FMO DATABASE

FMODB ID: R5J38

Calculation Name: 5J9U-F-Xray372

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

Total energy (hartree)

FMO2-HF: Electronic energy	-397396.596843
FMO2-HF: Nuclear repulsion	366354.572554
FMO2-HF: Total energy	-31042.024289
FMO2-MP2: Total energy	-31133.187608

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.
-1.589	1.832	0.067	-1.073	-2.416	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 : 0.071 / q_NPA : 0.014

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].
3	F	3	ASP	-1	-0.850	-0.915	2.896	-1.646	0.496	0.024	-0.826	-1.341	0.002
4	F	4	GLU	-1	-0.917	-0.945	3.174	-0.285	0.827	0.044	-0.221	-0.935	0.000
5	F	5	LEU	0	-0.007	-0.001	4.802	0.247	0.414	-0.001	-0.026	-0.140	0.000
6	F	6	LYS	1	0.879	0.924	6.749	-0.231	-0.231	0.000	0.000	0.000	0.000
7	F	7	SER	0	0.014	-0.002	7.614	0.130	0.130	0.000	0.000	0.000	0.000
8	F	8	TYR	0	0.026	0.016	9.117	0.069	0.069	0.000	0.000	0.000	0.000
9	F	9	GLU	-1	-0.837	-0.915	10.910	-0.039	-0.039	0.000	0.000	0.000	0.000
10	F	10	ALA	0	-0.049	-0.016	12.323	0.033	0.033	0.000	0.000	0.000	0.000
11	F	11	LEU	0	0.065	0.017	12.945	0.009	0.009	0.000	0.000	0.000	0.000
12	F	12	LYS	1	0.796	0.900	13.753	0.133	0.133	0.000	0.000	0.000	0.000
13	F	13	ALA	0	-0.063	-0.033	16.995	0.010	0.010	0.000	0.000	0.000	0.000
14	F	14	GLU	-1	-0.913	-0.958	18.006	-0.002	-0.002	0.000	0.000	0.000	0.000
15	F	15	LEU	0	0.003	0.004	19.447	0.001	0.001	0.000	0.000	0.000	0.000
16	F	16	LYS	1	0.913	0.949	19.155	0.009	0.009	0.000	0.000	0.000	0.000
17	F	17	LYS	1	0.954	0.988	22.908	-0.028	-0.028	0.000	0.000	0.000	0.000
18	F	18	SER	0	0.032	0.012	23.075	-0.001	-0.001	0.000	0.000	0.000	0.000
19	F	19	LEU	0	-0.035	-0.012	24.694	-0.001	-0.001	0.000	0.000	0.000	0.000
20	F	20	GLN	0	-0.080	-0.049	27.325	-0.002	-0.002	0.000	0.000	0.000	0.000
21	F	21	ASP	-1	-0.869	-0.934	28.620	-0.001	-0.001	0.000	0.000	0.000	0.000
22	F	22	ARG	1	0.831	0.897	29.274	0.033	0.033	0.000	0.000	0.000	0.000
23	F	23	ARG	1	0.770	0.861	31.485	0.014	0.014	0.000	0.000	0.000	0.000
24	F	24	GLU	-1	-0.830	-0.901	33.232	0.008	0.008	0.000	0.000	0.000	0.000
25	F	25	GLN	0	-0.056	-0.042	33.315	0.001	0.001	0.000	0.000	0.000	0.000
26	F	26	GLU	-1	-0.842	-0.909	33.840	-0.025	-0.025	0.000	0.000	0.000	0.000
27	F	27	ASP	-1	-0.780	-0.852	37.514	-0.008	-0.008	0.000	0.000	0.000	0.000
28	F	28	THR	0	-0.025	-0.014	38.778	0.002	0.002	0.000	0.000	0.000	0.000
29	F	29	PHE	0	-0.081	-0.032	40.166	0.001	0.001	0.000	0.000	0.000	0.000
30	F	30	ASP	-1	-0.892	-0.951	41.864	-0.013	-0.013	0.000	0.000	0.000	0.000
31	F	31	ASN	0	-0.103	-0.057	43.312	0.001	0.001	0.000	0.000	0.000	0.000
32	F	32	LEU	0	0.014	0.015	43.092	0.001	0.001	0.000	0.000	0.000	0.000
33	F	33	GLN	0	0.036	0.019	46.492	0.001	0.001	0.000	0.000	0.000	0.000
34	F	34	GLN	0	-0.033	-0.017	48.473	-0.001	-0.001	0.000	0.000	0.000	0.000
35	F	35	GLU	-1	-0.860	-0.939	49.498	0.002	0.002	0.000	0.000	0.000	0.000
36	F	36	ILE	0	-0.074	-0.041	48.395	0.000	0.000	0.000	0.000	0.000	0.000
37	F	37	TYR	0	-0.018	-0.004	52.166	0.000	0.000	0.000	0.000	0.000	0.000
38	F	38	ASP	-1	-0.825	-0.919	54.109	-0.003	-0.003	0.000	0.000	0.000	0.000
39	F	39	LYS	1	0.806	0.888	54.090	-0.002	-0.002	0.000	0.000	0.000	0.000
40	F	40	GLU	-1	-0.787	-0.886	56.098	-0.006	-0.006	0.000	0.000	0.000	0.000
41	F	41	THR	0	-0.030	-0.005	58.362	0.000	0.000	0.000	0.000	0.000	0.000
42	F	42	GLU	-1	-0.847	-0.876	58.718	0.002	0.002	0.000	0.000	0.000	0.000
43	F	43	TYR	0	-0.081	-0.053	57.164	0.001	0.001	0.000	0.000	0.000	0.000
44	F	44	PHE	0	-0.045	-0.018	58.804	0.000	0.000	0.000	0.000	0.000	0.000
45	F	45	SER	0	-0.059	-0.024	63.991	-0.001	-0.001	0.000	0.000	0.000	0.000
46	F	65	TYR	0	0.010	-0.002	68.461	0.000	0.000	0.000	0.000	0.000	0.000
47	F	66	SER	0	-0.045	-0.044	70.477	0.000	0.000	0.000	0.000	0.000	0.000
48	F	67	GLY	0	-0.006	0.013	68.611	0.000	0.000	0.000	0.000	0.000	0.000
49	F	68	ASN	0	-0.084	-0.043	64.011	0.000	0.000	0.000	0.000	0.000	0.000
50	F	69	ILE	0	0.055	0.021	58.562	0.000	0.000	0.000	0.000	0.000	0.000
51	F	70	ILE	0	-0.004	0.009	60.213	0.000	0.000	0.000	0.000	0.000	0.000
52	F	71	LYS	1	0.901	0.949	63.416	0.003	0.003	0.000	0.000	0.000	0.000
53	F	72	GLY	0	0.038	0.026	66.516	0.000	0.000	0.000	0.000	0.000	0.000
54	F	73	PHE	0	0.018	0.004	62.422	0.000	0.000	0.000	0.000	0.000	0.000
55	F	74	ASP	-1	-0.920	-0.948	68.406	0.000	0.000	0.000	0.000	0.000	0.000
56	F	75	THR	0	0.009	-0.006	71.406	0.000	0.000	0.000	0.000	0.000	0.000
57	F	76	PHE	0	-0.050	-0.008	72.419	0.000	0.000	0.000	0.000	0.000	0.000
58	F	77	SER	0	-0.013	-0.006	76.961	0.000	0.000	0.000	0.000	0.000	0.000
59	F	86	SER	0	0.016	0.003	70.334	0.000	0.000	0.000	0.000	0.000	0.000
60	F	87	ALA	0	-0.008	-0.012	70.065	0.001	0.001	0.000	0.000	0.000	0.000
61	F	88	PHE	0	0.037	0.022	60.414	0.000	0.000	0.000	0.000	0.000	0.000
62	F	89	ASN	0	-0.049	-0.035	64.981	0.000	0.000	0.000	0.000	0.000	0.000
63	F	90	ASN	0	0.059	0.025	60.288	0.001	0.001	0.000	0.000	0.000	0.000
64	F	91	ASN	0	-0.034	-0.022	59.916	-0.001	-0.001	0.000	0.000	0.000	0.000
65	F	92	ASP	-1	-0.844	-0.917	60.934	-0.007	-0.007	0.000	0.000	0.000	0.000
66	F	93	ARG	1	0.797	0.906	57.045	0.006	0.006	0.000	0.000	0.000	0.000
67	F	94	ILE	0	-0.009	-0.025	56.323	-0.001	-0.001	0.000	0.000	0.000	0.000
68	F	95	PHE	0	-0.025	-0.007	53.022	0.000	0.000	0.000	0.000	0.000	0.000
69	F	96	SER	0	0.045	0.018	51.848	-0.001	-0.001	0.000	0.000	0.000	0.000
70	F	97	LEU	0	-0.091	-0.044	51.729	-0.001	-0.001	0.000	0.000	0.000	0.000
71	F	98	SER	0	-0.098	-0.041	50.402	-0.001	-0.001	0.000	0.000	0.000	0.000
72	F	99	SER	0	-0.003	-0.001	46.730	-0.001	-0.001	0.000	0.000	0.000	0.000
73	F	100	ALA	0	0.008	-0.011	46.464	0.000	0.000	0.000	0.000	0.000	0.000
74	F	101	THR	0	-0.045	-0.018	44.495	0.000	0.000	0.000	0.000	0.000	0.000
75	F	102	TYR	0	-0.012	0.006	47.206	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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