FMO DATABASE

FMODB ID: 349ML

Calculation Name: 3FXT-A-Xray549

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3FXT

Chain ID: A

ChEMBL ID:

UniProt ID: P53370

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-623412.075793
FMO2-HF: Nuclear repulsion	588452.546407
FMO2-HF: Total energy	-34959.529386
FMO2-MP2: Total energy	-35062.615176

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:42:GLN)

Summations of interaction energy for fragment #1(A:42: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.
-13.051	-11.197	-0.02	-0.866	-0.968	0.001

Interaction energy analysis for fragmet #1(A:42:GLN)

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 : 0.918

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	44	MET	0	-0.002	0.010	3.849	-2.332	-0.478	-0.020	-0.866	-0.968	0.001
4	A	45	ASP	-1	-0.850	-0.916	6.543	-28.197	-28.197	0.000	0.000	0.000	0.000
5	A	46	LEU	0	0.000	-0.010	8.422	2.017	2.017	0.000	0.000	0.000	0.000
6	A	47	GLN	0	-0.023	-0.017	11.619	3.473	3.473	0.000	0.000	0.000	0.000
7	A	48	GLY	0	-0.010	0.004	13.481	1.516	1.516	0.000	0.000	0.000	0.000
8	A	49	GLU	-1	-0.842	-0.896	15.524	-15.175	-15.175	0.000	0.000	0.000	0.000
9	A	50	LEU	0	0.000	0.006	18.807	0.291	0.291	0.000	0.000	0.000	0.000
10	A	51	ASP	-1	-0.795	-0.888	20.232	-12.639	-12.639	0.000	0.000	0.000	0.000
11	A	52	ARG	1	0.916	0.937	23.852	10.607	10.607	0.000	0.000	0.000	0.000
12	A	53	PHE	0	-0.019	-0.015	25.936	0.527	0.527	0.000	0.000	0.000	0.000
13	A	54	GLY	0	0.030	0.037	22.703	0.056	0.056	0.000	0.000	0.000	0.000
14	A	55	GLY	0	-0.002	0.007	21.294	-0.620	-0.620	0.000	0.000	0.000	0.000
15	A	56	ILE	0	-0.007	-0.001	16.185	-0.144	-0.144	0.000	0.000	0.000	0.000
16	A	57	SER	0	-0.002	-0.003	19.606	0.411	0.411	0.000	0.000	0.000	0.000
17	A	58	VAL	0	0.007	0.004	15.981	-0.804	-0.804	0.000	0.000	0.000	0.000
18	A	59	ARG	1	0.850	0.915	18.450	14.748	14.748	0.000	0.000	0.000	0.000
19	A	60	LEU	0	0.016	0.017	17.243	-0.654	-0.654	0.000	0.000	0.000	0.000
20	A	61	ALA	0	0.034	0.018	19.344	-0.284	-0.284	0.000	0.000	0.000	0.000
21	A	62	ARG	1	0.814	0.904	15.817	18.458	18.458	0.000	0.000	0.000	0.000
22	A	63	LEU	0	-0.057	-0.023	12.167	-0.410	-0.410	0.000	0.000	0.000	0.000
23	A	64	ASP	-1	-0.753	-0.885	14.745	-18.443	-18.443	0.000	0.000	0.000	0.000
24	A	65	ALA	0	0.021	0.020	17.134	0.891	0.891	0.000	0.000	0.000	0.000
25	A	66	LEU	0	-0.067	-0.039	17.414	0.708	0.708	0.000	0.000	0.000	0.000
26	A	67	ASP	-1	-0.843	-0.882	19.908	-13.685	-13.685	0.000	0.000	0.000	0.000
27	A	68	ARG	1	0.905	0.937	16.336	15.489	15.489	0.000	0.000	0.000	0.000
28	A	69	LEU	0	-0.052	-0.005	12.121	-0.774	-0.774	0.000	0.000	0.000	0.000
29	A	70	ASP	-1	-0.758	-0.902	14.428	-17.813	-17.813	0.000	0.000	0.000	0.000
30	A	71	ALA	0	0.013	0.008	15.243	-1.015	-1.015	0.000	0.000	0.000	0.000
31	A	72	ALA	0	0.047	0.021	15.887	-0.375	-0.375	0.000	0.000	0.000	0.000
32	A	73	ALA	0	-0.053	-0.033	11.043	-1.677	-1.677	0.000	0.000	0.000	0.000
33	A	74	PHE	0	0.027	0.001	11.387	-2.497	-2.497	0.000	0.000	0.000	0.000
34	A	75	GLN	0	0.021	0.020	13.565	-0.703	-0.703	0.000	0.000	0.000	0.000
35	A	76	LYS	1	0.966	0.980	7.381	36.281	36.281	0.000	0.000	0.000	0.000
36	A	77	GLY	0	-0.008	-0.007	8.868	-2.587	-2.587	0.000	0.000	0.000	0.000
37	A	78	LEU	0	0.018	0.012	9.954	-0.864	-0.864	0.000	0.000	0.000	0.000
38	A	79	GLN	0	-0.001	0.002	11.859	0.873	0.873	0.000	0.000	0.000	0.000
39	A	80	ALA	0	-0.035	-0.023	6.876	-0.090	-0.090	0.000	0.000	0.000	0.000
40	A	81	ALA	0	0.009	0.008	9.028	-0.113	-0.113	0.000	0.000	0.000	0.000
41	A	82	VAL	0	0.033	0.014	10.633	1.365	1.365	0.000	0.000	0.000	0.000
42	A	83	GLN	0	-0.027	-0.005	9.557	2.831	2.831	0.000	0.000	0.000	0.000
43	A	84	GLN	0	-0.034	-0.018	9.015	-1.192	-1.192	0.000	0.000	0.000	0.000
44	A	85	TRP	0	0.038	0.003	11.041	1.495	1.495	0.000	0.000	0.000	0.000
45	A	86	ARG	1	0.971	0.994	14.495	17.634	17.634	0.000	0.000	0.000	0.000
46	A	87	SER	0	-0.078	-0.033	12.732	0.641	0.641	0.000	0.000	0.000	0.000
47	A	88	GLU	-1	-0.820	-0.892	13.142	-21.421	-21.421	0.000	0.000	0.000	0.000
48	A	89	GLY	0	-0.025	-0.012	16.128	0.843	0.843	0.000	0.000	0.000	0.000
49	A	90	ARG	1	0.806	0.891	16.261	18.601	18.601	0.000	0.000	0.000	0.000
50	A	91	THR	0	-0.034	-0.037	19.662	0.082	0.082	0.000	0.000	0.000	0.000
51	A	92	ALA	0	0.021	0.002	21.716	0.324	0.324	0.000	0.000	0.000	0.000
52	A	93	VAL	0	-0.020	-0.003	17.102	-0.705	-0.705	0.000	0.000	0.000	0.000
53	A	94	TRP	0	-0.009	0.004	20.216	0.632	0.632	0.000	0.000	0.000	0.000
54	A	95	LEU	0	0.014	0.003	18.018	-0.552	-0.552	0.000	0.000	0.000	0.000
55	A	96	HIS	0	-0.008	-0.004	21.660	0.430	0.430	0.000	0.000	0.000	0.000
56	A	97	ILE	0	0.016	-0.002	21.474	-0.710	-0.710	0.000	0.000	0.000	0.000
57	A	98	PRO	0	0.065	0.034	23.230	0.567	0.567	0.000	0.000	0.000	0.000
58	A	99	ILE	0	0.041	0.018	25.741	-0.321	-0.321	0.000	0.000	0.000	0.000
59	A	100	LEU	0	0.009	0.013	26.641	-0.040	-0.040	0.000	0.000	0.000	0.000
60	A	101	GLN	0	-0.037	-0.031	20.399	-0.147	-0.147	0.000	0.000	0.000	0.000
61	A	102	SER	0	0.005	-0.031	22.673	-0.562	-0.562	0.000	0.000	0.000	0.000
62	A	103	ARG	1	0.753	0.872	18.582	15.377	15.377	0.000	0.000	0.000	0.000
63	A	104	PHE	0	-0.016	-0.013	16.837	-0.460	-0.460	0.000	0.000	0.000	0.000
64	A	105	ILE	0	0.011	0.010	20.689	-0.443	-0.443	0.000	0.000	0.000	0.000
65	A	106	ALA	0	0.038	0.023	23.438	-0.046	-0.046	0.000	0.000	0.000	0.000
66	A	107	PRO	0	0.007	0.005	18.532	-0.054	-0.054	0.000	0.000	0.000	0.000
67	A	108	ALA	0	0.018	0.013	19.235	-0.512	-0.512	0.000	0.000	0.000	0.000
68	A	109	ALA	0	0.002	0.005	20.246	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	110	SER	0	-0.069	-0.041	20.483	0.379	0.379	0.000	0.000	0.000	0.000
70	A	111	LEU	0	-0.097	-0.044	15.406	-0.483	-0.483	0.000	0.000	0.000	0.000
71	A	112	GLY	0	0.009	0.010	19.393	-0.227	-0.227	0.000	0.000	0.000	0.000
72	A	113	PHE	0	-0.027	-0.020	17.893	0.266	0.266	0.000	0.000	0.000	0.000
73	A	114	CYS	0	-0.030	-0.006	23.158	0.466	0.466	0.000	0.000	0.000	0.000
74	A	115	PHE	0	0.024	-0.013	26.521	-0.338	-0.338	0.000	0.000	0.000	0.000
75	A	116	HIS	0	-0.020	-0.003	28.146	0.048	0.048	0.000	0.000	0.000	0.000
76	A	117	HIS	0	-0.009	-0.021	29.882	0.286	0.286	0.000	0.000	0.000	0.000
77	A	118	ALA	0	-0.033	-0.031	30.419	-0.493	-0.493	0.000	0.000	0.000	0.000
78	A	119	GLU	-1	-0.897	-0.932	32.512	-8.422	-8.422	0.000	0.000	0.000	0.000
79	A	120	SER	0	-0.032	-0.013	33.392	-0.137	-0.137	0.000	0.000	0.000	0.000
80	A	121	ASP	-1	-0.873	-0.928	31.488	-10.088	-10.088	0.000	0.000	0.000	0.000
81	A	122	SER	0	-0.019	-0.011	27.614	-0.637	-0.637	0.000	0.000	0.000	0.000
82	A	123	SER	0	-0.034	-0.006	26.858	0.259	0.259	0.000	0.000	0.000	0.000
83	A	124	THR	0	-0.026	-0.020	25.601	-0.446	-0.446	0.000	0.000	0.000	0.000
84	A	125	LEU	0	0.011	0.015	22.702	0.429	0.429	0.000	0.000	0.000	0.000
85	A	126	THR	0	-0.011	-0.025	23.785	-0.412	-0.412	0.000	0.000	0.000	0.000
86	A	127	LEU	0	0.022	0.027	18.596	0.172	0.172	0.000	0.000	0.000	0.000
87	A	128	TRP	0	0.034	0.010	21.989	-0.430	-0.430	0.000	0.000	0.000	0.000
88	A	129	LEU	0	-0.060	-0.045	17.682	-0.390	-0.390	0.000	0.000	0.000	0.000
89	A	130	ARG	1	0.806	0.917	21.476	13.146	13.146	0.000	0.000	0.000	0.000
90	A	131	GLU	-2	-1.858	-1.916	23.991	-24.073	-24.073	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:42:GLN)