FMO DATABASE

FMODB ID: KQ313

Calculation Name: 6YTF-k-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: k

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-671578.429546
FMO2-HF: Nuclear repulsion	631849.63561
FMO2-HF: Total energy	-39728.793936
FMO2-MP2: Total energy	-39844.762371

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:4:GLN)

Summations of interaction energy for fragment #1(A:4:GLN)

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.
-37.233	-32.767	0.117	-1.677	-2.908	-0.003

Interaction energy analysis for fragmet #1(A:4:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.925

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	6	ILE	0	0.027	0.020	3.824	0.362	1.997	-0.007	-0.621	-1.007	0.000
75	A	78	GLN	0	-0.043	-0.030	3.109	-12.961	-11.966	0.046	-0.553	-0.489	-0.004
76	A	79	PRO	0	0.002	0.021	3.405	7.865	8.527	0.005	-0.174	-0.493	-0.001
77	A	80	THR	0	0.016	0.010	4.692	-7.544	-7.494	-0.001	-0.007	-0.043	0.000
81	A	84	VAL	0	0.026	0.005	4.499	1.554	1.612	-0.001	-0.002	-0.054	0.000
99	A	102	LEU	0	-0.005	-0.004	3.337	-3.022	-2.127	0.076	-0.313	-0.658	0.002
100	A	103	GLY	-1	-0.870	-0.912	4.769	-31.881	-31.710	-0.001	-0.007	-0.164	0.000
4	A	7	ARG	1	0.805	0.893	5.875	28.596	28.596	0.000	0.000	0.000	0.000
5	A	8	ILE	0	0.059	0.031	9.552	0.800	0.800	0.000	0.000	0.000	0.000
6	A	9	ARG	1	0.834	0.911	12.016	20.862	20.862	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.054	0.046	15.483	0.215	0.215	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.950	0.947	18.501	14.100	14.100	0.000	0.000	0.000	0.000
9	A	12	SER	0	0.063	0.019	21.919	0.041	0.041	0.000	0.000	0.000	0.000
10	A	13	PHE	0	0.025	0.012	25.308	0.067	0.067	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.830	-0.916	28.196	-10.073	-10.073	0.000	0.000	0.000	0.000
12	A	15	HIS	0	0.012	0.018	27.007	-0.532	-0.532	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.960	0.980	26.942	9.300	9.300	0.000	0.000	0.000	0.000
14	A	17	LEU	0	0.059	0.037	26.096	-0.245	-0.245	0.000	0.000	0.000	0.000
15	A	18	ILE	0	-0.064	-0.012	21.703	-0.560	-0.560	0.000	0.000	0.000	0.000
16	A	19	ASP	-1	-0.821	-0.887	22.076	-13.554	-13.554	0.000	0.000	0.000	0.000
17	A	20	GLN	0	-0.030	-0.004	23.102	-0.407	-0.407	0.000	0.000	0.000	0.000
18	A	21	SER	0	0.073	0.023	20.287	-0.678	-0.678	0.000	0.000	0.000	0.000
19	A	22	ALA	0	-0.042	-0.029	18.412	-1.025	-1.025	0.000	0.000	0.000	0.000
20	A	23	GLN	0	-0.075	-0.047	18.403	-0.557	-0.557	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.836	-0.908	20.429	-13.707	-13.707	0.000	0.000	0.000	0.000
22	A	25	ILE	0	0.006	-0.001	13.859	-0.862	-0.862	0.000	0.000	0.000	0.000
23	A	26	VAL	0	-0.057	-0.036	15.166	-1.433	-1.433	0.000	0.000	0.000	0.000
24	A	27	GLU	-1	-0.943	-0.972	16.117	-15.685	-15.685	0.000	0.000	0.000	0.000
25	A	28	THR	0	-0.042	-0.029	14.957	-0.190	-0.190	0.000	0.000	0.000	0.000
26	A	29	ALA	0	0.000	-0.001	11.482	-0.615	-0.615	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.923	0.956	13.142	18.234	18.234	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.952	0.992	15.007	17.101	17.101	0.000	0.000	0.000	0.000
29	A	32	THR	0	-0.084	-0.053	12.518	0.909	0.909	0.000	0.000	0.000	0.000
30	A	33	GLY	0	0.040	0.014	10.709	-1.908	-1.908	0.000	0.000	0.000	0.000
31	A	34	ALA	0	0.009	0.005	10.134	2.433	2.433	0.000	0.000	0.000	0.000
32	A	35	GLN	0	-0.043	-0.023	7.918	-0.440	-0.440	0.000	0.000	0.000	0.000
33	A	36	VAL	0	0.023	0.015	8.837	-3.106	-3.106	0.000	0.000	0.000	0.000
34	A	37	CYS	0	-0.057	-0.037	11.591	1.357	1.357	0.000	0.000	0.000	0.000
35	A	38	GLY	0	0.011	0.022	13.635	1.429	1.429	0.000	0.000	0.000	0.000
36	A	39	PRO	0	0.018	0.000	15.878	-0.929	-0.929	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.036	0.015	15.750	1.023	1.023	0.000	0.000	0.000	0.000
38	A	41	PRO	0	-0.006	-0.005	19.567	-0.171	-0.171	0.000	0.000	0.000	0.000
39	A	42	MET	0	-0.034	-0.019	19.799	-0.085	-0.085	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.007	-0.004	22.873	0.412	0.412	0.000	0.000	0.000	0.000
41	A	44	THR	0	-0.027	-0.012	25.718	-0.254	-0.254	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.819	0.885	27.907	10.294	10.294	0.000	0.000	0.000	0.000
43	A	46	ILE	0	0.000	-0.006	29.644	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	47	GLU	-1	-0.836	-0.871	32.284	-9.495	-9.495	0.000	0.000	0.000	0.000
45	A	48	ARG	1	0.881	0.917	35.574	8.138	8.138	0.000	0.000	0.000	0.000
46	A	49	PHE	0	0.023	0.014	36.296	0.026	0.026	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.041	-0.023	41.948	-0.053	-0.053	0.000	0.000	0.000	0.000
48	A	51	VAL	0	0.033	0.014	44.895	0.033	0.033	0.000	0.000	0.000	0.000
49	A	52	LEU	0	-0.032	-0.019	47.532	0.073	0.073	0.000	0.000	0.000	0.000
50	A	53	THR	0	0.013	0.002	50.537	0.027	0.027	0.000	0.000	0.000	0.000
51	A	54	SER	0	-0.017	0.001	52.568	0.091	0.091	0.000	0.000	0.000	0.000
52	A	55	PRO	0	0.009	-0.010	55.306	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	56	HIS	0	0.015	0.016	56.487	-0.043	-0.043	0.000	0.000	0.000	0.000
54	A	57	VAL	0	-0.023	-0.008	57.991	-0.072	-0.072	0.000	0.000	0.000	0.000
55	A	58	ASN	0	0.024	-0.002	57.760	0.112	0.112	0.000	0.000	0.000	0.000
56	A	59	LYS	1	0.960	0.989	53.196	5.755	5.755	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.871	-0.936	54.562	-5.712	-5.712	0.000	0.000	0.000	0.000
58	A	61	ALA	0	0.004	0.017	54.066	-0.092	-0.092	0.000	0.000	0.000	0.000
59	A	62	ARG	1	0.832	0.904	49.377	6.178	6.178	0.000	0.000	0.000	0.000
60	A	63	ASP	-1	-0.764	-0.845	46.771	-6.604	-6.604	0.000	0.000	0.000	0.000
61	A	64	GLN	0	-0.068	-0.037	44.480	-0.062	-0.062	0.000	0.000	0.000	0.000
62	A	65	TYR	0	-0.039	-0.036	40.712	-0.112	-0.112	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.779	-0.881	36.658	-8.541	-8.541	0.000	0.000	0.000	0.000
64	A	67	ILE	0	0.012	0.019	32.408	0.010	0.010	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.849	0.904	31.283	9.081	9.081	0.000	0.000	0.000	0.000
66	A	69	THR	0	-0.001	0.004	25.512	-0.137	-0.137	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.012	-0.003	25.850	-0.089	-0.089	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.956	0.969	18.393	15.555	15.555	0.000	0.000	0.000	0.000
69	A	72	ARG	1	0.822	0.883	19.160	13.491	13.491	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.068	-0.023	13.937	-0.321	-0.321	0.000	0.000	0.000	0.000
71	A	74	ILE	0	0.039	0.032	12.045	0.621	0.621	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.808	-0.886	10.062	-29.472	-29.472	0.000	0.000	0.000	0.000
73	A	76	ILE	0	0.049	0.017	7.270	2.029	2.029	0.000	0.000	0.000	0.000
74	A	77	VAL	0	0.018	0.000	5.299	-7.109	-7.109	0.000	0.000	0.000	0.000
78	A	81	ASP	-1	-0.886	-0.947	5.994	-41.393	-41.393	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.921	0.976	6.833	23.923	23.923	0.000	0.000	0.000	0.000
80	A	83	THR	0	-0.017	-0.006	7.767	0.398	0.398	0.000	0.000	0.000	0.000
82	A	85	ASP	-1	-0.817	-0.909	7.807	-23.557	-23.557	0.000	0.000	0.000	0.000
83	A	86	ALA	0	-0.056	-0.041	10.367	2.075	2.075	0.000	0.000	0.000	0.000
84	A	87	LEU	0	-0.033	-0.014	9.055	1.152	1.152	0.000	0.000	0.000	0.000
85	A	88	MET	0	0.002	0.003	9.894	1.624	1.624	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.849	0.933	13.179	19.117	19.117	0.000	0.000	0.000	0.000
87	A	90	LEU	0	-0.013	-0.011	15.768	0.316	0.316	0.000	0.000	0.000	0.000
88	A	91	ASP	-1	-0.919	-0.936	17.788	-13.250	-13.250	0.000	0.000	0.000	0.000
89	A	92	LEU	0	-0.036	-0.015	18.078	-0.173	-0.173	0.000	0.000	0.000	0.000
90	A	93	ALA	0	0.040	0.020	21.134	0.503	0.503	0.000	0.000	0.000	0.000
91	A	94	ALA	0	0.046	0.016	24.000	-0.186	-0.186	0.000	0.000	0.000	0.000
92	A	95	GLY	0	-0.029	-0.022	26.681	0.088	0.088	0.000	0.000	0.000	0.000
93	A	96	VAL	0	-0.055	-0.029	20.745	0.024	0.024	0.000	0.000	0.000	0.000
94	A	97	ASP	-1	-0.892	-0.937	20.032	-14.744	-14.744	0.000	0.000	0.000	0.000
95	A	98	VAL	0	-0.006	-0.023	14.630	-0.481	-0.481	0.000	0.000	0.000	0.000
96	A	99	GLN	0	0.014	0.021	14.442	-0.532	-0.532	0.000	0.000	0.000	0.000
97	A	100	ILE	0	0.022	-0.007	8.545	-0.906	-0.906	0.000	0.000	0.000	0.000
98	A	101	ALA	0	0.003	0.005	9.173	0.985	0.985	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLN)