FMO DATABASE

FMODB ID: 16RMZ

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	OptHSide
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	-408732.642492
FMO2-HF: Nuclear repulsion	377236.685969
FMO2-HF: Total energy	-31495.956523
FMO2-MP2: Total energy	-31588.13433

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.
-3.142	-0.443	0.165	-1.12	-1.745	0.003

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 : 0.148 / q_NPA : -0.008

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	-0.025	0.066	4.504	1.076	1.355	-0.001	-0.108	-0.170	0.000
5	J	3	ASP	0	0.160	-0.066	2.786	-2.479	-0.880	0.080	-0.763	-0.916	0.002
6	J	3	ASP	-1	-0.910	-0.796	3.620	1.692	1.850	0.002	-0.040	-0.121	0.000
7	J	4	GLU	0	0.086	-0.148	3.018	0.061	0.422	0.060	-0.116	-0.305	0.001
8	J	4	GLU	-1	-0.978	-0.808	3.514	-2.979	-2.727	0.026	-0.078	-0.200	0.000
9	J	5	LEU	0	0.080	-0.114	4.731	0.085	0.135	-0.002	-0.015	-0.033	0.000
10	J	5	LEU	0	-0.090	0.111	6.149	-0.029	-0.029	0.000	0.000	0.000	0.000
11	J	6	LYS	0	0.102	-0.082	6.580	0.150	0.150	0.000	0.000	0.000	0.000
12	J	6	LYS	1	0.732	0.996	7.045	-1.054	-1.054	0.000	0.000	0.000	0.000
13	J	7	SER	0	0.021	-0.091	7.683	0.074	0.074	0.000	0.000	0.000	0.000
14	J	7	SER	0	-0.022	0.086	7.536	0.025	0.025	0.000	0.000	0.000	0.000
15	J	8	TYR	0	0.099	-0.070	8.944	0.096	0.096	0.000	0.000	0.000	0.000
16	J	8	TYR	0	-0.084	0.095	9.594	-0.015	-0.015	0.000	0.000	0.000	0.000
17	J	9	GLU	0	0.017	-0.142	10.578	0.016	0.016	0.000	0.000	0.000	0.000
18	J	9	GLU	-1	-0.896	-0.799	10.993	-0.257	-0.257	0.000	0.000	0.000	0.000
19	J	10	ALA	0	0.089	-0.098	12.007	0.029	0.029	0.000	0.000	0.000	0.000
20	J	10	ALA	0	-0.076	0.105	12.672	0.013	0.013	0.000	0.000	0.000	0.000
21	J	11	LEU	0	0.081	-0.107	13.265	0.039	0.039	0.000	0.000	0.000	0.000
22	J	11	LEU	0	-0.067	0.107	12.398	-0.013	-0.013	0.000	0.000	0.000	0.000
23	J	12	LYS	0	0.079	-0.104	14.942	0.012	0.012	0.000	0.000	0.000	0.000
24	J	12	LYS	1	0.715	0.986	13.900	0.294	0.294	0.000	0.000	0.000	0.000
25	J	13	ALA	0	0.027	-0.102	16.800	-0.001	-0.001	0.000	0.000	0.000	0.000
26	J	13	ALA	0	-0.062	0.101	17.684	0.007	0.007	0.000	0.000	0.000	0.000
27	J	14	GLU	0	0.079	-0.152	17.785	0.014	0.014	0.000	0.000	0.000	0.000
28	J	14	GLU	-1	-1.006	-0.822	17.452	-0.026	-0.026	0.000	0.000	0.000	0.000
29	J	15	LEU	0	0.109	-0.103	19.171	0.016	0.016	0.000	0.000	0.000	0.000
30	J	15	LEU	0	-0.102	0.109	19.497	-0.006	-0.006	0.000	0.000	0.000	0.000
31	J	16	LYS	0	0.080	-0.103	21.022	0.001	0.001	0.000	0.000	0.000	0.000
32	J	16	LYS	1	0.864	1.056	21.290	0.093	0.093	0.000	0.000	0.000	0.000
33	J	17	LYS	0	0.096	-0.052	22.744	0.003	0.003	0.000	0.000	0.000	0.000
34	J	17	LYS	1	0.863	1.063	23.240	-0.020	-0.020	0.000	0.000	0.000	0.000
35	J	18	SER	0	0.044	-0.067	23.531	0.009	0.009	0.000	0.000	0.000	0.000
36	J	18	SER	0	-0.007	0.077	23.554	-0.006	-0.006	0.000	0.000	0.000	0.000
37	J	19	LEU	0	0.018	-0.123	24.997	0.004	0.004	0.000	0.000	0.000	0.000
38	J	19	LEU	0	-0.109	0.075	24.701	-0.003	-0.003	0.000	0.000	0.000	0.000
39	J	20	GLN	0	0.123	-0.057	26.923	-0.001	-0.001	0.000	0.000	0.000	0.000
40	J	20	GLN	0	-0.172	0.033	28.071	-0.005	-0.005	0.000	0.000	0.000	0.000
41	J	21	ASP	0	0.127	-0.100	28.383	0.003	0.003	0.000	0.000	0.000	0.000
42	J	21	ASP	-1	-0.988	-0.835	28.597	-0.023	-0.023	0.000	0.000	0.000	0.000
43	J	22	ARG	0	0.128	-0.064	29.317	0.004	0.004	0.000	0.000	0.000	0.000
44	J	22	ARG	1	0.737	0.994	29.076	0.071	0.071	0.000	0.000	0.000	0.000
45	J	23	ARG	0	0.067	-0.101	31.029	0.000	0.000	0.000	0.000	0.000	0.000
46	J	23	ARG	1	0.682	0.943	32.167	0.040	0.040	0.000	0.000	0.000	0.000
47	J	24	GLU	0	0.101	-0.105	32.935	0.000	0.000	0.000	0.000	0.000	0.000
48	J	24	GLU	-1	-0.945	-0.805	32.966	-0.012	-0.012	0.000	0.000	0.000	0.000
49	J	25	GLN	0	0.036	-0.122	34.109	0.003	0.003	0.000	0.000	0.000	0.000
50	J	25	GLN	0	-0.093	0.060	33.238	0.001	0.001	0.000	0.000	0.000	0.000
51	J	26	GLU	0	0.029	-0.124	35.481	0.003	0.003	0.000	0.000	0.000	0.000
52	J	26	GLU	-1	-0.879	-0.805	33.713	-0.057	-0.057	0.000	0.000	0.000	0.000
53	J	27	ASP	0	0.109	-0.051	37.404	0.000	0.000	0.000	0.000	0.000	0.000
54	J	27	ASP	-1	-0.924	-0.794	37.481	-0.031	-0.031	0.000	0.000	0.000	0.000
55	J	28	THR	0	0.022	-0.090	39.076	0.001	0.001	0.000	0.000	0.000	0.000
56	J	28	THR	0	-0.042	0.079	38.811	0.001	0.001	0.000	0.000	0.000	0.000
57	J	29	PHE	0	0.105	-0.057	40.155	0.003	0.003	0.000	0.000	0.000	0.000
58	J	29	PHE	0	-0.101	0.073	40.175	-0.001	-0.001	0.000	0.000	0.000	0.000
59	J	30	ASP	0	0.079	-0.120	41.852	0.001	0.001	0.000	0.000	0.000	0.000
60	J	30	ASP	-1	-0.994	-0.839	41.941	-0.034	-0.034	0.000	0.000	0.000	0.000
61	J	31	ASN	0	0.070	-0.057	43.760	0.000	0.000	0.000	0.000	0.000	0.000
62	J	31	ASN	0	-0.170	0.010	43.135	0.002	0.002	0.000	0.000	0.000	0.000
63	J	32	LEU	0	0.104	-0.098	44.834	0.001	0.001	0.000	0.000	0.000	0.000
64	J	32	LEU	0	-0.116	0.091	43.406	0.000	0.000	0.000	0.000	0.000	0.000
65	J	33	GLN	0	0.157	-0.089	45.941	0.002	0.002	0.000	0.000	0.000	0.000
66	J	33	GLN	0	-0.129	0.083	45.859	0.001	0.001	0.000	0.000	0.000	0.000
67	J	34	GLN	0	0.061	-0.103	47.685	0.000	0.000	0.000	0.000	0.000	0.000
68	J	34	GLN	0	-0.143	0.059	49.358	-0.002	-0.002	0.000	0.000	0.000	0.000
69	J	35	GLU	0	0.105	-0.088	49.393	0.000	0.000	0.000	0.000	0.000	0.000
70	J	35	GLU	-1	-0.987	-0.862	49.432	-0.009	-0.009	0.000	0.000	0.000	0.000
71	J	36	ILE	0	0.044	-0.102	50.367	0.002	0.002	0.000	0.000	0.000	0.000
72	J	36	ILE	0	-0.086	0.086	48.289	0.000	0.000	0.000	0.000	0.000	0.000
73	J	37	TYR	0	0.130	-0.078	52.091	0.001	0.001	0.000	0.000	0.000	0.000
74	J	37	TYR	0	-0.115	0.087	53.134	0.000	0.000	0.000	0.000	0.000	0.000
75	J	38	ASP	0	0.141	-0.115	53.926	0.000	0.000	0.000	0.000	0.000	0.000
76	J	38	ASP	-1	-0.932	-0.791	54.261	-0.015	-0.015	0.000	0.000	0.000	0.000
77	J	39	LYS	0	0.070	-0.125	54.867	0.001	0.001	0.000	0.000	0.000	0.000
78	J	39	LYS	1	0.776	1.050	54.327	0.007	0.007	0.000	0.000	0.000	0.000
79	J	40	GLU	0	0.029	-0.124	56.315	0.001	0.001	0.000	0.000	0.000	0.000
80	J	40	GLU	-1	-0.806	-0.771	55.975	-0.017	-0.017	0.000	0.000	0.000	0.000
81	J	41	THR	0	-0.059	-0.103	58.206	0.000	0.000	0.000	0.000	0.000	0.000
82	J	41	THR	0	-0.055	0.032	58.371	0.000	0.000	0.000	0.000	0.000	0.000
83	J	42	GLU	0	0.077	-0.085	59.635	0.000	0.000	0.000	0.000	0.000	0.000
84	J	42	GLU	-1	-0.927	-0.799	58.392	-0.006	-0.006	0.000	0.000	0.000	0.000
85	J	43	TYR	0	0.008	-0.122	60.621	0.001	0.001	0.000	0.000	0.000	0.000
86	J	43	TYR	0	-0.132	0.070	57.299	0.000	0.000	0.000	0.000	0.000	0.000
87	J	44	PHE	0	-0.046	-0.113	62.050	0.001	0.001	0.000	0.000	0.000	0.000
88	J	44	PHE	0	-0.048	0.082	58.706	0.000	0.000	0.000	0.000	0.000	0.000
89	J	45	SER	0	0.098	-0.058	63.738	-0.001	-0.001	0.000	0.000	0.000	0.000
90	J	45	SER	0	-0.059	0.067	64.853	0.000	0.000	0.000	0.000	0.000	0.000
91	J	46	HIS	0	-0.075	-0.138	65.528	-0.001	-0.001	0.000	0.000	0.000	0.000
92	J	46	HIS	0	0.026	0.022	67.638	0.000	0.000	0.000	0.000	0.000	0.000
93	J	65	TYR	0	0.137	0.016	72.784	0.000	0.000	0.000	0.000	0.000	0.000
94	J	65	TYR	0	-0.106	0.061	68.455	0.000	0.000	0.000	0.000	0.000	0.000
95	J	66	SER	0	-0.065	-0.132	70.270	0.000	0.000	0.000	0.000	0.000	0.000
96	J	66	SER	0	-0.047	0.087	71.046	0.000	0.000	0.000	0.000	0.000	0.000
97	J	67	GLY	0	0.031	-0.071	68.501	0.000	0.000	0.000	0.000	0.000	0.000
98	J	68	ASN	0	0.019	-0.002	64.472	0.000	0.000	0.000	0.000	0.000	0.000
99	J	68	ASN	0	-0.131	0.024	63.701	-0.001	-0.001	0.000	0.000	0.000	0.000
100	J	69	ILE	0	0.112	-0.068	60.772	0.000	0.000	0.000	0.000	0.000	0.000
101	J	69	ILE	0	-0.050	0.098	58.652	0.000	0.000	0.000	0.000	0.000	0.000
102	J	70	ILE	0	0.071	-0.094	62.230	0.000	0.000	0.000	0.000	0.000	0.000
103	J	70	ILE	0	-0.090	0.099	59.831	0.000	0.000	0.000	0.000	0.000	0.000
104	J	71	LYS	0	0.075	-0.089	63.027	-0.001	-0.001	0.000	0.000	0.000	0.000
105	J	71	LYS	1	0.767	1.030	66.106	0.012	0.012	0.000	0.000	0.000	0.000
106	J	72	GLY	0	0.026	-0.097	66.271	0.000	0.000	0.000	0.000	0.000	0.000
107	J	73	PHE	0	0.090	0.005	67.214	0.000	0.000	0.000	0.000	0.000	0.000
108	J	73	PHE	0	-0.077	0.109	62.352	0.000	0.000	0.000	0.000	0.000	0.000
109	J	74	ASP	0	0.128	-0.103	68.257	0.001	0.001	0.000	0.000	0.000	0.000
110	J	74	ASP	-1	-0.955	-0.812	71.159	-0.005	-0.005	0.000	0.000	0.000	0.000
111	J	75	THR	0	0.018	-0.091	71.734	0.000	0.000	0.000	0.000	0.000	0.000
112	J	75	THR	0	-0.034	0.054	72.011	0.000	0.000	0.000	0.000	0.000	0.000
113	J	76	PHE	0	-0.020	-0.079	74.092	0.000	0.000	0.000	0.000	0.000	0.000
114	J	76	PHE	0	-0.101	0.071	72.239	0.000	0.000	0.000	0.000	0.000	0.000
115	J	77	SER	0	-0.069	-0.173	76.837	0.000	0.000	0.000	0.000	0.000	0.000
116	J	77	SER	0	0.095	0.083	77.106	0.000	0.000	0.000	0.000	0.000	0.000
117	J	86	SER	0	0.056	0.019	70.370	0.000	0.000	0.000	0.000	0.000	0.000
118	J	86	SER	0	-0.022	0.064	73.146	0.000	0.000	0.000	0.000	0.000	0.000
119	J	87	ALA	0	0.108	-0.054	69.951	0.001	0.001	0.000	0.000	0.000	0.000
120	J	87	ALA	0	-0.061	0.093	70.047	0.000	0.000	0.000	0.000	0.000	0.000
121	J	88	PHE	0	0.049	-0.110	65.634	0.000	0.000	0.000	0.000	0.000	0.000
122	J	88	PHE	0	-0.033	0.153	60.258	0.000	0.000	0.000	0.000	0.000	0.000
123	J	89	ASN	0	0.093	-0.074	65.018	0.000	0.000	0.000	0.000	0.000	0.000
124	J	89	ASN	0	-0.185	0.006	64.611	0.000	0.000	0.000	0.000	0.000	0.000
125	J	90	ASN	0	0.122	-0.050	61.087	0.000	0.000	0.000	0.000	0.000	0.000
126	J	90	ASN	0	-0.063	0.089	60.028	0.000	0.000	0.000	0.000	0.000	0.000
127	J	91	ASN	0	0.127	-0.070	59.576	-0.001	-0.001	0.000	0.000	0.000	0.000
128	J	91	ASN	0	-0.128	0.048	61.976	-0.001	-0.001	0.000	0.000	0.000	0.000
129	J	92	ASP	0	0.065	-0.110	60.592	-0.001	-0.001	0.000	0.000	0.000	0.000
130	J	92	ASP	-1	-0.871	-0.821	62.680	-0.014	-0.014	0.000	0.000	0.000	0.000
131	J	93	ARG	0	0.047	-0.072	57.744	0.001	0.001	0.000	0.000	0.000	0.000
132	J	93	ARG	1	0.729	1.000	56.742	0.017	0.017	0.000	0.000	0.000	0.000
133	J	94	ILE	0	0.096	-0.110	56.065	-0.001	-0.001	0.000	0.000	0.000	0.000
134	J	94	ILE	0	-0.090	0.098	56.513	0.000	0.000	0.000	0.000	0.000	0.000
135	J	95	PHE	0	0.093	-0.069	53.206	-0.001	-0.001	0.000	0.000	0.000	0.000
136	J	95	PHE	0	-0.108	0.061	52.883	0.001	0.001	0.000	0.000	0.000	0.000
137	J	96	SER	0	0.072	-0.057	51.611	-0.001	-0.001	0.000	0.000	0.000	0.000
138	J	96	SER	0	-0.045	0.047	52.962	0.000	0.000	0.000	0.000	0.000	0.000
139	J	97	LEU	0	0.055	-0.098	51.298	-0.002	-0.002	0.000	0.000	0.000	0.000
140	J	97	LEU	0	-0.099	0.085	54.500	0.000	0.000	0.000	0.000	0.000	0.000
141	J	98	SER	0	-0.017	-0.112	50.622	-0.001	-0.001	0.000	0.000	0.000	0.000
142	J	98	SER	0	-0.069	0.059	50.049	0.000	0.000	0.000	0.000	0.000	0.000
143	J	99	SER	0	-0.002	-0.103	47.088	-0.001	-0.001	0.000	0.000	0.000	0.000
144	J	99	SER	0	-0.014	0.111	46.289	-0.001	-0.001	0.000	0.000	0.000	0.000
145	J	100	ALA	0	0.141	-0.084	46.684	0.001	0.001	0.000	0.000	0.000	0.000
146	J	100	ALA	0	-0.097	0.097	45.765	-0.001	-0.001	0.000	0.000	0.000	0.000
147	J	101	THR	0	-0.052	-0.111	45.586	-0.001	-0.001	0.000	0.000	0.000	0.000
148	J	101	THR	0	-0.013	0.061	43.877	0.001	0.001	0.000	0.000	0.000	0.000
149	J	102	TYR	0	-0.096	-0.095	46.600	-0.001	-0.001	0.000	0.000	0.000	0.000
150	J	102	TYR	0	0.043	0.034	49.986	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)