FMO DATABASE

FMODB ID: 3Q55L

Calculation Name: 5J9T-B-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9T

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-423302.068065
FMO2-HF: Nuclear repulsion	391510.05772
FMO2-HF: Total energy	-31792.010345
FMO2-MP2: Total energy	-31885.442961

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.
-5.175	-0.989	0.09	-1.585	-2.691	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 : 0.067 / q_NPA : 0.017

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	-0.842	-0.916	3.522	-0.104	2.469	0.009	-1.166	-1.415	0.004
4	B	4	GLU	-1	-0.947	-0.965	3.066	-2.610	-1.163	0.082	-0.392	-1.138	-0.001
5	B	5	LEU	0	-0.008	-0.001	4.689	-0.278	-0.112	-0.001	-0.027	-0.138	0.000
6	B	6	LYS	1	0.890	0.931	6.780	-1.970	-1.970	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.005	-0.006	7.663	-0.134	-0.134	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.031	0.016	9.045	-0.095	-0.095	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.829	-0.911	10.868	-0.053	-0.053	0.000	0.000	0.000	0.000
10	B	10	ALA	0	-0.035	-0.011	12.427	-0.020	-0.020	0.000	0.000	0.000	0.000
11	B	11	LEU	0	0.059	0.015	13.067	-0.038	-0.038	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.777	0.891	13.624	0.028	0.028	0.000	0.000	0.000	0.000
13	B	13	ALA	0	-0.057	-0.029	17.198	-0.020	-0.020	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.926	-0.960	18.295	0.257	0.257	0.000	0.000	0.000	0.000
15	B	15	LEU	0	0.017	0.021	19.481	-0.016	-0.016	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.950	0.965	20.503	-0.055	-0.055	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.961	0.991	22.934	-0.198	-0.198	0.000	0.000	0.000	0.000
18	B	18	SER	0	0.011	-0.007	22.871	-0.011	-0.011	0.000	0.000	0.000	0.000
19	B	19	LEU	0	-0.038	-0.023	24.685	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	20	GLN	0	-0.003	0.014	27.135	-0.014	-0.014	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.860	-0.913	28.662	0.083	0.083	0.000	0.000	0.000	0.000
22	B	22	ARG	1	0.845	0.894	29.309	-0.021	-0.021	0.000	0.000	0.000	0.000
23	B	23	ARG	1	0.807	0.901	31.540	-0.048	-0.048	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.890	-0.941	33.303	0.068	0.068	0.000	0.000	0.000	0.000
25	B	25	GLN	0	-0.049	-0.045	32.815	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	26	GLU	-1	-0.857	-0.914	34.174	0.014	0.014	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.820	-0.903	37.604	0.028	0.028	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.035	-0.016	38.805	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	29	PHE	0	-0.065	-0.025	40.173	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	30	ASP	-1	-0.874	-0.943	41.853	0.014	0.014	0.000	0.000	0.000	0.000
31	B	31	ASN	0	-0.087	-0.053	43.185	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	32	LEU	0	0.029	0.024	43.037	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	33	GLN	0	0.018	0.033	45.057	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	34	GLN	0	-0.060	-0.038	47.983	-0.003	-0.003	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.905	-0.959	49.306	0.030	0.030	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.052	-0.037	48.516	0.000	0.000	0.000	0.000	0.000	0.000
37	B	37	TYR	0	-0.022	0.000	52.141	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.790	-0.897	54.018	0.017	0.017	0.000	0.000	0.000	0.000
39	B	39	LYS	1	0.788	0.889	53.853	-0.028	-0.028	0.000	0.000	0.000	0.000
40	B	40	GLU	-1	-0.784	-0.867	55.813	0.017	0.017	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.026	-0.010	58.321	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.855	-0.900	58.901	0.025	0.025	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.032	-0.021	57.051	0.000	0.000	0.000	0.000	0.000	0.000
44	B	44	PHE	0	-0.050	-0.027	58.750	0.000	0.000	0.000	0.000	0.000	0.000
45	B	45	SER	0	-0.071	-0.029	63.867	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	66	SER	0	-0.023	-0.030	71.402	0.000	0.000	0.000	0.000	0.000	0.000
47	B	67	GLY	0	0.029	0.022	69.364	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	68	ASN	0	-0.072	-0.039	64.609	0.000	0.000	0.000	0.000	0.000	0.000
49	B	69	ILE	0	0.069	0.035	59.314	0.000	0.000	0.000	0.000	0.000	0.000
50	B	70	ILE	0	-0.008	0.004	59.979	0.000	0.000	0.000	0.000	0.000	0.000
51	B	71	LYS	1	0.928	0.952	63.291	-0.015	-0.015	0.000	0.000	0.000	0.000
52	B	72	GLY	0	0.018	0.032	66.275	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	73	PHE	0	-0.027	-0.033	62.750	0.000	0.000	0.000	0.000	0.000	0.000
54	B	74	ASP	-1	-0.946	-0.951	68.724	0.017	0.017	0.000	0.000	0.000	0.000
55	B	87	ALA	0	-0.054	-0.040	70.316	0.000	0.000	0.000	0.000	0.000	0.000
56	B	88	PHE	0	0.057	0.039	60.461	0.000	0.000	0.000	0.000	0.000	0.000
57	B	89	ASN	0	0.051	0.020	64.436	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	90	ASN	0	0.057	0.023	60.349	0.002	0.002	0.000	0.000	0.000	0.000
59	B	91	ASN	0	-0.090	-0.053	59.810	0.000	0.000	0.000	0.000	0.000	0.000
60	B	92	ASP	-1	-0.883	-0.944	61.267	0.011	0.011	0.000	0.000	0.000	0.000
61	B	93	ARG	1	0.759	0.902	56.850	-0.012	-0.012	0.000	0.000	0.000	0.000
62	B	94	ILE	0	0.007	-0.023	56.677	0.000	0.000	0.000	0.000	0.000	0.000
63	B	95	PHE	0	-0.026	-0.006	53.065	0.001	0.001	0.000	0.000	0.000	0.000
64	B	96	SER	0	0.029	-0.008	51.861	0.001	0.001	0.000	0.000	0.000	0.000
65	B	97	LEU	0	-0.065	-0.028	51.636	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	98	SER	0	-0.081	-0.029	50.453	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	99	SER	0	-0.005	-0.016	47.218	0.000	0.000	0.000	0.000	0.000	0.000
68	B	100	ALA	0	0.037	-0.002	46.319	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	101	THR	0	-0.051	-0.032	43.523	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	102	TYR	0	0.084	0.045	46.872	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	103	VAL	0	0.023	0.009	50.072	-0.002	-0.002	0.000	0.000	0.000	0.000
72	B	104	LYS	1	0.925	0.957	44.159	0.007	0.007	0.000	0.000	0.000	0.000
73	B	105	GLN	0	-0.004	-0.009	47.609	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	106	GLN	0	-0.030	-0.003	50.809	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	107	HIS	0	-0.027	-0.021	53.296	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	108	GLY	0	-0.038	0.003	53.003	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	109	GLN	0	-0.051	-0.015	52.537	-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)