FMO DATABASE

FMODB ID: 6GMKZ

Calculation Name: 5J9U-B-Xray540

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9U

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	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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-442971.991864
FMO2-HF: Nuclear repulsion	410151.138806
FMO2-HF: Total energy	-32820.853059
FMO2-MP2: Total energy	-32917.010907

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(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.
-2.921	0.63	0.08	-1.644	-1.989	-0.002

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 : 0.185 / q_NPA : 0.002

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	-0.039	0.065	4.418	1.247	1.553	0.000	-0.117	-0.189	0.000
5	B	3	ASP	0	0.031	-0.135	2.878	-2.157	-0.518	0.033	-0.791	-0.881	0.002
6	B	3	ASP	-1	-0.912	-0.808	3.301	0.170	1.263	0.030	-0.605	-0.519	-0.005
7	B	4	GLU	0	0.108	-0.137	3.340	0.218	0.479	0.013	-0.079	-0.196	0.001
8	B	4	GLU	-1	-0.993	-0.800	3.832	-2.305	-2.086	0.006	-0.047	-0.178	0.000
9	B	5	LEU	0	0.087	-0.111	5.054	0.172	0.205	-0.002	-0.005	-0.026	0.000
10	B	5	LEU	0	-0.099	0.103	6.431	-0.007	-0.007	0.000	0.000	0.000	0.000
11	B	6	LYS	0	0.028	-0.103	6.959	0.146	0.146	0.000	0.000	0.000	0.000
12	B	6	LYS	1	0.871	1.060	7.643	-0.848	-0.848	0.000	0.000	0.000	0.000
13	B	7	SER	0	0.052	-0.092	8.032	0.094	0.094	0.000	0.000	0.000	0.000
14	B	7	SER	0	-0.023	0.093	7.980	0.030	0.030	0.000	0.000	0.000	0.000
15	B	8	TYR	0	0.089	-0.076	9.226	0.093	0.093	0.000	0.000	0.000	0.000
16	B	8	TYR	0	-0.081	0.096	9.901	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	9	GLU	0	0.048	-0.139	11.140	0.016	0.016	0.000	0.000	0.000	0.000
18	B	9	GLU	-1	-0.983	-0.841	11.790	-0.202	-0.202	0.000	0.000	0.000	0.000
19	B	10	ALA	0	0.098	-0.101	12.685	0.030	0.030	0.000	0.000	0.000	0.000
20	B	10	ALA	0	-0.070	0.115	13.318	0.010	0.010	0.000	0.000	0.000	0.000
21	B	11	LEU	0	0.094	-0.104	13.634	0.037	0.037	0.000	0.000	0.000	0.000
22	B	11	LEU	0	-0.074	0.114	12.603	-0.012	-0.012	0.000	0.000	0.000	0.000
23	B	12	LYS	0	0.074	-0.105	15.169	0.015	0.015	0.000	0.000	0.000	0.000
24	B	12	LYS	1	0.787	1.047	14.587	0.286	0.286	0.000	0.000	0.000	0.000
25	B	13	ALA	0	0.073	-0.105	17.086	0.005	0.005	0.000	0.000	0.000	0.000
26	B	13	ALA	0	-0.047	0.117	18.113	0.006	0.006	0.000	0.000	0.000	0.000
27	B	14	GLU	0	0.086	-0.167	18.208	0.017	0.017	0.000	0.000	0.000	0.000
28	B	14	GLU	-1	-1.000	-0.803	18.065	-0.073	-0.073	0.000	0.000	0.000	0.000
29	B	15	LEU	0	0.105	-0.129	19.428	0.016	0.016	0.000	0.000	0.000	0.000
30	B	15	LEU	0	-0.122	0.113	19.630	-0.005	-0.005	0.000	0.000	0.000	0.000
31	B	16	LYS	0	0.001	-0.128	21.229	0.002	0.002	0.000	0.000	0.000	0.000
32	B	16	LYS	1	0.827	1.060	21.015	0.108	0.108	0.000	0.000	0.000	0.000
33	B	17	LYS	0	0.132	-0.058	23.182	0.004	0.004	0.000	0.000	0.000	0.000
34	B	17	LYS	1	0.887	1.075	24.127	0.011	0.011	0.000	0.000	0.000	0.000
35	B	18	SER	0	0.111	-0.040	23.887	0.009	0.009	0.000	0.000	0.000	0.000
36	B	18	SER	0	-0.036	0.065	23.740	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	19	LEU	0	-0.020	-0.137	25.201	0.004	0.004	0.000	0.000	0.000	0.000
38	B	19	LEU	0	-0.121	0.078	24.622	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	20	GLN	0	0.120	-0.073	27.050	0.000	0.000	0.000	0.000	0.000	0.000
40	B	20	GLN	0	-0.139	0.072	28.336	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	21	ASP	0	0.154	-0.103	28.676	0.003	0.003	0.000	0.000	0.000	0.000
42	B	21	ASP	-1	-1.000	-0.835	29.050	-0.038	-0.038	0.000	0.000	0.000	0.000
43	B	22	ARG	0	0.141	-0.073	29.605	0.005	0.005	0.000	0.000	0.000	0.000
44	B	22	ARG	1	0.790	1.049	28.600	0.084	0.084	0.000	0.000	0.000	0.000
45	B	23	ARG	0	0.064	-0.110	31.322	0.001	0.001	0.000	0.000	0.000	0.000
46	B	23	ARG	1	0.815	1.056	32.316	0.049	0.049	0.000	0.000	0.000	0.000
47	B	24	GLU	0	0.062	-0.122	33.159	0.001	0.001	0.000	0.000	0.000	0.000
48	B	24	GLU	-1	-0.958	-0.825	32.841	-0.028	-0.028	0.000	0.000	0.000	0.000
49	B	25	GLN	0	0.115	-0.089	34.349	0.004	0.004	0.000	0.000	0.000	0.000
50	B	25	GLN	0	-0.102	0.092	33.909	0.000	0.000	0.000	0.000	0.000	0.000
51	B	26	GLU	0	0.039	-0.138	35.674	0.003	0.003	0.000	0.000	0.000	0.000
52	B	26	GLU	-1	-1.009	-0.860	34.268	-0.064	-0.064	0.000	0.000	0.000	0.000
53	B	27	ASP	0	0.216	-0.068	37.574	0.001	0.001	0.000	0.000	0.000	0.000
54	B	27	ASP	-1	-1.065	-0.857	38.430	-0.039	-0.039	0.000	0.000	0.000	0.000
55	B	28	THR	0	-0.038	-0.122	39.109	0.002	0.002	0.000	0.000	0.000	0.000
56	B	28	THR	0	-0.086	0.055	38.632	0.002	0.002	0.000	0.000	0.000	0.000
57	B	29	PHE	0	0.086	-0.081	40.158	0.003	0.003	0.000	0.000	0.000	0.000
58	B	29	PHE	0	-0.133	0.064	40.134	0.000	0.000	0.000	0.000	0.000	0.000
59	B	30	ASP	0	0.016	-0.157	41.825	0.002	0.002	0.000	0.000	0.000	0.000
60	B	30	ASP	-1	-0.964	-0.821	41.732	-0.040	-0.040	0.000	0.000	0.000	0.000
61	B	31	ASN	0	0.100	-0.075	43.867	0.001	0.001	0.000	0.000	0.000	0.000
62	B	31	ASN	0	-0.112	0.064	44.064	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	32	LEU	0	0.110	-0.089	44.945	0.002	0.002	0.000	0.000	0.000	0.000
64	B	32	LEU	0	-0.115	0.103	43.188	0.000	0.000	0.000	0.000	0.000	0.000
65	B	33	GLN	0	0.112	-0.096	46.291	0.002	0.002	0.000	0.000	0.000	0.000
66	B	33	GLN	0	-0.054	0.100	45.792	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	34	GLN	0	0.087	-0.092	48.186	0.001	0.001	0.000	0.000	0.000	0.000
68	B	34	GLN	0	-0.100	0.101	49.381	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	35	GLU	0	0.127	-0.096	49.636	0.001	0.001	0.000	0.000	0.000	0.000
70	B	35	GLU	-1	-1.024	-0.856	49.747	-0.015	-0.015	0.000	0.000	0.000	0.000
71	B	36	ILE	0	0.029	-0.107	50.617	0.002	0.002	0.000	0.000	0.000	0.000
72	B	36	ILE	0	-0.098	0.080	48.614	0.000	0.000	0.000	0.000	0.000	0.000
73	B	37	TYR	0	0.132	-0.085	52.331	0.001	0.001	0.000	0.000	0.000	0.000
74	B	37	TYR	0	-0.124	0.085	53.254	0.000	0.000	0.000	0.000	0.000	0.000
75	B	38	ASP	0	0.095	-0.138	54.229	0.001	0.001	0.000	0.000	0.000	0.000
76	B	38	ASP	-1	-0.962	-0.814	54.353	-0.019	-0.019	0.000	0.000	0.000	0.000
77	B	39	LYS	0	0.088	-0.117	55.203	0.001	0.001	0.000	0.000	0.000	0.000
78	B	39	LYS	1	0.783	1.064	54.420	0.012	0.012	0.000	0.000	0.000	0.000
79	B	40	GLU	0	0.038	-0.112	56.596	0.001	0.001	0.000	0.000	0.000	0.000
80	B	40	GLU	-1	-0.832	-0.777	55.887	-0.021	-0.021	0.000	0.000	0.000	0.000
81	B	41	THR	0	-0.043	-0.088	58.463	0.001	0.001	0.000	0.000	0.000	0.000
82	B	41	THR	0	-0.024	0.068	58.860	0.000	0.000	0.000	0.000	0.000	0.000
83	B	42	GLU	0	0.105	-0.099	59.899	0.000	0.000	0.000	0.000	0.000	0.000
84	B	42	GLU	-1	-0.991	-0.839	59.188	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	43	TYR	0	0.031	-0.112	60.923	0.001	0.001	0.000	0.000	0.000	0.000
86	B	43	TYR	0	-0.081	0.089	57.592	0.000	0.000	0.000	0.000	0.000	0.000
87	B	44	PHE	0	0.041	-0.063	62.489	0.001	0.001	0.000	0.000	0.000	0.000
88	B	44	PHE	0	-0.089	0.045	59.482	0.000	0.000	0.000	0.000	0.000	0.000
89	B	45	SER	0	-0.013	-0.069	64.181	0.000	0.000	0.000	0.000	0.000	0.000
90	B	45	SER	0	-0.014	0.045	64.512	0.000	0.000	0.000	0.000	0.000	0.000
91	B	46	HIS	0	-0.103	-0.137	66.175	0.000	0.000	0.000	0.000	0.000	0.000
92	B	46	HIS	0	0.075	0.042	68.173	0.000	0.000	0.000	0.000	0.000	0.000
93	B	65	TYR	0	0.167	0.012	73.473	0.000	0.000	0.000	0.000	0.000	0.000
94	B	65	TYR	0	-0.127	0.074	69.094	0.000	0.000	0.000	0.000	0.000	0.000
95	B	66	SER	0	-0.029	-0.107	70.828	0.000	0.000	0.000	0.000	0.000	0.000
96	B	66	SER	0	-0.045	0.091	71.479	0.000	0.000	0.000	0.000	0.000	0.000
97	B	67	GLY	0	0.039	-0.071	69.016	0.000	0.000	0.000	0.000	0.000	0.000
98	B	68	ASN	0	0.043	0.007	64.985	0.000	0.000	0.000	0.000	0.000	0.000
99	B	68	ASN	0	-0.122	0.025	64.116	-0.001	-0.001	0.000	0.000	0.000	0.000
100	B	69	ILE	0	0.076	-0.111	61.103	0.001	0.001	0.000	0.000	0.000	0.000
101	B	69	ILE	0	-0.021	0.130	58.823	0.000	0.000	0.000	0.000	0.000	0.000
102	B	70	ILE	0	0.049	-0.100	62.607	0.000	0.000	0.000	0.000	0.000	0.000
103	B	70	ILE	0	-0.094	0.130	60.246	0.000	0.000	0.000	0.000	0.000	0.000
104	B	71	LYS	0	0.051	-0.111	63.417	0.000	0.000	0.000	0.000	0.000	0.000
105	B	71	LYS	1	0.849	1.075	67.060	0.013	0.013	0.000	0.000	0.000	0.000
106	B	72	GLY	0	0.035	-0.078	66.584	0.000	0.000	0.000	0.000	0.000	0.000
107	B	73	PHE	0	0.090	-0.009	67.447	0.000	0.000	0.000	0.000	0.000	0.000
108	B	73	PHE	0	-0.081	0.105	62.740	0.000	0.000	0.000	0.000	0.000	0.000
109	B	74	ASP	0	0.115	-0.123	68.597	0.001	0.001	0.000	0.000	0.000	0.000
110	B	74	ASP	-1	-1.007	-0.828	71.281	-0.007	-0.007	0.000	0.000	0.000	0.000
111	B	75	THR	0	-0.006	-0.119	71.983	0.000	0.000	0.000	0.000	0.000	0.000
112	B	75	THR	0	-0.079	0.072	71.801	0.000	0.000	0.000	0.000	0.000	0.000
113	B	76	PHE	0	-0.029	-0.094	74.306	0.000	0.000	0.000	0.000	0.000	0.000
114	B	76	PHE	0	0.032	0.022	73.029	0.000	0.000	0.000	0.000	0.000	0.000
115	B	86	SER	0	0.081	0.015	70.417	0.000	0.000	0.000	0.000	0.000	0.000
116	B	86	SER	0	-0.053	0.051	72.709	0.000	0.000	0.000	0.000	0.000	0.000
117	B	87	ALA	0	0.087	-0.121	69.953	0.001	0.001	0.000	0.000	0.000	0.000
118	B	87	ALA	0	-0.051	0.126	69.758	0.000	0.000	0.000	0.000	0.000	0.000
119	B	88	PHE	0	-0.011	-0.098	65.824	0.000	0.000	0.000	0.000	0.000	0.000
120	B	88	PHE	0	-0.035	0.129	60.529	0.000	0.000	0.000	0.000	0.000	0.000
121	B	89	ASN	0	0.156	-0.029	64.962	0.000	0.000	0.000	0.000	0.000	0.000
122	B	89	ASN	0	-0.147	0.037	64.862	0.000	0.000	0.000	0.000	0.000	0.000
123	B	90	ASN	0	0.157	-0.066	60.813	0.000	0.000	0.000	0.000	0.000	0.000
124	B	90	ASN	0	-0.061	0.101	59.739	0.001	0.001	0.000	0.000	0.000	0.000
125	B	91	ASN	0	0.104	-0.077	59.541	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	91	ASN	0	-0.124	0.054	61.835	-0.001	-0.001	0.000	0.000	0.000	0.000
127	B	92	ASP	0	0.110	-0.089	60.707	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	92	ASP	-1	-0.999	-0.874	62.841	-0.017	-0.017	0.000	0.000	0.000	0.000
129	B	93	ARG	0	0.029	-0.089	57.898	0.001	0.001	0.000	0.000	0.000	0.000
130	B	93	ARG	1	0.717	0.999	56.917	0.019	0.019	0.000	0.000	0.000	0.000
131	B	94	ILE	0	0.107	-0.133	56.233	-0.002	-0.002	0.000	0.000	0.000	0.000
132	B	94	ILE	0	-0.095	0.102	56.872	0.000	0.000	0.000	0.000	0.000	0.000
133	B	95	PHE	0	0.110	-0.069	53.470	-0.001	-0.001	0.000	0.000	0.000	0.000
134	B	95	PHE	0	-0.103	0.071	53.162	0.000	0.000	0.000	0.000	0.000	0.000
135	B	96	SER	0	0.099	-0.045	51.834	-0.001	-0.001	0.000	0.000	0.000	0.000
136	B	96	SER	0	-0.059	0.054	53.186	0.000	0.000	0.000	0.000	0.000	0.000
137	B	97	LEU	0	0.016	-0.124	51.442	-0.002	-0.002	0.000	0.000	0.000	0.000
138	B	97	LEU	0	-0.091	0.096	54.717	0.000	0.000	0.000	0.000	0.000	0.000
139	B	98	SER	0	-0.014	-0.104	50.798	-0.001	-0.001	0.000	0.000	0.000	0.000
140	B	98	SER	0	-0.099	0.039	50.038	0.000	0.000	0.000	0.000	0.000	0.000
141	B	99	SER	0	0.005	-0.104	47.242	-0.001	-0.001	0.000	0.000	0.000	0.000
142	B	99	SER	0	-0.023	0.093	46.439	0.000	0.000	0.000	0.000	0.000	0.000
143	B	100	ALA	0	0.182	-0.075	46.909	0.001	0.001	0.000	0.000	0.000	0.000
144	B	100	ALA	0	-0.078	0.110	46.011	0.000	0.000	0.000	0.000	0.000	0.000
145	B	101	THR	0	-0.093	-0.132	45.508	-0.001	-0.001	0.000	0.000	0.000	0.000
146	B	101	THR	0	-0.002	0.081	43.755	-0.001	-0.001	0.000	0.000	0.000	0.000
147	B	102	TYR	0	0.155	-0.086	46.604	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	102	TYR	0	-0.057	0.133	50.091	0.001	0.001	0.000	0.000	0.000	0.000
149	B	103	VAL	0	0.051	-0.101	50.110	0.001	0.001	0.000	0.000	0.000	0.000
150	B	103	VAL	0	-0.109	0.092	50.602	0.000	0.000	0.000	0.000	0.000	0.000
151	B	104	LYS	0	0.066	-0.087	48.791	0.001	0.001	0.000	0.000	0.000	0.000
152	B	104	LYS	1	0.837	1.028	44.226	0.047	0.047	0.000	0.000	0.000	0.000
153	B	105	GLN	0	0.056	-0.115	50.207	-0.001	-0.001	0.000	0.000	0.000	0.000
154	B	105	GLN	0	-0.076	0.124	49.308	0.000	0.000	0.000	0.000	0.000	0.000
155	B	106	GLN	0	-0.119	-0.146	50.986	0.001	0.001	0.000	0.000	0.000	0.000
156	B	106	GLN	0	0.054	0.045	54.263	-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)