FMO DATABASE

FMODB ID: VN5Z1

Calculation Name: 3E9V-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3E9V

Chain ID: A

ChEMBL ID:

UniProt ID: P78543

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	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1009713.298553
FMO2-HF: Nuclear repulsion	962024.398705
FMO2-HF: Total energy	-47688.899848
FMO2-MP2: Total energy	-47827.225086

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:9:ASP)

Summations of interaction energy for fragment #1(A:9:ASP)

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.
-26.83	-19.01	2.236	-4.26	-5.795	0.023

Interaction energy analysis for fragmet #1(A:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : -0.038

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	11	LEU	0	0.030	0.035	3.028	-3.141	2.171	0.350	-2.766	-2.895	0.012
4	A	12	PRO	0	0.029	0.013	2.477	-5.068	-3.635	1.881	-1.029	-2.286	0.014
5	A	13	GLU	-1	-0.782	-0.895	3.790	-16.658	-16.074	0.002	-0.334	-0.251	-0.002
47	A	55	TRP	0	0.062	0.056	3.601	0.632	1.123	0.003	-0.131	-0.363	-0.001
6	A	14	ILE	0	-0.007	-0.009	7.017	0.515	0.515	0.000	0.000	0.000	0.000
7	A	15	ALA	0	-0.012	-0.011	7.842	0.008	0.008	0.000	0.000	0.000	0.000
8	A	16	ALA	0	0.008	0.016	9.507	-0.187	-0.187	0.000	0.000	0.000	0.000
9	A	17	ALA	0	0.017	0.010	11.366	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	18	VAL	0	-0.045	-0.020	12.507	0.030	0.030	0.000	0.000	0.000	0.000
11	A	19	GLY	0	0.006	0.008	13.525	0.007	0.007	0.000	0.000	0.000	0.000
12	A	20	PHE	0	0.004	0.002	15.352	-0.051	-0.051	0.000	0.000	0.000	0.000
13	A	21	LEU	0	0.012	0.004	16.704	0.003	0.003	0.000	0.000	0.000	0.000
14	A	22	SER	0	0.007	-0.031	17.629	-0.062	-0.062	0.000	0.000	0.000	0.000
15	A	23	SER	0	-0.041	-0.006	19.426	0.026	0.026	0.000	0.000	0.000	0.000
16	A	24	LEU	0	0.014	0.020	21.248	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	25	LEU	0	-0.020	-0.016	22.146	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	26	ARG	1	0.790	0.858	20.231	-0.741	-0.741	0.000	0.000	0.000	0.000
19	A	27	THR	0	-0.028	-0.012	24.832	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	28	ARG	1	0.883	0.963	27.221	-0.097	-0.097	0.000	0.000	0.000	0.000
21	A	29	GLY	0	0.019	-0.002	28.200	-0.026	-0.026	0.000	0.000	0.000	0.000
22	A	30	CYS	0	-0.030	-0.008	29.625	0.019	0.019	0.000	0.000	0.000	0.000
23	A	31	VAL	0	-0.019	-0.016	25.142	0.001	0.001	0.000	0.000	0.000	0.000
24	A	32	SER	0	0.053	0.026	27.149	0.025	0.025	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.710	-0.843	22.685	0.823	0.823	0.000	0.000	0.000	0.000
26	A	34	GLN	0	-0.048	-0.017	22.787	0.058	0.058	0.000	0.000	0.000	0.000
27	A	35	ARG	1	0.893	0.954	23.186	-0.328	-0.328	0.000	0.000	0.000	0.000
28	A	36	LEU	0	0.070	0.032	21.215	0.028	0.028	0.000	0.000	0.000	0.000
29	A	37	LYS	1	0.951	0.999	18.071	-1.273	-1.273	0.000	0.000	0.000	0.000
30	A	38	VAL	0	-0.020	-0.005	18.177	0.149	0.149	0.000	0.000	0.000	0.000
31	A	39	PHE	0	0.017	0.006	19.020	0.025	0.025	0.000	0.000	0.000	0.000
32	A	40	SER	0	0.023	-0.013	15.198	-0.068	-0.068	0.000	0.000	0.000	0.000
33	A	41	GLY	0	0.012	0.011	14.131	0.119	0.119	0.000	0.000	0.000	0.000
34	A	42	ALA	0	0.014	0.000	14.284	0.087	0.087	0.000	0.000	0.000	0.000
35	A	43	LEU	0	0.001	0.000	14.578	-0.165	-0.165	0.000	0.000	0.000	0.000
36	A	44	GLN	0	-0.008	-0.015	9.774	-0.592	-0.592	0.000	0.000	0.000	0.000
37	A	45	GLU	-1	-0.898	-0.930	10.775	1.709	1.709	0.000	0.000	0.000	0.000
38	A	46	ALA	0	-0.007	0.001	12.142	-0.399	-0.399	0.000	0.000	0.000	0.000
39	A	47	LEU	0	-0.012	-0.014	11.273	-0.314	-0.314	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.013	-0.009	6.939	-0.800	-0.800	0.000	0.000	0.000	0.000
41	A	49	GLU	-1	-0.911	-0.967	9.437	-0.434	-0.434	0.000	0.000	0.000	0.000
42	A	50	HIS	0	-0.004	0.013	12.404	-0.256	-0.256	0.000	0.000	0.000	0.000
43	A	51	TYR	0	0.029	-0.023	8.554	-0.104	-0.104	0.000	0.000	0.000	0.000
44	A	52	LYS	1	0.996	1.016	7.702	-0.139	-0.139	0.000	0.000	0.000	0.000
45	A	53	HIS	0	-0.032	-0.018	8.720	-0.683	-0.683	0.000	0.000	0.000	0.000
46	A	54	HIS	1	0.799	0.897	10.073	2.374	2.374	0.000	0.000	0.000	0.000
48	A	56	PHE	0	-0.014	-0.026	8.030	0.291	0.291	0.000	0.000	0.000	0.000
49	A	57	PRO	0	0.050	0.028	5.050	0.410	0.410	0.000	0.000	0.000	0.000
50	A	58	GLU	-1	-0.835	-0.915	7.359	-5.162	-5.162	0.000	0.000	0.000	0.000
51	A	59	LYS	1	0.848	0.917	10.677	3.303	3.303	0.000	0.000	0.000	0.000
52	A	60	PRO	0	0.109	0.062	9.457	0.279	0.279	0.000	0.000	0.000	0.000
53	A	61	SER	0	0.082	0.036	10.794	0.046	0.046	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.881	0.960	13.246	2.764	2.764	0.000	0.000	0.000	0.000
55	A	63	GLY	0	0.012	-0.002	12.500	-0.449	-0.449	0.000	0.000	0.000	0.000
56	A	64	SER	0	0.009	-0.011	13.304	0.188	0.188	0.000	0.000	0.000	0.000
57	A	65	GLY	0	-0.009	-0.019	14.213	0.169	0.169	0.000	0.000	0.000	0.000
58	A	66	TYR	0	-0.116	-0.061	13.962	0.199	0.199	0.000	0.000	0.000	0.000
59	A	67	ARG	1	0.731	0.816	9.780	4.196	4.196	0.000	0.000	0.000	0.000
60	A	68	CYS	0	-0.091	-0.013	13.917	0.193	0.193	0.000	0.000	0.000	0.000
61	A	69	ILE	0	0.023	0.032	14.587	0.171	0.171	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.942	0.950	18.022	0.681	0.681	0.000	0.000	0.000	0.000
63	A	71	ILE	0	-0.080	-0.032	21.771	0.064	0.064	0.000	0.000	0.000	0.000
64	A	72	ASN	0	-0.016	-0.006	24.963	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	73	HIS	0	0.006	-0.001	28.350	0.041	0.041	0.000	0.000	0.000	0.000
66	A	74	LYS	1	0.909	0.957	25.897	0.410	0.410	0.000	0.000	0.000	0.000
67	A	75	MET	0	0.026	0.031	25.046	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	76	ASP	-1	-0.732	-0.872	19.811	-0.544	-0.544	0.000	0.000	0.000	0.000
69	A	77	PRO	0	-0.035	-0.012	21.303	0.097	0.097	0.000	0.000	0.000	0.000
70	A	78	ILE	0	-0.003	-0.001	16.272	0.100	0.100	0.000	0.000	0.000	0.000
71	A	79	ILE	0	0.037	0.012	19.470	0.139	0.139	0.000	0.000	0.000	0.000
72	A	80	SER	0	-0.034	-0.042	21.160	0.097	0.097	0.000	0.000	0.000	0.000
73	A	81	ARG	1	0.862	0.941	17.509	0.040	0.040	0.000	0.000	0.000	0.000
74	A	82	VAL	0	0.036	0.018	18.267	0.058	0.058	0.000	0.000	0.000	0.000
75	A	83	ALA	0	0.007	0.001	21.609	0.081	0.081	0.000	0.000	0.000	0.000
76	A	84	SER	0	-0.014	-0.013	24.221	0.024	0.024	0.000	0.000	0.000	0.000
77	A	85	GLN	0	-0.055	-0.027	21.245	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	86	ILE	0	-0.042	0.000	22.998	0.063	0.063	0.000	0.000	0.000	0.000
79	A	87	GLY	0	0.018	0.014	26.001	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	88	LEU	0	-0.087	-0.039	25.350	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	89	SER	0	0.023	-0.008	28.073	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	90	GLN	0	0.046	0.002	27.892	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	91	PRO	0	0.039	0.009	29.897	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	92	GLN	0	0.073	0.061	30.585	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	93	LEU	0	0.010	-0.007	24.653	0.003	0.003	0.000	0.000	0.000	0.000
86	A	94	HIS	0	0.011	0.003	27.986	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	95	GLN	0	-0.047	-0.011	30.096	0.001	0.001	0.000	0.000	0.000	0.000
88	A	96	LEU	0	-0.085	-0.039	27.492	0.016	0.016	0.000	0.000	0.000	0.000
89	A	97	LEU	0	-0.002	0.002	22.761	0.019	0.019	0.000	0.000	0.000	0.000
90	A	98	PRO	0	0.002	-0.007	24.195	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	99	SER	0	0.034	0.007	26.309	-0.033	-0.033	0.000	0.000	0.000	0.000
92	A	100	GLU	-1	-0.805	-0.887	27.184	-0.418	-0.418	0.000	0.000	0.000	0.000
93	A	101	LEU	0	-0.028	0.004	20.243	-0.029	-0.029	0.000	0.000	0.000	0.000
94	A	102	THR	0	-0.036	-0.023	19.904	-0.024	-0.024	0.000	0.000	0.000	0.000
95	A	103	LEU	0	0.023	0.007	14.892	0.042	0.042	0.000	0.000	0.000	0.000
96	A	104	TRP	0	0.001	0.002	14.330	0.044	0.044	0.000	0.000	0.000	0.000
97	A	105	VAL	0	0.027	0.004	8.956	0.121	0.121	0.000	0.000	0.000	0.000
98	A	106	ASP	-1	-0.741	-0.836	9.199	-3.448	-3.448	0.000	0.000	0.000	0.000
99	A	107	PRO	0	-0.090	-0.044	5.458	-0.360	-0.360	0.000	0.000	0.000	0.000
100	A	108	TYR	0	0.003	0.003	5.603	0.155	0.155	0.000	0.000	0.000	0.000
101	A	109	GLU	-1	-0.831	-0.879	7.410	-0.835	-0.835	0.000	0.000	0.000	0.000
102	A	110	VAL	0	-0.048	-0.014	9.634	-0.210	-0.210	0.000	0.000	0.000	0.000
103	A	111	SER	0	0.011	0.009	11.969	0.353	0.353	0.000	0.000	0.000	0.000
104	A	112	TYR	0	-0.015	-0.022	15.662	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	113	ARG	1	0.913	0.985	18.787	0.702	0.702	0.000	0.000	0.000	0.000
106	A	114	ILE	0	-0.011	-0.011	22.567	0.021	0.021	0.000	0.000	0.000	0.000
107	A	115	GLY	0	0.031	0.013	25.560	0.023	0.023	0.000	0.000	0.000	0.000
108	A	116	GLU	-1	-0.964	-0.996	26.854	-0.515	-0.515	0.000	0.000	0.000	0.000
109	A	117	ASP	-1	-0.914	-0.962	27.831	-0.473	-0.473	0.000	0.000	0.000	0.000
110	A	118	GLY	0	-0.048	-0.007	27.051	0.017	0.017	0.000	0.000	0.000	0.000
111	A	119	SER	0	-0.008	-0.022	25.202	-0.031	-0.031	0.000	0.000	0.000	0.000
112	A	120	ILE	0	-0.009	-0.012	19.693	0.011	0.011	0.000	0.000	0.000	0.000
113	A	121	CYS	0	-0.046	-0.013	20.622	0.044	0.044	0.000	0.000	0.000	0.000
114	A	122	VAL	0	0.038	0.007	14.867	-0.083	-0.083	0.000	0.000	0.000	0.000
115	A	123	LEU	0	-0.079	-0.037	14.517	0.176	0.176	0.000	0.000	0.000	0.000
116	A	124	TYR	0	-0.012	-0.015	6.625	1.009	1.009	0.000	0.000	0.000	0.000
117	A	125	GLU	0	-0.040	-0.057	11.459	-0.528	-0.528	0.000	0.000	0.000	0.000
118	A	126	GLU	-1	-0.932	-0.937	8.041	-0.686	-0.686	0.000	0.000	0.000	0.000
119	A	127	ALA	0	-0.030	-0.031	10.416	-0.402	-0.402	0.000	0.000	0.000	0.000
120	A	128	PRO	-1	-0.971	-0.975	8.388	-4.221	-4.221	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ASP)