FMO DATABASE

FMODB ID: 1Y6LZ

Calculation Name: 3OW2-Y-Xray547

Preferred Name:

Target Type:

Ligand Name: (2r,3s,4r,5r,8r,10r,11r,12s,13s,14r)-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-15-oxo-11-[(3,4,6-trideoxy-3-{[3-(1-{(1s,2r)-1-(fluoromethyl)-2-hydroxy-2-[4-(methylsulfonyl)phenyl]ethyl}-1h-1,2,3-triazol-4-yl)propyl](methyl)amino}-beta-d-xylo-hexopyranosyl)oxy]-1-oxa-6-azacyclopentadecan-13-yl 2,6-dideoxy-3-c-methyl-3-o-methyl-alpha-l-ribo-hexopyranoside | cadmium ion | magnesium ion | strontium ion | chloride ion | potassium ion

Ligand 3-letter code: EMK | CD | MG | SR | CL | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3OW2

Chain ID: Y

ChEMBL ID:

UniProt ID: P15825

Base Structure: X-ray

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	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-401862.811962
FMO2-HF: Nuclear repulsion	372582.038894
FMO2-HF: Total energy	-29280.773068
FMO2-MP2: Total energy	-29362.047136

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:10:ARG)

Summations of interaction energy for fragment #1(A:10:ARG)

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.
468.743	477.632	5.302	-5.524	-8.667	-0.055

Interaction energy analysis for fragmet #1(A:10:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.850 / q_NPA : 1.922

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	12	GLY	0	-0.001	0.030	2.276	8.591	12.036	0.651	-1.763	-2.333	-0.008
4	A	13	ARG	1	0.959	0.973	3.763	94.994	95.608	0.003	-0.140	-0.477	0.000
15	A	24	VAL	0	0.008	0.005	4.498	-13.812	-13.596	-0.001	-0.010	-0.205	0.000
17	A	26	VAL	0	0.016	0.008	3.939	0.172	0.348	0.000	-0.031	-0.145	0.000
18	A	27	ALA	0	-0.062	-0.040	2.256	-14.823	-13.575	3.269	-1.694	-2.823	-0.017
19	A	28	ASP	-1	-0.848	-0.922	3.124	-68.561	-68.748	0.010	0.576	-0.399	-0.002
21	A	30	GLU	-1	-0.860	-0.950	2.529	-110.412	-107.330	1.372	-2.424	-2.030	-0.028
22	A	31	ILE	0	-0.027	-0.007	4.216	1.204	1.429	-0.001	-0.032	-0.192	0.000
25	A	34	LYS	1	0.916	0.959	4.198	86.264	86.334	-0.001	-0.006	-0.063	0.000
5	A	14	PHE	0	-0.021	-0.023	6.398	5.933	5.933	0.000	0.000	0.000	0.000
6	A	15	GLY	0	0.052	0.036	7.491	6.044	6.044	0.000	0.000	0.000	0.000
7	A	16	PRO	0	0.034	0.013	8.127	-4.457	-4.457	0.000	0.000	0.000	0.000
8	A	17	ARG	1	0.977	0.994	10.477	49.609	49.609	0.000	0.000	0.000	0.000
9	A	18	TYR	0	0.048	0.015	10.130	-5.958	-5.958	0.000	0.000	0.000	0.000
10	A	19	GLY	0	0.061	0.043	10.937	1.561	1.561	0.000	0.000	0.000	0.000
11	A	20	LEU	0	0.040	0.007	6.765	-4.259	-4.259	0.000	0.000	0.000	0.000
12	A	21	LYS	1	0.998	1.001	7.754	31.109	31.109	0.000	0.000	0.000	0.000
13	A	22	ILE	0	0.043	0.025	9.627	-1.707	-1.707	0.000	0.000	0.000	0.000
14	A	23	ARG	1	0.890	0.939	5.679	60.363	60.363	0.000	0.000	0.000	0.000
16	A	25	ARG	1	1.010	1.010	5.600	38.549	38.549	0.000	0.000	0.000	0.000
20	A	29	VAL	0	-0.017	-0.011	6.630	4.309	4.309	0.000	0.000	0.000	0.000
23	A	32	LYS	1	0.879	0.924	5.477	50.584	50.584	0.000	0.000	0.000	0.000
24	A	33	HIS	0	-0.041	-0.007	7.190	-0.673	-0.673	0.000	0.000	0.000	0.000
26	A	35	LYS	1	0.951	0.985	8.485	50.604	50.604	0.000	0.000	0.000	0.000
27	A	36	LYS	1	0.980	0.996	10.853	37.056	37.056	0.000	0.000	0.000	0.000
28	A	37	HIS	0	-0.021	-0.016	11.918	2.952	2.952	0.000	0.000	0.000	0.000
29	A	38	LYS	1	0.921	0.952	16.302	31.763	31.763	0.000	0.000	0.000	0.000
30	A	39	CYS	0	-0.066	-0.020	20.113	0.000	0.000	0.000	0.000	0.000	0.000
31	A	40	PRO	0	0.051	0.015	22.242	0.314	0.314	0.000	0.000	0.000	0.000
32	A	41	VAL	0	0.040	0.038	25.258	0.574	0.574	0.000	0.000	0.000	0.000
33	A	42	CYS	0	-0.011	0.000	24.698	0.344	0.344	0.000	0.000	0.000	0.000
34	A	43	GLY	0	0.109	0.050	25.152	-0.709	-0.709	0.000	0.000	0.000	0.000
35	A	44	PHE	0	0.011	-0.006	22.309	-1.136	-1.136	0.000	0.000	0.000	0.000
36	A	45	LYS	0	-0.010	0.002	17.804	-1.007	-1.007	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.866	0.924	17.502	24.464	24.464	0.000	0.000	0.000	0.000
38	A	47	LEU	0	0.002	0.024	16.808	0.274	0.274	0.000	0.000	0.000	0.000
39	A	48	LYS	1	0.903	0.947	10.489	42.037	42.037	0.000	0.000	0.000	0.000
40	A	49	ARG	1	0.874	0.957	11.876	42.304	42.304	0.000	0.000	0.000	0.000
41	A	50	ALA	0	0.004	-0.007	13.817	-1.318	-1.318	0.000	0.000	0.000	0.000
42	A	51	GLY	0	0.054	0.023	15.741	0.491	0.491	0.000	0.000	0.000	0.000
43	A	52	THR	0	-0.059	-0.044	15.226	-1.940	-1.940	0.000	0.000	0.000	0.000
44	A	53	GLY	0	0.059	0.042	16.104	1.472	1.472	0.000	0.000	0.000	0.000
45	A	54	ILE	0	-0.005	0.016	17.375	1.353	1.353	0.000	0.000	0.000	0.000
46	A	55	TRP	0	-0.048	-0.026	12.281	-3.755	-3.755	0.000	0.000	0.000	0.000
47	A	56	MET	0	0.035	0.013	17.874	1.923	1.923	0.000	0.000	0.000	0.000
48	A	57	CYS	0	-0.038	0.003	18.402	-1.845	-1.845	0.000	0.000	0.000	0.000
49	A	58	GLY	0	0.007	0.011	19.257	0.931	0.931	0.000	0.000	0.000	0.000
50	A	59	HIS	0	-0.004	-0.032	20.447	-0.530	-0.530	0.000	0.000	0.000	0.000
51	A	60	CYS	0	0.085	0.038	23.538	0.179	0.179	0.000	0.000	0.000	0.000
52	A	61	GLY	0	0.060	0.045	24.128	0.647	0.647	0.000	0.000	0.000	0.000
53	A	62	TYR	0	0.046	0.013	24.169	-0.121	-0.121	0.000	0.000	0.000	0.000
54	A	63	LYS	1	0.961	0.975	22.021	23.136	23.136	0.000	0.000	0.000	0.000
55	A	64	ILE	0	0.028	0.007	20.937	0.733	0.733	0.000	0.000	0.000	0.000
56	A	65	ALA	0	0.030	0.028	21.326	-1.165	-1.165	0.000	0.000	0.000	0.000
57	A	66	GLY	0	0.029	0.002	19.496	0.271	0.271	0.000	0.000	0.000	0.000
58	A	67	GLY	0	0.022	0.017	17.348	0.194	0.194	0.000	0.000	0.000	0.000
59	A	68	CYS	0	-0.008	-0.010	14.738	-0.729	-0.729	0.000	0.000	0.000	0.000
60	A	69	TYR	0	0.011	-0.013	10.323	-2.212	-2.212	0.000	0.000	0.000	0.000
61	A	70	GLN	0	0.026	0.006	11.440	-4.471	-4.471	0.000	0.000	0.000	0.000
62	A	71	PRO	0	0.014	0.030	14.186	1.157	1.157	0.000	0.000	0.000	0.000
63	A	72	GLU	-1	-0.815	-0.919	17.508	-25.958	-25.958	0.000	0.000	0.000	0.000
64	A	73	THR	0	-0.046	-0.032	18.349	-1.394	-1.394	0.000	0.000	0.000	0.000
65	A	74	VAL	0	0.011	-0.006	19.710	0.591	0.591	0.000	0.000	0.000	0.000
66	A	75	ALA	0	0.062	0.034	22.199	0.724	0.724	0.000	0.000	0.000	0.000
67	A	76	GLY	0	0.026	0.015	23.475	0.814	0.814	0.000	0.000	0.000	0.000
68	A	77	LYS	1	0.923	0.948	20.088	28.869	28.869	0.000	0.000	0.000	0.000
69	A	78	ALA	0	-0.034	-0.014	25.626	0.505	0.505	0.000	0.000	0.000	0.000
70	A	79	VAL	0	0.033	0.013	28.211	0.548	0.548	0.000	0.000	0.000	0.000
71	A	80	MET	0	-0.069	-0.032	26.491	0.215	0.215	0.000	0.000	0.000	0.000
72	A	81	LYS	1	0.858	0.936	27.649	21.666	21.666	0.000	0.000	0.000	0.000
73	A	82	ALA	-1	-0.879	-0.905	32.987	-16.696	-16.696	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ARG)