FMO DATABASE

FMODB ID: 8NLRY

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	OptH
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	-408119.782539
FMO2-HF: Nuclear repulsion	376625.456102
FMO2-HF: Total energy	-31494.326436
FMO2-MP2: Total energy	-31586.454848

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.
-1.56	1.388	0.139	-1.309	-1.779	0.001

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 : 0.170 / q_NPA : -0.009

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	-0.028	0.087	4.417	1.374	1.672	-0.001	-0.109	-0.188	0.000
5	J	3	ASP	0	0.098	-0.137	2.849	-2.338	-0.721	0.058	-0.803	-0.871	0.001
6	J	3	ASP	-1	-0.965	-0.808	3.837	1.426	1.822	0.004	-0.200	-0.201	-0.001
7	J	4	GLU	0	0.073	-0.151	3.000	0.174	0.525	0.059	-0.113	-0.296	0.001
8	J	4	GLU	-1	-0.975	-0.799	3.607	-2.416	-2.178	0.021	-0.069	-0.191	0.000
9	J	5	LEU	0	0.078	-0.126	4.707	0.161	0.209	-0.002	-0.015	-0.032	0.000
10	J	5	LEU	0	-0.098	0.119	6.137	-0.021	-0.021	0.000	0.000	0.000	0.000
11	J	6	LYS	0	0.099	-0.086	6.561	0.209	0.209	0.000	0.000	0.000	0.000
12	J	6	LYS	1	0.858	1.068	7.713	-0.575	-0.575	0.000	0.000	0.000	0.000
13	J	7	SER	0	0.013	-0.093	7.663	0.099	0.099	0.000	0.000	0.000	0.000
14	J	7	SER	0	-0.017	0.095	7.743	0.031	0.031	0.000	0.000	0.000	0.000
15	J	8	TYR	0	0.112	-0.072	8.918	0.106	0.106	0.000	0.000	0.000	0.000
16	J	8	TYR	0	-0.072	0.099	9.675	-0.006	-0.006	0.000	0.000	0.000	0.000
17	J	9	GLU	0	0.021	-0.151	10.553	0.030	0.030	0.000	0.000	0.000	0.000
18	J	9	GLU	-1	-0.976	-0.836	11.105	-0.229	-0.229	0.000	0.000	0.000	0.000
19	J	10	ALA	0	0.094	-0.106	11.986	0.039	0.039	0.000	0.000	0.000	0.000
20	J	10	ALA	0	-0.079	0.107	12.692	0.011	0.011	0.000	0.000	0.000	0.000
21	J	11	LEU	0	0.085	-0.113	13.243	0.043	0.043	0.000	0.000	0.000	0.000
22	J	11	LEU	0	-0.083	0.114	12.580	-0.012	-0.012	0.000	0.000	0.000	0.000
23	J	12	LYS	0	0.069	-0.102	14.916	0.018	0.018	0.000	0.000	0.000	0.000
24	J	12	LYS	1	0.765	1.032	14.270	0.294	0.294	0.000	0.000	0.000	0.000
25	J	13	ALA	0	0.039	-0.112	16.775	0.005	0.005	0.000	0.000	0.000	0.000
26	J	13	ALA	0	-0.057	0.107	17.724	0.006	0.006	0.000	0.000	0.000	0.000
27	J	14	GLU	0	0.086	-0.166	17.763	0.017	0.017	0.000	0.000	0.000	0.000
28	J	14	GLU	-1	-0.993	-0.806	17.297	-0.073	-0.073	0.000	0.000	0.000	0.000
29	J	15	LEU	0	0.108	-0.113	19.137	0.017	0.017	0.000	0.000	0.000	0.000
30	J	15	LEU	0	-0.113	0.113	19.437	-0.004	-0.004	0.000	0.000	0.000	0.000
31	J	16	LYS	0	0.077	-0.096	20.999	0.003	0.003	0.000	0.000	0.000	0.000
32	J	16	LYS	1	0.854	1.055	21.111	0.108	0.108	0.000	0.000	0.000	0.000
33	J	17	LYS	0	0.099	-0.065	22.721	0.005	0.005	0.000	0.000	0.000	0.000
34	J	17	LYS	1	0.869	1.070	23.334	0.004	0.004	0.000	0.000	0.000	0.000
35	J	18	SER	0	0.110	-0.038	23.509	0.009	0.009	0.000	0.000	0.000	0.000
36	J	18	SER	0	-0.043	0.059	23.455	0.000	0.000	0.000	0.000	0.000	0.000
37	J	19	LEU	0	-0.024	-0.136	24.972	0.004	0.004	0.000	0.000	0.000	0.000
38	J	19	LEU	0	-0.124	0.072	24.652	-0.002	-0.002	0.000	0.000	0.000	0.000
39	J	20	GLN	0	0.130	-0.070	26.899	0.000	0.000	0.000	0.000	0.000	0.000
40	J	20	GLN	0	-0.120	0.084	28.046	0.002	0.002	0.000	0.000	0.000	0.000
41	J	21	ASP	0	0.176	-0.088	28.368	0.003	0.003	0.000	0.000	0.000	0.000
42	J	21	ASP	-1	-1.017	-0.840	28.768	-0.033	-0.033	0.000	0.000	0.000	0.000
43	J	22	ARG	0	0.129	-0.076	29.289	0.004	0.004	0.000	0.000	0.000	0.000
44	J	22	ARG	1	0.782	1.031	28.765	0.080	0.080	0.000	0.000	0.000	0.000
45	J	23	ARG	0	0.059	-0.102	31.007	0.001	0.001	0.000	0.000	0.000	0.000
46	J	23	ARG	1	0.807	1.051	32.068	0.046	0.046	0.000	0.000	0.000	0.000
47	J	24	GLU	0	0.082	-0.122	32.917	0.000	0.000	0.000	0.000	0.000	0.000
48	J	24	GLU	-1	-0.982	-0.829	32.764	-0.024	-0.024	0.000	0.000	0.000	0.000
49	J	25	GLN	0	0.101	-0.091	34.088	0.004	0.004	0.000	0.000	0.000	0.000
50	J	25	GLN	0	-0.106	0.079	33.666	0.002	0.002	0.000	0.000	0.000	0.000
51	J	26	GLU	0	0.038	-0.142	35.466	0.003	0.003	0.000	0.000	0.000	0.000
52	J	26	GLU	-1	-1.000	-0.869	34.192	-0.060	-0.060	0.000	0.000	0.000	0.000
53	J	27	ASP	0	0.199	-0.059	37.380	0.001	0.001	0.000	0.000	0.000	0.000
54	J	27	ASP	-1	-1.063	-0.858	37.918	-0.037	-0.037	0.000	0.000	0.000	0.000
55	J	28	THR	0	-0.028	-0.117	39.052	0.002	0.002	0.000	0.000	0.000	0.000
56	J	28	THR	0	-0.066	0.069	38.462	0.001	0.001	0.000	0.000	0.000	0.000
57	J	29	PHE	0	0.110	-0.062	40.157	0.003	0.003	0.000	0.000	0.000	0.000
58	J	29	PHE	0	-0.106	0.074	40.119	-0.001	-0.001	0.000	0.000	0.000	0.000
59	J	30	ASP	0	0.039	-0.134	41.830	0.002	0.002	0.000	0.000	0.000	0.000
60	J	30	ASP	-1	-0.967	-0.833	41.529	-0.038	-0.038	0.000	0.000	0.000	0.000
61	J	31	ASN	0	0.093	-0.063	43.739	0.001	0.001	0.000	0.000	0.000	0.000
62	J	31	ASN	0	-0.121	0.049	43.995	-0.001	-0.001	0.000	0.000	0.000	0.000
63	J	32	LEU	0	0.069	-0.110	44.812	0.002	0.002	0.000	0.000	0.000	0.000
64	J	32	LEU	0	-0.117	0.098	43.097	0.000	0.000	0.000	0.000	0.000	0.000
65	J	33	GLN	0	0.173	-0.088	45.917	0.002	0.002	0.000	0.000	0.000	0.000
66	J	33	GLN	0	-0.122	0.100	45.834	0.001	0.001	0.000	0.000	0.000	0.000
67	J	34	GLN	0	0.055	-0.112	47.663	0.000	0.000	0.000	0.000	0.000	0.000
68	J	34	GLN	0	-0.121	0.086	49.360	-0.002	-0.002	0.000	0.000	0.000	0.000
69	J	35	GLU	0	0.120	-0.101	49.376	0.001	0.001	0.000	0.000	0.000	0.000
70	J	35	GLU	-1	-1.024	-0.856	49.431	-0.013	-0.013	0.000	0.000	0.000	0.000
71	J	36	ILE	0	0.036	-0.105	50.347	0.002	0.002	0.000	0.000	0.000	0.000
72	J	36	ILE	0	-0.084	0.094	48.399	0.000	0.000	0.000	0.000	0.000	0.000
73	J	37	TYR	0	0.136	-0.082	52.071	0.001	0.001	0.000	0.000	0.000	0.000
74	J	37	TYR	0	-0.122	0.088	53.102	0.000	0.000	0.000	0.000	0.000	0.000
75	J	38	ASP	0	0.133	-0.128	53.906	0.001	0.001	0.000	0.000	0.000	0.000
76	J	38	ASP	-1	-0.947	-0.799	53.973	-0.018	-0.018	0.000	0.000	0.000	0.000
77	J	39	LYS	0	0.119	-0.085	54.846	0.001	0.001	0.000	0.000	0.000	0.000
78	J	39	LYS	1	0.798	1.075	54.489	0.010	0.010	0.000	0.000	0.000	0.000
79	J	40	GLU	0	0.038	-0.127	56.293	0.001	0.001	0.000	0.000	0.000	0.000
80	J	40	GLU	-1	-0.826	-0.782	55.759	-0.019	-0.019	0.000	0.000	0.000	0.000
81	J	41	THR	0	-0.039	-0.109	58.186	0.001	0.001	0.000	0.000	0.000	0.000
82	J	41	THR	0	-0.113	0.007	58.302	0.000	0.000	0.000	0.000	0.000	0.000
83	J	42	GLU	0	0.074	-0.116	59.617	0.000	0.000	0.000	0.000	0.000	0.000
84	J	42	GLU	-1	-0.986	-0.824	58.777	-0.010	-0.010	0.000	0.000	0.000	0.000
85	J	43	TYR	0	0.009	-0.136	60.593	0.001	0.001	0.000	0.000	0.000	0.000
86	J	43	TYR	0	-0.082	0.101	57.406	0.000	0.000	0.000	0.000	0.000	0.000
87	J	44	PHE	0	-0.050	-0.118	62.025	0.001	0.001	0.000	0.000	0.000	0.000
88	J	44	PHE	0	-0.040	0.089	58.996	0.000	0.000	0.000	0.000	0.000	0.000
89	J	45	SER	0	0.090	-0.053	63.718	-0.001	-0.001	0.000	0.000	0.000	0.000
90	J	45	SER	0	-0.059	0.068	64.773	0.000	0.000	0.000	0.000	0.000	0.000
91	J	46	HIS	0	-0.065	-0.137	65.507	-0.001	-0.001	0.000	0.000	0.000	0.000
92	J	46	HIS	0	0.019	0.026	67.868	0.000	0.000	0.000	0.000	0.000	0.000
93	J	65	TYR	0	0.173	0.009	72.770	0.000	0.000	0.000	0.000	0.000	0.000
94	J	65	TYR	0	-0.161	0.037	68.549	0.000	0.000	0.000	0.000	0.000	0.000
95	J	66	SER	0	-0.050	-0.113	70.250	0.000	0.000	0.000	0.000	0.000	0.000
96	J	66	SER	0	-0.040	0.094	71.003	0.000	0.000	0.000	0.000	0.000	0.000
97	J	67	GLY	0	0.036	-0.068	68.485	0.000	0.000	0.000	0.000	0.000	0.000
98	J	68	ASN	0	0.045	-0.005	64.445	0.000	0.000	0.000	0.000	0.000	0.000
99	J	68	ASN	0	-0.119	0.030	63.649	-0.001	-0.001	0.000	0.000	0.000	0.000
100	J	69	ILE	0	0.064	-0.096	60.769	0.001	0.001	0.000	0.000	0.000	0.000
101	J	69	ILE	0	-0.037	0.116	58.659	0.000	0.000	0.000	0.000	0.000	0.000
102	J	70	ILE	0	0.067	-0.104	62.223	0.000	0.000	0.000	0.000	0.000	0.000
103	J	70	ILE	0	-0.077	0.130	59.786	0.000	0.000	0.000	0.000	0.000	0.000
104	J	71	LYS	0	0.046	-0.117	63.009	0.000	0.000	0.000	0.000	0.000	0.000
105	J	71	LYS	1	0.801	1.046	66.473	0.013	0.013	0.000	0.000	0.000	0.000
106	J	72	GLY	0	0.036	-0.082	66.258	0.000	0.000	0.000	0.000	0.000	0.000
107	J	73	PHE	0	0.096	0.000	67.198	0.000	0.000	0.000	0.000	0.000	0.000
108	J	73	PHE	0	-0.064	0.112	62.286	0.000	0.000	0.000	0.000	0.000	0.000
109	J	74	ASP	0	0.112	-0.101	68.241	0.001	0.001	0.000	0.000	0.000	0.000
110	J	74	ASP	-1	-0.987	-0.820	71.103	-0.007	-0.007	0.000	0.000	0.000	0.000
111	J	75	THR	0	0.025	-0.083	71.719	0.000	0.000	0.000	0.000	0.000	0.000
112	J	75	THR	0	-0.034	0.058	71.966	0.000	0.000	0.000	0.000	0.000	0.000
113	J	76	PHE	0	-0.004	-0.091	74.076	0.000	0.000	0.000	0.000	0.000	0.000
114	J	76	PHE	0	-0.100	0.083	72.479	0.000	0.000	0.000	0.000	0.000	0.000
115	J	77	SER	0	-0.070	-0.174	76.822	0.000	0.000	0.000	0.000	0.000	0.000
116	J	77	SER	0	0.098	0.087	77.112	0.000	0.000	0.000	0.000	0.000	0.000
117	J	86	SER	0	0.070	0.011	70.345	0.000	0.000	0.000	0.000	0.000	0.000
118	J	86	SER	0	-0.023	0.076	73.224	0.000	0.000	0.000	0.000	0.000	0.000
119	J	87	ALA	0	0.094	-0.070	69.930	0.001	0.001	0.000	0.000	0.000	0.000
120	J	87	ALA	0	-0.055	0.102	69.989	0.000	0.000	0.000	0.000	0.000	0.000
121	J	88	PHE	0	0.064	-0.129	65.627	0.000	0.000	0.000	0.000	0.000	0.000
122	J	88	PHE	0	-0.043	0.160	60.327	0.000	0.000	0.000	0.000	0.000	0.000
123	J	89	ASN	0	0.141	-0.057	64.996	0.000	0.000	0.000	0.000	0.000	0.000
124	J	89	ASN	0	-0.148	0.044	64.779	0.000	0.000	0.000	0.000	0.000	0.000
125	J	90	ASN	0	0.142	-0.071	61.062	0.000	0.000	0.000	0.000	0.000	0.000
126	J	90	ASN	0	-0.068	0.094	59.987	0.001	0.001	0.000	0.000	0.000	0.000
127	J	91	ASN	0	0.089	-0.072	59.554	-0.001	-0.001	0.000	0.000	0.000	0.000
128	J	91	ASN	0	-0.129	0.051	61.711	-0.001	-0.001	0.000	0.000	0.000	0.000
129	J	92	ASP	0	0.128	-0.092	60.571	-0.001	-0.001	0.000	0.000	0.000	0.000
130	J	92	ASP	-1	-1.011	-0.866	62.645	-0.016	-0.016	0.000	0.000	0.000	0.000
131	J	93	ARG	0	0.023	-0.093	57.725	0.001	0.001	0.000	0.000	0.000	0.000
132	J	93	ARG	1	0.760	1.033	56.768	0.018	0.018	0.000	0.000	0.000	0.000
133	J	94	ILE	0	0.107	-0.130	56.045	-0.001	-0.001	0.000	0.000	0.000	0.000
134	J	94	ILE	0	-0.095	0.100	56.567	0.000	0.000	0.000	0.000	0.000	0.000
135	J	95	PHE	0	0.103	-0.072	53.184	-0.001	-0.001	0.000	0.000	0.000	0.000
136	J	95	PHE	0	-0.103	0.066	52.822	0.000	0.000	0.000	0.000	0.000	0.000
137	J	96	SER	0	0.095	-0.034	51.592	-0.001	-0.001	0.000	0.000	0.000	0.000
138	J	96	SER	0	-0.044	0.067	53.019	0.000	0.000	0.000	0.000	0.000	0.000
139	J	97	LEU	0	0.056	-0.112	51.277	-0.002	-0.002	0.000	0.000	0.000	0.000
140	J	97	LEU	0	-0.097	0.096	54.624	0.000	0.000	0.000	0.000	0.000	0.000
141	J	98	SER	0	-0.017	-0.102	50.602	-0.001	-0.001	0.000	0.000	0.000	0.000
142	J	98	SER	0	-0.115	0.024	49.831	0.000	0.000	0.000	0.000	0.000	0.000
143	J	99	SER	0	-0.033	-0.122	47.050	-0.001	-0.001	0.000	0.000	0.000	0.000
144	J	99	SER	0	-0.017	0.101	46.276	-0.001	-0.001	0.000	0.000	0.000	0.000
145	J	100	ALA	0	0.158	-0.079	46.666	0.001	0.001	0.000	0.000	0.000	0.000
146	J	100	ALA	0	-0.091	0.102	45.759	0.000	0.000	0.000	0.000	0.000	0.000
147	J	101	THR	0	-0.050	-0.097	45.535	-0.001	-0.001	0.000	0.000	0.000	0.000
148	J	101	THR	0	-0.034	0.056	43.598	0.000	0.000	0.000	0.000	0.000	0.000
149	J	102	TYR	0	-0.075	-0.103	46.576	-0.001	-0.001	0.000	0.000	0.000	0.000
150	J	102	TYR	0	0.032	0.021	50.098	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)