FMO DATABASE

FMODB ID: N1MMQ

Calculation Name: 5J9T-F-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9T

Chain ID: F

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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-370063.764289
FMO2-HF: Nuclear repulsion	341943.826553
FMO2-HF: Total energy	-28119.937736
FMO2-MP2: Total energy	-28203.569197

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(F:7:SER)

Summations of interaction energy for fragment #1(F:7:SER)

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.
-2.57	0.189	0.068	-1.006	-1.82	0.001

Interaction energy analysis for fragmet #1(F:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.004

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	F	9	GLU	-1	-0.754	-0.886	3.889	-1.463	0.050	0.000	-0.640	-0.873	0.002
4	F	10	ALA	0	0.002	0.014	3.024	-0.679	0.073	0.065	-0.233	-0.584	-0.001
5	F	11	LEU	0	0.054	0.028	4.017	0.411	0.905	0.003	-0.133	-0.363	0.000
6	F	12	LYS	1	0.772	0.877	6.204	-0.710	-0.710	0.000	0.000	0.000	0.000
7	F	13	ALA	0	-0.030	-0.010	7.580	0.047	0.047	0.000	0.000	0.000	0.000
8	F	14	GLU	-1	-0.914	-0.977	7.660	-0.135	-0.135	0.000	0.000	0.000	0.000
9	F	15	LEU	0	0.031	0.032	10.149	0.036	0.036	0.000	0.000	0.000	0.000
10	F	16	LYS	1	0.920	0.960	12.110	-0.216	-0.216	0.000	0.000	0.000	0.000
11	F	17	LYS	1	0.963	0.992	13.022	0.154	0.154	0.000	0.000	0.000	0.000
12	F	18	SER	0	0.011	-0.007	13.503	0.011	0.011	0.000	0.000	0.000	0.000
13	F	19	LEU	0	-0.033	-0.020	16.066	0.003	0.003	0.000	0.000	0.000	0.000
14	F	20	GLN	0	-0.077	-0.048	17.882	0.008	0.008	0.000	0.000	0.000	0.000
15	F	21	ASP	-1	-0.855	-0.919	18.926	0.009	0.009	0.000	0.000	0.000	0.000
16	F	22	ARG	1	0.797	0.864	20.104	-0.084	-0.084	0.000	0.000	0.000	0.000
17	F	23	ARG	1	0.802	0.872	22.024	-0.050	-0.050	0.000	0.000	0.000	0.000
18	F	24	GLU	-1	-0.847	-0.909	23.125	0.007	0.007	0.000	0.000	0.000	0.000
19	F	25	GLN	0	-0.053	-0.047	23.516	-0.003	-0.003	0.000	0.000	0.000	0.000
20	F	26	GLU	-1	-0.841	-0.887	25.581	0.066	0.066	0.000	0.000	0.000	0.000
21	F	27	ASP	-1	-0.779	-0.850	28.042	0.036	0.036	0.000	0.000	0.000	0.000
22	F	28	THR	0	-0.009	-0.005	28.928	-0.003	-0.003	0.000	0.000	0.000	0.000
23	F	29	PHE	0	-0.061	-0.015	30.563	-0.003	-0.003	0.000	0.000	0.000	0.000
24	F	30	ASP	-1	-0.875	-0.949	32.281	0.032	0.032	0.000	0.000	0.000	0.000
25	F	31	ASN	0	-0.085	-0.056	33.474	-0.003	-0.003	0.000	0.000	0.000	0.000
26	F	32	LEU	0	0.006	0.007	33.300	-0.002	-0.002	0.000	0.000	0.000	0.000
27	F	33	GLN	0	-0.019	0.011	36.310	0.000	0.000	0.000	0.000	0.000	0.000
28	F	34	GLN	0	-0.059	-0.035	38.378	0.001	0.001	0.000	0.000	0.000	0.000
29	F	35	GLU	-1	-0.849	-0.934	39.626	0.006	0.006	0.000	0.000	0.000	0.000
30	F	36	ILE	0	-0.046	-0.023	38.896	-0.001	-0.001	0.000	0.000	0.000	0.000
31	F	37	TYR	0	-0.015	0.009	42.522	-0.001	-0.001	0.000	0.000	0.000	0.000
32	F	38	ASP	-1	-0.799	-0.889	44.472	0.013	0.013	0.000	0.000	0.000	0.000
33	F	39	LYS	1	0.804	0.893	44.321	-0.006	-0.006	0.000	0.000	0.000	0.000
34	F	40	GLU	-1	-0.777	-0.862	46.491	0.010	0.010	0.000	0.000	0.000	0.000
35	F	41	THR	0	-0.027	-0.012	48.647	0.000	0.000	0.000	0.000	0.000	0.000
36	F	42	GLU	-1	-0.832	-0.884	48.590	0.005	0.005	0.000	0.000	0.000	0.000
37	F	43	TYR	0	-0.060	-0.046	46.970	-0.001	-0.001	0.000	0.000	0.000	0.000
38	F	44	PHE	0	-0.011	-0.010	49.117	-0.001	-0.001	0.000	0.000	0.000	0.000
39	F	45	SER	0	-0.095	-0.043	54.088	0.000	0.000	0.000	0.000	0.000	0.000
40	F	66	SER	0	-0.010	-0.018	61.507	0.000	0.000	0.000	0.000	0.000	0.000
41	F	67	GLY	0	0.044	0.038	59.868	0.000	0.000	0.000	0.000	0.000	0.000
42	F	68	ASN	0	0.015	-0.005	54.427	0.000	0.000	0.000	0.000	0.000	0.000
43	F	69	ILE	0	0.059	0.034	49.961	0.000	0.000	0.000	0.000	0.000	0.000
44	F	70	ILE	0	-0.050	-0.019	50.372	0.000	0.000	0.000	0.000	0.000	0.000
45	F	71	LYS	1	0.797	0.866	53.833	-0.006	-0.006	0.000	0.000	0.000	0.000
46	F	72	GLY	0	0.042	0.033	56.776	0.000	0.000	0.000	0.000	0.000	0.000
47	F	73	PHE	0	-0.104	-0.047	52.677	-0.001	-0.001	0.000	0.000	0.000	0.000
48	F	74	ASP	-1	-0.937	-0.955	58.712	0.000	0.000	0.000	0.000	0.000	0.000
49	F	88	PHE	0	0.046	0.028	51.114	0.000	0.000	0.000	0.000	0.000	0.000
50	F	89	ASN	0	-0.043	-0.053	55.323	0.001	0.001	0.000	0.000	0.000	0.000
51	F	90	ASN	0	0.014	0.008	49.712	0.000	0.000	0.000	0.000	0.000	0.000
52	F	91	ASN	0	-0.054	-0.038	50.791	0.001	0.001	0.000	0.000	0.000	0.000
53	F	92	ASP	-1	-0.796	-0.874	51.942	0.008	0.008	0.000	0.000	0.000	0.000
54	F	93	ARG	1	0.792	0.897	47.713	-0.013	-0.013	0.000	0.000	0.000	0.000
55	F	94	ILE	0	0.007	-0.009	47.208	0.001	0.001	0.000	0.000	0.000	0.000
56	F	95	PHE	0	-0.011	0.009	43.678	0.000	0.000	0.000	0.000	0.000	0.000
57	F	96	SER	0	0.008	-0.026	42.586	0.001	0.001	0.000	0.000	0.000	0.000
58	F	97	LEU	0	-0.068	-0.047	42.633	0.002	0.002	0.000	0.000	0.000	0.000
59	F	98	SER	0	-0.060	-0.019	41.167	0.000	0.000	0.000	0.000	0.000	0.000
60	F	99	SER	0	-0.027	-0.021	37.874	0.001	0.001	0.000	0.000	0.000	0.000
61	F	100	ALA	0	0.031	-0.003	37.816	0.000	0.000	0.000	0.000	0.000	0.000
62	F	101	THR	0	-0.007	-0.003	35.333	0.002	0.002	0.000	0.000	0.000	0.000
63	F	102	TYR	0	0.030	0.011	38.382	0.000	0.000	0.000	0.000	0.000	0.000
64	F	103	VAL	0	-0.003	-0.006	41.650	0.000	0.000	0.000	0.000	0.000	0.000
65	F	104	LYS	1	0.929	0.960	36.718	-0.037	-0.037	0.000	0.000	0.000	0.000
66	F	105	GLN	0	0.032	0.036	41.439	-0.001	-0.001	0.000	0.000	0.000	0.000
67	F	106	GLN	0	0.048	0.044	43.058	-0.002	-0.002	0.000	0.000	0.000	0.000
68	F	107	HIS	1	0.835	0.918	45.023	-0.021	-0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:7:SER)