FMO DATABASE

FMODB ID: 55K3Z

Calculation Name: 5VS7-A-Xray547

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine | chloride ion

Ligand 3-letter code: ALY | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5VS7

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IK82

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1091412.715728
FMO2-HF: Nuclear repulsion	1041241.354356
FMO2-HF: Total energy	-50171.361371
FMO2-MP2: Total energy	-50318.63737

3D Structure Molmil

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(A:1:GLY)

Summations of interaction energy for fragment #1(A:1:GLY)

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.
-115.34	-115.204	16.269	-9.38	-7.027	-0.121

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.774 / q_NPA : 0.862

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

Sort

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	A	3	ASP	-1	-0.791	-0.905	3.835	-43.746	-42.843	-0.003	-0.287	-0.614	-0.001
4	A	4	GLU	-1	-0.786	-0.884	1.739	-120.464	-121.429	16.273	-9.046	-6.263	-0.120
5	A	5	ILE	0	-0.050	-0.027	4.337	10.376	10.574	-0.001	-0.047	-0.150	0.000
6	A	6	GLU	-1	-0.809	-0.893	6.109	-24.207	-24.207	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.814	-0.887	7.575	-26.556	-26.556	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.013	-0.014	6.874	4.433	4.433	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.841	0.922	9.580	34.809	34.809	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.048	0.026	11.903	2.836	2.836	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.798	0.882	11.269	27.641	27.641	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.000	-0.016	13.940	2.108	2.108	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.937	-0.949	15.807	-18.112	-18.112	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.072	-0.035	17.584	1.605	1.605	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.001	0.003	17.334	1.102	1.102	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.027	-0.024	19.210	1.142	1.142	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.029	-0.028	21.635	0.836	0.836	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.033	-0.002	23.551	0.705	0.705	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.029	0.016	23.571	0.579	0.579	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.010	-0.001	24.788	0.501	0.501	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.915	0.970	27.635	11.578	11.578	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.007	0.010	27.465	0.436	0.436	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.021	0.006	27.810	0.379	0.379	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.041	-0.015	31.547	0.331	0.331	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.030	-0.014	33.536	0.337	0.337	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.736	-0.854	34.391	-8.667	-8.667	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.929	0.955	36.235	8.266	8.266	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.907	0.949	38.687	7.472	7.472	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.860	0.945	35.453	8.553	8.553	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.034	-0.017	37.101	0.073	0.073	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.030	0.001	33.140	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.004	0.000	30.357	-0.328	-0.328	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.021	0.019	30.897	-0.428	-0.428	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.008	0.008	31.175	0.186	0.186	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.013	0.018	33.699	0.192	0.192	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.021	0.006	37.365	0.004	0.004	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.065	0.029	38.462	0.197	0.197	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.045	-0.020	41.171	0.154	0.154	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.050	-0.026	43.086	0.193	0.193	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.019	0.004	42.172	0.138	0.138	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.020	-0.001	42.898	-0.170	-0.170	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.835	-0.895	44.054	-7.195	-7.195	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.052	0.025	35.799	-0.111	-0.111	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.022	0.007	35.911	-0.131	-0.131	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.018	-0.005	39.201	-0.181	-0.181	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.002	0.016	41.088	0.019	0.019	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.048	-0.020	35.272	-0.132	-0.132	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.831	0.902	35.204	8.136	8.136	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.843	-0.903	29.181	-11.353	-11.353	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.002	0.014	31.809	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.027	-0.016	26.173	-0.619	-0.619	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.724	-0.835	28.787	-10.679	-10.679	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.032	-0.020	27.478	-0.509	-0.509	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.028	-0.018	26.364	-0.555	-0.555	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.037	-0.049	25.155	-0.701	-0.701	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.033	-0.012	23.214	-0.473	-0.473	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.902	0.956	21.725	12.656	12.656	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.025	0.011	20.912	-0.437	-0.437	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.812	0.904	19.240	12.823	12.823	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.009	0.003	17.370	-1.051	-1.051	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.010	0.005	16.066	-0.922	-0.922	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.069	-0.035	15.315	-1.099	-1.099	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.016	0.007	11.472	-1.351	-1.351	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.937	0.977	12.971	14.771	14.771	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.069	-0.069	15.293	-0.219	-0.219	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.862	0.922	10.116	24.475	24.475	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.012	-0.023	13.914	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.006	-0.005	16.814	0.442	0.442	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.003	0.002	19.683	0.833	0.833	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.763	-0.853	17.277	-18.043	-18.043	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.013	0.002	20.480	0.539	0.539	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.794	-0.882	22.230	-11.460	-11.460	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.901	0.940	24.551	12.395	12.395	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.759	-0.853	23.607	-13.020	-13.020	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.004	-0.010	26.144	0.476	0.476	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.022	0.007	28.597	0.466	0.466	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.025	0.019	28.607	0.380	0.380	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.042	-0.017	28.883	0.343	0.343	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.015	0.000	32.224	0.317	0.317	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.006	-0.024	33.625	0.521	0.521	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.001	0.000	32.955	0.387	0.387	0.000	0.000	0.000	0.000
82	A	82	CYS	0	-0.096	-0.025	36.568	0.344	0.344	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.001	-0.045	37.932	0.274	0.274	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.040	-0.021	38.642	0.188	0.188	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.082	-0.064	40.803	0.117	0.117	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.080	-0.044	41.368	0.301	0.301	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.733	-0.833	44.506	-6.492	-6.492	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.043	0.028	46.615	-0.063	-0.063	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.067	-0.057	47.633	0.016	0.016	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.023	-0.025	46.147	-0.044	-0.044	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.009	-0.023	44.963	-0.058	-0.058	0.000	0.000	0.000	0.000
92	A	92	TYR	0	0.001	0.002	41.675	-0.141	-0.141	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.044	0.039	41.274	-0.220	-0.220	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.878	0.945	41.860	6.702	6.702	0.000	0.000	0.000	0.000
95	A	95	PHE	0	0.000	-0.009	39.878	-0.083	-0.083	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.007	0.000	37.591	-0.269	-0.269	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.802	-0.910	37.607	-7.610	-7.610	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.926	-0.954	39.114	-7.857	-7.857	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.068	-0.040	33.051	-0.207	-0.207	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.805	-0.877	34.164	-9.309	-9.309	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.046	-0.033	34.736	-0.169	-0.169	0.000	0.000	0.000	0.000
102	A	102	TYR	0	-0.080	-0.046	32.333	-0.215	-0.215	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.047	-0.065	26.405	-0.333	-0.333	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.901	0.944	30.798	8.769	8.769	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.924	0.986	32.905	8.539	8.539	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.061	-0.035	28.890	-0.105	-0.105	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.006	-0.012	26.846	-0.079	-0.079	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.083	0.054	25.950	-0.564	-0.564	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.969	0.991	26.160	10.637	10.637	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.042	-0.030	22.256	-0.420	-0.420	0.000	0.000	0.000	0.000
111	A	111	GLN	0	0.023	0.019	21.755	-0.470	-0.470	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.002	-0.016	21.091	-0.614	-0.614	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.903	0.950	20.304	13.800	13.800	0.000	0.000	0.000	0.000
114	A	114	TYR	0	0.022	-0.004	15.130	-0.795	-0.795	0.000	0.000	0.000	0.000
115	A	115	MET	0	-0.014	-0.010	16.324	-1.520	-1.520	0.000	0.000	0.000	0.000
116	A	116	ASN	0	-0.023	-0.013	16.694	-0.683	-0.683	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.072	-0.024	12.389	0.029	0.029	0.000	0.000	0.000	0.000
118	A	118	HIS	0	-0.001	0.009	12.088	-1.857	-1.857	0.000	0.000	0.000	0.000
119	A	119	LEU	-1	-0.933	-0.946	13.345	-19.028	-19.028	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLY)