FMO DATABASE

FMODB ID: Q519Y

Calculation Name: 6YTF-n-Other547

Preferred Name:

Target Type:

Ligand Name: tigecycline | magnesium ion

Ligand 3-letter code: T1C | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6YTF

Chain ID: n

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-793742.21811
FMO2-HF: Nuclear repulsion	748938.444933
FMO2-HF: Total energy	-44803.773177
FMO2-MP2: Total energy	-44935.261455

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:2:ALA)

Summations of interaction energy for fragment #1(A:2: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.
-35.8	-31.453	23.312	-14.675	-12.982	-0.158

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.915

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	4	ILE	0	0.096	0.036	3.882	5.160	6.511	-0.012	-0.528	-0.810	0.000
7	A	8	ASN	0	-0.009	-0.017	2.943	-22.241	-20.790	0.306	-0.797	-0.960	-0.008
8	A	9	ILE	0	0.011	0.016	2.384	5.662	6.584	1.398	-0.808	-1.511	-0.006
9	A	10	PRO	0	-0.042	-0.020	2.057	-28.491	-27.195	3.756	-2.704	-2.349	-0.037
10	A	11	ASP	-1	-0.733	-0.874	1.683	-122.642	-124.536	16.592	-8.999	-5.699	-0.097
11	A	12	ASN	0	-0.027	-0.015	4.037	6.575	6.649	0.000	-0.038	-0.036	0.000
44	A	45	ILE	0	0.011	0.006	2.566	-1.863	-1.298	0.658	-0.433	-0.791	-0.004
52	A	53	LEU	0	-0.030	-0.020	2.559	-3.444	-2.950	0.615	-0.359	-0.749	-0.006
56	A	57	ARG	1	0.740	0.858	4.486	39.040	39.128	-0.001	-0.009	-0.077	0.000
4	A	5	ALA	0	0.038	0.018	6.225	0.996	0.996	0.000	0.000	0.000	0.000
5	A	6	GLY	0	-0.011	0.007	8.846	2.801	2.801	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.044	-0.019	6.871	1.474	1.474	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.897	0.937	7.284	33.762	33.762	0.000	0.000	0.000	0.000
13	A	14	HIS	0	0.086	0.046	8.012	-4.588	-4.588	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.084	0.059	7.778	-1.790	-1.790	0.000	0.000	0.000	0.000
15	A	16	VAL	0	0.011	-0.004	8.855	-0.357	-0.357	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.069	-0.036	10.710	1.650	1.650	0.000	0.000	0.000	0.000
17	A	18	SER	0	0.002	-0.001	5.499	-0.032	-0.032	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.082	0.029	6.633	-2.103	-2.103	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.106	-0.063	8.235	2.479	2.479	0.000	0.000	0.000	0.000
20	A	21	TYR	0	-0.029	-0.019	7.526	1.802	1.802	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.014	0.020	7.269	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.036	-0.031	10.810	2.332	2.332	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.061	0.015	14.494	0.457	0.457	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.056	-0.015	10.445	1.116	1.116	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.046	0.029	14.112	-0.351	-0.351	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.949	0.952	15.293	18.055	18.055	0.000	0.000	0.000	0.000
27	A	28	HIS	0	-0.011	0.003	16.701	-0.587	-0.587	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.070	0.029	14.859	0.277	0.277	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.015	0.015	12.336	-0.480	-0.480	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.965	0.977	13.605	15.170	15.170	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.003	0.003	16.244	0.323	0.323	0.000	0.000	0.000	0.000
32	A	33	ILE	0	0.002	0.005	11.126	0.238	0.238	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.002	-0.008	9.968	-0.282	-0.282	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.001	0.003	13.956	0.447	0.447	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.049	-0.016	16.878	0.672	0.672	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.015	-0.014	12.543	0.320	0.320	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.021	0.027	15.716	0.303	0.303	0.000	0.000	0.000	0.000
38	A	39	ILE	0	-0.034	-0.003	10.542	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.039	0.025	14.296	-0.251	-0.251	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.882	-0.966	13.116	-20.309	-20.309	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.082	-0.055	13.278	-1.220	-1.220	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.018	0.020	11.193	-0.911	-0.911	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.921	0.957	8.821	23.046	23.046	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.879	0.943	5.603	32.809	32.809	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.886	-0.943	6.849	-27.761	-27.761	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.054	-0.011	6.348	2.402	2.402	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.783	-0.880	6.745	-28.025	-28.025	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.894	-0.975	5.991	-39.790	-39.790	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.021	0.002	7.869	0.916	0.916	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.040	-0.038	9.594	2.117	2.117	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.822	-0.914	6.698	-29.850	-29.850	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.033	0.031	9.338	1.520	1.520	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.001	-0.007	6.353	0.575	0.575	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.009	0.006	9.783	1.354	1.354	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.823	-0.893	12.881	-16.701	-16.701	0.000	0.000	0.000	0.000
59	A	60	VAL	0	-0.055	-0.026	9.677	0.710	0.710	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.031	-0.012	12.869	0.885	0.885	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.825	0.904	15.087	18.074	18.074	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.055	-0.023	15.085	0.917	0.917	0.000	0.000	0.000	0.000
63	A	64	PRO	0	-0.012	0.013	16.466	-0.526	-0.526	0.000	0.000	0.000	0.000
64	A	65	THR	0	0.059	0.002	13.253	-1.088	-1.088	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.776	-0.886	12.158	-22.268	-22.268	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.007	0.002	15.418	1.210	1.210	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.890	-0.961	18.143	-15.981	-15.981	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.045	0.037	18.055	1.016	1.016	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.830	0.903	14.919	19.871	19.871	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.968	1.004	21.207	14.965	14.965	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.848	-0.935	23.465	-12.054	-12.054	0.000	0.000	0.000	0.000
72	A	73	ILE	0	0.028	0.022	23.029	0.760	0.760	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.090	-0.053	25.440	0.669	0.669	0.000	0.000	0.000	0.000
74	A	75	MET	0	0.024	0.012	27.323	0.639	0.639	0.000	0.000	0.000	0.000
75	A	76	ASN	0	0.023	0.014	28.436	0.958	0.958	0.000	0.000	0.000	0.000
76	A	77	ILE	0	-0.064	-0.030	27.880	0.471	0.471	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.946	0.978	31.355	10.296	10.296	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.994	0.988	32.226	9.908	9.908	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.053	-0.031	33.677	0.311	0.311	0.000	0.000	0.000	0.000
80	A	81	MET	0	-0.056	-0.033	34.169	0.304	0.304	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.868	-0.936	37.206	-8.423	-8.423	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.014	0.000	39.332	0.195	0.195	0.000	0.000	0.000	0.000
83	A	84	GLY	0	0.005	0.021	41.223	0.179	0.179	0.000	0.000	0.000	0.000
84	A	85	CYS	0	0.028	0.027	39.677	0.087	0.087	0.000	0.000	0.000	0.000
85	A	86	TYR	0	0.089	0.038	41.438	-0.215	-0.215	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.976	0.968	33.486	9.091	9.091	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.075	0.048	37.243	-0.241	-0.241	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.016	0.006	38.310	-0.105	-0.105	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.831	0.912	38.174	7.780	7.780	0.000	0.000	0.000	0.000
90	A	91	HIS	0	0.019	0.003	31.554	-0.088	-0.088	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.946	0.962	35.532	7.816	7.816	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.942	0.991	37.772	7.391	7.391	0.000	0.000	0.000	0.000
93	A	94	SER	0	-0.032	0.003	34.688	0.020	0.020	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.013	-0.004	35.873	0.071	0.071	0.000	0.000	0.000	0.000
95	A	96	PRO	0	-0.008	-0.013	35.451	-0.261	-0.261	0.000	0.000	0.000	0.000
96	A	97	VAL	0	-0.014	-0.017	34.073	0.232	0.232	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.922	0.954	29.192	10.459	10.459	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.079	0.062	36.957	0.059	0.059	0.000	0.000	0.000	0.000
99	A	100	GLN	0	0.043	0.021	34.331	0.245	0.245	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.957	0.983	39.453	7.393	7.393	0.000	0.000	0.000	0.000
101	A	102	THR	0	0.029	-0.005	40.539	-0.167	-0.167	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.992	1.004	42.537	6.346	6.346	0.000	0.000	0.000	0.000
103	A	104	THR	0	0.045	0.015	42.622	0.034	0.034	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.004	-0.019	38.605	0.088	0.088	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.049	0.029	37.110	-0.163	-0.163	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.823	0.898	34.994	8.304	8.304	0.000	0.000	0.000	0.000
107	A	108	THR	0	0.039	0.033	29.602	-0.131	-0.131	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.822	0.924	31.211	9.587	9.587	0.000	0.000	0.000	0.000
109	A	110	LYS	1	0.952	0.968	33.494	7.836	7.836	0.000	0.000	0.000	0.000
110	A	111	GLY	0	0.079	0.068	33.362	0.150	0.150	0.000	0.000	0.000	0.000
111	A	112	PRO	0	0.077	0.030	33.506	0.183	0.183	0.000	0.000	0.000	0.000
112	A	113	ARG	1	0.917	0.952	35.935	8.016	8.016	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.975	0.989	39.506	7.292	7.292	0.000	0.000	0.000	0.000
114	A	115	PRO	0	0.007	0.012	41.880	0.041	0.041	0.000	0.000	0.000	0.000
115	A	116	ILE	-1	-0.894	-0.939	45.439	-6.696	-6.696	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)