FMO DATABASE

FMODB ID: 4QM2N

Calculation Name: 2KO7-A-Other547

Preferred Name:

Target Type:

Ligand Name: ethyl (4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}-2,6-dioxopiperidin-1-yl)acetate

Ligand 3-letter code: JZF

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KO7

Chain ID: A

ChEMBL ID:

UniProt ID: Q63J95

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	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-834020.874327
FMO2-HF: Nuclear repulsion	791117.645398
FMO2-HF: Total energy	-42903.228928
FMO2-MP2: Total energy	-43028.449376

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.
-185.756	-188.326	21.077	-9.935	-8.572	-0.124

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 : 0.789 / q_NPA : 0.892

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	GLY	0	0.023	0.000	3.847	3.518	4.080	-0.004	-0.157	-0.402	0.000
43	A	43	ASP	-1	-0.902	-0.938	1.925	-128.878	-132.469	16.143	-6.879	-5.672	-0.088
44	A	44	GLY	0	0.031	0.009	2.282	-28.993	-28.605	4.939	-2.897	-2.430	-0.036
45	A	45	GLN	0	-0.037	-0.006	4.665	3.994	4.065	-0.001	-0.002	-0.068	0.000
4	A	4	SER	0	-0.059	-0.018	6.513	2.781	2.781	0.000	0.000	0.000	0.000
5	A	5	MET	0	0.017	-0.001	6.438	-5.594	-5.594	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.010	0.005	8.124	2.045	2.045	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.013	-0.012	11.110	-1.157	-1.157	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.027	0.032	13.061	0.545	0.545	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.059	-0.036	15.622	-0.610	-0.610	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.016	-0.023	17.661	0.954	0.954	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.913	-0.964	21.144	-11.917	-11.917	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.019	0.013	22.795	0.035	0.035	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.013	-0.006	19.544	-0.134	-0.134	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.028	-0.006	17.614	-1.313	-1.313	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.871	0.949	12.659	22.222	22.222	0.000	0.000	0.000	0.000
16	A	16	TYR	0	0.018	0.008	15.883	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.834	-0.936	12.186	-23.046	-23.046	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.969	-0.971	14.936	-17.593	-17.593	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.004	-0.002	12.369	-1.638	-1.638	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.048	-0.031	16.518	0.244	0.244	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.929	-0.951	20.220	-12.353	-12.353	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.030	0.003	23.657	-0.088	-0.088	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.096	-0.047	26.455	0.422	0.422	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.082	0.060	29.110	0.402	0.402	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.030	-0.029	31.060	0.163	0.163	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.936	-0.963	28.439	-11.155	-11.155	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.030	0.035	28.802	0.407	0.407	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.856	0.909	30.578	9.618	9.618	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.044	0.010	32.437	0.006	0.006	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.031	-0.013	33.466	0.301	0.301	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.011	0.008	33.364	0.201	0.201	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.031	-0.023	33.504	-0.241	-0.241	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.024	0.023	28.741	0.107	0.107	0.000	0.000	0.000	0.000
34	A	34	SER	0	0.008	-0.004	28.933	-0.211	-0.211	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.002	-0.003	23.678	-0.147	-0.147	0.000	0.000	0.000	0.000
36	A	36	HIS	0	0.047	0.040	20.809	-0.146	-0.146	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.004	-0.003	18.414	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.036	-0.045	13.946	0.600	0.600	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.021	0.023	13.979	-0.869	-0.869	0.000	0.000	0.000	0.000
40	A	40	TRP	0	-0.019	-0.025	8.746	-2.460	-2.460	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.045	0.014	7.088	1.719	1.719	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.005	-0.012	6.309	-1.305	-1.305	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.926	0.949	6.462	23.175	23.175	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.080	-0.045	10.267	0.213	0.213	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.873	-0.930	12.840	-15.600	-15.600	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.044	-0.031	15.270	-1.404	-1.404	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.069	0.045	17.919	0.082	0.082	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.913	0.938	19.281	15.259	15.259	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.857	-0.934	21.796	-13.073	-13.073	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.868	0.943	23.232	12.450	12.450	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.109	-0.054	25.131	0.654	0.654	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.873	-0.938	26.095	-10.535	-10.535	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.069	-0.018	25.713	-0.579	-0.579	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.034	0.010	24.766	0.384	0.384	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.041	0.021	26.766	-0.080	-0.080	0.000	0.000	0.000	0.000
59	A	59	PHE	0	-0.068	-0.039	26.302	0.090	0.090	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.003	0.001	30.973	0.049	0.049	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.004	0.026	27.974	-0.210	-0.210	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.007	-0.008	29.994	0.382	0.382	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.043	-0.025	31.728	0.361	0.361	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.023	0.033	30.001	0.161	0.161	0.000	0.000	0.000	0.000
65	A	65	MET	0	-0.067	-0.047	29.029	0.206	0.206	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.003	0.019	24.320	-0.392	-0.392	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.017	0.007	19.162	0.238	0.238	0.000	0.000	0.000	0.000
68	A	68	LYS	1	1.011	0.990	23.752	11.712	11.712	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.031	-0.001	20.148	0.174	0.174	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.046	-0.011	18.680	-0.231	-0.231	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.823	-0.915	22.388	-11.376	-11.376	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.928	-0.969	22.949	-12.450	-12.450	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.012	-0.027	21.452	-0.109	-0.109	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.017	-0.023	22.238	0.114	0.114	0.000	0.000	0.000	0.000
75	A	75	GLN	0	-0.061	-0.033	24.964	0.599	0.599	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.012	0.018	25.293	0.324	0.324	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.098	-0.022	21.103	-0.327	-0.327	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.964	0.961	24.767	11.776	11.776	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.033	0.005	26.043	-0.452	-0.452	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.024	0.011	26.616	0.176	0.176	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.026	0.005	23.489	-0.245	-0.245	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.014	-0.001	17.254	-0.078	-0.078	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.923	0.945	16.935	15.186	15.186	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.935	0.993	9.756	28.350	28.350	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.010	0.025	14.245	0.606	0.606	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.052	-0.038	11.463	-1.275	-1.275	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.046	0.015	13.989	1.416	1.416	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.018	0.018	15.553	-0.902	-0.902	0.000	0.000	0.000	0.000
89	A	89	PRO	0	0.034	0.024	16.077	0.907	0.907	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.026	-0.023	18.635	1.246	1.246	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.008	-0.009	20.369	0.698	0.698	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.027	0.003	19.178	-0.045	-0.045	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.007	-0.002	17.366	0.382	0.382	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.009	0.020	20.533	0.743	0.743	0.000	0.000	0.000	0.000
95	A	95	ALA	0	-0.020	-0.028	20.810	-0.527	-0.527	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.913	0.962	22.578	12.094	12.094	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.029	0.025	19.317	0.173	0.173	0.000	0.000	0.000	0.000
98	A	98	ALA	0	-0.014	-0.016	18.121	0.596	0.596	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.046	0.017	18.557	0.029	0.029	0.000	0.000	0.000	0.000
100	A	100	GLY	0	-0.022	-0.005	18.167	-0.355	-0.355	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.002	0.003	11.769	-0.070	-0.070	0.000	0.000	0.000	0.000
102	A	102	ILE	0	-0.026	-0.006	13.172	-1.831	-1.831	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.047	0.020	13.996	1.491	1.491	0.000	0.000	0.000	0.000
104	A	104	PRO	0	0.016	0.005	17.123	-0.397	-0.397	0.000	0.000	0.000	0.000
105	A	105	ASN	0	0.008	-0.012	15.882	1.059	1.059	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.021	-0.002	13.437	-1.277	-1.277	0.000	0.000	0.000	0.000
107	A	107	THR	0	-0.014	-0.012	11.945	1.610	1.610	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.021	0.002	11.377	-2.262	-2.262	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.036	-0.027	9.260	1.103	1.103	0.000	0.000	0.000	0.000
110	A	110	PHE	0	0.030	0.017	12.196	-0.476	-0.476	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.824	-0.893	13.837	-21.242	-21.242	0.000	0.000	0.000	0.000
112	A	112	VAL	0	-0.012	-0.011	15.357	0.742	0.742	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.891	-0.954	18.520	-16.637	-16.637	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.017	-0.001	21.398	0.361	0.361	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.068	-0.028	24.866	0.084	0.084	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.878	-0.955	27.395	-9.463	-9.463	0.000	0.000	0.000	0.000
117	A	117	VAL	-1	-0.947	-0.972	30.548	-9.664	-9.664	0.000	0.000	0.000	0.000

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