FMO DATABASE

FMODB ID: 9QKV2

Calculation Name: 5LTL-B-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5LTL

Chain ID: B

ChEMBL ID:

UniProt ID: O15467

Base Structure: X-ray

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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-422859.64519
FMO2-HF: Nuclear repulsion	394746.661652
FMO2-HF: Total energy	-28112.983538
FMO2-MP2: Total energy	-28193.547512

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(B:8:VAL)

Summations of interaction energy for fragment #1(B:8:VAL)

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.
-0.166	4.849	3.633	-3.402	-5.246	-0.026

Interaction energy analysis for fragmet #1(B:8:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / 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	B	10	THR	0	0.027	0.034	2.076	3.786	7.217	3.427	-2.561	-4.298	-0.016
4	B	11	PRO	0	0.028	0.013	2.920	-9.493	-8.092	0.207	-0.829	-0.778	-0.010
5	B	12	SER	0	-0.027	-0.028	4.313	-5.674	-5.491	-0.001	-0.012	-0.170	0.000
6	B	13	THR	0	-0.002	0.006	6.513	1.716	1.716	0.000	0.000	0.000	0.000
7	B	14	CYS	0	-0.035	-0.011	7.852	-4.836	-4.836	0.000	0.000	0.000	0.000
8	B	15	CYS	0	-0.021	0.016	11.633	0.989	0.989	0.000	0.000	0.000	0.000
9	B	16	LEU	0	0.020	0.003	15.044	-0.564	-0.564	0.000	0.000	0.000	0.000
10	B	17	LYS	1	0.839	0.906	17.577	13.138	13.138	0.000	0.000	0.000	0.000
11	B	18	TYR	0	-0.031	-0.041	18.090	-0.253	-0.253	0.000	0.000	0.000	0.000
12	B	19	TYR	-1	-0.826	-0.923	22.000	-10.732	-10.732	0.000	0.000	0.000	0.000
13	B	20	GLU	-1	-0.813	-0.893	24.829	-11.590	-11.590	0.000	0.000	0.000	0.000
14	B	21	LYS	0	-0.048	-0.017	27.880	0.467	0.467	0.000	0.000	0.000	0.000
15	B	22	VAL	0	0.033	0.031	28.042	-0.356	-0.356	0.000	0.000	0.000	0.000
16	B	23	LEU	0	0.000	0.009	24.516	0.301	0.301	0.000	0.000	0.000	0.000
17	B	24	PRO	0	0.000	-0.002	28.941	0.087	0.087	0.000	0.000	0.000	0.000
18	B	25	ARG	1	0.911	0.959	28.413	10.538	10.538	0.000	0.000	0.000	0.000
19	B	26	ARG	1	0.961	0.976	29.968	8.414	8.414	0.000	0.000	0.000	0.000
20	B	27	LEU	0	-0.064	-0.039	29.791	0.110	0.110	0.000	0.000	0.000	0.000
21	B	28	VAL	0	-0.005	0.014	24.476	-0.251	-0.251	0.000	0.000	0.000	0.000
22	B	29	VAL	0	-0.045	-0.042	23.742	0.370	0.370	0.000	0.000	0.000	0.000
23	B	30	GLY	0	0.067	0.026	21.426	0.009	0.009	0.000	0.000	0.000	0.000
24	B	31	TYR	0	-0.007	0.005	17.905	-0.267	-0.267	0.000	0.000	0.000	0.000
25	B	32	ARG	1	0.843	0.886	13.816	17.068	17.068	0.000	0.000	0.000	0.000
26	B	33	LYS	1	0.921	0.961	12.129	22.588	22.588	0.000	0.000	0.000	0.000
27	B	34	ALA	0	0.053	0.028	10.580	-1.916	-1.916	0.000	0.000	0.000	0.000
28	B	35	LEU	0	0.002	-0.009	11.211	0.215	0.215	0.000	0.000	0.000	0.000
29	B	36	ASN	0	-0.023	-0.007	6.095	3.699	3.699	0.000	0.000	0.000	0.000
30	B	38	HIS	0	0.040	0.010	10.164	0.250	0.250	0.000	0.000	0.000	0.000
31	B	39	LEU	0	-0.007	0.018	12.591	1.468	1.468	0.000	0.000	0.000	0.000
32	B	40	PRO	0	-0.014	0.007	13.428	-0.379	-0.379	0.000	0.000	0.000	0.000
33	B	41	ALA	0	0.020	0.000	13.964	1.737	1.737	0.000	0.000	0.000	0.000
34	B	42	ILE	0	0.008	0.012	14.767	-1.285	-1.285	0.000	0.000	0.000	0.000
35	B	43	ILE	0	0.011	0.007	13.880	0.671	0.671	0.000	0.000	0.000	0.000
36	B	44	PHE	0	0.013	0.007	17.631	-0.055	-0.055	0.000	0.000	0.000	0.000
37	B	45	VAL	0	0.033	0.026	19.168	0.120	0.120	0.000	0.000	0.000	0.000
38	B	46	THR	0	-0.007	-0.022	21.769	0.742	0.742	0.000	0.000	0.000	0.000
39	B	47	LYS	1	0.968	0.975	25.486	9.716	9.716	0.000	0.000	0.000	0.000
40	B	48	ARG	1	0.821	0.901	27.998	9.982	9.982	0.000	0.000	0.000	0.000
41	B	49	ASN	0	0.023	0.017	24.840	0.030	0.030	0.000	0.000	0.000	0.000
42	B	50	ARG	1	0.855	0.942	23.781	11.018	11.018	0.000	0.000	0.000	0.000
43	B	51	GLU	-1	-0.714	-0.820	17.962	-15.882	-15.882	0.000	0.000	0.000	0.000
44	B	52	VAL	0	-0.034	-0.024	20.635	0.147	0.147	0.000	0.000	0.000	0.000
45	B	54	THR	0	-0.010	-0.012	19.242	0.858	0.858	0.000	0.000	0.000	0.000
46	B	55	ASN	0	0.115	0.044	19.310	-1.402	-1.402	0.000	0.000	0.000	0.000
47	B	56	PRO	0	-0.001	0.000	17.197	0.503	0.503	0.000	0.000	0.000	0.000
48	B	57	ASN	0	-0.073	-0.037	20.002	0.186	0.186	0.000	0.000	0.000	0.000
49	B	58	ASP	-1	-0.848	-0.911	23.058	-11.017	-11.017	0.000	0.000	0.000	0.000
50	B	59	ASP	-1	-0.854	-0.920	25.466	-10.584	-10.584	0.000	0.000	0.000	0.000
51	B	60	TRP	0	0.039	-0.009	25.477	-0.247	-0.247	0.000	0.000	0.000	0.000
52	B	61	VAL	0	-0.046	-0.013	21.447	-0.149	-0.149	0.000	0.000	0.000	0.000
53	B	62	GLN	0	-0.014	-0.034	22.823	0.081	0.081	0.000	0.000	0.000	0.000
54	B	63	GLU	-1	-0.989	-0.989	24.713	-9.878	-9.878	0.000	0.000	0.000	0.000
55	B	64	TYR	0	-0.055	-0.062	25.019	0.122	0.122	0.000	0.000	0.000	0.000
56	B	65	ILE	0	-0.043	-0.019	19.905	-0.135	-0.135	0.000	0.000	0.000	0.000
57	B	66	LYS	1	0.908	0.959	23.137	11.092	11.092	0.000	0.000	0.000	0.000
58	B	67	ASP	-1	-0.766	-0.853	26.089	-9.971	-9.971	0.000	0.000	0.000	0.000
59	B	68	PRO	0	-0.017	-0.009	26.643	-0.349	-0.349	0.000	0.000	0.000	0.000
60	B	69	ASN	0	-0.067	-0.031	28.100	0.090	0.090	0.000	0.000	0.000	0.000
61	B	70	LEU	0	-0.063	-0.022	23.447	0.014	0.014	0.000	0.000	0.000	0.000
62	B	71	PRO	0	-0.008	0.009	21.154	-0.323	-0.323	0.000	0.000	0.000	0.000
63	B	72	LEU	0	0.019	0.009	15.077	-0.420	-0.420	0.000	0.000	0.000	0.000
64	B	73	LEU	0	-0.059	-0.032	16.562	0.294	0.294	0.000	0.000	0.000	0.000
65	B	74	PRO	0	-0.008	-0.004	11.907	-0.783	-0.783	0.000	0.000	0.000	0.000
66	B	75	THR	-1	-0.881	-0.931	8.954	-23.991	-23.991	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:VAL)