FMO DATABASE

FMODB ID: GY1J1

Calculation Name: 5J9U-J-Xray540

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: 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	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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-409984.340657
FMO2-HF: Nuclear repulsion	378488.29113
FMO2-HF: Total energy	-31496.049527
FMO2-MP2: Total energy	-31588.20047

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.
-3.426	-1.14	0.031	-0.955	-1.363	0.002

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 : 0.120 / q_NPA : -0.004

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	J	2	THR	0	-0.015	0.061	4.314	1.410	1.691	0.000	-0.101	-0.180	0.000
5	J	3	ASP	0	0.117	-0.068	3.557	-1.939	-0.661	0.022	-0.648	-0.652	0.002
6	J	3	ASP	-1	-0.883	-0.797	4.330	0.935	1.039	-0.001	-0.011	-0.093	0.000
7	J	4	GLU	0	0.138	-0.104	3.417	0.696	1.064	0.009	-0.148	-0.229	0.000
8	J	4	GLU	-1	-0.995	-0.824	3.889	-5.146	-4.945	0.003	-0.039	-0.165	0.000
9	J	5	LEU	0	0.092	-0.103	5.032	0.388	0.442	-0.002	-0.008	-0.044	0.000
10	J	5	LEU	0	-0.093	0.104	6.276	-0.010	-0.010	0.000	0.000	0.000	0.000
11	J	6	LYS	0	0.095	-0.091	6.865	0.236	0.236	0.000	0.000	0.000	0.000
12	J	6	LYS	1	0.717	0.982	7.649	-0.576	-0.576	0.000	0.000	0.000	0.000
13	J	7	SER	0	0.021	-0.095	7.963	0.166	0.166	0.000	0.000	0.000	0.000
14	J	7	SER	0	-0.034	0.070	7.723	0.051	0.051	0.000	0.000	0.000	0.000
15	J	8	TYR	0	0.108	-0.058	9.299	0.158	0.158	0.000	0.000	0.000	0.000
16	J	8	TYR	0	-0.105	0.087	9.825	-0.002	-0.002	0.000	0.000	0.000	0.000
17	J	9	GLU	0	0.034	-0.137	11.079	0.053	0.053	0.000	0.000	0.000	0.000
18	J	9	GLU	-1	-0.897	-0.807	11.183	-0.380	-0.380	0.000	0.000	0.000	0.000
19	J	10	ALA	0	0.126	-0.084	12.509	0.052	0.052	0.000	0.000	0.000	0.000
20	J	10	ALA	0	-0.088	0.104	12.981	0.010	0.010	0.000	0.000	0.000	0.000
21	J	11	LEU	0	0.078	-0.107	13.689	0.067	0.067	0.000	0.000	0.000	0.000
22	J	11	LEU	0	-0.069	0.107	12.640	-0.015	-0.015	0.000	0.000	0.000	0.000
23	J	12	LYS	0	0.082	-0.093	15.358	0.026	0.026	0.000	0.000	0.000	0.000
24	J	12	LYS	1	0.705	0.983	14.094	0.418	0.418	0.000	0.000	0.000	0.000
25	J	13	ALA	0	0.042	-0.099	17.210	0.015	0.015	0.000	0.000	0.000	0.000
26	J	13	ALA	0	-0.075	0.094	18.066	0.007	0.007	0.000	0.000	0.000	0.000
27	J	14	GLU	0	0.084	-0.135	18.275	0.026	0.026	0.000	0.000	0.000	0.000
28	J	14	GLU	-1	-1.019	-0.833	18.026	-0.151	-0.151	0.000	0.000	0.000	0.000
29	J	15	LEU	0	0.144	-0.092	19.405	0.026	0.026	0.000	0.000	0.000	0.000
30	J	15	LEU	0	-0.103	0.105	19.730	-0.007	-0.007	0.000	0.000	0.000	0.000
31	J	16	LYS	0	0.058	-0.104	21.265	0.009	0.009	0.000	0.000	0.000	0.000
32	J	16	LYS	1	0.853	1.048	21.621	0.152	0.152	0.000	0.000	0.000	0.000
33	J	17	LYS	0	0.100	-0.055	22.928	0.010	0.010	0.000	0.000	0.000	0.000
34	J	17	LYS	1	0.852	1.052	23.229	0.051	0.051	0.000	0.000	0.000	0.000
35	J	18	SER	0	0.039	-0.069	23.839	0.016	0.016	0.000	0.000	0.000	0.000
36	J	18	SER	0	-0.022	0.069	23.918	-0.007	-0.007	0.000	0.000	0.000	0.000
37	J	19	LEU	0	0.046	-0.108	25.390	0.009	0.009	0.000	0.000	0.000	0.000
38	J	19	LEU	0	-0.115	0.070	25.044	-0.003	-0.003	0.000	0.000	0.000	0.000
39	J	20	GLN	0	0.122	-0.047	27.372	0.002	0.002	0.000	0.000	0.000	0.000
40	J	20	GLN	0	-0.178	0.024	28.447	-0.005	-0.005	0.000	0.000	0.000	0.000
41	J	21	ASP	0	0.127	-0.087	28.901	0.006	0.006	0.000	0.000	0.000	0.000
42	J	21	ASP	-1	-0.984	-0.843	28.901	-0.073	-0.073	0.000	0.000	0.000	0.000
43	J	22	ARG	0	0.122	-0.069	29.585	0.007	0.007	0.000	0.000	0.000	0.000
44	J	22	ARG	1	0.676	0.954	29.124	0.108	0.108	0.000	0.000	0.000	0.000
45	J	23	ARG	0	0.062	-0.089	31.169	0.001	0.001	0.000	0.000	0.000	0.000
46	J	23	ARG	1	0.656	0.929	32.961	0.066	0.066	0.000	0.000	0.000	0.000
47	J	24	GLU	0	0.097	-0.097	33.367	0.003	0.003	0.000	0.000	0.000	0.000
48	J	24	GLU	-1	-0.928	-0.808	33.418	-0.049	-0.049	0.000	0.000	0.000	0.000
49	J	25	GLN	0	0.074	-0.091	34.415	0.007	0.007	0.000	0.000	0.000	0.000
50	J	25	GLN	0	-0.108	0.051	33.436	0.002	0.002	0.000	0.000	0.000	0.000
51	J	26	GLU	0	0.034	-0.104	35.913	0.004	0.004	0.000	0.000	0.000	0.000
52	J	26	GLU	-1	-0.849	-0.786	34.197	-0.091	-0.091	0.000	0.000	0.000	0.000
53	J	27	ASP	0	0.136	-0.061	37.744	0.002	0.002	0.000	0.000	0.000	0.000
54	J	27	ASP	-1	-0.912	-0.799	37.843	-0.057	-0.057	0.000	0.000	0.000	0.000
55	J	28	THR	0	0.007	-0.080	39.148	0.004	0.004	0.000	0.000	0.000	0.000
56	J	28	THR	0	-0.077	0.060	38.452	0.000	0.000	0.000	0.000	0.000	0.000
57	J	29	PHE	0	0.113	-0.062	40.226	0.005	0.005	0.000	0.000	0.000	0.000
58	J	29	PHE	0	-0.114	0.059	40.448	-0.001	-0.001	0.000	0.000	0.000	0.000
59	J	30	ASP	0	0.065	-0.118	41.861	0.002	0.002	0.000	0.000	0.000	0.000
60	J	30	ASP	-1	-0.967	-0.846	41.543	-0.059	-0.059	0.000	0.000	0.000	0.000
61	J	31	ASN	0	0.072	-0.058	43.798	0.001	0.001	0.000	0.000	0.000	0.000
62	J	31	ASN	0	-0.167	0.013	43.308	0.003	0.003	0.000	0.000	0.000	0.000
63	J	32	LEU	0	0.085	-0.106	44.900	0.003	0.003	0.000	0.000	0.000	0.000
64	J	32	LEU	0	-0.112	0.093	43.671	0.000	0.000	0.000	0.000	0.000	0.000
65	J	33	GLN	0	0.159	-0.088	46.136	0.003	0.003	0.000	0.000	0.000	0.000
66	J	33	GLN	0	-0.131	0.080	46.103	0.000	0.000	0.000	0.000	0.000	0.000
67	J	34	GLN	0	0.062	-0.100	47.891	0.001	0.001	0.000	0.000	0.000	0.000
68	J	34	GLN	0	-0.150	0.055	49.635	-0.002	-0.002	0.000	0.000	0.000	0.000
69	J	35	GLU	0	0.134	-0.079	49.828	0.001	0.001	0.000	0.000	0.000	0.000
70	J	35	GLU	-1	-0.932	-0.825	49.828	-0.025	-0.025	0.000	0.000	0.000	0.000
71	J	36	ILE	0	0.039	-0.100	50.652	0.002	0.002	0.000	0.000	0.000	0.000
72	J	36	ILE	0	-0.089	0.085	48.330	0.000	0.000	0.000	0.000	0.000	0.000
73	J	37	TYR	0	0.128	-0.084	52.260	0.002	0.002	0.000	0.000	0.000	0.000
74	J	37	TYR	0	-0.109	0.093	53.223	0.000	0.000	0.000	0.000	0.000	0.000
75	J	38	ASP	0	0.149	-0.092	54.284	0.001	0.001	0.000	0.000	0.000	0.000
76	J	38	ASP	-1	-0.933	-0.788	54.576	-0.029	-0.029	0.000	0.000	0.000	0.000
77	J	39	LYS	0	0.081	-0.099	55.291	0.002	0.002	0.000	0.000	0.000	0.000
78	J	39	LYS	1	0.705	1.012	54.585	0.023	0.023	0.000	0.000	0.000	0.000
79	J	40	GLU	0	0.070	-0.113	56.763	0.002	0.002	0.000	0.000	0.000	0.000
80	J	40	GLU	-1	-0.809	-0.751	56.343	-0.032	-0.032	0.000	0.000	0.000	0.000
81	J	41	THR	0	-0.040	-0.101	58.686	0.001	0.001	0.000	0.000	0.000	0.000
82	J	41	THR	0	-0.081	0.020	59.120	0.000	0.000	0.000	0.000	0.000	0.000
83	J	42	GLU	0	0.085	-0.087	59.863	0.001	0.001	0.000	0.000	0.000	0.000
84	J	42	GLU	-1	-0.915	-0.784	58.258	-0.021	-0.021	0.000	0.000	0.000	0.000
85	J	43	TYR	0	0.019	-0.122	61.139	0.001	0.001	0.000	0.000	0.000	0.000
86	J	43	TYR	0	-0.132	0.054	57.585	0.000	0.000	0.000	0.000	0.000	0.000
87	J	44	PHE	0	0.003	-0.103	62.536	0.001	0.001	0.000	0.000	0.000	0.000
88	J	44	PHE	0	-0.009	0.099	59.101	0.000	0.000	0.000	0.000	0.000	0.000
89	J	45	SER	0	0.046	-0.079	64.181	0.000	0.000	0.000	0.000	0.000	0.000
90	J	45	SER	0	-0.048	0.072	64.742	0.000	0.000	0.000	0.000	0.000	0.000
91	J	46	HIS	0	-0.137	-0.170	65.624	0.000	0.000	0.000	0.000	0.000	0.000
92	J	46	HIS	0	0.031	0.028	67.053	0.000	0.000	0.000	0.000	0.000	0.000
93	J	65	TYR	0	0.128	0.016	72.986	0.000	0.000	0.000	0.000	0.000	0.000
94	J	65	TYR	0	-0.106	0.054	68.533	0.000	0.000	0.000	0.000	0.000	0.000
95	J	66	SER	0	-0.069	-0.123	70.711	0.000	0.000	0.000	0.000	0.000	0.000
96	J	66	SER	0	-0.019	0.089	71.615	0.000	0.000	0.000	0.000	0.000	0.000
97	J	67	GLY	0	0.041	-0.069	68.908	-0.001	-0.001	0.000	0.000	0.000	0.000
98	J	68	ASN	0	0.035	-0.038	64.810	0.000	0.000	0.000	0.000	0.000	0.000
99	J	68	ASN	0	-0.075	0.066	63.975	-0.001	-0.001	0.000	0.000	0.000	0.000
100	J	69	ILE	0	0.081	-0.048	60.754	0.000	0.000	0.000	0.000	0.000	0.000
101	J	69	ILE	0	-0.045	0.090	58.447	0.000	0.000	0.000	0.000	0.000	0.000
102	J	70	ILE	0	0.036	-0.110	62.215	0.000	0.000	0.000	0.000	0.000	0.000
103	J	70	ILE	0	-0.072	0.103	59.994	0.000	0.000	0.000	0.000	0.000	0.000
104	J	71	LYS	0	-0.021	-0.125	63.032	-0.001	-0.001	0.000	0.000	0.000	0.000
105	J	71	LYS	1	0.775	1.015	66.127	0.022	0.022	0.000	0.000	0.000	0.000
106	J	72	GLY	0	0.029	-0.078	65.930	0.000	0.000	0.000	0.000	0.000	0.000
107	J	73	PHE	0	0.074	0.003	67.240	0.000	0.000	0.000	0.000	0.000	0.000
108	J	73	PHE	0	-0.080	0.098	62.287	0.000	0.000	0.000	0.000	0.000	0.000
109	J	74	ASP	0	0.190	-0.078	68.145	0.001	0.001	0.000	0.000	0.000	0.000
110	J	74	ASP	-1	-0.934	-0.812	71.514	-0.014	-0.014	0.000	0.000	0.000	0.000
111	J	75	THR	0	-0.093	-0.087	71.757	-0.001	-0.001	0.000	0.000	0.000	0.000
112	J	75	THR	0	-0.008	0.040	72.412	0.000	0.000	0.000	0.000	0.000	0.000
113	J	76	PHE	0	-0.010	-0.086	74.511	0.000	0.000	0.000	0.000	0.000	0.000
114	J	76	PHE	0	-0.099	0.080	72.172	0.000	0.000	0.000	0.000	0.000	0.000
115	J	77	SER	0	-0.054	-0.174	77.213	0.001	0.001	0.000	0.000	0.000	0.000
116	J	77	SER	0	0.085	0.073	76.913	0.000	0.000	0.000	0.000	0.000	0.000
117	J	86	SER	0	0.045	0.050	71.015	0.000	0.000	0.000	0.000	0.000	0.000
118	J	86	SER	0	-0.053	0.034	73.391	0.000	0.000	0.000	0.000	0.000	0.000
119	J	87	ALA	0	0.168	-0.059	70.159	0.000	0.000	0.000	0.000	0.000	0.000
120	J	87	ALA	0	-0.065	0.094	70.050	0.000	0.000	0.000	0.000	0.000	0.000
121	J	88	PHE	0	0.066	-0.097	65.635	0.000	0.000	0.000	0.000	0.000	0.000
122	J	88	PHE	0	-0.057	0.149	60.237	0.000	0.000	0.000	0.000	0.000	0.000
123	J	89	ASN	0	0.075	-0.072	65.091	0.000	0.000	0.000	0.000	0.000	0.000
124	J	89	ASN	0	-0.187	0.013	64.715	0.000	0.000	0.000	0.000	0.000	0.000
125	J	90	ASN	0	0.122	-0.060	61.168	0.000	0.000	0.000	0.000	0.000	0.000
126	J	90	ASN	0	-0.076	0.083	60.294	0.000	0.000	0.000	0.000	0.000	0.000
127	J	91	ASN	0	0.150	-0.058	59.776	-0.001	-0.001	0.000	0.000	0.000	0.000
128	J	91	ASN	0	-0.127	0.039	62.405	0.000	0.000	0.000	0.000	0.000	0.000
129	J	92	ASP	0	0.058	-0.092	60.590	-0.001	-0.001	0.000	0.000	0.000	0.000
130	J	92	ASP	-1	-0.822	-0.799	62.828	-0.025	-0.025	0.000	0.000	0.000	0.000
131	J	93	ARG	0	0.041	-0.062	57.904	0.001	0.001	0.000	0.000	0.000	0.000
132	J	93	ARG	1	0.699	0.969	56.892	0.030	0.030	0.000	0.000	0.000	0.000
133	J	94	ILE	0	0.101	-0.119	56.171	-0.002	-0.002	0.000	0.000	0.000	0.000
134	J	94	ILE	0	-0.086	0.096	56.783	0.000	0.000	0.000	0.000	0.000	0.000
135	J	95	PHE	0	0.114	-0.056	53.323	-0.001	-0.001	0.000	0.000	0.000	0.000
136	J	95	PHE	0	-0.117	0.060	53.173	0.001	0.001	0.000	0.000	0.000	0.000
137	J	96	SER	0	0.080	-0.072	51.835	-0.002	-0.002	0.000	0.000	0.000	0.000
138	J	96	SER	0	-0.057	0.038	53.315	0.000	0.000	0.000	0.000	0.000	0.000
139	J	97	LEU	0	0.056	-0.087	51.478	-0.003	-0.003	0.000	0.000	0.000	0.000
140	J	97	LEU	0	-0.088	0.083	54.677	0.000	0.000	0.000	0.000	0.000	0.000
141	J	98	SER	0	-0.021	-0.098	50.784	-0.001	-0.001	0.000	0.000	0.000	0.000
142	J	98	SER	0	-0.068	0.055	50.122	0.000	0.000	0.000	0.000	0.000	0.000
143	J	99	SER	0	-0.007	-0.103	47.497	-0.002	-0.002	0.000	0.000	0.000	0.000
144	J	99	SER	0	-0.028	0.101	46.887	-0.001	-0.001	0.000	0.000	0.000	0.000
145	J	100	ALA	0	0.140	-0.080	46.895	0.002	0.002	0.000	0.000	0.000	0.000
146	J	100	ALA	0	-0.094	0.096	45.861	-0.001	-0.001	0.000	0.000	0.000	0.000
147	J	101	THR	0	-0.102	-0.110	45.829	-0.001	-0.001	0.000	0.000	0.000	0.000
148	J	101	THR	0	0.004	0.072	44.036	0.000	0.000	0.000	0.000	0.000	0.000
149	J	102	TYR	0	-0.073	-0.117	46.925	0.000	0.000	0.000	0.000	0.000	0.000
150	J	102	TYR	0	0.056	0.029	50.520	0.001	0.001	0.000	0.000	0.000	0.000

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