FMO DATABASE

FMODB ID: 53KLZ

Calculation Name: 5J9U-B-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9U

Chain ID: B

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	OptAll
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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-445370.902845
FMO2-HF: Nuclear repulsion	412532.049206
FMO2-HF: Total energy	-32838.85364
FMO2-MP2: Total energy	-32935.499321

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-2.508	0.231	0.008	-0.983	-1.764	0.001

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / 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

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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	B	3	ASP	-1	-0.815	-0.902	3.513	-1.753	0.027	0.001	-0.701	-1.080	0.001
4	B	4	GLU	-1	-0.903	-0.921	3.699	-1.803	-0.844	0.007	-0.282	-0.684	0.000
5	B	5	LEU	0	0.005	0.005	5.347	0.587	0.587	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.835	0.891	6.892	-0.060	-0.060	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.011	-0.002	7.980	0.193	0.193	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.015	0.008	9.431	0.117	0.117	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.841	-0.916	11.135	-0.132	-0.132	0.000	0.000	0.000	0.000
10	B	10	ALA	0	-0.018	-0.004	12.940	0.044	0.044	0.000	0.000	0.000	0.000
11	B	11	LEU	0	0.042	0.016	12.503	0.023	0.023	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.783	0.892	13.757	0.239	0.239	0.000	0.000	0.000	0.000
13	B	13	ALA	0	-0.024	-0.011	17.192	0.020	0.020	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.929	-0.964	18.402	-0.059	-0.059	0.000	0.000	0.000	0.000
15	B	15	LEU	0	0.017	0.010	19.591	0.010	0.010	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.894	0.937	21.161	0.076	0.076	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.977	0.996	23.217	0.024	0.024	0.000	0.000	0.000	0.000
18	B	18	SER	0	0.004	0.007	24.127	0.003	0.003	0.000	0.000	0.000	0.000
19	B	19	LEU	0	-0.034	-0.034	23.868	0.003	0.003	0.000	0.000	0.000	0.000
20	B	20	GLN	0	-0.077	-0.041	27.104	-0.001	-0.001	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.860	-0.927	28.890	-0.030	-0.030	0.000	0.000	0.000	0.000
22	B	22	ARG	1	0.871	0.928	28.750	0.058	0.058	0.000	0.000	0.000	0.000
23	B	23	ARG	1	0.758	0.847	31.402	0.035	0.035	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.823	-0.899	33.435	-0.019	-0.019	0.000	0.000	0.000	0.000
25	B	25	GLN	0	-0.048	-0.026	33.411	0.004	0.004	0.000	0.000	0.000	0.000
26	B	26	GLU	-1	-0.861	-0.907	34.068	-0.044	-0.044	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.794	-0.872	37.479	-0.026	-0.026	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.033	-0.019	38.774	0.003	0.003	0.000	0.000	0.000	0.000
29	B	29	PHE	0	-0.052	-0.027	40.116	0.001	0.001	0.000	0.000	0.000	0.000
30	B	30	ASP	-1	-0.908	-0.964	41.698	-0.027	-0.027	0.000	0.000	0.000	0.000
31	B	31	ASN	0	-0.076	-0.053	43.208	0.002	0.002	0.000	0.000	0.000	0.000
32	B	32	LEU	0	-0.003	0.001	43.081	0.001	0.001	0.000	0.000	0.000	0.000
33	B	33	GLN	0	0.015	0.014	44.800	0.001	0.001	0.000	0.000	0.000	0.000
34	B	34	GLN	0	-0.065	-0.032	48.035	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.844	-0.932	49.746	-0.009	-0.009	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.054	-0.024	48.617	0.001	0.001	0.000	0.000	0.000	0.000
37	B	37	TYR	0	-0.011	0.010	52.383	0.001	0.001	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.804	-0.888	54.234	-0.013	-0.013	0.000	0.000	0.000	0.000
39	B	39	LYS	1	0.795	0.887	54.701	0.009	0.009	0.000	0.000	0.000	0.000
40	B	40	GLU	-1	-0.793	-0.874	56.382	-0.014	-0.014	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.038	-0.027	58.380	0.000	0.000	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.844	-0.877	59.043	-0.007	-0.007	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.082	-0.056	57.701	0.001	0.001	0.000	0.000	0.000	0.000
44	B	44	PHE	0	-0.008	-0.009	59.490	0.000	0.000	0.000	0.000	0.000	0.000
45	B	45	SER	0	-0.028	-0.011	64.005	0.000	0.000	0.000	0.000	0.000	0.000
46	B	46	HIS	0	-0.023	0.007	66.052	0.000	0.000	0.000	0.000	0.000	0.000
47	B	65	TYR	0	0.000	-0.017	68.923	0.000	0.000	0.000	0.000	0.000	0.000
48	B	66	SER	0	-0.034	-0.033	71.194	0.000	0.000	0.000	0.000	0.000	0.000
49	B	67	GLY	0	0.014	0.028	69.258	0.000	0.000	0.000	0.000	0.000	0.000
50	B	68	ASN	0	-0.053	-0.038	64.485	0.000	0.000	0.000	0.000	0.000	0.000
51	B	69	ILE	0	0.046	0.017	58.772	0.000	0.000	0.000	0.000	0.000	0.000
52	B	70	ILE	0	-0.045	-0.011	60.332	0.000	0.000	0.000	0.000	0.000	0.000
53	B	71	LYS	1	0.793	0.880	63.366	0.010	0.010	0.000	0.000	0.000	0.000
54	B	72	GLY	0	0.022	0.034	66.334	0.000	0.000	0.000	0.000	0.000	0.000
55	B	73	PHE	0	0.011	-0.008	62.930	0.000	0.000	0.000	0.000	0.000	0.000
56	B	74	ASP	-1	-0.834	-0.872	68.766	-0.005	-0.005	0.000	0.000	0.000	0.000
57	B	75	THR	0	-0.029	-0.014	72.105	0.000	0.000	0.000	0.000	0.000	0.000
58	B	76	PHE	0	-0.086	-0.064	72.687	0.000	0.000	0.000	0.000	0.000	0.000
59	B	86	SER	0	0.007	0.002	70.152	0.000	0.000	0.000	0.000	0.000	0.000
60	B	87	ALA	0	0.018	-0.007	69.700	0.000	0.000	0.000	0.000	0.000	0.000
61	B	88	PHE	0	0.010	0.017	60.277	0.000	0.000	0.000	0.000	0.000	0.000
62	B	89	ASN	0	-0.033	-0.013	64.412	0.000	0.000	0.000	0.000	0.000	0.000
63	B	90	ASN	0	0.074	0.024	59.562	0.000	0.000	0.000	0.000	0.000	0.000
64	B	91	ASN	0	-0.021	-0.017	59.379	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	92	ASP	-1	-0.781	-0.882	60.460	-0.012	-0.012	0.000	0.000	0.000	0.000
66	B	93	ARG	1	0.800	0.901	56.870	0.014	0.014	0.000	0.000	0.000	0.000
67	B	94	ILE	0	-0.009	-0.025	56.258	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	95	PHE	0	-0.021	0.000	53.498	0.000	0.000	0.000	0.000	0.000	0.000
69	B	96	SER	0	0.026	-0.009	52.034	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	97	LEU	0	-0.064	-0.039	51.448	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	98	SER	0	-0.085	-0.032	49.893	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	99	SER	0	0.000	-0.002	46.669	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	100	ALA	0	0.042	-0.002	45.825	0.000	0.000	0.000	0.000	0.000	0.000
74	B	101	THR	0	-0.054	-0.027	43.378	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	102	TYR	0	0.096	0.052	46.356	0.000	0.000	0.000	0.000	0.000	0.000
76	B	103	VAL	0	-0.006	-0.007	49.831	0.000	0.000	0.000	0.000	0.000	0.000
77	B	104	LYS	1	0.877	0.933	43.332	0.034	0.034	0.000	0.000	0.000	0.000
78	B	105	GLN	0	-0.012	0.015	48.809	-0.001	-0.001	0.000	0.000	0.000	0.000
79	B	106	GLN	0	-0.075	-0.032	50.353	0.002	0.002	0.000	0.000	0.000	0.000

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