FMO DATABASE

FMODB ID: VR111

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

Total energy (hartree)

FMO2-HF: Electronic energy	-405789.692726
FMO2-HF: Nuclear repulsion	374652.508079
FMO2-HF: Total energy	-31137.184647
FMO2-MP2: Total energy	-31228.774991

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.
-6.502	-1.654	7.509	-3.763	-8.594	-0.018

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 : 0.059 / q_NPA : 0.039

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	-0.830	-0.920	2.049	-1.951	1.466	3.776	-2.600	-4.592	-0.004
4	J	4	GLU	-1	-0.909	-0.967	1.854	-6.162	-5.300	3.731	-1.035	-3.558	-0.014
5	J	5	LEU	0	-0.026	-0.007	3.859	0.459	1.028	0.002	-0.128	-0.444	0.000
6	J	6	LYS	1	0.876	0.926	5.450	-0.013	-0.013	0.000	0.000	0.000	0.000
7	J	7	SER	0	0.006	0.004	6.568	0.319	0.319	0.000	0.000	0.000	0.000
8	J	8	TYR	0	0.009	0.009	7.956	0.273	0.273	0.000	0.000	0.000	0.000
9	J	9	GLU	-1	-0.812	-0.899	9.724	-0.553	-0.553	0.000	0.000	0.000	0.000
10	J	10	ALA	0	-0.021	-0.001	11.337	0.129	0.129	0.000	0.000	0.000	0.000
11	J	11	LEU	0	0.073	0.029	12.241	0.067	0.067	0.000	0.000	0.000	0.000
12	J	12	LYS	1	0.778	0.887	12.127	0.790	0.790	0.000	0.000	0.000	0.000
13	J	13	ALA	0	-0.052	-0.024	15.799	0.063	0.063	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.921	-0.963	16.898	-0.303	-0.303	0.000	0.000	0.000	0.000
15	J	15	LEU	0	0.009	0.003	18.365	0.034	0.034	0.000	0.000	0.000	0.000
16	J	16	LYS	1	0.934	0.956	18.759	0.321	0.321	0.000	0.000	0.000	0.000
17	J	17	LYS	1	0.957	0.992	21.783	0.170	0.170	0.000	0.000	0.000	0.000
18	J	18	SER	0	0.024	0.009	22.304	0.015	0.015	0.000	0.000	0.000	0.000
19	J	19	LEU	0	-0.035	-0.022	23.166	0.012	0.012	0.000	0.000	0.000	0.000
20	J	20	GLN	0	-0.087	-0.050	26.031	0.004	0.004	0.000	0.000	0.000	0.000
21	J	21	ASP	-1	-0.857	-0.919	27.692	-0.121	-0.121	0.000	0.000	0.000	0.000
22	J	22	ARG	1	0.826	0.885	28.468	0.164	0.164	0.000	0.000	0.000	0.000
23	J	23	ARG	1	0.901	0.952	27.463	0.155	0.155	0.000	0.000	0.000	0.000
24	J	24	GLU	-1	-0.822	-0.885	31.801	-0.100	-0.100	0.000	0.000	0.000	0.000
25	J	25	GLN	0	-0.049	-0.035	32.117	0.015	0.015	0.000	0.000	0.000	0.000
26	J	26	GLU	-1	-0.857	-0.910	33.308	-0.126	-0.126	0.000	0.000	0.000	0.000
27	J	27	ASP	-1	-0.865	-0.923	36.614	-0.085	-0.085	0.000	0.000	0.000	0.000
28	J	28	THR	0	-0.065	-0.036	37.711	0.008	0.008	0.000	0.000	0.000	0.000
29	J	29	PHE	0	-0.078	-0.033	39.325	0.005	0.005	0.000	0.000	0.000	0.000
30	J	30	ASP	-1	-0.864	-0.942	41.022	-0.076	-0.076	0.000	0.000	0.000	0.000
31	J	31	ASN	0	-0.096	-0.054	42.118	0.008	0.008	0.000	0.000	0.000	0.000
32	J	32	LEU	0	0.030	0.017	42.527	0.004	0.004	0.000	0.000	0.000	0.000
33	J	33	GLN	0	-0.001	0.031	45.221	0.001	0.001	0.000	0.000	0.000	0.000
34	J	34	GLN	0	-0.042	-0.035	47.037	0.001	0.001	0.000	0.000	0.000	0.000
35	J	35	GLU	-1	-0.920	-0.966	48.611	-0.045	-0.045	0.000	0.000	0.000	0.000
36	J	36	ILE	0	-0.041	-0.030	47.743	0.003	0.003	0.000	0.000	0.000	0.000
37	J	37	TYR	0	-0.010	0.006	51.356	0.003	0.003	0.000	0.000	0.000	0.000
38	J	38	ASP	-1	-0.831	-0.916	53.163	-0.042	-0.042	0.000	0.000	0.000	0.000
39	J	39	LYS	1	0.826	0.899	53.223	0.041	0.041	0.000	0.000	0.000	0.000
40	J	40	GLU	-1	-0.781	-0.857	55.284	-0.046	-0.046	0.000	0.000	0.000	0.000
41	J	41	THR	0	-0.017	-0.007	57.389	0.002	0.002	0.000	0.000	0.000	0.000
42	J	42	GLU	-1	-0.884	-0.926	58.207	-0.034	-0.034	0.000	0.000	0.000	0.000
43	J	43	TYR	0	-0.014	-0.012	56.391	0.001	0.001	0.000	0.000	0.000	0.000
44	J	44	PHE	0	-0.039	-0.024	58.017	0.001	0.001	0.000	0.000	0.000	0.000
45	J	45	SER	0	-0.073	-0.015	62.697	0.001	0.001	0.000	0.000	0.000	0.000
46	J	46	HIS	0	-0.033	-0.006	62.765	0.002	0.002	0.000	0.000	0.000	0.000
47	J	65	TYR	0	-0.005	-0.021	72.069	0.000	0.000	0.000	0.000	0.000	0.000
48	J	66	SER	0	0.029	0.004	69.332	0.001	0.001	0.000	0.000	0.000	0.000
49	J	67	GLY	0	-0.008	0.018	68.813	-0.001	-0.001	0.000	0.000	0.000	0.000
50	J	68	ASN	0	0.012	-0.011	63.612	-0.001	-0.001	0.000	0.000	0.000	0.000
51	J	69	ILE	0	0.029	0.006	58.840	0.000	0.000	0.000	0.000	0.000	0.000
52	J	70	ILE	0	-0.043	0.001	59.495	-0.001	-0.001	0.000	0.000	0.000	0.000
53	J	71	LYS	1	0.820	0.901	62.884	0.034	0.034	0.000	0.000	0.000	0.000
54	J	72	GLY	0	0.005	0.012	66.353	0.000	0.000	0.000	0.000	0.000	0.000
55	J	73	PHE	0	0.004	-0.012	62.469	0.000	0.000	0.000	0.000	0.000	0.000
56	J	74	ASP	-1	-0.954	-0.936	68.548	-0.024	-0.024	0.000	0.000	0.000	0.000
57	J	75	THR	0	-0.051	-0.036	71.882	0.001	0.001	0.000	0.000	0.000	0.000
58	J	87	ALA	0	-0.023	-0.024	69.526	0.000	0.000	0.000	0.000	0.000	0.000
59	J	88	PHE	0	-0.001	0.008	59.678	0.000	0.000	0.000	0.000	0.000	0.000
60	J	89	ASN	0	0.031	0.003	64.156	0.000	0.000	0.000	0.000	0.000	0.000
61	J	90	ASN	0	0.057	0.018	59.394	-0.001	-0.001	0.000	0.000	0.000	0.000
62	J	91	ASN	0	-0.049	-0.028	58.876	-0.001	-0.001	0.000	0.000	0.000	0.000
63	J	92	ASP	-1	-0.780	-0.882	60.019	-0.037	-0.037	0.000	0.000	0.000	0.000
64	J	93	ARG	1	0.801	0.903	55.931	0.044	0.044	0.000	0.000	0.000	0.000
65	J	94	ILE	0	0.016	-0.005	55.401	-0.002	-0.002	0.000	0.000	0.000	0.000
66	J	95	PHE	0	-0.012	-0.004	52.566	-0.002	-0.002	0.000	0.000	0.000	0.000
67	J	96	SER	0	0.013	-0.019	51.046	-0.003	-0.003	0.000	0.000	0.000	0.000
68	J	97	LEU	0	-0.051	-0.034	50.594	-0.003	-0.003	0.000	0.000	0.000	0.000
69	J	98	SER	0	-0.113	-0.038	49.619	-0.002	-0.002	0.000	0.000	0.000	0.000
70	J	99	SER	0	0.001	-0.007	46.160	-0.004	-0.004	0.000	0.000	0.000	0.000
71	J	100	ALA	0	0.022	-0.015	45.627	0.002	0.002	0.000	0.000	0.000	0.000
72	J	101	THR	0	-0.036	-0.031	42.586	0.000	0.000	0.000	0.000	0.000	0.000
73	J	102	TYR	0	0.018	0.014	45.492	0.002	0.002	0.000	0.000	0.000	0.000
74	J	103	VAL	0	-0.040	-0.004	48.702	0.002	0.002	0.000	0.000	0.000	0.000
75	J	104	LYS	1	0.925	0.978	44.045	0.080	0.080	0.000	0.000	0.000	0.000

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