FMO DATABASE

FMODB ID: 24ZNR

Calculation Name: 2IDL-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2IDL

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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	113
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-888025.202047
FMO2-HF: Nuclear repulsion	843050.665744
FMO2-HF: Total energy	-44974.536303
FMO2-MP2: Total energy	-45103.793378

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:0:ALA)

Summations of interaction energy for fragment #1(A:0: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.
-310.306	-305.251	4.097	-3.118	-6.033	-0.017

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.922

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

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	2	ILE	0	0.024	0.017	2.970	4.042	5.794	0.040	-0.629	-1.164	-0.001
4	A	3	GLN	0	-0.038	-0.018	5.359	4.556	4.579	-0.001	-0.002	-0.019	0.000
22	A	21	GLY	0	0.014	0.006	4.688	-2.022	-2.015	-0.001	-0.007	0.001	0.000
23	A	22	HIS	0	-0.034	-0.029	3.246	-17.933	-16.342	0.073	-0.817	-0.847	-0.007
24	A	23	ALA	0	0.027	0.018	4.965	3.259	3.278	-0.001	-0.003	-0.014	0.000
25	A	24	GLU	-1	-0.996	-0.981	5.029	-31.225	-31.101	-0.001	-0.006	-0.117	0.000
27	A	26	GLY	0	-0.057	-0.020	4.467	-5.699	-5.557	-0.001	-0.014	-0.128	0.000
31	A	30	LEU	0	-0.008	-0.021	2.180	-4.090	-3.919	3.224	-1.005	-2.389	-0.006
32	A	31	ASP	-1	-0.641	-0.833	4.280	-42.097	-41.862	-0.001	-0.020	-0.214	0.000
34	A	33	VAL	0	-0.003	0.022	4.467	2.756	2.812	-0.001	-0.005	-0.050	0.000
35	A	34	CYS	0	0.016	0.012	3.206	-1.392	-0.886	0.764	-0.481	-0.789	-0.003
106	A	105	PHE	0	-0.081	-0.057	3.678	-6.386	-5.969	0.004	-0.116	-0.305	0.000
107	A	106	VAL	0	0.000	0.008	4.899	-5.628	-5.616	-0.001	-0.013	0.002	0.000
5	A	4	ALA	0	0.035	0.016	9.127	0.493	0.493	0.000	0.000	0.000	0.000
6	A	5	VAL	0	-0.024	-0.014	11.654	0.724	0.724	0.000	0.000	0.000	0.000
7	A	6	PHE	0	0.040	0.013	14.117	0.301	0.301	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.885	-0.917	18.256	-12.276	-12.276	0.000	0.000	0.000	0.000
9	A	8	ARG	1	0.758	0.833	21.785	12.783	12.783	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.002	0.008	24.931	0.101	0.101	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.949	-0.986	28.526	-9.095	-9.095	0.000	0.000	0.000	0.000
12	A	11	ASP	-1	-0.925	-0.963	30.933	-9.706	-9.706	0.000	0.000	0.000	0.000
13	A	12	GLY	0	-0.017	-0.004	28.212	0.094	0.094	0.000	0.000	0.000	0.000
14	A	13	GLU	-1	-0.904	-0.946	27.000	-10.403	-10.403	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.028	-0.009	20.920	-0.199	-0.199	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.914	0.962	23.376	11.219	11.219	0.000	0.000	0.000	0.000
17	A	16	SER	0	0.040	-0.020	20.501	-0.098	-0.098	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.019	-0.010	15.900	-0.078	-0.078	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.839	-0.884	13.599	-19.236	-19.236	0.000	0.000	0.000	0.000
20	A	19	ILE	0	-0.033	-0.039	8.679	-0.705	-0.705	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.009	0.002	8.699	0.208	0.208	0.000	0.000	0.000	0.000
26	A	25	SER	0	-0.054	-0.033	6.038	3.025	3.025	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.945	-0.990	5.606	-26.086	-26.086	0.000	0.000	0.000	0.000
29	A	28	TYR	0	-0.073	-0.040	7.068	0.756	0.756	0.000	0.000	0.000	0.000
30	A	29	GLY	0	-0.022	-0.002	7.603	-2.127	-2.127	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.040	-0.008	6.163	3.102	3.102	0.000	0.000	0.000	0.000
36	A	35	ALA	0	0.035	0.030	5.525	3.470	3.470	0.000	0.000	0.000	0.000
37	A	36	SER	0	-0.065	-0.031	9.004	3.146	3.146	0.000	0.000	0.000	0.000
38	A	37	VAL	0	0.022	-0.002	6.984	2.194	2.194	0.000	0.000	0.000	0.000
39	A	38	SER	0	0.021	-0.001	8.478	2.109	2.109	0.000	0.000	0.000	0.000
40	A	39	THR	0	-0.071	-0.046	10.802	2.257	2.257	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.052	-0.017	12.616	1.542	1.542	0.000	0.000	0.000	0.000
42	A	41	ALA	0	0.048	0.026	12.940	1.197	1.197	0.000	0.000	0.000	0.000
43	A	42	ILE	0	0.019	0.011	14.300	1.157	1.157	0.000	0.000	0.000	0.000
44	A	43	ASN	0	-0.033	-0.017	16.625	1.358	1.358	0.000	0.000	0.000	0.000
45	A	44	PHE	0	0.002	0.017	17.952	0.971	0.971	0.000	0.000	0.000	0.000
46	A	45	ILE	0	0.052	0.032	17.252	0.757	0.757	0.000	0.000	0.000	0.000
47	A	46	ASN	0	0.017	0.003	20.457	0.761	0.761	0.000	0.000	0.000	0.000
48	A	47	SER	0	-0.090	-0.057	22.341	0.774	0.774	0.000	0.000	0.000	0.000
49	A	48	ILE	0	-0.008	0.001	23.225	0.656	0.656	0.000	0.000	0.000	0.000
50	A	49	GLU	-1	-0.873	-0.944	24.092	-11.750	-11.750	0.000	0.000	0.000	0.000
51	A	50	LYS	1	0.836	0.927	26.544	10.717	10.717	0.000	0.000	0.000	0.000
52	A	51	PHE	0	-0.085	-0.051	26.309	0.482	0.482	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.047	0.022	28.259	0.353	0.353	0.000	0.000	0.000	0.000
54	A	53	GLY	0	-0.030	0.004	29.664	0.330	0.330	0.000	0.000	0.000	0.000
55	A	54	TYR	0	-0.071	-0.082	26.524	0.223	0.223	0.000	0.000	0.000	0.000
56	A	55	GLU	-1	-0.874	-0.932	26.387	-10.737	-10.737	0.000	0.000	0.000	0.000
57	A	56	PRO	0	-0.055	-0.024	22.363	0.265	0.265	0.000	0.000	0.000	0.000
58	A	57	ILE	0	-0.024	-0.007	22.994	0.036	0.036	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.002	-0.007	17.399	-0.501	-0.501	0.000	0.000	0.000	0.000
60	A	59	GLU	-1	-0.957	-0.968	17.614	-15.444	-15.444	0.000	0.000	0.000	0.000
61	A	60	LEU	0	-0.017	-0.026	14.419	-0.855	-0.855	0.000	0.000	0.000	0.000
62	A	61	ASN	0	-0.012	-0.005	14.201	0.591	0.591	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.883	-0.942	11.656	-24.489	-24.489	0.000	0.000	0.000	0.000
64	A	63	ASP	-1	-0.942	-0.964	10.779	-21.510	-21.510	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-1.027	-1.027	9.851	-23.641	-23.641	0.000	0.000	0.000	0.000
66	A	65	GLY	0	-0.005	0.003	6.054	-2.141	-2.141	0.000	0.000	0.000	0.000
67	A	66	GLY	0	-0.006	0.014	6.203	-3.677	-3.677	0.000	0.000	0.000	0.000
68	A	67	TYR	0	-0.071	-0.076	8.762	-1.902	-1.902	0.000	0.000	0.000	0.000
69	A	68	LEU	0	-0.025	-0.008	11.577	1.163	1.163	0.000	0.000	0.000	0.000
70	A	69	MET	0	0.035	0.031	13.601	-0.417	-0.417	0.000	0.000	0.000	0.000
71	A	70	VAL	0	-0.034	-0.012	16.762	0.680	0.680	0.000	0.000	0.000	0.000
72	A	71	GLU	-1	-0.917	-0.972	19.055	-12.531	-12.531	0.000	0.000	0.000	0.000
73	A	72	ILE	0	-0.042	-0.009	22.498	0.314	0.314	0.000	0.000	0.000	0.000
74	A	73	PRO	0	-0.013	-0.006	25.697	0.218	0.218	0.000	0.000	0.000	0.000
75	A	74	LYS	1	0.974	0.973	29.108	9.996	9.996	0.000	0.000	0.000	0.000
76	A	75	ASP	-1	-0.950	-0.971	31.006	-8.314	-8.314	0.000	0.000	0.000	0.000
77	A	76	LEU	0	0.015	0.035	28.930	0.211	0.211	0.000	0.000	0.000	0.000
78	A	77	PRO	0	-0.008	-0.001	33.293	0.172	0.172	0.000	0.000	0.000	0.000
79	A	78	SER	0	0.030	-0.003	34.678	-0.215	-0.215	0.000	0.000	0.000	0.000
80	A	79	HIS	0	0.022	0.009	34.751	-0.179	-0.179	0.000	0.000	0.000	0.000
81	A	80	GLN	0	-0.017	-0.011	31.531	-0.070	-0.070	0.000	0.000	0.000	0.000
82	A	81	ARG	1	0.816	0.927	30.436	9.074	9.074	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.921	-0.964	29.961	-9.015	-9.015	0.000	0.000	0.000	0.000
84	A	83	MET	0	-0.051	-0.022	29.091	-0.304	-0.304	0.000	0.000	0.000	0.000
85	A	84	THR	0	0.021	0.004	25.369	-0.423	-0.423	0.000	0.000	0.000	0.000
86	A	85	GLN	0	0.026	0.017	25.351	-0.766	-0.766	0.000	0.000	0.000	0.000
87	A	86	LEU	0	-0.030	-0.004	25.408	-0.380	-0.380	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.012	-0.017	23.077	-0.301	-0.301	0.000	0.000	0.000	0.000
89	A	88	PHE	0	0.015	0.011	18.626	-0.664	-0.664	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.761	-0.859	20.602	-13.182	-13.182	0.000	0.000	0.000	0.000
91	A	90	SER	0	-0.085	-0.026	21.068	-0.650	-0.650	0.000	0.000	0.000	0.000
92	A	91	PHE	0	0.022	0.006	13.690	-0.718	-0.718	0.000	0.000	0.000	0.000
93	A	92	PHE	0	0.029	0.012	16.255	-0.997	-0.997	0.000	0.000	0.000	0.000
94	A	93	LEU	0	-0.004	-0.002	16.861	-0.701	-0.701	0.000	0.000	0.000	0.000
95	A	94	GLY	0	-0.007	-0.006	16.047	-0.427	-0.427	0.000	0.000	0.000	0.000
96	A	95	MET	0	0.016	0.008	9.259	-1.212	-1.212	0.000	0.000	0.000	0.000
97	A	96	ALA	0	-0.010	0.015	12.658	-1.451	-1.451	0.000	0.000	0.000	0.000
98	A	97	ASN	0	0.014	-0.003	14.776	-0.397	-0.397	0.000	0.000	0.000	0.000
99	A	98	LEU	0	-0.018	-0.009	9.799	-0.627	-0.627	0.000	0.000	0.000	0.000
100	A	99	SER	0	-0.040	-0.019	10.677	-1.772	-1.772	0.000	0.000	0.000	0.000
101	A	100	GLU	-1	-0.955	-0.967	11.804	-18.173	-18.173	0.000	0.000	0.000	0.000
102	A	101	ASN	0	-0.114	-0.072	13.116	0.516	0.516	0.000	0.000	0.000	0.000
103	A	102	TYR	0	-0.006	-0.005	7.478	-0.203	-0.203	0.000	0.000	0.000	0.000
104	A	103	SER	0	0.039	0.046	8.401	-3.050	-3.050	0.000	0.000	0.000	0.000
105	A	104	GLU	-1	-0.959	-0.985	7.804	-29.050	-29.050	0.000	0.000	0.000	0.000
108	A	107	GLN	0	-0.005	0.005	7.528	4.933	4.933	0.000	0.000	0.000	0.000
109	A	108	THR	0	0.035	0.001	10.572	-0.601	-0.601	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.851	0.923	13.077	21.333	21.333	0.000	0.000	0.000	0.000
111	A	110	VAL	0	-0.003	0.004	16.337	-0.137	-0.137	0.000	0.000	0.000	0.000
112	A	111	ILE	0	-0.043	-0.010	19.629	-0.053	-0.053	0.000	0.000	0.000	0.000
113	A	112	THR	-1	-0.918	-0.957	21.896	-11.573	-11.573	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)