FMO DATABASE

FMODB ID: 4YKLN

Calculation Name: 3DFE-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol | isopropyl alcohol

Ligand 3-letter code: EDO | IPA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DFE

Chain ID: B

ChEMBL ID:

UniProt ID: Q3M8P8

Base Structure: X-ray

Registration Date: 2025-10-05

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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-530462.976065
FMO2-HF: Nuclear repulsion	498326.413443
FMO2-HF: Total energy	-32136.562623
FMO2-MP2: Total energy	-32229.922903

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:1:MET)

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

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.
-68.25	-66.041	-0.02	-1.09	-1.099	-0.004

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.814 / q_NPA : 0.894

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

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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	3	LYS	1	0.869	0.945	3.838	28.875	30.948	-0.018	-1.045	-1.011	-0.004
81	A	99	LEU	0	-0.019	-0.019	4.436	-5.662	-5.560	-0.001	-0.031	-0.070	0.000
82	A	100	TYR	0	-0.041	-0.032	4.783	-9.041	-9.007	-0.001	-0.014	-0.018	0.000
4	A	4	ARG	1	0.838	0.909	6.437	28.443	28.443	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.018	0.010	9.650	0.704	0.704	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.037	0.017	12.733	1.391	1.391	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.897	0.954	16.473	16.848	16.848	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.022	0.021	18.017	0.672	0.672	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.065	-0.033	21.490	-0.308	-0.308	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.037	0.023	24.060	0.402	0.402	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.034	-0.018	27.702	-0.148	-0.148	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.005	-0.014	30.373	0.232	0.232	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.755	-0.871	33.762	-8.236	-8.236	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.822	0.885	33.515	9.442	9.442	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.008	-0.006	36.313	-0.107	-0.107	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.010	0.010	35.260	0.075	0.075	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.010	0.019	31.087	-0.184	-0.184	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.858	0.904	30.491	10.222	10.222	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.957	0.975	33.373	8.114	8.114	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.053	0.029	29.154	-0.090	-0.090	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.007	0.004	28.509	-0.311	-0.311	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.793	0.913	28.710	10.001	10.001	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.045	0.025	28.853	-0.090	-0.090	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.001	0.002	23.878	-0.291	-0.291	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.797	-0.882	25.152	-11.413	-11.413	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.940	-0.985	26.536	-9.969	-9.969	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.025	-0.004	25.177	0.028	0.028	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.001	-0.002	23.504	-0.311	-0.311	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.001	-0.006	20.504	-0.740	-0.740	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.023	-0.018	16.169	0.641	0.641	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.016	0.010	19.367	0.033	0.033	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.075	-0.056	20.519	-0.099	-0.099	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.009	0.015	19.823	0.156	0.156	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.017	-0.017	22.413	0.275	0.275	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.021	-0.008	24.719	-0.065	-0.065	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.811	-0.870	27.723	-9.753	-9.753	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.042	-0.035	29.430	-0.168	-0.168	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.030	0.008	32.320	0.296	0.296	0.000	0.000	0.000	0.000
39	A	39	GLY	-1	-0.917	-0.947	34.312	-8.800	-8.800	0.000	0.000	0.000	0.000
40	A	58	SER	0	-0.032	-0.016	37.167	0.084	0.084	0.000	0.000	0.000	0.000
41	A	59	ASN	0	-0.024	-0.009	33.546	0.192	0.192	0.000	0.000	0.000	0.000
42	A	60	VAL	0	-0.021	-0.016	29.908	-0.044	-0.044	0.000	0.000	0.000	0.000
43	A	61	LYS	1	0.877	0.935	23.485	13.399	13.399	0.000	0.000	0.000	0.000
44	A	62	PHE	0	0.006	-0.007	25.522	-0.113	-0.113	0.000	0.000	0.000	0.000
45	A	63	GLU	-1	-0.840	-0.918	20.647	-15.451	-15.451	0.000	0.000	0.000	0.000
46	A	64	VAL	0	0.014	-0.001	19.954	-0.146	-0.146	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.007	0.000	13.528	-0.069	-0.069	0.000	0.000	0.000	0.000
48	A	66	THR	0	0.000	-0.017	16.659	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	67	GLU	-1	-0.821	-0.900	12.486	-24.846	-24.846	0.000	0.000	0.000	0.000
50	A	68	ASN	0	-0.015	-0.015	14.232	-0.491	-0.491	0.000	0.000	0.000	0.000
51	A	69	ARG	1	0.856	0.921	16.634	14.479	14.479	0.000	0.000	0.000	0.000
52	A	70	GLU	-1	-0.794	-0.891	19.232	-12.628	-12.628	0.000	0.000	0.000	0.000
53	A	71	MET	0	0.010	0.025	19.804	0.218	0.218	0.000	0.000	0.000	0.000
54	A	72	ALA	0	-0.008	-0.007	20.363	0.370	0.370	0.000	0.000	0.000	0.000
55	A	73	GLU	-1	-0.811	-0.897	22.293	-12.426	-12.426	0.000	0.000	0.000	0.000
56	A	74	LYS	1	0.826	0.922	24.227	13.116	13.116	0.000	0.000	0.000	0.000
57	A	75	ILE	0	0.001	-0.005	23.222	0.429	0.429	0.000	0.000	0.000	0.000
58	A	76	ALA	0	-0.016	-0.012	26.529	0.398	0.398	0.000	0.000	0.000	0.000
59	A	77	ASP	-1	-0.874	-0.933	28.205	-10.075	-10.075	0.000	0.000	0.000	0.000
60	A	78	GLN	0	-0.049	-0.038	29.141	0.099	0.099	0.000	0.000	0.000	0.000
61	A	79	VAL	0	-0.045	-0.024	29.907	0.319	0.319	0.000	0.000	0.000	0.000
62	A	80	ALA	0	0.004	0.000	32.213	0.330	0.330	0.000	0.000	0.000	0.000
63	A	81	ILE	0	-0.003	-0.012	34.051	0.323	0.323	0.000	0.000	0.000	0.000
64	A	82	LYS	1	0.899	0.966	35.199	9.282	9.282	0.000	0.000	0.000	0.000
65	A	83	PHE	0	-0.007	-0.017	34.809	0.162	0.162	0.000	0.000	0.000	0.000
66	A	84	PHE	0	-0.001	-0.001	32.486	0.045	0.045	0.000	0.000	0.000	0.000
67	A	85	THR	0	-0.039	-0.033	37.805	0.001	0.001	0.000	0.000	0.000	0.000
68	A	86	ASP	-1	-0.929	-0.928	41.055	-7.295	-7.295	0.000	0.000	0.000	0.000
69	A	87	TYR	0	-0.060	-0.032	38.624	0.104	0.104	0.000	0.000	0.000	0.000
70	A	88	ALA	0	0.014	0.009	38.470	-0.132	-0.132	0.000	0.000	0.000	0.000
71	A	89	GLY	0	0.022	-0.006	34.332	-0.181	-0.181	0.000	0.000	0.000	0.000
72	A	90	ILE	0	-0.052	-0.011	30.087	0.102	0.102	0.000	0.000	0.000	0.000
73	A	91	ILE	0	0.001	-0.001	26.770	-0.301	-0.301	0.000	0.000	0.000	0.000
74	A	92	TYR	0	-0.015	-0.005	23.633	0.008	0.008	0.000	0.000	0.000	0.000
75	A	93	ILE	0	0.006	-0.004	19.647	-0.274	-0.274	0.000	0.000	0.000	0.000
76	A	94	CYS	0	-0.061	-0.019	18.605	0.558	0.558	0.000	0.000	0.000	0.000
77	A	95	GLU	-1	-0.827	-0.912	13.783	-22.329	-22.329	0.000	0.000	0.000	0.000
78	A	96	ALA	0	-0.030	-0.015	13.308	0.278	0.278	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.846	-0.894	6.267	-40.844	-40.844	0.000	0.000	0.000	0.000
80	A	98	VAL	0	0.006	0.005	8.592	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	101	GLY	-1	-0.895	-0.930	7.578	-25.931	-25.931	0.000	0.000	0.000	0.000

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