FMO DATABASE

FMODB ID: 434MN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-443685.090075
FMO2-HF: Nuclear repulsion	410846.481324
FMO2-HF: Total energy	-32838.60875
FMO2-MP2: Total energy	-32935.281703

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.
-3.476	0.674	0.083	-1.541	-2.69	-0.003

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 : 0.071 / 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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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	-0.898	-0.954	2.895	-3.595	-0.418	0.068	-1.389	-1.856	-0.003
4	B	4	GLU	-1	-0.915	-0.939	3.353	-0.057	0.793	0.016	-0.141	-0.724	0.000
5	B	5	LEU	0	-0.001	0.002	5.072	0.314	0.437	-0.001	-0.011	-0.110	0.000
6	B	6	LYS	1	0.949	0.965	6.959	-0.488	-0.488	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.010	-0.005	7.788	0.136	0.136	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.007	0.011	9.247	0.074	0.074	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.839	-0.916	11.162	-0.041	-0.041	0.000	0.000	0.000	0.000
10	B	10	ALA	0	-0.017	0.003	12.698	0.029	0.029	0.000	0.000	0.000	0.000
11	B	11	LEU	0	0.048	0.017	12.309	0.008	0.008	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.801	0.899	13.811	0.118	0.118	0.000	0.000	0.000	0.000
13	B	13	ALA	0	-0.028	-0.013	17.105	0.010	0.010	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.935	-0.976	18.100	-0.007	-0.007	0.000	0.000	0.000	0.000
15	B	15	LEU	0	0.010	0.007	19.455	0.002	0.002	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.892	0.941	21.234	0.029	0.029	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.991	0.998	23.199	-0.016	-0.016	0.000	0.000	0.000	0.000
18	B	18	SER	0	0.005	0.015	23.717	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	19	LEU	0	-0.036	-0.031	24.209	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	20	GLN	0	-0.088	-0.054	27.071	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.852	-0.923	28.690	-0.005	-0.005	0.000	0.000	0.000	0.000
22	B	22	ARG	1	0.935	0.982	29.075	0.032	0.032	0.000	0.000	0.000	0.000
23	B	23	ARG	1	0.746	0.844	31.340	0.014	0.014	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.829	-0.903	33.099	0.003	0.003	0.000	0.000	0.000	0.000
25	B	25	GLN	0	-0.045	-0.033	33.600	0.001	0.001	0.000	0.000	0.000	0.000
26	B	26	GLU	-1	-0.916	-0.960	34.502	-0.023	-0.023	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.790	-0.865	37.594	-0.009	-0.009	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.043	-0.018	38.743	0.002	0.002	0.000	0.000	0.000	0.000
29	B	29	PHE	0	-0.055	-0.030	40.114	0.000	0.000	0.000	0.000	0.000	0.000
30	B	30	ASP	-1	-0.901	-0.958	41.843	-0.013	-0.013	0.000	0.000	0.000	0.000
31	B	31	ASN	0	-0.086	-0.052	43.275	0.001	0.001	0.000	0.000	0.000	0.000
32	B	32	LEU	0	0.003	0.013	43.074	0.001	0.001	0.000	0.000	0.000	0.000
33	B	33	GLN	0	0.038	0.023	45.271	0.000	0.000	0.000	0.000	0.000	0.000
34	B	34	GLN	0	-0.054	-0.027	48.205	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.869	-0.944	49.652	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.054	-0.033	48.635	0.000	0.000	0.000	0.000	0.000	0.000
37	B	37	TYR	0	-0.016	0.005	52.347	0.000	0.000	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.807	-0.903	54.246	-0.004	-0.004	0.000	0.000	0.000	0.000
39	B	39	LYS	1	0.814	0.898	54.360	0.001	0.001	0.000	0.000	0.000	0.000
40	B	40	GLU	-1	-0.793	-0.886	56.184	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.037	-0.015	58.480	0.000	0.000	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.846	-0.877	58.964	0.000	0.000	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.081	-0.048	57.467	0.000	0.000	0.000	0.000	0.000	0.000
44	B	44	PHE	0	-0.033	-0.022	59.350	0.000	0.000	0.000	0.000	0.000	0.000
45	B	45	SER	0	-0.030	-0.010	64.188	0.000	0.000	0.000	0.000	0.000	0.000
46	B	46	HIS	0	-0.011	0.010	66.192	0.000	0.000	0.000	0.000	0.000	0.000
47	B	65	TYR	0	0.011	0.005	69.068	0.000	0.000	0.000	0.000	0.000	0.000
48	B	66	SER	0	-0.041	-0.041	70.841	0.000	0.000	0.000	0.000	0.000	0.000
49	B	67	GLY	0	0.018	0.032	69.029	0.000	0.000	0.000	0.000	0.000	0.000
50	B	68	ASN	0	-0.117	-0.061	64.174	0.000	0.000	0.000	0.000	0.000	0.000
51	B	69	ILE	0	0.056	0.024	58.903	0.000	0.000	0.000	0.000	0.000	0.000
52	B	70	ILE	0	-0.027	-0.003	60.311	0.000	0.000	0.000	0.000	0.000	0.000
53	B	71	LYS	1	0.839	0.908	63.432	0.005	0.005	0.000	0.000	0.000	0.000
54	B	72	GLY	0	0.042	0.038	66.596	0.000	0.000	0.000	0.000	0.000	0.000
55	B	73	PHE	0	0.024	-0.001	62.825	0.000	0.000	0.000	0.000	0.000	0.000
56	B	74	ASP	-1	-0.911	-0.949	68.608	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	75	THR	0	0.013	-0.004	71.845	0.000	0.000	0.000	0.000	0.000	0.000
58	B	76	PHE	0	-0.075	-0.018	72.804	0.000	0.000	0.000	0.000	0.000	0.000
59	B	86	SER	0	-0.007	-0.018	70.434	0.000	0.000	0.000	0.000	0.000	0.000
60	B	87	ALA	0	0.033	0.003	69.821	0.000	0.000	0.000	0.000	0.000	0.000
61	B	88	PHE	0	-0.030	0.000	60.464	0.000	0.000	0.000	0.000	0.000	0.000
62	B	89	ASN	0	-0.001	0.002	64.637	0.000	0.000	0.000	0.000	0.000	0.000
63	B	90	ASN	0	0.062	0.030	59.791	0.000	0.000	0.000	0.000	0.000	0.000
64	B	91	ASN	0	-0.014	-0.016	59.560	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	92	ASP	-1	-0.798	-0.908	60.725	-0.007	-0.007	0.000	0.000	0.000	0.000
66	B	93	ARG	1	0.794	0.900	56.898	0.007	0.007	0.000	0.000	0.000	0.000
67	B	94	ILE	0	-0.012	-0.026	56.251	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	95	PHE	0	-0.016	-0.003	53.193	0.000	0.000	0.000	0.000	0.000	0.000
69	B	96	SER	0	0.034	0.004	51.851	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	97	LEU	0	-0.086	-0.044	51.460	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	98	SER	0	-0.083	-0.033	50.243	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	99	SER	0	0.012	0.007	46.609	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	100	ALA	0	0.036	-0.009	46.016	0.000	0.000	0.000	0.000	0.000	0.000
74	B	101	THR	0	-0.052	-0.036	43.699	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	102	TYR	0	0.077	0.041	46.625	0.000	0.000	0.000	0.000	0.000	0.000
76	B	103	VAL	0	-0.009	-0.003	50.131	0.000	0.000	0.000	0.000	0.000	0.000
77	B	104	LYS	1	0.893	0.940	44.112	0.023	0.023	0.000	0.000	0.000	0.000
78	B	105	GLN	0	-0.018	0.012	49.332	0.000	0.000	0.000	0.000	0.000	0.000
79	B	106	GLN	0	-0.056	-0.011	50.986	0.001	0.001	0.000	0.000	0.000	0.000

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