FMO DATABASE

FMODB ID: 9G652

Calculation Name: 5J9U-J-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9U

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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-408748.249947
FMO2-HF: Nuclear repulsion	377236.685969
FMO2-HF: Total energy	-31511.563978
FMO2-MP2: Total energy	-31604.177222

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.
-2.272	1.264	0.122	-1.149	-2.508	0.001

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 : 0.064 / q_NPA : 0.011

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	-0.814	-0.906	2.786	-1.351	0.813	0.052	-0.862	-1.354	0.002
4	J	4	GLU	-1	-0.919	-0.945	3.018	-0.909	0.309	0.071	-0.265	-1.024	-0.001
5	J	5	LEU	0	0.001	0.000	4.731	0.173	0.327	-0.001	-0.022	-0.130	0.000
6	J	6	LYS	1	0.849	0.917	6.580	-0.458	-0.458	0.000	0.000	0.000	0.000
7	J	7	SER	0	0.022	0.010	7.536	0.102	0.102	0.000	0.000	0.000	0.000
8	J	8	TYR	0	0.013	0.011	8.944	0.047	0.047	0.000	0.000	0.000	0.000
9	J	9	GLU	-1	-0.846	-0.926	10.578	-0.061	-0.061	0.000	0.000	0.000	0.000
10	J	10	ALA	0	-0.040	-0.013	12.007	0.031	0.031	0.000	0.000	0.000	0.000
11	J	11	LEU	0	0.038	0.012	12.398	0.001	0.001	0.000	0.000	0.000	0.000
12	J	12	LYS	1	0.784	0.892	13.622	0.136	0.136	0.000	0.000	0.000	0.000
13	J	13	ALA	0	-0.047	-0.023	16.800	0.007	0.007	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.935	-0.974	17.452	0.032	0.032	0.000	0.000	0.000	0.000
15	J	15	LEU	0	0.014	0.008	19.171	0.000	0.000	0.000	0.000	0.000	0.000
16	J	16	LYS	1	0.947	0.966	21.022	0.024	0.024	0.000	0.000	0.000	0.000
17	J	17	LYS	1	0.971	0.995	22.744	-0.046	-0.046	0.000	0.000	0.000	0.000
18	J	18	SER	0	-0.003	0.007	23.531	-0.002	-0.002	0.000	0.000	0.000	0.000
19	J	19	LEU	0	-0.020	-0.026	24.701	-0.003	-0.003	0.000	0.000	0.000	0.000
20	J	20	GLN	0	-0.081	-0.048	26.923	-0.004	-0.004	0.000	0.000	0.000	0.000
21	J	21	ASP	-1	-0.861	-0.923	28.383	0.003	0.003	0.000	0.000	0.000	0.000
22	J	22	ARG	1	0.856	0.921	29.076	0.035	0.035	0.000	0.000	0.000	0.000
23	J	23	ARG	1	0.768	0.852	31.029	0.015	0.015	0.000	0.000	0.000	0.000
24	J	24	GLU	-1	-0.846	-0.912	32.935	0.012	0.012	0.000	0.000	0.000	0.000
25	J	25	GLN	0	-0.056	-0.044	33.238	0.000	0.000	0.000	0.000	0.000	0.000
26	J	26	GLU	-1	-0.873	-0.922	33.713	-0.027	-0.027	0.000	0.000	0.000	0.000
27	J	27	ASP	-1	-0.785	-0.858	37.404	-0.009	-0.009	0.000	0.000	0.000	0.000
28	J	28	THR	0	-0.039	-0.013	38.811	0.001	0.001	0.000	0.000	0.000	0.000
29	J	29	PHE	0	-0.019	0.000	40.155	0.000	0.000	0.000	0.000	0.000	0.000
30	J	30	ASP	-1	-0.881	-0.942	41.852	-0.015	-0.015	0.000	0.000	0.000	0.000
31	J	31	ASN	0	-0.102	-0.061	43.135	0.001	0.001	0.000	0.000	0.000	0.000
32	J	32	LEU	0	0.005	-0.003	43.406	0.001	0.001	0.000	0.000	0.000	0.000
33	J	33	GLN	0	-0.011	-0.002	45.859	0.001	0.001	0.000	0.000	0.000	0.000
34	J	34	GLN	0	-0.075	-0.043	47.685	-0.001	-0.001	0.000	0.000	0.000	0.000
35	J	35	GLU	-1	-0.870	-0.947	49.393	0.002	0.002	0.000	0.000	0.000	0.000
36	J	36	ILE	0	-0.035	-0.022	48.289	0.001	0.001	0.000	0.000	0.000	0.000
37	J	37	TYR	0	-0.003	0.007	52.091	0.000	0.000	0.000	0.000	0.000	0.000
38	J	38	ASP	-1	-0.800	-0.912	53.926	-0.004	-0.004	0.000	0.000	0.000	0.000
39	J	39	LYS	1	0.858	0.929	54.327	-0.001	-0.001	0.000	0.000	0.000	0.000
40	J	40	GLU	-1	-0.795	-0.888	55.975	-0.007	-0.007	0.000	0.000	0.000	0.000
41	J	41	THR	0	-0.127	-0.063	58.206	0.000	0.000	0.000	0.000	0.000	0.000
42	J	42	GLU	-1	-0.857	-0.913	58.392	0.002	0.002	0.000	0.000	0.000	0.000
43	J	43	TYR	0	-0.080	-0.051	57.299	0.001	0.001	0.000	0.000	0.000	0.000
44	J	44	PHE	0	-0.052	-0.031	58.706	0.000	0.000	0.000	0.000	0.000	0.000
45	J	45	SER	0	0.008	0.024	63.738	-0.001	-0.001	0.000	0.000	0.000	0.000
46	J	46	HIS	0	-0.053	-0.024	65.528	-0.001	-0.001	0.000	0.000	0.000	0.000
47	J	65	TYR	0	-0.013	-0.026	68.455	0.000	0.000	0.000	0.000	0.000	0.000
48	J	66	SER	0	-0.040	-0.037	70.270	0.000	0.000	0.000	0.000	0.000	0.000
49	J	67	GLY	0	0.018	0.037	68.501	0.000	0.000	0.000	0.000	0.000	0.000
50	J	68	ASN	0	-0.110	-0.068	63.701	0.000	0.000	0.000	0.000	0.000	0.000
51	J	69	ILE	0	0.044	0.016	58.652	0.000	0.000	0.000	0.000	0.000	0.000
52	J	70	ILE	0	-0.025	-0.003	59.831	0.000	0.000	0.000	0.000	0.000	0.000
53	J	71	LYS	1	0.858	0.921	63.027	0.005	0.005	0.000	0.000	0.000	0.000
54	J	72	GLY	0	0.040	0.031	66.271	0.000	0.000	0.000	0.000	0.000	0.000
55	J	73	PHE	0	0.023	0.009	62.352	0.000	0.000	0.000	0.000	0.000	0.000
56	J	74	ASP	-1	-0.901	-0.939	68.257	0.000	0.000	0.000	0.000	0.000	0.000
57	J	75	THR	0	-0.031	-0.017	71.734	0.000	0.000	0.000	0.000	0.000	0.000
58	J	76	PHE	0	-0.037	-0.017	72.239	0.000	0.000	0.000	0.000	0.000	0.000
59	J	77	SER	0	0.011	0.019	76.837	0.000	0.000	0.000	0.000	0.000	0.000
60	J	86	SER	0	-0.015	-0.021	70.370	0.000	0.000	0.000	0.000	0.000	0.000
61	J	87	ALA	0	0.053	0.035	69.951	0.000	0.000	0.000	0.000	0.000	0.000
62	J	88	PHE	0	0.020	0.019	60.258	0.000	0.000	0.000	0.000	0.000	0.000
63	J	89	ASN	0	-0.038	-0.024	64.611	0.000	0.000	0.000	0.000	0.000	0.000
64	J	90	ASN	0	0.058	0.025	60.028	0.001	0.001	0.000	0.000	0.000	0.000
65	J	91	ASN	0	-0.020	-0.018	59.576	-0.001	-0.001	0.000	0.000	0.000	0.000
66	J	92	ASP	-1	-0.818	-0.910	60.592	-0.008	-0.008	0.000	0.000	0.000	0.000
67	J	93	ARG	1	0.802	0.919	56.742	0.008	0.008	0.000	0.000	0.000	0.000
68	J	94	ILE	0	-0.011	-0.023	56.065	-0.001	-0.001	0.000	0.000	0.000	0.000
69	J	95	PHE	0	-0.020	-0.004	52.883	0.000	0.000	0.000	0.000	0.000	0.000
70	J	96	SER	0	0.042	0.020	51.611	-0.001	-0.001	0.000	0.000	0.000	0.000
71	J	97	LEU	0	-0.069	-0.038	51.298	-0.001	-0.001	0.000	0.000	0.000	0.000
72	J	98	SER	0	-0.085	-0.034	50.049	-0.001	-0.001	0.000	0.000	0.000	0.000
73	J	99	SER	0	-0.002	0.012	46.289	-0.001	-0.001	0.000	0.000	0.000	0.000
74	J	100	ALA	0	0.014	-0.010	45.765	0.000	0.000	0.000	0.000	0.000	0.000
75	J	101	THR	0	-0.049	-0.020	43.877	0.000	0.000	0.000	0.000	0.000	0.000
76	J	102	TYR	0	-0.005	0.011	46.600	0.000	0.000	0.000	0.000	0.000	0.000

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