FMO DATABASE

FMODB ID: M37KZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-410000.079788
FMO2-HF: Nuclear repulsion	378488.29113
FMO2-HF: Total energy	-31511.788658
FMO2-MP2: Total energy	-31604.376737

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.
-4.765	-1.047	0.071	-1.433	-2.354	-0.003

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 : 0.069 / q_NPA : 0.015

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	-0.791	-0.892	3.557	-1.257	0.424	0.008	-0.690	-0.998	0.001
4	J	4	GLU	-1	-0.917	-0.926	3.246	-4.426	-2.533	0.064	-0.728	-1.229	-0.004
5	J	5	LEU	0	0.002	0.000	4.768	0.464	0.608	-0.001	-0.015	-0.127	0.000
6	J	6	LYS	1	0.820	0.892	6.752	-0.053	-0.053	0.000	0.000	0.000	0.000
7	J	7	SER	0	0.012	-0.003	7.723	0.198	0.198	0.000	0.000	0.000	0.000
8	J	8	TYR	0	0.020	0.008	8.970	0.117	0.117	0.000	0.000	0.000	0.000
9	J	9	GLU	-1	-0.848	-0.923	10.723	-0.160	-0.160	0.000	0.000	0.000	0.000
10	J	10	ALA	0	-0.017	-0.006	12.509	0.048	0.048	0.000	0.000	0.000	0.000
11	J	11	LEU	0	0.041	0.015	12.307	0.023	0.023	0.000	0.000	0.000	0.000
12	J	12	LYS	1	0.777	0.889	13.356	0.289	0.289	0.000	0.000	0.000	0.000
13	J	13	ALA	0	-0.044	-0.015	16.890	0.021	0.021	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.939	-0.972	18.026	-0.065	-0.065	0.000	0.000	0.000	0.000
15	J	15	LEU	0	0.026	0.015	19.157	0.010	0.010	0.000	0.000	0.000	0.000
16	J	16	LYS	1	0.934	0.959	20.910	0.098	0.098	0.000	0.000	0.000	0.000
17	J	17	LYS	1	0.964	0.985	22.787	0.021	0.021	0.000	0.000	0.000	0.000
18	J	18	SER	0	-0.015	-0.001	23.722	0.003	0.003	0.000	0.000	0.000	0.000
19	J	19	LEU	0	-0.012	-0.024	24.332	0.003	0.003	0.000	0.000	0.000	0.000
20	J	20	GLN	0	-0.079	-0.040	26.937	-0.001	-0.001	0.000	0.000	0.000	0.000
21	J	21	ASP	-1	-0.853	-0.916	28.786	-0.039	-0.039	0.000	0.000	0.000	0.000
22	J	22	ARG	1	0.794	0.877	28.760	0.076	0.076	0.000	0.000	0.000	0.000
23	J	23	ARG	1	0.743	0.847	30.845	0.043	0.043	0.000	0.000	0.000	0.000
24	J	24	GLU	-1	-0.843	-0.907	33.113	-0.021	-0.021	0.000	0.000	0.000	0.000
25	J	25	GLN	0	-0.040	-0.035	33.372	0.004	0.004	0.000	0.000	0.000	0.000
26	J	26	GLU	-1	-0.823	-0.874	33.587	-0.060	-0.060	0.000	0.000	0.000	0.000
27	J	27	ASP	-1	-0.788	-0.871	37.381	-0.032	-0.032	0.000	0.000	0.000	0.000
28	J	28	THR	0	-0.051	-0.029	38.347	0.003	0.003	0.000	0.000	0.000	0.000
29	J	29	PHE	0	-0.028	-0.007	39.980	0.002	0.002	0.000	0.000	0.000	0.000
30	J	30	ASP	-1	-0.870	-0.945	40.985	-0.037	-0.037	0.000	0.000	0.000	0.000
31	J	31	ASN	0	-0.092	-0.058	43.019	0.003	0.003	0.000	0.000	0.000	0.000
32	J	32	LEU	0	-0.007	-0.012	43.643	0.002	0.002	0.000	0.000	0.000	0.000
33	J	33	GLN	0	-0.017	-0.008	45.722	0.002	0.002	0.000	0.000	0.000	0.000
34	J	34	GLN	0	-0.080	-0.044	47.560	-0.001	-0.001	0.000	0.000	0.000	0.000
35	J	35	GLU	-1	-0.796	-0.903	49.590	-0.013	-0.013	0.000	0.000	0.000	0.000
36	J	36	ILE	0	-0.036	-0.018	48.224	0.001	0.001	0.000	0.000	0.000	0.000
37	J	37	TYR	0	-0.005	0.007	52.082	0.001	0.001	0.000	0.000	0.000	0.000
38	J	38	ASP	-1	-0.788	-0.880	54.005	-0.017	-0.017	0.000	0.000	0.000	0.000
39	J	39	LYS	1	0.796	0.898	54.513	0.013	0.013	0.000	0.000	0.000	0.000
40	J	40	GLU	-1	-0.784	-0.858	56.095	-0.021	-0.021	0.000	0.000	0.000	0.000
41	J	41	THR	0	-0.102	-0.065	58.496	0.001	0.001	0.000	0.000	0.000	0.000
42	J	42	GLU	-1	-0.838	-0.904	58.197	-0.010	-0.010	0.000	0.000	0.000	0.000
43	J	43	TYR	0	-0.076	-0.056	57.585	0.001	0.001	0.000	0.000	0.000	0.000
44	J	44	PHE	0	0.014	-0.004	59.014	0.001	0.001	0.000	0.000	0.000	0.000
45	J	45	SER	0	-0.016	0.010	64.037	0.000	0.000	0.000	0.000	0.000	0.000
46	J	46	HIS	0	-0.104	-0.046	65.376	0.000	0.000	0.000	0.000	0.000	0.000
47	J	65	TYR	0	-0.021	-0.034	68.533	0.000	0.000	0.000	0.000	0.000	0.000
48	J	66	SER	0	-0.022	-0.027	70.711	0.000	0.000	0.000	0.000	0.000	0.000
49	J	67	GLY	0	0.027	0.040	68.908	-0.001	-0.001	0.000	0.000	0.000	0.000
50	J	68	ASN	0	-0.062	-0.049	63.963	0.000	0.000	0.000	0.000	0.000	0.000
51	J	69	ILE	0	0.028	0.006	58.447	0.000	0.000	0.000	0.000	0.000	0.000
52	J	70	ILE	0	-0.041	-0.012	59.873	0.000	0.000	0.000	0.000	0.000	0.000
53	J	71	LYS	1	0.817	0.900	62.948	0.015	0.015	0.000	0.000	0.000	0.000
54	J	72	GLY	0	0.014	0.031	65.930	0.000	0.000	0.000	0.000	0.000	0.000
55	J	73	PHE	0	0.013	-0.005	62.287	0.000	0.000	0.000	0.000	0.000	0.000
56	J	74	ASP	-1	-0.840	-0.903	68.145	-0.008	-0.008	0.000	0.000	0.000	0.000
57	J	75	THR	0	-0.065	-0.046	71.757	0.000	0.000	0.000	0.000	0.000	0.000
58	J	76	PHE	0	-0.045	-0.014	72.172	0.000	0.000	0.000	0.000	0.000	0.000
59	J	77	SER	0	-0.004	0.013	76.913	0.000	0.000	0.000	0.000	0.000	0.000
60	J	86	SER	0	-0.013	-0.022	70.730	0.000	0.000	0.000	0.000	0.000	0.000
61	J	87	ALA	0	0.050	0.026	69.680	0.000	0.000	0.000	0.000	0.000	0.000
62	J	88	PHE	0	0.028	0.035	59.963	0.000	0.000	0.000	0.000	0.000	0.000
63	J	89	ASN	0	-0.057	-0.029	64.263	0.000	0.000	0.000	0.000	0.000	0.000
64	J	90	ASN	0	0.043	0.007	59.731	0.000	0.000	0.000	0.000	0.000	0.000
65	J	91	ASN	0	-0.006	-0.012	59.290	-0.001	-0.001	0.000	0.000	0.000	0.000
66	J	92	ASP	-1	-0.776	-0.878	60.185	-0.018	-0.018	0.000	0.000	0.000	0.000
67	J	93	ARG	1	0.790	0.901	56.523	0.021	0.021	0.000	0.000	0.000	0.000
68	J	94	ILE	0	-0.005	-0.021	55.839	-0.001	-0.001	0.000	0.000	0.000	0.000
69	J	95	PHE	0	-0.020	0.000	53.049	-0.001	-0.001	0.000	0.000	0.000	0.000
70	J	96	SER	0	0.027	0.000	51.594	-0.001	-0.001	0.000	0.000	0.000	0.000
71	J	97	LEU	0	-0.051	-0.032	51.082	-0.002	-0.002	0.000	0.000	0.000	0.000
72	J	98	SER	0	-0.098	-0.037	49.908	-0.001	-0.001	0.000	0.000	0.000	0.000
73	J	99	SER	0	0.000	0.008	46.465	-0.002	-0.002	0.000	0.000	0.000	0.000
74	J	100	ALA	0	0.020	-0.007	45.277	0.000	0.000	0.000	0.000	0.000	0.000
75	J	101	THR	0	-0.044	-0.017	43.450	-0.001	-0.001	0.000	0.000	0.000	0.000
76	J	102	TYR	0	-0.016	0.000	46.298	0.001	0.001	0.000	0.000	0.000	0.000

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