.322	0.008	0.008	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.860	-0.940	32.841	0.001	0.001	0.000	0.000	0.000	0.000
25	B	25	GLN	0	-0.025	-0.010	33.909	0.000	0.000	0.000	0.000	0.000	0.000
26	B	26	GLU	-1	-0.960	-0.992	34.268	-0.015	-0.015	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.859	-0.918	37.574	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.100	-0.062	38.632	0.001	0.001	0.000	0.000	0.000	0.000
29	B	29	PHE	0	-0.062	-0.032	40.134	0.000	0.000	0.000	0.000	0.000	0.000
30	B	30	ASP	-1	-0.912	-0.961	41.732	-0.009	-0.009	0.000	0.000	0.000	0.000
31	B	31	ASN	0	-0.030	-0.015	43.867	0.000	0.000	0.000	0.000	0.000	0.000
32	B	32	LEU	0	-0.008	0.006	43.188	0.000	0.000	0.000	0.000	0.000	0.000
33	B	33	GLN	0	0.039	0.010	45.792	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	34	GLN	0	-0.028	0.002	48.186	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.882	-0.946	49.636	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.059	-0.037	48.614	0.000	0.000	0.000	0.000	0.000	0.000
37	B	37	TYR	0	-0.020	-0.001	52.331	0.000	0.000	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.846	-0.941	54.229	-0.003	-0.003	0.000	0.000	0.000	0.000
39	B	39	LYS	1	0.868	0.940	54.420	0.001	0.001	0.000	0.000	0.000	0.000
40	B	40	GLU	-1	-0.802	-0.894	55.887	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.049	-0.023	58.463	0.000	0.000	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.927	-0.954	59.188	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.042	-0.015	57.592	0.000	0.000	0.000	0.000	0.000	0.000
44	B	44	PHE	0	-0.022	-0.018	59.482	0.000	0.000	0.000	0.000	0.000	0.000
45	B	45	SER	0	-0.043	-0.021	64.181	0.000	0.000	0.000	0.000	0.000	0.000
46	B	46	HIS	0	-0.006	0.013	66.175	0.000	0.000	0.000	0.000	0.000	0.000
47	B	65	TYR	0	-0.019	-0.022	69.094	0.000	0.000	0.000	0.000	0.000	0.000
48	B	66	SER	0	0.005	-0.001	70.828	0.000	0.000	0.000	0.000	0.000	0.000
49	B	67	GLY	0	0.024	0.036	69.016	0.000	0.000	0.000	0.000	0.000	0.000
50	B	68	ASN	0	-0.118	-0.066	64.116	0.000	0.000	0.000	0.000	0.000	0.000
51	B	69	ILE	0	0.069	0.028	58.823	0.000	0.000	0.000	0.000	0.000	0.000
52	B	70	ILE	0	-0.019	0.000	60.246	0.000	0.000	0.000	0.000	0.000	0.000
53	B	71	LYS	1	0.911	0.969	63.417	0.004	0.004	0.000	0.000	0.000	0.000
54	B	72	GLY	0	0.042	0.031	66.584	0.000	0.000	0.000	0.000	0.000	0.000
55	B	73	PHE	0	0.018	-0.006	62.740	0.000	0.000	0.000	0.000	0.000	0.000
56	B	74	ASP	-1	-0.966	-0.974	68.597	-0.003	-0.003	0.000	0.000	0.000	0.000
57	B	75	THR	0	-0.017	-0.014	71.801	0.000	0.000	0.000	0.000	0.000	0.000
58	B	76	PHE	0	-0.002	0.009	73.029	0.000	0.000	0.000	0.000	0.000	0.000
59	B	86	SER	0	-0.039	-0.050	70.417	0.000	0.000	0.000	0.000	0.000	0.000
60	B	87	ALA	0	0.041	0.009	69.758	0.000	0.000	0.000	0.000	0.000	0.000
61	B	88	PHE	0	-0.025	0.011	60.529	0.000	0.000	0.000	0.000	0.000	0.000
62	B	89	ASN	0	0.051	0.026	64.862	0.000	0.000	0.000	0.000	0.000	0.000
63	B	90	ASN	0	0.077	0.033	59.739	0.000	0.000	0.000	0.000	0.000	0.000
64	B	91	ASN	0	-0.033	-0.026	59.541	0.000	0.000	0.000	0.000	0.000	0.000
65	B	92	ASP	-1	-0.888	-0.947	60.707	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	93	ARG	1	0.782	0.911	56.917	0.005	0.005	0.000	0.000	0.000	0.000
67	B	94	ILE	0	-0.008	-0.028	56.233	0.000	0.000	0.000	0.000	0.000	0.000
68	B	95	PHE	0	-0.010	0.001	53.162	0.000	0.000	0.000	0.000	0.000	0.000
69	B	96	SER	0	0.041	0.026	51.834	0.000	0.000	0.000	0.000	0.000	0.000
70	B	97	LEU	0	-0.086	-0.040	51.442	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	98	SER	0	-0.084	-0.054	50.038	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	99	SER	0	0.015	0.009	46.439	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	100	ALA	0	0.048	0.004	46.011	0.000	0.000	0.000	0.000	0.000	0.000
74	B	101	THR	0	-0.059	-0.043	43.755	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	102	TYR	0	0.080	0.046	46.604	0.000	0.000	0.000	0.000	0.000	0.000
76	B	103	VAL	0	-0.032	-0.012	50.110	0.000	0.000	0.000	0.000	0.000	0.000
77	B	104	LYS	1	0.883	0.935	44.182	0.016	0.016	0.000	0.000	0.000	0.000
78	B	105	GLN	0	-0.019	0.012	49.308	0.000	0.000	0.000	0.000	0.000	0.000
79	B	106	GLN	0	-0.025	0.005	50.986	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)