FMO DATABASE

FMODB ID: YYKK2

Calculation Name: 5J9T-J-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9T

Chain ID: J

ChEMBL ID:

UniProt ID: P47128

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-405212.035246
FMO2-HF: Nuclear repulsion	374075.380485
FMO2-HF: Total energy	-31136.654761
FMO2-MP2: Total energy	-31228.178106

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.
-1.933	-1.495	10.852	-3.053	-8.238	-0.029

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 : 0.011 / 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

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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].
3	J	3	ASP	-1	-0.880	-0.947	1.783	-0.465	-0.474	7.647	-2.770	-4.869	-0.019
4	J	4	GLU	-1	-0.916	-0.978	2.045	-5.009	-5.134	3.202	-0.190	-2.887	-0.010
5	J	5	LEU	0	-0.022	0.001	3.645	0.809	1.381	0.003	-0.093	-0.482	0.000
6	J	6	LYS	1	0.969	0.977	5.441	1.330	1.330	0.000	0.000	0.000	0.000
7	J	7	SER	0	-0.008	-0.004	6.726	0.485	0.485	0.000	0.000	0.000	0.000
8	J	8	TYR	0	0.003	0.010	7.800	0.374	0.374	0.000	0.000	0.000	0.000
9	J	9	GLU	-1	-0.909	-0.964	9.598	-0.373	-0.373	0.000	0.000	0.000	0.000
10	J	10	ALA	0	-0.035	-0.008	11.504	0.156	0.156	0.000	0.000	0.000	0.000
11	J	11	LEU	0	0.070	0.026	12.101	0.099	0.099	0.000	0.000	0.000	0.000
12	J	12	LYS	1	0.902	0.965	12.611	0.622	0.622	0.000	0.000	0.000	0.000
13	J	13	ALA	0	-0.049	-0.021	15.672	0.079	0.079	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.919	-0.964	17.184	-0.436	-0.436	0.000	0.000	0.000	0.000
15	J	15	LEU	0	0.004	0.001	18.229	0.042	0.042	0.000	0.000	0.000	0.000
16	J	16	LYS	1	0.921	0.948	18.905	0.306	0.306	0.000	0.000	0.000	0.000
17	J	17	LYS	1	0.962	0.993	21.685	0.236	0.236	0.000	0.000	0.000	0.000
18	J	18	SER	0	0.031	0.016	22.178	0.022	0.022	0.000	0.000	0.000	0.000
19	J	19	LEU	0	-0.055	-0.031	22.904	0.017	0.017	0.000	0.000	0.000	0.000
20	J	20	GLN	0	-0.081	-0.036	25.920	0.011	0.011	0.000	0.000	0.000	0.000
21	J	21	ASP	-1	-0.866	-0.937	27.587	-0.161	-0.161	0.000	0.000	0.000	0.000
22	J	22	ARG	1	0.938	0.969	28.065	0.218	0.218	0.000	0.000	0.000	0.000
23	J	23	ARG	1	0.934	0.969	27.420	0.170	0.170	0.000	0.000	0.000	0.000
24	J	24	GLU	-1	-0.839	-0.905	31.935	-0.124	-0.124	0.000	0.000	0.000	0.000
25	J	25	GLN	0	-0.046	-0.028	32.484	0.016	0.016	0.000	0.000	0.000	0.000
26	J	26	GLU	-1	-0.980	-0.993	33.564	-0.144	-0.144	0.000	0.000	0.000	0.000
27	J	27	ASP	-1	-0.866	-0.924	36.495	-0.101	-0.101	0.000	0.000	0.000	0.000
28	J	28	THR	0	-0.083	-0.054	37.709	0.009	0.009	0.000	0.000	0.000	0.000
29	J	29	PHE	0	-0.079	-0.035	39.213	0.005	0.005	0.000	0.000	0.000	0.000
30	J	30	ASP	-1	-0.868	-0.942	40.669	-0.095	-0.095	0.000	0.000	0.000	0.000
31	J	31	ASN	0	-0.035	-0.013	42.551	0.007	0.007	0.000	0.000	0.000	0.000
32	J	32	LEU	0	0.011	0.007	42.422	0.004	0.004	0.000	0.000	0.000	0.000
33	J	33	GLN	0	0.031	0.043	45.112	0.000	0.000	0.000	0.000	0.000	0.000
34	J	34	GLN	0	-0.016	-0.007	46.932	0.001	0.001	0.000	0.000	0.000	0.000
35	J	35	GLU	-1	-0.932	-0.968	48.488	-0.061	-0.061	0.000	0.000	0.000	0.000
36	J	36	ILE	0	-0.049	-0.034	47.594	0.003	0.003	0.000	0.000	0.000	0.000
37	J	37	TYR	0	-0.013	0.003	51.240	0.004	0.004	0.000	0.000	0.000	0.000
38	J	38	ASP	-1	-0.860	-0.947	53.050	-0.052	-0.052	0.000	0.000	0.000	0.000
39	J	39	LYS	1	0.921	0.951	53.221	0.056	0.056	0.000	0.000	0.000	0.000
40	J	40	GLU	-1	-0.776	-0.850	55.139	-0.060	-0.060	0.000	0.000	0.000	0.000
41	J	41	THR	0	-0.029	-0.013	57.419	0.002	0.002	0.000	0.000	0.000	0.000
42	J	42	GLU	-1	-0.967	-0.982	58.587	-0.042	-0.042	0.000	0.000	0.000	0.000
43	J	43	TYR	0	-0.018	-0.009	56.802	0.001	0.001	0.000	0.000	0.000	0.000
44	J	44	PHE	0	-0.052	-0.032	58.242	0.001	0.001	0.000	0.000	0.000	0.000
45	J	45	SER	0	-0.072	-0.014	62.604	0.001	0.001	0.000	0.000	0.000	0.000
46	J	46	HIS	0	-0.011	0.003	62.368	0.003	0.003	0.000	0.000	0.000	0.000
47	J	65	TYR	0	-0.007	-0.021	72.204	0.000	0.000	0.000	0.000	0.000	0.000
48	J	66	SER	0	0.041	0.011	69.567	0.001	0.001	0.000	0.000	0.000	0.000
49	J	67	GLY	0	-0.014	0.014	68.864	-0.001	-0.001	0.000	0.000	0.000	0.000
50	J	68	ASN	0	0.004	-0.013	63.532	-0.001	-0.001	0.000	0.000	0.000	0.000
51	J	69	ILE	0	0.037	0.011	58.912	0.000	0.000	0.000	0.000	0.000	0.000
52	J	70	ILE	0	-0.044	0.000	59.338	-0.001	-0.001	0.000	0.000	0.000	0.000
53	J	71	LYS	1	0.921	0.956	62.789	0.045	0.045	0.000	0.000	0.000	0.000
54	J	72	GLY	0	0.005	0.011	66.255	0.000	0.000	0.000	0.000	0.000	0.000
55	J	73	PHE	0	-0.007	-0.017	62.738	0.000	0.000	0.000	0.000	0.000	0.000
56	J	74	ASP	-1	-0.986	-0.964	68.591	-0.036	-0.036	0.000	0.000	0.000	0.000
57	J	75	THR	0	-0.015	-0.006	71.930	0.001	0.001	0.000	0.000	0.000	0.000
58	J	87	ALA	0	-0.022	-0.019	69.437	0.000	0.000	0.000	0.000	0.000	0.000
59	J	88	PHE	0	-0.009	-0.006	59.594	-0.001	-0.001	0.000	0.000	0.000	0.000
60	J	89	ASN	0	0.051	0.036	64.106	0.001	0.001	0.000	0.000	0.000	0.000
61	J	90	ASN	0	0.053	0.006	59.351	-0.001	-0.001	0.000	0.000	0.000	0.000
62	J	91	ASN	0	-0.062	-0.039	58.808	-0.001	-0.001	0.000	0.000	0.000	0.000
63	J	92	ASP	-1	-0.853	-0.928	59.954	-0.050	-0.050	0.000	0.000	0.000	0.000
64	J	93	ARG	1	0.798	0.917	55.870	0.055	0.055	0.000	0.000	0.000	0.000
65	J	94	ILE	0	0.017	-0.006	55.323	-0.003	-0.003	0.000	0.000	0.000	0.000
66	J	95	PHE	0	-0.010	-0.002	52.447	-0.002	-0.002	0.000	0.000	0.000	0.000
67	J	96	SER	0	0.003	-0.025	50.960	-0.004	-0.004	0.000	0.000	0.000	0.000
68	J	97	LEU	0	-0.046	-0.032	50.519	-0.003	-0.003	0.000	0.000	0.000	0.000
69	J	98	SER	0	-0.117	-0.049	49.437	-0.003	-0.003	0.000	0.000	0.000	0.000
70	J	99	SER	0	-0.041	-0.029	45.934	-0.006	-0.006	0.000	0.000	0.000	0.000
71	J	100	ALA	0	0.027	-0.013	45.600	0.003	0.003	0.000	0.000	0.000	0.000
72	J	101	THR	0	-0.033	-0.027	42.431	0.000	0.000	0.000	0.000	0.000	0.000
73	J	102	TYR	0	0.018	0.013	45.441	0.003	0.003	0.000	0.000	0.000	0.000
74	J	103	VAL	0	-0.039	-0.004	48.639	0.003	0.003	0.000	0.000	0.000	0.000
75	J	104	LYS	1	0.925	0.978	44.177	0.102	0.102	0.000	0.000	0.000	0.000

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