FMO DATABASE

FMODB ID: Q139Y

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	OptAll
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	-398568.338837
FMO2-HF: Nuclear repulsion	367526.109135
FMO2-HF: Total energy	-31042.229703
FMO2-MP2: Total energy	-31133.365764

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.
-3.341	-0.213	0.036	-1.195	-1.968	-0.001

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 : 0.016

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	F	3	ASP	-1	-0.799	-0.897	3.584	-1.292	0.335	0.006	-0.660	-0.972	0.001
4	F	4	GLU	-1	-0.910	-0.923	3.437	-3.128	-1.627	0.030	-0.535	-0.996	-0.002
5	F	5	LEU	0	0.003	-0.001	4.921	0.604	0.604	0.000	0.000	0.000	0.000
6	F	6	LYS	1	0.819	0.890	6.877	-0.033	-0.033	0.000	0.000	0.000	0.000
7	F	7	SER	0	0.013	-0.005	7.845	0.194	0.194	0.000	0.000	0.000	0.000
8	F	8	TYR	0	0.026	0.015	9.090	0.117	0.117	0.000	0.000	0.000	0.000
9	F	9	GLU	-1	-0.835	-0.913	10.828	-0.110	-0.110	0.000	0.000	0.000	0.000
10	F	10	ALA	0	-0.033	-0.008	12.646	0.047	0.047	0.000	0.000	0.000	0.000
11	F	11	LEU	0	0.070	0.025	13.131	0.023	0.023	0.000	0.000	0.000	0.000
12	F	12	LYS	1	0.783	0.887	13.559	0.253	0.253	0.000	0.000	0.000	0.000
13	F	13	ALA	0	-0.077	-0.039	16.951	0.022	0.022	0.000	0.000	0.000	0.000
14	F	14	GLU	-1	-0.906	-0.954	18.215	-0.075	-0.075	0.000	0.000	0.000	0.000
15	F	15	LEU	0	0.005	0.020	19.364	0.009	0.009	0.000	0.000	0.000	0.000
16	F	16	LYS	1	0.909	0.950	18.609	0.081	0.081	0.000	0.000	0.000	0.000
17	F	17	LYS	1	0.962	0.986	22.984	0.015	0.015	0.000	0.000	0.000	0.000
18	F	18	SER	0	0.013	-0.012	23.122	0.002	0.002	0.000	0.000	0.000	0.000
19	F	19	LEU	0	-0.033	-0.018	24.334	0.001	0.001	0.000	0.000	0.000	0.000
20	F	20	GLN	0	-0.076	-0.043	27.112	-0.001	-0.001	0.000	0.000	0.000	0.000
21	F	21	ASP	-1	-0.865	-0.928	28.832	-0.030	-0.030	0.000	0.000	0.000	0.000
22	F	22	ARG	1	0.823	0.891	29.127	0.065	0.065	0.000	0.000	0.000	0.000
23	F	23	ARG	1	0.754	0.853	31.332	0.036	0.036	0.000	0.000	0.000	0.000
24	F	24	GLU	-1	-0.848	-0.907	33.316	-0.015	-0.015	0.000	0.000	0.000	0.000
25	F	25	GLN	0	-0.060	-0.050	33.416	0.004	0.004	0.000	0.000	0.000	0.000
26	F	26	GLU	-1	-0.824	-0.881	33.616	-0.049	-0.049	0.000	0.000	0.000	0.000
27	F	27	ASP	-1	-0.779	-0.865	37.478	-0.026	-0.026	0.000	0.000	0.000	0.000
28	F	28	THR	0	-0.018	-0.004	38.801	0.003	0.003	0.000	0.000	0.000	0.000
29	F	29	PHE	0	-0.069	-0.024	40.145	0.002	0.002	0.000	0.000	0.000	0.000
30	F	30	ASP	-1	-0.881	-0.951	41.168	-0.030	-0.030	0.000	0.000	0.000	0.000
31	F	31	ASN	0	-0.091	-0.059	43.036	0.003	0.003	0.000	0.000	0.000	0.000
32	F	32	LEU	0	-0.007	-0.005	43.075	0.001	0.001	0.000	0.000	0.000	0.000
33	F	33	GLN	0	-0.002	-0.003	46.223	0.001	0.001	0.000	0.000	0.000	0.000
34	F	34	GLN	0	-0.051	-0.028	48.081	-0.001	-0.001	0.000	0.000	0.000	0.000
35	F	35	GLU	-1	-0.847	-0.934	49.625	-0.009	-0.009	0.000	0.000	0.000	0.000
36	F	36	ILE	0	-0.047	-0.020	48.361	0.001	0.001	0.000	0.000	0.000	0.000
37	F	37	TYR	0	0.003	0.016	52.170	0.001	0.001	0.000	0.000	0.000	0.000
38	F	38	ASP	-1	-0.815	-0.894	54.211	-0.012	-0.012	0.000	0.000	0.000	0.000
39	F	39	LYS	1	0.792	0.885	54.434	0.008	0.008	0.000	0.000	0.000	0.000
40	F	40	GLU	-1	-0.772	-0.864	56.071	-0.016	-0.016	0.000	0.000	0.000	0.000
41	F	41	THR	0	-0.036	-0.015	58.333	0.000	0.000	0.000	0.000	0.000	0.000
42	F	42	GLU	-1	-0.847	-0.887	58.776	-0.006	-0.006	0.000	0.000	0.000	0.000
43	F	43	TYR	0	-0.083	-0.055	57.362	0.001	0.001	0.000	0.000	0.000	0.000
44	F	44	PHE	0	-0.014	-0.003	58.788	0.000	0.000	0.000	0.000	0.000	0.000
45	F	45	SER	0	-0.089	-0.036	63.541	0.000	0.000	0.000	0.000	0.000	0.000
46	F	65	TYR	0	-0.006	-0.016	68.493	0.000	0.000	0.000	0.000	0.000	0.000
47	F	66	SER	0	-0.026	-0.028	70.810	0.000	0.000	0.000	0.000	0.000	0.000
48	F	67	GLY	0	-0.012	0.010	68.973	-0.001	-0.001	0.000	0.000	0.000	0.000
49	F	68	ASN	0	-0.041	-0.037	64.848	0.000	0.000	0.000	0.000	0.000	0.000
50	F	69	ILE	0	0.034	0.013	58.477	0.000	0.000	0.000	0.000	0.000	0.000
51	F	70	ILE	0	-0.015	0.002	60.289	0.000	0.000	0.000	0.000	0.000	0.000
52	F	71	LYS	1	0.826	0.909	63.482	0.010	0.010	0.000	0.000	0.000	0.000
53	F	72	GLY	0	0.022	0.036	66.155	0.000	0.000	0.000	0.000	0.000	0.000
54	F	73	PHE	0	0.013	-0.006	62.297	0.000	0.000	0.000	0.000	0.000	0.000
55	F	74	ASP	-1	-0.875	-0.926	68.219	-0.005	-0.005	0.000	0.000	0.000	0.000
56	F	75	THR	0	-0.012	-0.014	71.747	0.000	0.000	0.000	0.000	0.000	0.000
57	F	76	PHE	0	-0.036	-0.008	72.362	0.000	0.000	0.000	0.000	0.000	0.000
58	F	77	SER	0	-0.020	-0.002	77.172	0.000	0.000	0.000	0.000	0.000	0.000
59	F	86	SER	0	0.012	-0.005	70.238	0.000	0.000	0.000	0.000	0.000	0.000
60	F	87	ALA	0	0.014	0.005	69.613	0.001	0.001	0.000	0.000	0.000	0.000
61	F	88	PHE	0	0.062	0.033	60.331	0.000	0.000	0.000	0.000	0.000	0.000
62	F	89	ASN	0	-0.075	-0.036	64.532	0.000	0.000	0.000	0.000	0.000	0.000
63	F	90	ASN	0	0.059	0.012	59.755	0.000	0.000	0.000	0.000	0.000	0.000
64	F	91	ASN	0	-0.014	-0.014	59.418	-0.001	-0.001	0.000	0.000	0.000	0.000
65	F	92	ASP	-1	-0.810	-0.899	60.395	-0.014	-0.014	0.000	0.000	0.000	0.000
66	F	93	ARG	1	0.782	0.893	56.885	0.015	0.015	0.000	0.000	0.000	0.000
67	F	94	ILE	0	-0.004	-0.023	56.155	-0.001	-0.001	0.000	0.000	0.000	0.000
68	F	95	PHE	0	-0.028	-0.003	53.225	0.000	0.000	0.000	0.000	0.000	0.000
69	F	96	SER	0	0.034	0.001	51.860	-0.001	-0.001	0.000	0.000	0.000	0.000
70	F	97	LEU	0	-0.066	-0.038	51.475	-0.002	-0.002	0.000	0.000	0.000	0.000
71	F	98	SER	0	-0.103	-0.043	50.133	-0.001	-0.001	0.000	0.000	0.000	0.000
72	F	99	SER	0	0.002	0.007	46.707	-0.002	-0.002	0.000	0.000	0.000	0.000
73	F	100	ALA	0	0.010	-0.008	45.890	0.000	0.000	0.000	0.000	0.000	0.000
74	F	101	THR	0	-0.043	-0.017	44.293	-0.001	-0.001	0.000	0.000	0.000	0.000
75	F	102	TYR	0	-0.027	-0.006	46.908	0.001	0.001	0.000	0.000	0.000	0.000

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