FMO DATABASE

FMODB ID: 9M3Z2

Calculation Name: 5J9U-F-Xray540

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: 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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-398552.857541
FMO2-HF: Nuclear repulsion	367526.109135
FMO2-HF: Total energy	-31026.748406
FMO2-MP2: Total energy	-31117.457744

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.
-2.883	-0.674	0.019	-0.914	-1.313	0.002

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 : 0.131 / q_NPA : -0.003

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	F	2	THR	0	-0.018	0.060	4.312	1.380	1.674	0.000	-0.107	-0.187	0.000
5	F	3	ASP	0	0.115	-0.071	3.584	-1.924	-0.700	0.016	-0.612	-0.627	0.002
6	F	3	ASP	-1	-0.886	-0.796	4.324	1.019	1.124	-0.001	-0.011	-0.093	0.000
7	F	4	GLU	0	0.133	-0.107	3.531	0.648	0.997	0.005	-0.146	-0.208	0.000
8	F	4	GLU	-1	-0.990	-0.820	3.967	-4.502	-4.317	0.001	-0.032	-0.154	0.000
9	F	5	LEU	0	0.089	-0.107	5.123	0.355	0.407	-0.002	-0.006	-0.044	0.000
10	F	5	LEU	0	-0.092	0.105	6.285	-0.012	-0.012	0.000	0.000	0.000	0.000
11	F	6	LYS	0	0.098	-0.088	6.932	0.230	0.230	0.000	0.000	0.000	0.000
12	F	6	LYS	1	0.716	0.982	7.388	-0.635	-0.635	0.000	0.000	0.000	0.000
13	F	7	SER	0	0.022	-0.099	8.076	0.154	0.154	0.000	0.000	0.000	0.000
14	F	7	SER	0	-0.035	0.071	7.845	0.051	0.051	0.000	0.000	0.000	0.000
15	F	8	TYR	0	0.109	-0.056	9.377	0.147	0.147	0.000	0.000	0.000	0.000
16	F	8	TYR	0	-0.105	0.090	9.856	-0.002	-0.002	0.000	0.000	0.000	0.000
17	F	9	GLU	0	0.054	-0.135	11.238	0.048	0.048	0.000	0.000	0.000	0.000
18	F	9	GLU	-1	-0.895	-0.799	11.629	-0.317	-0.317	0.000	0.000	0.000	0.000
19	F	10	ALA	0	0.098	-0.088	12.646	0.053	0.053	0.000	0.000	0.000	0.000
20	F	10	ALA	0	-0.088	0.103	13.081	0.009	0.009	0.000	0.000	0.000	0.000
21	F	11	LEU	0	0.100	-0.098	13.824	0.062	0.062	0.000	0.000	0.000	0.000
22	F	11	LEU	0	-0.072	0.112	13.208	-0.014	-0.014	0.000	0.000	0.000	0.000
23	F	12	LYS	0	0.124	-0.085	15.386	0.025	0.025	0.000	0.000	0.000	0.000
24	F	12	LYS	1	0.691	0.970	14.252	0.388	0.388	0.000	0.000	0.000	0.000
25	F	13	ALA	0	0.025	-0.109	17.137	0.016	0.016	0.000	0.000	0.000	0.000
26	F	13	ALA	0	-0.077	0.089	18.035	0.007	0.007	0.000	0.000	0.000	0.000
27	F	14	GLU	0	0.123	-0.119	18.437	0.029	0.029	0.000	0.000	0.000	0.000
28	F	14	GLU	-1	-1.020	-0.832	18.215	-0.174	-0.174	0.000	0.000	0.000	0.000
29	F	15	LEU	0	0.120	-0.080	19.654	0.025	0.025	0.000	0.000	0.000	0.000
30	F	15	LEU	0	-0.101	0.104	20.005	-0.007	-0.007	0.000	0.000	0.000	0.000
31	F	16	LYS	0	0.043	-0.112	21.412	0.007	0.007	0.000	0.000	0.000	0.000
32	F	16	LYS	1	0.828	1.032	18.882	0.146	0.146	0.000	0.000	0.000	0.000
33	F	17	LYS	0	0.097	-0.045	23.125	0.009	0.009	0.000	0.000	0.000	0.000
34	F	17	LYS	1	0.863	1.053	23.724	0.045	0.045	0.000	0.000	0.000	0.000
35	F	18	SER	0	0.064	-0.073	24.214	0.015	0.015	0.000	0.000	0.000	0.000
36	F	18	SER	0	-0.060	0.053	23.307	-0.006	-0.006	0.000	0.000	0.000	0.000
37	F	19	LEU	0	0.036	-0.111	25.640	0.007	0.007	0.000	0.000	0.000	0.000
38	F	19	LEU	0	-0.099	0.079	25.083	-0.002	-0.002	0.000	0.000	0.000	0.000
39	F	20	GLN	0	0.116	-0.056	27.569	0.002	0.002	0.000	0.000	0.000	0.000
40	F	20	GLN	0	-0.175	0.027	28.570	-0.005	-0.005	0.000	0.000	0.000	0.000
41	F	21	ASP	0	0.123	-0.089	28.978	0.006	0.006	0.000	0.000	0.000	0.000
42	F	21	ASP	-1	-0.996	-0.850	28.954	-0.068	-0.068	0.000	0.000	0.000	0.000
43	F	22	ARG	0	0.135	-0.063	29.881	0.007	0.007	0.000	0.000	0.000	0.000
44	F	22	ARG	1	0.711	0.963	29.772	0.104	0.104	0.000	0.000	0.000	0.000
45	F	23	ARG	0	0.063	-0.089	31.644	0.002	0.002	0.000	0.000	0.000	0.000
46	F	23	ARG	1	0.670	0.938	33.154	0.062	0.062	0.000	0.000	0.000	0.000
47	F	24	GLU	0	0.089	-0.095	33.579	0.002	0.002	0.000	0.000	0.000	0.000
48	F	24	GLU	-1	-0.940	-0.813	33.488	-0.045	-0.045	0.000	0.000	0.000	0.000
49	F	25	GLN	0	0.059	-0.104	34.529	0.006	0.006	0.000	0.000	0.000	0.000
50	F	25	GLN	0	-0.124	0.044	33.453	0.002	0.002	0.000	0.000	0.000	0.000
51	F	26	GLU	0	0.053	-0.103	35.945	0.004	0.004	0.000	0.000	0.000	0.000
52	F	26	GLU	-1	-0.865	-0.786	34.207	-0.087	-0.087	0.000	0.000	0.000	0.000
53	F	27	ASP	0	0.140	-0.065	37.877	0.002	0.002	0.000	0.000	0.000	0.000
54	F	27	ASP	-1	-0.917	-0.792	38.108	-0.053	-0.053	0.000	0.000	0.000	0.000
55	F	28	THR	0	0.034	-0.056	39.265	0.003	0.003	0.000	0.000	0.000	0.000
56	F	28	THR	0	-0.048	0.065	38.901	0.002	0.002	0.000	0.000	0.000	0.000
57	F	29	PHE	0	0.073	-0.078	40.390	0.004	0.004	0.000	0.000	0.000	0.000
58	F	29	PHE	0	-0.119	0.058	40.492	-0.001	-0.001	0.000	0.000	0.000	0.000
59	F	30	ASP	0	0.052	-0.120	42.005	0.002	0.002	0.000	0.000	0.000	0.000
60	F	30	ASP	-1	-0.973	-0.850	41.721	-0.056	-0.056	0.000	0.000	0.000	0.000
61	F	31	ASN	0	0.068	-0.067	43.857	0.001	0.001	0.000	0.000	0.000	0.000
62	F	31	ASN	0	-0.164	0.017	43.334	0.003	0.003	0.000	0.000	0.000	0.000
63	F	32	LEU	0	0.099	-0.106	44.917	0.003	0.003	0.000	0.000	0.000	0.000
64	F	32	LEU	0	-0.097	0.098	43.126	0.000	0.000	0.000	0.000	0.000	0.000
65	F	33	GLN	0	0.121	-0.085	46.498	0.002	0.002	0.000	0.000	0.000	0.000
66	F	33	GLN	0	-0.090	0.098	46.767	0.001	0.001	0.000	0.000	0.000	0.000
67	F	34	GLN	0	0.085	-0.092	48.373	0.001	0.001	0.000	0.000	0.000	0.000
68	F	34	GLN	0	-0.143	0.057	49.835	-0.002	-0.002	0.000	0.000	0.000	0.000
69	F	35	GLU	0	0.121	-0.082	49.920	0.001	0.001	0.000	0.000	0.000	0.000
70	F	35	GLU	-1	-0.977	-0.858	49.721	-0.023	-0.023	0.000	0.000	0.000	0.000
71	F	36	ILE	0	0.043	-0.088	50.686	0.002	0.002	0.000	0.000	0.000	0.000
72	F	36	ILE	0	-0.103	0.080	48.446	0.000	0.000	0.000	0.000	0.000	0.000
73	F	37	TYR	0	0.145	-0.083	52.317	0.002	0.002	0.000	0.000	0.000	0.000
74	F	37	TYR	0	-0.109	0.092	53.671	0.000	0.000	0.000	0.000	0.000	0.000
75	F	38	ASP	0	0.117	-0.097	54.452	0.001	0.001	0.000	0.000	0.000	0.000
76	F	38	ASP	-1	-0.937	-0.794	54.716	-0.026	-0.026	0.000	0.000	0.000	0.000
77	F	39	LYS	0	0.066	-0.119	55.224	0.002	0.002	0.000	0.000	0.000	0.000
78	F	39	LYS	1	0.727	1.015	54.468	0.019	0.019	0.000	0.000	0.000	0.000
79	F	40	GLU	0	0.071	-0.118	56.555	0.001	0.001	0.000	0.000	0.000	0.000
80	F	40	GLU	-1	-0.812	-0.765	56.212	-0.029	-0.029	0.000	0.000	0.000	0.000
81	F	41	THR	0	-0.051	-0.091	58.466	0.001	0.001	0.000	0.000	0.000	0.000
82	F	41	THR	0	-0.011	0.076	58.667	0.000	0.000	0.000	0.000	0.000	0.000
83	F	42	GLU	0	0.075	-0.087	59.812	0.001	0.001	0.000	0.000	0.000	0.000
84	F	42	GLU	-1	-0.883	-0.771	58.796	-0.018	-0.018	0.000	0.000	0.000	0.000
85	F	43	TYR	0	-0.008	-0.126	61.022	0.001	0.001	0.000	0.000	0.000	0.000
86	F	43	TYR	0	-0.125	0.056	57.362	0.000	0.000	0.000	0.000	0.000	0.000
87	F	44	PHE	0	0.031	-0.078	62.440	0.001	0.001	0.000	0.000	0.000	0.000
88	F	44	PHE	0	-0.047	0.085	58.846	0.000	0.000	0.000	0.000	0.000	0.000
89	F	45	SER	0	-0.131	-0.179	64.046	0.000	0.000	0.000	0.000	0.000	0.000
90	F	45	SER	0	0.032	0.028	63.745	-0.001	-0.001	0.000	0.000	0.000	0.000
91	F	65	TYR	0	0.140	0.020	72.990	0.000	0.000	0.000	0.000	0.000	0.000
92	F	65	TYR	0	-0.102	0.063	68.493	0.000	0.000	0.000	0.000	0.000	0.000
93	F	66	SER	0	-0.064	-0.115	70.810	0.000	0.000	0.000	0.000	0.000	0.000
94	F	66	SER	0	-0.035	0.083	71.614	0.000	0.000	0.000	0.000	0.000	0.000
95	F	67	GLY	0	0.009	-0.099	68.973	-0.001	-0.001	0.000	0.000	0.000	0.000
96	F	68	ASN	0	0.070	-0.008	64.957	0.000	0.000	0.000	0.000	0.000	0.000
97	F	68	ASN	0	-0.102	0.062	64.848	-0.001	-0.001	0.000	0.000	0.000	0.000
98	F	69	ILE	0	0.096	-0.059	60.915	0.000	0.000	0.000	0.000	0.000	0.000
99	F	69	ILE	0	-0.038	0.099	58.477	0.000	0.000	0.000	0.000	0.000	0.000
100	F	70	ILE	0	0.051	-0.105	62.424	0.000	0.000	0.000	0.000	0.000	0.000
101	F	70	ILE	0	-0.076	0.108	60.374	0.000	0.000	0.000	0.000	0.000	0.000
102	F	71	LYS	0	-0.015	-0.124	63.521	-0.001	-0.001	0.000	0.000	0.000	0.000
103	F	71	LYS	1	0.788	1.017	66.809	0.019	0.019	0.000	0.000	0.000	0.000
104	F	72	GLY	0	0.034	-0.073	66.155	0.000	0.000	0.000	0.000	0.000	0.000
105	F	73	PHE	0	0.069	0.000	67.232	0.000	0.000	0.000	0.000	0.000	0.000
106	F	73	PHE	0	-0.086	0.100	62.297	0.000	0.000	0.000	0.000	0.000	0.000
107	F	74	ASP	0	0.168	-0.104	68.219	0.001	0.001	0.000	0.000	0.000	0.000
108	F	74	ASP	-1	-0.943	-0.811	71.739	-0.013	-0.013	0.000	0.000	0.000	0.000
109	F	75	THR	0	-0.061	-0.094	71.855	-0.001	-0.001	0.000	0.000	0.000	0.000
110	F	75	THR	0	-0.034	0.073	71.747	0.000	0.000	0.000	0.000	0.000	0.000
111	F	76	PHE	0	0.021	-0.087	74.371	0.000	0.000	0.000	0.000	0.000	0.000
112	F	76	PHE	0	-0.075	0.086	72.362	0.000	0.000	0.000	0.000	0.000	0.000
113	F	77	SER	0	-0.034	-0.167	77.172	0.001	0.001	0.000	0.000	0.000	0.000
114	F	77	SER	0	0.054	0.064	78.360	0.000	0.000	0.000	0.000	0.000	0.000
115	F	86	SER	0	0.077	0.031	70.524	0.000	0.000	0.000	0.000	0.000	0.000
116	F	86	SER	0	-0.022	0.063	73.288	0.000	0.000	0.000	0.000	0.000	0.000
117	F	87	ALA	0	0.086	-0.058	70.313	0.001	0.001	0.000	0.000	0.000	0.000
118	F	87	ALA	0	-0.084	0.078	69.971	0.000	0.000	0.000	0.000	0.000	0.000
119	F	88	PHE	0	0.095	-0.098	65.934	0.000	0.000	0.000	0.000	0.000	0.000
120	F	88	PHE	0	-0.032	0.147	60.549	0.000	0.000	0.000	0.000	0.000	0.000
121	F	89	ASN	0	0.086	-0.060	65.174	0.000	0.000	0.000	0.000	0.000	0.000
122	F	89	ASN	0	-0.205	-0.001	64.948	0.000	0.000	0.000	0.000	0.000	0.000
123	F	90	ASN	0	0.127	-0.058	61.191	0.000	0.000	0.000	0.000	0.000	0.000
124	F	90	ASN	0	-0.068	0.084	60.271	0.000	0.000	0.000	0.000	0.000	0.000
125	F	91	ASN	0	0.142	-0.067	59.864	-0.001	-0.001	0.000	0.000	0.000	0.000
126	F	91	ASN	0	-0.125	0.035	62.759	0.000	0.000	0.000	0.000	0.000	0.000
127	F	92	ASP	0	0.060	-0.082	60.757	-0.001	-0.001	0.000	0.000	0.000	0.000
128	F	92	ASP	-1	-0.856	-0.815	63.145	-0.023	-0.023	0.000	0.000	0.000	0.000
129	F	93	ARG	0	0.065	-0.059	58.220	0.001	0.001	0.000	0.000	0.000	0.000
130	F	93	ARG	1	0.682	0.966	57.208	0.027	0.027	0.000	0.000	0.000	0.000
131	F	94	ILE	0	0.094	-0.124	56.448	-0.002	-0.002	0.000	0.000	0.000	0.000
132	F	94	ILE	0	-0.091	0.093	57.016	0.000	0.000	0.000	0.000	0.000	0.000
133	F	95	PHE	0	0.098	-0.059	53.509	-0.001	-0.001	0.000	0.000	0.000	0.000
134	F	95	PHE	0	-0.120	0.053	53.315	0.001	0.001	0.000	0.000	0.000	0.000
135	F	96	SER	0	0.091	-0.067	52.067	-0.002	-0.002	0.000	0.000	0.000	0.000
136	F	96	SER	0	-0.063	0.036	53.672	0.000	0.000	0.000	0.000	0.000	0.000
137	F	97	LEU	0	0.047	-0.094	51.838	-0.003	-0.003	0.000	0.000	0.000	0.000
138	F	97	LEU	0	-0.104	0.080	55.095	0.000	0.000	0.000	0.000	0.000	0.000
139	F	98	SER	0	-0.015	-0.097	50.914	-0.001	-0.001	0.000	0.000	0.000	0.000
140	F	98	SER	0	-0.077	0.050	50.299	0.000	0.000	0.000	0.000	0.000	0.000
141	F	99	SER	0	0.043	-0.091	47.716	-0.002	-0.002	0.000	0.000	0.000	0.000
142	F	99	SER	0	-0.053	0.078	47.106	-0.001	-0.001	0.000	0.000	0.000	0.000
143	F	100	ALA	0	0.124	-0.076	47.494	0.002	0.002	0.000	0.000	0.000	0.000
144	F	100	ALA	0	-0.102	0.094	46.437	-0.001	-0.001	0.000	0.000	0.000	0.000
145	F	101	THR	0	-0.053	-0.110	46.483	-0.001	-0.001	0.000	0.000	0.000	0.000
146	F	101	THR	0	0.001	0.072	44.879	0.000	0.000	0.000	0.000	0.000	0.000
147	F	102	TYR	0	-0.121	-0.125	47.511	0.000	0.000	0.000	0.000	0.000	0.000
148	F	102	TYR	0	0.047	0.033	51.093	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)