FMO DATABASE

FMODB ID: 82ZZY

Calculation Name: 5J9T-F-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9T

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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-368848.458154
FMO2-HF: Nuclear repulsion	340728.649418
FMO2-HF: Total energy	-28119.808736
FMO2-MP2: Total energy	-28203.465431

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:7:SER)

Summations of interaction energy for fragment #1(F:7:SER)

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.
-4.588	-0.505	0.261	-1.764	-2.577	0.002

Interaction energy analysis for fragmet #1(F:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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].
3	F	9	GLU	-1	-0.788	-0.900	3.067	-3.199	-0.508	0.084	-1.316	-1.458	0.004
4	F	10	ALA	0	-0.007	0.005	2.548	-1.032	-0.022	0.177	-0.362	-0.824	-0.002
5	F	11	LEU	0	0.050	0.026	4.270	0.379	0.761	0.000	-0.086	-0.295	0.000
6	F	12	LYS	1	0.820	0.897	6.248	-0.711	-0.711	0.000	0.000	0.000	0.000
7	F	13	ALA	0	-0.041	-0.019	7.276	0.028	0.028	0.000	0.000	0.000	0.000
8	F	14	GLU	-1	-0.913	-0.966	8.030	0.063	0.063	0.000	0.000	0.000	0.000
9	F	15	LEU	0	0.021	0.022	10.246	0.032	0.032	0.000	0.000	0.000	0.000
10	F	16	LYS	1	0.950	0.963	12.035	-0.233	-0.233	0.000	0.000	0.000	0.000
11	F	17	LYS	1	0.956	0.993	13.053	0.070	0.070	0.000	0.000	0.000	0.000
12	F	18	SER	0	0.028	0.006	13.556	0.005	0.005	0.000	0.000	0.000	0.000
13	F	19	LEU	0	-0.048	-0.025	16.073	0.001	0.001	0.000	0.000	0.000	0.000
14	F	20	GLN	0	-0.075	-0.047	17.696	0.006	0.006	0.000	0.000	0.000	0.000
15	F	21	ASP	-1	-0.859	-0.919	18.926	0.032	0.032	0.000	0.000	0.000	0.000
16	F	22	ARG	1	0.811	0.883	20.285	-0.098	-0.098	0.000	0.000	0.000	0.000
17	F	23	ARG	1	0.812	0.881	22.150	-0.060	-0.060	0.000	0.000	0.000	0.000
18	F	24	GLU	-1	-0.860	-0.917	23.059	0.022	0.022	0.000	0.000	0.000	0.000
19	F	25	GLN	0	-0.057	-0.051	23.592	-0.005	-0.005	0.000	0.000	0.000	0.000
20	F	26	GLU	-1	-0.848	-0.906	25.725	0.074	0.074	0.000	0.000	0.000	0.000
21	F	27	ASP	-1	-0.768	-0.841	28.161	0.045	0.045	0.000	0.000	0.000	0.000
22	F	28	THR	0	-0.007	0.000	29.046	-0.004	-0.004	0.000	0.000	0.000	0.000
23	F	29	PHE	0	-0.069	-0.025	30.710	-0.003	-0.003	0.000	0.000	0.000	0.000
24	F	30	ASP	-1	-0.877	-0.948	32.438	0.039	0.039	0.000	0.000	0.000	0.000
25	F	31	ASN	0	-0.094	-0.059	33.474	-0.003	-0.003	0.000	0.000	0.000	0.000
26	F	32	LEU	0	0.024	0.023	33.526	-0.002	-0.002	0.000	0.000	0.000	0.000
27	F	33	GLN	0	0.014	0.033	36.516	0.000	0.000	0.000	0.000	0.000	0.000
28	F	34	GLN	0	-0.046	-0.030	38.755	0.000	0.000	0.000	0.000	0.000	0.000
29	F	35	GLU	-1	-0.876	-0.948	39.735	0.013	0.013	0.000	0.000	0.000	0.000
30	F	36	ILE	0	-0.050	-0.033	39.238	-0.002	-0.002	0.000	0.000	0.000	0.000
31	F	37	TYR	0	-0.026	0.000	42.703	-0.001	-0.001	0.000	0.000	0.000	0.000
32	F	38	ASP	-1	-0.797	-0.897	44.535	0.018	0.018	0.000	0.000	0.000	0.000
33	F	39	LYS	1	0.807	0.899	44.554	-0.012	-0.012	0.000	0.000	0.000	0.000
34	F	40	GLU	-1	-0.788	-0.870	46.613	0.016	0.016	0.000	0.000	0.000	0.000
35	F	41	THR	0	-0.037	-0.016	48.838	0.000	0.000	0.000	0.000	0.000	0.000
36	F	42	GLU	-1	-0.859	-0.921	48.917	0.010	0.010	0.000	0.000	0.000	0.000
37	F	43	TYR	0	-0.031	-0.018	47.199	-0.001	-0.001	0.000	0.000	0.000	0.000
38	F	44	PHE	0	-0.035	-0.016	49.488	-0.001	-0.001	0.000	0.000	0.000	0.000
39	F	45	SER	0	-0.064	-0.018	54.382	0.000	0.000	0.000	0.000	0.000	0.000
40	F	66	SER	0	-0.028	-0.025	61.912	0.000	0.000	0.000	0.000	0.000	0.000
41	F	67	GLY	0	0.053	0.040	59.856	0.000	0.000	0.000	0.000	0.000	0.000
42	F	68	ASN	0	-0.029	-0.030	54.471	0.000	0.000	0.000	0.000	0.000	0.000
43	F	69	ILE	0	0.091	0.049	50.031	0.000	0.000	0.000	0.000	0.000	0.000
44	F	70	ILE	0	-0.046	-0.019	50.699	0.000	0.000	0.000	0.000	0.000	0.000
45	F	71	LYS	1	0.812	0.873	54.146	-0.010	-0.010	0.000	0.000	0.000	0.000
46	F	72	GLY	0	0.030	0.017	57.417	0.000	0.000	0.000	0.000	0.000	0.000
47	F	73	PHE	0	-0.097	-0.034	53.166	0.000	0.000	0.000	0.000	0.000	0.000
48	F	74	ASP	-1	-0.930	-0.942	59.277	0.003	0.003	0.000	0.000	0.000	0.000
49	F	88	PHE	0	0.053	0.028	51.627	0.000	0.000	0.000	0.000	0.000	0.000
50	F	89	ASN	0	-0.068	-0.063	55.649	0.001	0.001	0.000	0.000	0.000	0.000
51	F	90	ASN	0	0.060	0.031	50.287	0.000	0.000	0.000	0.000	0.000	0.000
52	F	91	ASN	0	-0.060	-0.037	51.169	0.001	0.001	0.000	0.000	0.000	0.000
53	F	92	ASP	-1	-0.815	-0.884	52.326	0.011	0.011	0.000	0.000	0.000	0.000
54	F	93	ARG	1	0.808	0.911	47.843	-0.018	-0.018	0.000	0.000	0.000	0.000
55	F	94	ILE	0	0.010	-0.007	47.443	0.001	0.001	0.000	0.000	0.000	0.000
56	F	95	PHE	0	-0.004	0.003	43.959	0.000	0.000	0.000	0.000	0.000	0.000
57	F	96	SER	0	0.018	-0.027	42.816	0.001	0.001	0.000	0.000	0.000	0.000
58	F	97	LEU	0	-0.091	-0.049	42.832	0.002	0.002	0.000	0.000	0.000	0.000
59	F	98	SER	0	-0.042	-0.007	41.382	0.000	0.000	0.000	0.000	0.000	0.000
60	F	99	SER	0	-0.054	-0.028	38.103	0.002	0.002	0.000	0.000	0.000	0.000
61	F	100	ALA	0	0.033	-0.008	38.345	0.000	0.000	0.000	0.000	0.000	0.000
62	F	101	THR	0	-0.004	-0.011	35.521	0.001	0.001	0.000	0.000	0.000	0.000
63	F	102	TYR	0	0.022	0.001	38.567	0.000	0.000	0.000	0.000	0.000	0.000
64	F	103	VAL	0	0.006	0.003	41.735	0.000	0.000	0.000	0.000	0.000	0.000
65	F	104	LYS	1	0.921	0.951	37.029	-0.042	-0.042	0.000	0.000	0.000	0.000
66	F	105	GLN	0	0.010	0.019	41.532	-0.001	-0.001	0.000	0.000	0.000	0.000
67	F	106	GLN	0	0.024	0.028	43.323	-0.002	-0.002	0.000	0.000	0.000	0.000
68	F	107	HIS	1	0.870	0.955	45.557	-0.024	-0.024	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(F:7:SER)