FMO DATABASE

FMODB ID: 1Y2VZ

Calculation Name: 2NQW-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2NQW

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXD1

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-624409.439846
FMO2-HF: Nuclear repulsion	589943.4908
FMO2-HF: Total energy	-34465.949046
FMO2-MP2: Total energy	-34568.641853

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:LEU)

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

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.
-134.719	-126.692	3.608	-4.119	-7.515	-0.044

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.822 / q_NPA : 0.907

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	PHE	0	0.030	0.016	2.484	4.625	9.743	2.074	-2.662	-4.530	-0.026
4	A	7	LYS	1	0.894	0.953	3.328	29.941	30.760	0.062	-0.389	-0.492	-0.003
25	A	28	TYR	0	-0.055	-0.056	2.862	-8.453	-6.363	1.472	-1.068	-2.493	-0.015
5	A	8	VAL	0	0.070	0.041	5.646	2.408	2.408	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.034	-0.015	8.123	0.193	0.193	0.000	0.000	0.000	0.000
7	A	10	GLY	0	-0.008	-0.010	11.708	0.660	0.660	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.853	-0.902	14.453	-17.585	-17.585	0.000	0.000	0.000	0.000
9	A	12	GLY	0	0.026	0.017	13.913	0.786	0.786	0.000	0.000	0.000	0.000
10	A	13	SER	0	-0.097	-0.064	13.560	-0.248	-0.248	0.000	0.000	0.000	0.000
11	A	14	TYR	0	0.071	0.017	7.938	-2.447	-2.447	0.000	0.000	0.000	0.000
12	A	15	LEU	0	-0.070	-0.015	8.941	1.869	1.869	0.000	0.000	0.000	0.000
13	A	16	PHE	0	0.067	0.014	6.491	-5.608	-5.608	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.866	-0.928	5.990	-43.761	-43.761	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.018	0.015	9.237	0.726	0.726	0.000	0.000	0.000	0.000
16	A	19	LYS	1	0.871	0.932	7.340	38.328	38.328	0.000	0.000	0.000	0.000
17	A	20	THR	0	-0.043	-0.027	7.317	-2.342	-2.342	0.000	0.000	0.000	0.000
18	A	21	SER	0	0.054	0.017	9.523	2.698	2.698	0.000	0.000	0.000	0.000
19	A	22	LEU	0	0.044	0.011	10.964	-1.850	-1.850	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.012	-0.003	12.196	0.590	0.590	0.000	0.000	0.000	0.000
21	A	24	ASP	-1	-0.873	-0.918	6.832	-31.589	-31.589	0.000	0.000	0.000	0.000
22	A	25	VAL	0	-0.049	-0.035	7.447	-2.154	-2.154	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.913	0.954	9.515	18.070	18.070	0.000	0.000	0.000	0.000
24	A	27	HIS	0	-0.032	-0.007	5.688	1.782	1.782	0.000	0.000	0.000	0.000
26	A	29	LEU	0	-0.046	-0.015	6.363	-0.974	-0.974	0.000	0.000	0.000	0.000
27	A	30	ASP	-1	-0.928	-0.944	9.615	-20.832	-20.832	0.000	0.000	0.000	0.000
28	A	31	LEU	0	-0.046	-0.011	11.969	1.619	1.619	0.000	0.000	0.000	0.000
29	A	32	PRO	0	-0.004	-0.003	14.324	-0.154	-0.154	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.918	-0.979	16.910	-14.799	-14.799	0.000	0.000	0.000	0.000
31	A	34	ASN	0	0.006	-0.005	17.901	-0.677	-0.677	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.022	0.003	16.606	0.427	0.427	0.000	0.000	0.000	0.000
33	A	36	PHE	0	-0.007	-0.018	13.866	-0.241	-0.241	0.000	0.000	0.000	0.000
34	A	37	GLY	0	0.011	0.010	19.751	0.351	0.351	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.925	-0.964	22.462	-10.833	-10.833	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.015	0.000	23.075	-0.141	-0.141	0.000	0.000	0.000	0.000
37	A	40	GLY	0	-0.024	-0.028	19.971	-0.411	-0.411	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.958	-0.972	19.800	-14.057	-14.057	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.967	-0.976	22.068	-11.450	-11.450	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.084	-0.035	19.052	-0.128	-0.128	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.899	-0.947	15.281	-19.968	-19.968	0.000	0.000	0.000	0.000
42	A	45	THR	0	-0.029	-0.013	13.661	-0.976	-0.976	0.000	0.000	0.000	0.000
43	A	46	LEU	0	0.032	0.016	10.855	1.049	1.049	0.000	0.000	0.000	0.000
44	A	47	SER	0	-0.068	-0.063	14.119	1.421	1.421	0.000	0.000	0.000	0.000
45	A	48	GLY	0	0.004	0.010	16.495	1.040	1.040	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.086	0.043	16.758	0.769	0.769	0.000	0.000	0.000	0.000
47	A	50	PHE	0	-0.057	-0.037	17.677	0.737	0.737	0.000	0.000	0.000	0.000
48	A	51	LEU	0	-0.059	-0.041	19.576	0.702	0.702	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.868	-0.927	22.024	-11.842	-11.842	0.000	0.000	0.000	0.000
50	A	53	ILE	0	-0.065	-0.025	20.501	0.557	0.557	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.793	0.904	23.332	12.776	12.776	0.000	0.000	0.000	0.000
52	A	55	GLN	0	-0.007	0.001	25.728	0.218	0.218	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.905	-0.945	26.775	-10.714	-10.714	0.000	0.000	0.000	0.000
54	A	57	LEU	0	-0.071	-0.049	26.100	-0.450	-0.450	0.000	0.000	0.000	0.000
55	A	58	PRO	0	0.002	0.013	21.851	0.198	0.198	0.000	0.000	0.000	0.000
56	A	59	HIS	0	-0.008	-0.019	23.971	-0.077	-0.077	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.017	-0.028	20.265	-0.484	-0.484	0.000	0.000	0.000	0.000
58	A	61	GLY	0	-0.044	-0.019	20.945	0.643	0.643	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.821	-0.893	22.124	-12.480	-12.480	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.091	-0.063	21.066	-0.624	-0.624	0.000	0.000	0.000	0.000
61	A	64	ALA	0	0.035	0.019	20.498	0.535	0.535	0.000	0.000	0.000	0.000
62	A	65	VAL	0	-0.038	-0.031	21.087	-0.475	-0.475	0.000	0.000	0.000	0.000
63	A	66	TYR	0	0.032	0.019	20.381	0.297	0.297	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.896	-0.938	20.802	-12.848	-12.848	0.000	0.000	0.000	0.000
65	A	68	PRO	0	-0.003	0.017	19.213	0.107	0.107	0.000	0.000	0.000	0.000
66	A	69	PHE	0	0.003	-0.003	15.366	-0.489	-0.489	0.000	0.000	0.000	0.000
67	A	70	ARG	1	0.947	0.978	18.430	13.851	13.851	0.000	0.000	0.000	0.000
68	A	71	PHE	0	0.023	0.010	14.808	-1.165	-1.165	0.000	0.000	0.000	0.000
69	A	72	GLN	0	-0.002	-0.019	16.646	1.051	1.051	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.009	0.019	16.410	-1.436	-1.436	0.000	0.000	0.000	0.000
71	A	74	THR	0	-0.034	-0.044	13.908	1.017	1.017	0.000	0.000	0.000	0.000
72	A	75	GLN	0	-0.079	-0.048	12.700	1.274	1.274	0.000	0.000	0.000	0.000
73	A	76	MET	0	0.024	0.016	16.700	-0.454	-0.454	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.810	-0.887	17.905	-16.840	-16.840	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.908	0.933	19.603	13.254	13.254	0.000	0.000	0.000	0.000
76	A	79	ARG	1	0.868	0.918	21.651	12.735	12.735	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.951	0.992	17.783	16.306	16.306	0.000	0.000	0.000	0.000
78	A	81	ILE	0	0.087	0.050	15.304	-0.071	-0.071	0.000	0.000	0.000	0.000
79	A	82	ILE	0	-0.058	-0.028	13.465	-0.752	-0.752	0.000	0.000	0.000	0.000
80	A	83	GLU	-1	-0.845	-0.907	10.593	-29.185	-29.185	0.000	0.000	0.000	0.000
81	A	84	ILE	0	0.026	0.014	11.856	2.235	2.235	0.000	0.000	0.000	0.000
82	A	85	LYS	1	0.869	0.953	11.752	15.763	15.763	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.016	0.013	10.698	1.293	1.293	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.028	-0.047	13.621	-0.521	-0.521	0.000	0.000	0.000	0.000
85	A	88	PRO	0	-0.006	-0.007	15.581	-0.579	-0.579	0.000	0.000	0.000	0.000
86	A	89	PHE	0	-0.042	-0.017	12.851	0.180	0.180	0.000	0.000	0.000	0.000
87	A	90	GLU	-2	-1.873	-1.927	17.720	-26.636	-26.636	0.000	0.000	0.000	0.000

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