FMO DATABASE

FMODB ID: 14GGZ

Calculation Name: 5J9T-J-Xray372

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

ligand 3-letter code: ALY

PDB ID: 5J9T

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-406689.983101
FMO2-HF: Nuclear repulsion	375552.663225
FMO2-HF: Total energy	-31137.319876
FMO2-MP2: Total energy	-31228.881492

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.
-14.269	-5.438	5.286	-5.476	-8.64	-0.037

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 : 0.057 / q_NPA : 0.043

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	-0.798	-0.891	2.708	-1.963	1.922	0.782	-1.693	-2.973	0.001
4	J	4	GLU	-1	-0.879	-0.926	1.935	-13.957	-9.588	4.501	-3.618	-5.252	-0.038
5	J	5	LEU	0	-0.009	0.000	3.803	0.808	1.385	0.003	-0.165	-0.415	0.000
6	J	6	LYS	1	0.843	0.890	5.774	-0.370	-0.370	0.000	0.000	0.000	0.000
7	J	7	SER	0	0.004	-0.005	6.305	0.330	0.330	0.000	0.000	0.000	0.000
8	J	8	TYR	0	0.009	0.003	7.802	0.300	0.300	0.000	0.000	0.000	0.000
9	J	9	GLU	-1	-0.831	-0.913	9.782	-0.546	-0.546	0.000	0.000	0.000	0.000
10	J	10	ALA	0	-0.011	0.002	11.216	0.122	0.122	0.000	0.000	0.000	0.000
11	J	11	LEU	0	0.070	0.024	11.658	0.069	0.069	0.000	0.000	0.000	0.000
12	J	12	LYS	1	0.764	0.883	11.310	0.827	0.827	0.000	0.000	0.000	0.000
13	J	13	ALA	0	-0.046	-0.018	15.693	0.066	0.066	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.920	-0.957	16.684	-0.331	-0.331	0.000	0.000	0.000	0.000
15	J	15	LEU	0	0.018	0.019	18.057	0.036	0.036	0.000	0.000	0.000	0.000
16	J	16	LYS	1	0.919	0.951	18.300	0.320	0.320	0.000	0.000	0.000	0.000
17	J	17	LYS	1	0.968	0.991	21.444	0.174	0.174	0.000	0.000	0.000	0.000
18	J	18	SER	0	0.005	-0.008	21.876	0.016	0.016	0.000	0.000	0.000	0.000
19	J	19	LEU	0	-0.030	-0.026	22.912	0.014	0.014	0.000	0.000	0.000	0.000
20	J	20	GLN	0	-0.086	-0.040	25.833	0.005	0.005	0.000	0.000	0.000	0.000
21	J	21	ASP	-1	-0.867	-0.924	27.296	-0.132	-0.132	0.000	0.000	0.000	0.000
22	J	22	ARG	1	0.825	0.862	28.529	0.170	0.170	0.000	0.000	0.000	0.000
23	J	23	ARG	1	0.887	0.947	27.081	0.157	0.157	0.000	0.000	0.000	0.000
24	J	24	GLU	-1	-0.802	-0.873	31.635	-0.099	-0.099	0.000	0.000	0.000	0.000
25	J	25	GLN	0	-0.061	-0.033	31.403	0.015	0.015	0.000	0.000	0.000	0.000
26	J	26	GLU	-1	-0.839	-0.882	33.464	-0.132	-0.132	0.000	0.000	0.000	0.000
27	J	27	ASP	-1	-0.884	-0.942	36.435	-0.086	-0.086	0.000	0.000	0.000	0.000
28	J	28	THR	0	-0.052	-0.035	37.327	0.009	0.009	0.000	0.000	0.000	0.000
29	J	29	PHE	0	-0.071	-0.028	39.017	0.005	0.005	0.000	0.000	0.000	0.000
30	J	30	ASP	-1	-0.858	-0.942	40.804	-0.078	-0.078	0.000	0.000	0.000	0.000
31	J	31	ASN	0	-0.091	-0.058	41.851	0.008	0.008	0.000	0.000	0.000	0.000
32	J	32	LEU	0	0.013	0.007	42.134	0.004	0.004	0.000	0.000	0.000	0.000
33	J	33	GLN	0	-0.040	-0.003	44.897	0.000	0.000	0.000	0.000	0.000	0.000
34	J	34	GLN	0	-0.050	-0.030	46.658	0.001	0.001	0.000	0.000	0.000	0.000
35	J	35	GLU	-1	-0.876	-0.948	48.432	-0.046	-0.046	0.000	0.000	0.000	0.000
36	J	36	ILE	0	-0.030	-0.020	47.427	0.003	0.003	0.000	0.000	0.000	0.000
37	J	37	TYR	0	0.014	0.019	51.131	0.003	0.003	0.000	0.000	0.000	0.000
38	J	38	ASP	-1	-0.821	-0.893	52.968	-0.044	-0.044	0.000	0.000	0.000	0.000
39	J	39	LYS	1	0.814	0.896	52.887	0.043	0.043	0.000	0.000	0.000	0.000
40	J	40	GLU	-1	-0.766	-0.856	55.107	-0.049	-0.049	0.000	0.000	0.000	0.000
41	J	41	THR	0	-0.028	-0.018	57.184	0.002	0.002	0.000	0.000	0.000	0.000
42	J	42	GLU	-1	-0.862	-0.914	57.758	-0.035	-0.035	0.000	0.000	0.000	0.000
43	J	43	TYR	0	-0.016	-0.008	56.145	0.001	0.001	0.000	0.000	0.000	0.000
44	J	44	PHE	0	-0.032	-0.024	57.573	0.001	0.001	0.000	0.000	0.000	0.000
45	J	45	SER	0	-0.077	-0.026	62.520	0.001	0.001	0.000	0.000	0.000	0.000
46	J	46	HIS	0	-0.054	-0.020	62.643	0.003	0.003	0.000	0.000	0.000	0.000
47	J	65	TYR	0	0.002	-0.017	71.797	0.000	0.000	0.000	0.000	0.000	0.000
48	J	66	SER	0	-0.011	-0.015	69.090	0.001	0.001	0.000	0.000	0.000	0.000
49	J	67	GLY	0	-0.001	0.022	68.258	-0.001	-0.001	0.000	0.000	0.000	0.000
50	J	68	ASN	0	0.021	-0.008	63.213	-0.001	-0.001	0.000	0.000	0.000	0.000
51	J	69	ILE	0	0.021	0.001	58.305	0.000	0.000	0.000	0.000	0.000	0.000
52	J	70	ILE	0	-0.037	0.008	59.147	-0.001	-0.001	0.000	0.000	0.000	0.000
53	J	71	LYS	1	0.795	0.880	62.327	0.036	0.036	0.000	0.000	0.000	0.000
54	J	72	GLY	0	0.001	0.027	65.338	0.001	0.001	0.000	0.000	0.000	0.000
55	J	73	PHE	0	0.007	-0.023	62.016	0.000	0.000	0.000	0.000	0.000	0.000
56	J	74	ASP	-1	-0.920	-0.920	68.193	-0.027	-0.027	0.000	0.000	0.000	0.000
57	J	75	THR	0	-0.073	-0.051	71.611	0.002	0.002	0.000	0.000	0.000	0.000
58	J	87	ALA	0	-0.007	-0.017	69.271	0.000	0.000	0.000	0.000	0.000	0.000
59	J	88	PHE	0	0.019	0.021	59.343	-0.001	-0.001	0.000	0.000	0.000	0.000
60	J	89	ASN	0	0.004	-0.012	63.809	0.001	0.001	0.000	0.000	0.000	0.000
61	J	90	ASN	0	0.051	0.017	58.891	-0.001	-0.001	0.000	0.000	0.000	0.000
62	J	91	ASN	0	-0.025	-0.017	58.547	-0.001	-0.001	0.000	0.000	0.000	0.000
63	J	92	ASP	-1	-0.765	-0.867	59.634	-0.040	-0.040	0.000	0.000	0.000	0.000
64	J	93	ARG	1	0.778	0.897	55.727	0.046	0.046	0.000	0.000	0.000	0.000
65	J	94	ILE	0	0.003	-0.020	55.104	-0.002	-0.002	0.000	0.000	0.000	0.000
66	J	95	PHE	0	-0.023	0.002	52.169	-0.002	-0.002	0.000	0.000	0.000	0.000
67	J	96	SER	0	0.007	-0.020	50.821	-0.004	-0.004	0.000	0.000	0.000	0.000
68	J	97	LEU	0	-0.054	-0.037	50.409	-0.003	-0.003	0.000	0.000	0.000	0.000
69	J	98	SER	0	-0.087	-0.034	49.017	-0.003	-0.003	0.000	0.000	0.000	0.000
70	J	99	SER	0	0.015	0.004	46.095	-0.005	-0.005	0.000	0.000	0.000	0.000
71	J	100	ALA	0	0.009	-0.020	45.159	0.002	0.002	0.000	0.000	0.000	0.000
72	J	101	THR	0	-0.032	-0.022	42.635	-0.001	-0.001	0.000	0.000	0.000	0.000
73	J	102	TYR	0	0.046	0.022	45.529	0.002	0.002	0.000	0.000	0.000	0.000
74	J	103	VAL	0	-0.049	-0.016	48.867	0.002	0.002	0.000	0.000	0.000	0.000
75	J	104	LYS	1	0.896	0.969	43.973	0.086	0.086	0.000	0.000	0.000	0.000

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