FMO DATABASE

FMODB ID: RQ3Z8

Calculation Name: 2KOO-A-Other547

Preferred Name:

Target Type:

Ligand Name: s-[2-({n-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] hexanethioate

Ligand 3-letter code: SXH

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KOO

Chain ID: A

ChEMBL ID:

UniProt ID: P72393

Base Structure: SolutionNMR

Registration Date: 2025-10-04

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	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-518213.443102
FMO2-HF: Nuclear repulsion	487583.765369
FMO2-HF: Total energy	-30629.677734
FMO2-MP2: Total energy	-30720.152031

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:ALA)

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

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.
-414.456	-413.847	30.642	-18.812	-12.436	-0.186

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.744 / q_NPA : 0.843

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	A	3	THR	0	-0.061	-0.077	3.836	3.904	5.122	-0.014	-0.515	-0.689	0.002
54	A	54	PHE	0	-0.038	-0.030	4.542	-5.250	-5.213	-0.001	-0.006	-0.029	0.000
55	A	55	ASP	-1	-0.925	-0.943	4.731	-45.042	-44.930	-0.001	-0.003	-0.107	0.000
80	A	80	GLN	0	-0.008	0.011	1.981	-25.583	-25.766	9.999	-6.103	-3.712	-0.042
81	A	81	ALA	-1	-0.817	-0.873	1.744	-140.475	-141.050	20.659	-12.185	-7.899	-0.146
4	A	4	GLN	0	0.033	-0.009	6.458	1.228	1.228	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.914	-0.963	9.982	-19.715	-19.715	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.831	-0.881	6.590	-45.177	-45.177	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.022	0.003	5.714	0.525	0.525	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.016	-0.004	9.108	1.985	1.985	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.002	-0.007	12.434	1.312	1.312	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.007	0.010	10.331	1.172	1.172	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.015	-0.019	11.412	1.003	1.003	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.009	-0.003	13.571	1.537	1.537	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.860	-0.902	13.148	-22.206	-22.206	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.040	0.031	12.808	1.059	1.059	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.009	-0.007	17.131	1.122	1.122	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.072	-0.057	19.407	1.351	1.351	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.984	-0.995	17.998	-16.059	-16.059	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.074	-0.028	19.620	0.744	0.744	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.015	-0.016	22.595	0.600	0.600	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.018	0.017	23.860	0.498	0.498	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.041	-0.018	22.144	0.247	0.247	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.022	0.007	21.946	-0.657	-0.657	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.018	0.010	18.113	-0.386	-0.386	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.954	-0.986	19.447	-14.069	-14.069	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.895	-0.942	22.173	-12.713	-12.713	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.015	0.014	16.899	-0.145	-0.145	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.824	0.898	17.714	15.587	15.587	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.042	0.018	15.800	0.126	0.126	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.931	-0.974	17.270	-14.607	-14.607	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.809	0.913	20.263	13.384	13.384	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.005	-0.011	20.477	-0.722	-0.722	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.070	-0.001	16.029	0.268	0.268	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.034	-0.029	21.927	0.336	0.336	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.989	-0.986	25.283	-10.710	-10.710	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.873	-0.919	24.500	-12.164	-12.164	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.053	-0.008	20.894	0.031	0.031	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.934	-0.970	25.482	-10.404	-10.404	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.008	-0.005	21.710	0.112	0.112	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.719	-0.816	24.965	-12.410	-12.410	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.105	-0.057	23.759	0.348	0.348	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.051	-0.020	24.047	-0.240	-0.240	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.011	-0.039	22.485	-0.555	-0.555	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.008	-0.003	18.327	-1.007	-1.007	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.004	0.007	18.912	-0.875	-0.875	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.910	-0.962	18.997	-15.188	-15.188	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.028	-0.023	15.548	-0.996	-0.996	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.003	0.001	14.761	-1.545	-1.545	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.009	0.015	13.919	-1.684	-1.684	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.030	0.009	13.646	-1.338	-1.338	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.013	-0.008	10.776	-2.034	-2.034	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.906	-0.948	9.202	-24.872	-24.872	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.947	-0.975	9.114	-26.776	-26.776	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.772	0.883	7.853	25.455	25.455	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.061	-0.041	5.618	4.274	4.274	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.760	0.876	8.092	24.180	24.180	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.026	0.017	10.177	1.075	1.075	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.022	0.013	13.689	0.651	0.651	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.852	-0.945	17.416	-14.677	-14.677	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.848	-0.916	19.725	-13.299	-13.299	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.829	-0.887	16.438	-17.748	-17.748	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.044	0.013	15.801	-0.077	-0.077	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.777	0.886	18.090	13.875	13.875	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.100	-0.066	18.655	1.319	1.319	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.087	-0.026	13.790	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.922	0.948	17.808	14.064	14.064	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.041	-0.022	18.819	0.572	0.572	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.061	0.044	14.596	-0.966	-0.966	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.038	0.024	14.337	-1.775	-1.775	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.897	-0.907	14.497	-17.631	-17.631	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.068	0.036	13.553	-0.994	-0.994	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.018	-0.014	9.748	-2.311	-2.311	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.805	0.896	9.678	16.802	16.802	0.000	0.000	0.000	0.000
75	A	75	TYR	0	-0.062	-0.057	10.551	-1.711	-1.711	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.024	-0.003	6.788	-1.709	-1.709	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.012	0.006	5.553	-5.535	-5.535	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.961	-0.988	5.826	-28.505	-28.505	0.000	0.000	0.000	0.000
79	A	79	HIS	1	0.828	0.915	7.704	27.362	27.362	0.000	0.000	0.000	0.000

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