FMO DATABASE

FMODB ID: YN3J2

Calculation Name: 5J9T-B-Xray540

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

Ligand 3-letter code: ALY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5J9T

Chain ID: B

ChEMBL ID:

UniProt ID: P47128

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-423286.502128
FMO2-HF: Nuclear repulsion	391510.05772
FMO2-HF: Total energy	-31776.444408
FMO2-MP2: Total energy	-31869.434013

3D Structure Molmil

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.
-7.467	-4.219	0.114	-1.5	-1.862	0.005

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 : 0.152 / q_NPA : 0.014

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

Sort

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].
4	B	2	THR	0	-0.014	0.083	3.592	-0.841	-0.450	0.001	-0.163	-0.229	0.000
5	B	3	ASP	0	0.038	-0.114	3.522	-4.787	-2.759	0.028	-1.093	-0.963	0.004
6	B	3	ASP	-1	-0.922	-0.799	4.308	4.932	5.063	-0.001	-0.014	-0.116	0.000
7	B	4	GLU	0	0.104	-0.152	3.066	-0.723	-0.369	0.051	-0.115	-0.290	0.001
8	B	4	GLU	-1	-0.992	-0.812	3.484	-3.316	-3.031	0.037	-0.095	-0.227	0.000
9	B	5	LEU	0	0.065	-0.116	4.689	-0.328	-0.269	-0.002	-0.020	-0.037	0.000
10	B	5	LEU	0	-0.094	0.113	5.933	-0.066	-0.066	0.000	0.000	0.000	0.000
11	B	6	LYS	0	0.109	-0.093	6.780	-0.164	-0.164	0.000	0.000	0.000	0.000
12	B	6	LYS	1	0.785	1.026	7.997	-2.102	-2.102	0.000	0.000	0.000	0.000
13	B	7	SER	0	0.005	-0.099	7.942	-0.122	-0.122	0.000	0.000	0.000	0.000
14	B	7	SER	0	-0.027	0.084	7.663	-0.004	-0.004	0.000	0.000	0.000	0.000
15	B	8	TYR	0	0.118	-0.076	9.045	0.007	0.007	0.000	0.000	0.000	0.000
16	B	8	TYR	0	-0.081	0.100	9.613	-0.046	-0.046	0.000	0.000	0.000	0.000
17	B	9	GLU	0	0.033	-0.138	10.868	-0.052	-0.052	0.000	0.000	0.000	0.000
18	B	9	GLU	-1	-0.886	-0.786	11.191	-0.206	-0.206	0.000	0.000	0.000	0.000
19	B	10	ALA	0	0.090	-0.100	12.427	-0.046	-0.046	0.000	0.000	0.000	0.000
20	B	10	ALA	0	-0.074	0.109	13.127	0.027	0.027	0.000	0.000	0.000	0.000
21	B	11	LEU	0	0.054	-0.114	13.611	0.008	0.008	0.000	0.000	0.000	0.000
22	B	11	LEU	0	-0.066	0.117	13.067	-0.013	-0.013	0.000	0.000	0.000	0.000
23	B	12	LYS	0	0.108	-0.107	15.271	-0.020	-0.020	0.000	0.000	0.000	0.000
24	B	12	LYS	1	0.714	0.992	14.034	0.247	0.247	0.000	0.000	0.000	0.000
25	B	13	ALA	0	0.004	-0.118	17.198	-0.032	-0.032	0.000	0.000	0.000	0.000
26	B	13	ALA	0	-0.042	0.111	18.182	0.008	0.008	0.000	0.000	0.000	0.000
27	B	14	GLU	0	0.087	-0.143	18.295	-0.010	-0.010	0.000	0.000	0.000	0.000
28	B	14	GLU	-1	-1.004	-0.818	18.340	0.216	0.216	0.000	0.000	0.000	0.000
29	B	15	LEU	0	0.120	-0.091	19.481	0.007	0.007	0.000	0.000	0.000	0.000
30	B	15	LEU	0	-0.084	0.112	19.562	-0.007	-0.007	0.000	0.000	0.000	0.000
31	B	16	LYS	0	0.073	-0.109	21.190	-0.011	-0.011	0.000	0.000	0.000	0.000
32	B	16	LYS	1	0.864	1.060	20.728	0.042	0.042	0.000	0.000	0.000	0.000
33	B	17	LYS	0	0.077	-0.070	22.934	-0.009	-0.009	0.000	0.000	0.000	0.000
34	B	17	LYS	1	0.868	1.070	23.285	-0.152	-0.152	0.000	0.000	0.000	0.000
35	B	18	SER	0	0.047	-0.072	23.885	0.003	0.003	0.000	0.000	0.000	0.000
36	B	18	SER	0	-0.043	0.069	22.871	-0.008	-0.008	0.000	0.000	0.000	0.000
37	B	19	LEU	0	0.021	-0.125	25.270	0.000	0.000	0.000	0.000	0.000	0.000
38	B	19	LEU	0	-0.105	0.080	24.850	-0.004	-0.004	0.000	0.000	0.000	0.000
39	B	20	GLN	0	0.118	-0.076	27.135	-0.008	-0.008	0.000	0.000	0.000	0.000
40	B	20	GLN	0	-0.075	0.107	28.296	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	21	ASP	0	0.114	-0.077	28.662	-0.004	-0.004	0.000	0.000	0.000	0.000
42	B	21	ASP	-1	-0.980	-0.834	28.993	0.059	0.059	0.000	0.000	0.000	0.000
43	B	22	ARG	0	0.131	-0.066	29.738	0.001	0.001	0.000	0.000	0.000	0.000
44	B	22	ARG	1	0.710	0.964	29.352	0.021	0.021	0.000	0.000	0.000	0.000
45	B	23	ARG	0	0.129	-0.074	31.540	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	23	ARG	1	0.703	0.958	32.634	-0.014	-0.014	0.000	0.000	0.000	0.000
47	B	24	GLU	0	0.105	-0.078	33.303	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	24	GLU	-1	-0.981	-0.825	33.579	0.044	0.044	0.000	0.000	0.000	0.000
49	B	25	GLN	0	0.012	-0.144	34.364	0.001	0.001	0.000	0.000	0.000	0.000
50	B	25	GLN	0	-0.095	0.048	32.815	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	26	GLU	0	0.053	-0.099	35.738	0.001	0.001	0.000	0.000	0.000	0.000
52	B	26	GLU	-1	-0.912	-0.794	34.174	-0.017	-0.017	0.000	0.000	0.000	0.000
53	B	27	ASP	0	0.124	-0.085	37.604	-0.003	-0.003	0.000	0.000	0.000	0.000
54	B	27	ASP	-1	-0.974	-0.836	37.756	0.005	0.005	0.000	0.000	0.000	0.000
55	B	28	THR	0	0.042	-0.063	39.136	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	28	THR	0	-0.041	0.070	38.805	0.002	0.002	0.000	0.000	0.000	0.000
57	B	29	PHE	0	0.052	-0.089	40.224	0.002	0.002	0.000	0.000	0.000	0.000
58	B	29	PHE	0	-0.104	0.068	40.173	0.000	0.000	0.000	0.000	0.000	0.000
59	B	30	ASP	0	0.085	-0.126	41.853	0.001	0.001	0.000	0.000	0.000	0.000
60	B	30	ASP	-1	-0.991	-0.827	42.806	-0.006	-0.006	0.000	0.000	0.000	0.000
61	B	31	ASN	0	0.072	-0.069	43.859	-0.002	-0.002	0.000	0.000	0.000	0.000
62	B	31	ASN	0	-0.156	0.022	43.185	0.000	0.000	0.000	0.000	0.000	0.000
63	B	32	LEU	0	0.138	-0.081	44.873	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	32	LEU	0	-0.097	0.099	43.037	0.001	0.001	0.000	0.000	0.000	0.000
65	B	33	GLN	0	0.108	-0.084	46.113	0.001	0.001	0.000	0.000	0.000	0.000
66	B	33	GLN	0	-0.055	0.117	45.057	0.000	0.000	0.000	0.000	0.000	0.000
67	B	34	GLN	0	0.069	-0.096	47.983	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	34	GLN	0	-0.132	0.062	49.174	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	35	GLU	0	0.095	-0.106	49.306	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	35	GLU	-1	-1.022	-0.867	49.349	0.019	0.019	0.000	0.000	0.000	0.000
71	B	36	ILE	0	0.037	-0.099	50.387	0.001	0.001	0.000	0.000	0.000	0.000
72	B	36	ILE	0	-0.102	0.077	48.516	0.000	0.000	0.000	0.000	0.000	0.000
73	B	37	TYR	0	0.128	-0.091	52.141	0.001	0.001	0.000	0.000	0.000	0.000
74	B	37	TYR	0	-0.116	0.089	53.179	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	38	ASP	0	0.140	-0.102	54.018	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	38	ASP	-1	-0.932	-0.785	54.283	0.006	0.006	0.000	0.000	0.000	0.000
77	B	39	LYS	0	0.030	-0.144	54.990	0.000	0.000	0.000	0.000	0.000	0.000
78	B	39	LYS	1	0.752	1.014	53.853	-0.017	-0.017	0.000	0.000	0.000	0.000
79	B	40	GLU	0	0.043	-0.103	56.424	0.001	0.001	0.000	0.000	0.000	0.000
80	B	40	GLU	-1	-0.808	-0.755	55.813	0.006	0.006	0.000	0.000	0.000	0.000
81	B	41	THR	0	-0.034	-0.089	58.321	0.000	0.000	0.000	0.000	0.000	0.000
82	B	41	THR	0	-0.020	0.080	58.408	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	42	GLU	0	0.121	-0.084	59.687	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	42	GLU	-1	-0.924	-0.799	58.901	0.016	0.016	0.000	0.000	0.000	0.000
85	B	43	TYR	0	0.008	-0.125	60.555	0.000	0.000	0.000	0.000	0.000	0.000
86	B	43	TYR	0	-0.088	0.096	57.051	0.001	0.001	0.000	0.000	0.000	0.000
87	B	44	PHE	0	-0.036	-0.097	62.133	0.000	0.000	0.000	0.000	0.000	0.000
88	B	44	PHE	0	-0.057	0.079	58.750	0.000	0.000	0.000	0.000	0.000	0.000
89	B	45	SER	0	-0.078	-0.177	63.867	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	45	SER	0	0.040	0.034	63.915	-0.001	-0.001	0.000	0.000	0.000	0.000
91	B	66	SER	0	0.066	0.024	71.742	0.000	0.000	0.000	0.000	0.000	0.000
92	B	66	SER	0	-0.079	0.026	71.402	0.000	0.000	0.000	0.000	0.000	0.000
93	B	67	GLY	0	0.016	-0.067	69.364	-0.001	-0.001	0.000	0.000	0.000	0.000
94	B	68	ASN	0	0.037	0.018	65.396	0.001	0.001	0.000	0.000	0.000	0.000
95	B	68	ASN	0	-0.105	0.045	64.609	-0.001	-0.001	0.000	0.000	0.000	0.000
96	B	69	ILE	0	0.130	-0.072	61.267	0.000	0.000	0.000	0.000	0.000	0.000
97	B	69	ILE	0	-0.050	0.117	59.314	0.000	0.000	0.000	0.000	0.000	0.000
98	B	70	ILE	0	0.047	-0.110	62.122	0.000	0.000	0.000	0.000	0.000	0.000
99	B	70	ILE	0	-0.069	0.108	59.979	0.000	0.000	0.000	0.000	0.000	0.000
100	B	71	LYS	0	0.108	-0.091	63.291	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	71	LYS	1	0.821	1.049	66.649	-0.008	-0.008	0.000	0.000	0.000	0.000
102	B	72	GLY	0	0.014	-0.081	66.275	0.000	0.000	0.000	0.000	0.000	0.000
103	B	73	PHE	0	0.032	-0.013	67.661	0.000	0.000	0.000	0.000	0.000	0.000
104	B	73	PHE	0	-0.089	0.087	62.750	0.000	0.000	0.000	0.000	0.000	0.000
105	B	74	ASP	0	-0.031	-0.111	68.724	0.000	0.000	0.000	0.000	0.000	0.000
106	B	74	ASP	-1	-0.881	-0.937	72.010	0.013	0.013	0.000	0.000	0.000	0.000
107	B	87	ALA	0	0.121	0.006	70.316	0.001	0.001	0.000	0.000	0.000	0.000
108	B	87	ALA	0	-0.144	0.077	71.013	0.000	0.000	0.000	0.000	0.000	0.000
109	B	88	PHE	0	0.112	-0.092	65.820	0.000	0.000	0.000	0.000	0.000	0.000
110	B	88	PHE	0	-0.053	0.114	60.461	0.000	0.000	0.000	0.000	0.000	0.000
111	B	89	ASN	0	0.096	-0.091	64.436	-0.001	-0.001	0.000	0.000	0.000	0.000
112	B	89	ASN	0	-0.073	0.102	64.856	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	90	ASN	0	0.139	-0.043	60.985	0.001	0.001	0.000	0.000	0.000	0.000
114	B	90	ASN	0	-0.091	0.078	60.349	0.001	0.001	0.000	0.000	0.000	0.000
115	B	91	ASN	0	0.067	-0.096	59.810	0.000	0.000	0.000	0.000	0.000	0.000
116	B	91	ASN	0	-0.138	0.035	62.142	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	92	ASP	0	0.121	-0.096	61.267	0.000	0.000	0.000	0.000	0.000	0.000
118	B	92	ASP	-1	-1.013	-0.860	63.284	0.003	0.003	0.000	0.000	0.000	0.000
119	B	93	ARG	0	0.091	-0.068	58.473	0.002	0.002	0.000	0.000	0.000	0.000
120	B	93	ARG	1	0.682	0.997	56.850	-0.003	-0.003	0.000	0.000	0.000	0.000
121	B	94	ILE	0	0.059	-0.149	56.677	-0.001	-0.001	0.000	0.000	0.000	0.000
122	B	94	ILE	0	-0.081	0.107	56.874	0.000	0.000	0.000	0.000	0.000	0.000
123	B	95	PHE	0	0.094	-0.070	53.603	0.000	0.000	0.000	0.000	0.000	0.000
124	B	95	PHE	0	-0.105	0.069	53.065	0.001	0.001	0.000	0.000	0.000	0.000
125	B	96	SER	0	0.067	-0.094	51.861	0.001	0.001	0.000	0.000	0.000	0.000
126	B	96	SER	0	-0.046	0.052	53.130	0.000	0.000	0.000	0.000	0.000	0.000
127	B	97	LEU	0	0.044	-0.096	51.636	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	97	LEU	0	-0.090	0.099	55.160	0.000	0.000	0.000	0.000	0.000	0.000
129	B	98	SER	0	-0.021	-0.111	51.076	-0.002	-0.002	0.000	0.000	0.000	0.000
130	B	98	SER	0	-0.061	0.068	50.453	0.001	0.001	0.000	0.000	0.000	0.000
131	B	99	SER	0	0.049	-0.091	47.665	0.001	0.001	0.000	0.000	0.000	0.000
132	B	99	SER	0	-0.061	0.055	47.218	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	100	ALA	0	0.122	-0.096	47.152	-0.001	-0.001	0.000	0.000	0.000	0.000
134	B	100	ALA	0	-0.074	0.115	46.319	0.000	0.000	0.000	0.000	0.000	0.000
135	B	101	THR	0	-0.077	-0.138	45.662	-0.003	-0.003	0.000	0.000	0.000	0.000
136	B	101	THR	0	0.007	0.091	43.523	0.000	0.000	0.000	0.000	0.000	0.000
137	B	102	TYR	0	0.121	-0.080	46.872	-0.003	-0.003	0.000	0.000	0.000	0.000
138	B	102	TYR	0	-0.040	0.136	49.950	0.001	0.001	0.000	0.000	0.000	0.000
139	B	103	VAL	0	0.093	-0.086	50.072	-0.001	-0.001	0.000	0.000	0.000	0.000
140	B	103	VAL	0	-0.095	0.108	51.163	0.000	0.000	0.000	0.000	0.000	0.000
141	B	104	LYS	0	0.112	-0.067	48.994	-0.001	-0.001	0.000	0.000	0.000	0.000
142	B	104	LYS	1	0.844	1.039	44.406	0.025	0.025	0.000	0.000	0.000	0.000
143	B	105	GLN	0	0.021	-0.140	50.046	-0.003	-0.003	0.000	0.000	0.000	0.000
144	B	105	GLN	0	-0.060	0.108	47.760	0.000	0.000	0.000	0.000	0.000	0.000
145	B	106	GLN	0	0.093	-0.087	50.944	-0.001	-0.001	0.000	0.000	0.000	0.000
146	B	106	GLN	0	-0.114	0.097	54.333	0.000	0.000	0.000	0.000	0.000	0.000
147	B	107	HIS	0	0.024	-0.107	53.712	0.000	0.000	0.000	0.000	0.000	0.000
148	B	107	HIS	0	-0.113	0.076	53.500	0.000	0.000	0.000	0.000	0.000	0.000
149	B	108	GLY	0	0.001	-0.103	53.345	-0.001	-0.001	0.000	0.000	0.000	0.000
150	B	109	GLN	0	-0.082	-0.023	54.240	-0.001	-0.001	0.000	0.000	0.000	0.000
151	B	109	GLN	0	0.022	0.012	52.838	-0.001	-0.001	0.000	0.000	0.000	0.000

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