FMO DATABASE

FMODB ID: LJ229

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

Total energy (hartree)

FMO2-HF: Electronic energy	-424949.023099
FMO2-HF: Nuclear repulsion	393156.787899
FMO2-HF: Total energy	-31792.2352
FMO2-MP2: Total energy	-31885.664458

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.
-6.771	-2.262	0.272	-1.884	-2.897	-0.009

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 : 0.060 / 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	-0.834	-0.913	3.636	0.623	2.297	0.004	-0.671	-1.008	0.002
4	B	4	GLU	-1	-0.919	-0.935	2.944	-7.580	-4.901	0.269	-1.193	-1.754	-0.011
5	B	5	LEU	0	0.008	0.004	4.620	0.463	0.619	-0.001	-0.020	-0.135	0.000
6	B	6	LYS	1	0.874	0.924	6.605	-0.888	-0.888	0.000	0.000	0.000	0.000
7	B	7	SER	0	-0.009	-0.016	7.904	0.159	0.159	0.000	0.000	0.000	0.000
8	B	8	TYR	0	0.025	0.010	8.758	0.086	0.086	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.830	-0.913	10.461	-0.392	-0.392	0.000	0.000	0.000	0.000
10	B	10	ALA	0	-0.010	0.002	12.488	0.052	0.052	0.000	0.000	0.000	0.000
11	B	11	LEU	0	0.031	0.005	12.799	0.019	0.019	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.780	0.888	13.074	0.504	0.504	0.000	0.000	0.000	0.000
13	B	13	ALA	0	-0.045	-0.014	16.649	0.015	0.015	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.813	-0.903	18.178	0.050	0.050	0.000	0.000	0.000	0.000
15	B	15	LEU	0	0.018	0.028	18.955	0.005	0.005	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.918	0.961	19.875	0.162	0.162	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.870	0.926	22.693	-0.037	-0.037	0.000	0.000	0.000	0.000
18	B	18	SER	0	0.000	-0.018	22.704	0.000	0.000	0.000	0.000	0.000	0.000
19	B	19	LEU	0	-0.025	-0.018	24.210	0.000	0.000	0.000	0.000	0.000	0.000
20	B	20	GLN	0	-0.003	0.012	26.786	-0.001	-0.001	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.861	-0.912	28.389	-0.012	-0.012	0.000	0.000	0.000	0.000
22	B	22	ARG	1	0.817	0.863	28.804	0.088	0.088	0.000	0.000	0.000	0.000
23	B	23	ARG	1	0.777	0.865	30.943	0.040	0.040	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.869	-0.912	32.972	-0.012	-0.012	0.000	0.000	0.000	0.000
25	B	25	GLN	0	-0.052	-0.044	32.340	0.005	0.005	0.000	0.000	0.000	0.000
26	B	26	GLU	-1	-0.841	-0.887	33.683	-0.072	-0.072	0.000	0.000	0.000	0.000
27	B	27	ASP	-1	-0.833	-0.913	37.096	-0.038	-0.038	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.029	-0.014	38.480	0.004	0.004	0.000	0.000	0.000	0.000
29	B	29	PHE	0	-0.052	-0.013	39.690	0.003	0.003	0.000	0.000	0.000	0.000
30	B	30	ASP	-1	-0.834	-0.927	41.402	-0.040	-0.040	0.000	0.000	0.000	0.000
31	B	31	ASN	0	-0.091	-0.053	42.726	0.003	0.003	0.000	0.000	0.000	0.000
32	B	32	LEU	0	0.007	0.004	42.855	0.002	0.002	0.000	0.000	0.000	0.000
33	B	33	GLN	0	-0.018	0.007	44.321	0.002	0.002	0.000	0.000	0.000	0.000
34	B	34	GLN	0	-0.073	-0.042	47.494	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.881	-0.943	49.103	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.050	-0.026	48.130	0.001	0.001	0.000	0.000	0.000	0.000
37	B	37	TYR	0	-0.002	0.011	51.796	0.001	0.001	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.791	-0.881	53.783	-0.016	-0.016	0.000	0.000	0.000	0.000
39	B	39	LYS	1	0.804	0.895	53.482	0.006	0.006	0.000	0.000	0.000	0.000
40	B	40	GLU	-1	-0.770	-0.857	55.388	-0.016	-0.016	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.015	-0.012	57.889	0.000	0.000	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.825	-0.877	58.771	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.061	-0.044	56.966	0.001	0.001	0.000	0.000	0.000	0.000
44	B	44	PHE	0	-0.033	-0.025	58.549	0.001	0.001	0.000	0.000	0.000	0.000
45	B	45	SER	0	-0.119	-0.058	63.296	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	66	SER	0	0.018	0.003	71.430	0.000	0.000	0.000	0.000	0.000	0.000
47	B	67	GLY	0	-0.017	-0.014	69.034	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	68	ASN	0	-0.017	-0.012	64.100	0.000	0.000	0.000	0.000	0.000	0.000
49	B	69	ILE	0	0.039	0.019	59.009	0.000	0.000	0.000	0.000	0.000	0.000
50	B	70	ILE	0	-0.013	0.005	59.516	0.000	0.000	0.000	0.000	0.000	0.000
51	B	71	LYS	1	0.893	0.939	62.783	0.007	0.007	0.000	0.000	0.000	0.000
52	B	72	GLY	0	0.021	0.037	65.719	0.000	0.000	0.000	0.000	0.000	0.000
53	B	73	PHE	0	-0.037	-0.044	62.722	0.000	0.000	0.000	0.000	0.000	0.000
54	B	74	ASP	-1	-0.939	-0.947	68.835	0.000	0.000	0.000	0.000	0.000	0.000
55	B	87	ALA	0	-0.048	-0.040	69.837	0.000	0.000	0.000	0.000	0.000	0.000
56	B	88	PHE	0	0.055	0.037	59.868	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	89	ASN	0	0.037	0.021	63.913	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	90	ASN	0	0.048	0.018	59.415	0.001	0.001	0.000	0.000	0.000	0.000
59	B	91	ASN	0	-0.062	-0.045	59.061	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	92	ASP	-1	-0.877	-0.936	60.242	-0.014	-0.014	0.000	0.000	0.000	0.000
61	B	93	ARG	1	0.766	0.896	56.163	0.020	0.020	0.000	0.000	0.000	0.000
62	B	94	ILE	0	0.011	-0.019	55.964	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	95	PHE	0	-0.028	-0.005	52.658	0.000	0.000	0.000	0.000	0.000	0.000
64	B	96	SER	0	0.028	-0.010	51.427	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	97	LEU	0	-0.076	-0.038	51.181	-0.003	-0.003	0.000	0.000	0.000	0.000
66	B	98	SER	0	-0.077	-0.031	49.811	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	99	SER	0	-0.005	-0.006	46.539	-0.003	-0.003	0.000	0.000	0.000	0.000
68	B	100	ALA	0	0.044	0.001	45.790	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	101	THR	0	-0.070	-0.034	42.948	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	102	TYR	0	0.077	0.030	46.310	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	103	VAL	0	0.015	0.006	49.614	0.000	0.000	0.000	0.000	0.000	0.000
72	B	104	LYS	1	0.923	0.958	43.514	0.060	0.060	0.000	0.000	0.000	0.000
73	B	105	GLN	0	0.012	0.000	47.073	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	106	GLN	0	-0.004	0.017	50.498	0.003	0.003	0.000	0.000	0.000	0.000
75	B	107	HIS	0	-0.019	-0.018	52.475	0.000	0.000	0.000	0.000	0.000	0.000
76	B	108	GLY	0	-0.041	-0.001	52.329	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	109	GLN	0	-0.082	-0.038	51.935	-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)