FMO DATABASE

FMODB ID: RLZV8

Calculation Name: 5DCL-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: 5DCL

Chain ID: A

ChEMBL ID:

UniProt ID: X5JZS1

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	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-996671.183087
FMO2-HF: Nuclear repulsion	949619.356319
FMO2-HF: Total energy	-47051.826768
FMO2-MP2: Total energy	-47187.221461

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:GLU)

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

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.
-5.149	-3.55	-0.009	-0.651	-0.939	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.136 / q_NPA : -0.075

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	GLY	0	0.048	0.034	3.855	-1.533	-0.205	-0.009	-0.570	-0.749	0.002
27	A	30	HIS	0	0.017	0.009	3.465	2.588	2.859	0.000	-0.081	-0.190	0.000
4	A	7	LYS	1	0.826	0.904	5.833	7.430	7.430	0.000	0.000	0.000	0.000
5	A	8	ILE	0	0.035	0.021	8.345	1.242	1.242	0.000	0.000	0.000	0.000
6	A	9	TYR	0	-0.066	-0.061	12.029	-0.131	-0.131	0.000	0.000	0.000	0.000
7	A	10	ILE	0	-0.008	-0.009	14.866	0.346	0.346	0.000	0.000	0.000	0.000
8	A	11	VAL	0	0.007	0.001	18.136	0.028	0.028	0.000	0.000	0.000	0.000
9	A	12	GLU	0	-0.028	-0.073	21.556	0.154	0.154	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.881	-0.941	23.923	-1.227	-1.227	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.808	-0.901	26.669	-1.200	-1.200	0.000	0.000	0.000	0.000
12	A	15	MET	0	0.018	-0.005	23.475	-0.158	-0.158	0.000	0.000	0.000	0.000
13	A	16	THR	0	-0.027	0.005	23.738	-0.105	-0.105	0.000	0.000	0.000	0.000
14	A	17	ILE	0	-0.016	-0.003	22.607	-0.081	-0.081	0.000	0.000	0.000	0.000
15	A	18	VAL	0	-0.007	-0.012	19.098	-0.166	-0.166	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.021	-0.016	19.042	-0.274	-0.274	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.001	0.008	19.380	-0.147	-0.147	0.000	0.000	0.000	0.000
18	A	21	LEU	0	-0.012	-0.013	17.692	-0.061	-0.061	0.000	0.000	0.000	0.000
19	A	22	LYS	1	0.912	0.960	14.904	2.817	2.817	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.899	-0.932	14.809	-2.595	-2.595	0.000	0.000	0.000	0.000
21	A	24	HIS	1	0.753	0.855	16.468	1.938	1.938	0.000	0.000	0.000	0.000
22	A	25	LEU	0	0.009	0.004	13.158	0.021	0.021	0.000	0.000	0.000	0.000
23	A	26	SER	0	-0.018	-0.039	10.563	-0.752	-0.752	0.000	0.000	0.000	0.000
24	A	27	ALA	0	-0.024	0.003	9.787	-0.716	-0.716	0.000	0.000	0.000	0.000
25	A	28	SER	0	-0.074	-0.044	8.682	0.200	0.200	0.000	0.000	0.000	0.000
26	A	29	TYR	0	0.003	0.001	7.734	-1.093	-1.093	0.000	0.000	0.000	0.000
28	A	31	VAL	0	0.009	0.008	7.835	1.043	1.043	0.000	0.000	0.000	0.000
29	A	32	SER	0	0.000	0.006	11.683	0.483	0.483	0.000	0.000	0.000	0.000
30	A	33	SER	0	0.015	-0.007	13.810	0.169	0.169	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.049	-0.005	17.618	-0.037	-0.037	0.000	0.000	0.000	0.000
32	A	35	SER	0	-0.058	-0.018	19.513	0.012	0.012	0.000	0.000	0.000	0.000
33	A	36	ASN	0	-0.016	-0.018	21.963	0.230	0.230	0.000	0.000	0.000	0.000
34	A	37	PHE	0	0.053	0.010	24.308	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	38	ARG	1	0.888	0.937	26.119	0.961	0.961	0.000	0.000	0.000	0.000
36	A	39	ASP	-1	-0.852	-0.917	23.378	-1.405	-1.405	0.000	0.000	0.000	0.000
37	A	40	VAL	0	0.035	0.027	20.868	-0.085	-0.085	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.818	0.904	20.250	0.892	0.892	0.000	0.000	0.000	0.000
39	A	42	GLN	0	-0.043	-0.025	20.113	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.716	-0.841	17.979	-2.285	-2.285	0.000	0.000	0.000	0.000
41	A	44	ILE	0	-0.005	-0.003	15.831	-0.358	-0.358	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.034	-0.019	15.054	-0.231	-0.231	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.027	-0.011	15.354	-0.067	-0.067	0.000	0.000	0.000	0.000
44	A	47	PHE	0	-0.035	-0.023	9.874	-0.346	-0.346	0.000	0.000	0.000	0.000
45	A	48	GLN	0	-0.037	-0.011	10.411	-1.091	-1.091	0.000	0.000	0.000	0.000
46	A	49	PRO	0	-0.026	-0.007	10.004	-0.821	-0.821	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.806	-0.904	7.285	-6.618	-6.618	0.000	0.000	0.000	0.000
48	A	51	LEU	0	-0.010	-0.007	10.669	0.665	0.665	0.000	0.000	0.000	0.000
49	A	52	ILE	0	-0.022	-0.010	13.652	-0.368	-0.368	0.000	0.000	0.000	0.000
50	A	53	LEU	0	-0.011	0.003	16.629	0.203	0.203	0.000	0.000	0.000	0.000
51	A	54	MET	0	0.021	0.011	18.935	-0.048	-0.048	0.000	0.000	0.000	0.000
52	A	55	ASP	-1	-0.723	-0.786	22.203	-1.054	-1.054	0.000	0.000	0.000	0.000
53	A	56	ILE	0	-0.017	-0.015	25.245	0.008	0.008	0.000	0.000	0.000	0.000
54	A	57	THR	0	-0.083	-0.063	28.439	0.074	0.074	0.000	0.000	0.000	0.000
55	A	58	LEU	0	-0.025	0.007	25.661	0.021	0.021	0.000	0.000	0.000	0.000
56	A	59	PRO	0	-0.007	0.007	30.347	0.032	0.032	0.000	0.000	0.000	0.000
57	A	60	TYR	0	-0.031	-0.029	32.170	0.055	0.055	0.000	0.000	0.000	0.000
58	A	61	PHE	0	-0.012	-0.009	24.778	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	62	ASN	0	0.063	0.035	29.466	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	63	GLY	0	0.097	0.040	26.817	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	64	PHE	0	0.033	0.027	27.162	-0.033	-0.033	0.000	0.000	0.000	0.000
62	A	65	TYR	0	-0.029	-0.013	29.267	0.030	0.030	0.000	0.000	0.000	0.000
63	A	66	TRP	0	0.024	-0.009	25.378	0.002	0.002	0.000	0.000	0.000	0.000
64	A	67	THR	0	0.030	0.012	23.839	-0.102	-0.102	0.000	0.000	0.000	0.000
65	A	68	ALA	0	0.032	0.019	25.479	0.013	0.013	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.849	-0.900	26.319	-0.797	-0.797	0.000	0.000	0.000	0.000
67	A	70	LEU	0	0.003	-0.018	20.823	0.004	0.004	0.000	0.000	0.000	0.000
68	A	71	ARG	1	0.784	0.861	19.891	1.039	1.039	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.817	0.915	24.443	0.768	0.768	0.000	0.000	0.000	0.000
70	A	73	PHE	0	-0.067	-0.038	21.631	0.058	0.058	0.000	0.000	0.000	0.000
71	A	74	LEU	0	-0.021	0.001	17.242	-0.045	-0.045	0.000	0.000	0.000	0.000
72	A	75	THR	0	0.022	0.003	18.021	0.013	0.013	0.000	0.000	0.000	0.000
73	A	76	ILE	0	-0.018	0.015	13.536	0.141	0.141	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.033	0.022	14.473	0.122	0.122	0.000	0.000	0.000	0.000
75	A	78	ILE	0	-0.033	-0.023	16.750	-0.317	-0.317	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.002	0.010	17.941	0.178	0.178	0.000	0.000	0.000	0.000
77	A	80	PHE	0	-0.033	-0.015	20.885	-0.107	-0.107	0.000	0.000	0.000	0.000
78	A	81	ILE	0	-0.005	-0.008	21.314	0.021	0.021	0.000	0.000	0.000	0.000
79	A	82	SER	0	0.070	0.029	25.177	0.015	0.015	0.000	0.000	0.000	0.000
80	A	83	SER	0	-0.007	-0.014	29.006	-0.035	-0.035	0.000	0.000	0.000	0.000
81	A	84	SER	0	0.008	-0.003	32.012	0.038	0.038	0.000	0.000	0.000	0.000
82	A	85	ASN	0	-0.061	-0.042	34.132	0.042	0.042	0.000	0.000	0.000	0.000
83	A	86	ASP	-1	-0.944	-0.977	32.925	-0.651	-0.651	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.973	-0.968	35.617	-0.388	-0.388	0.000	0.000	0.000	0.000
85	A	88	MET	0	0.007	0.008	29.117	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.817	-0.907	32.372	-0.442	-0.442	0.000	0.000	0.000	0.000
87	A	90	MET	0	0.001	-0.012	24.769	-0.048	-0.048	0.000	0.000	0.000	0.000
88	A	91	VAL	0	-0.011	0.000	29.740	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	92	MET	0	0.015	0.025	32.289	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	93	ALA	0	0.009	-0.006	27.077	-0.028	-0.028	0.000	0.000	0.000	0.000
91	A	94	LEU	0	0.030	0.014	26.503	-0.035	-0.035	0.000	0.000	0.000	0.000
92	A	95	ASN	0	-0.084	-0.054	28.612	0.009	0.009	0.000	0.000	0.000	0.000
93	A	96	MET	0	-0.072	-0.013	28.745	0.011	0.011	0.000	0.000	0.000	0.000
94	A	97	GLY	0	-0.004	0.006	26.467	-0.060	-0.060	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.013	0.008	23.552	-0.101	-0.101	0.000	0.000	0.000	0.000
96	A	99	ASP	-1	-0.833	-0.912	20.567	-0.954	-0.954	0.000	0.000	0.000	0.000
97	A	100	ASP	-1	-0.794	-0.898	21.930	-0.772	-0.772	0.000	0.000	0.000	0.000
98	A	101	PHE	0	-0.037	-0.019	23.803	-0.090	-0.090	0.000	0.000	0.000	0.000
99	A	102	ILE	0	-0.017	-0.001	22.962	0.050	0.050	0.000	0.000	0.000	0.000
100	A	103	SER	0	0.030	0.034	25.852	-0.029	-0.029	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.792	0.887	27.006	1.085	1.085	0.000	0.000	0.000	0.000
102	A	105	PRO	0	-0.017	-0.015	29.148	0.053	0.053	0.000	0.000	0.000	0.000
103	A	106	PHE	0	0.055	0.015	22.296	0.051	0.051	0.000	0.000	0.000	0.000
104	A	107	SER	0	-0.002	-0.002	25.766	-0.070	-0.070	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.055	0.008	19.991	-0.017	-0.017	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.042	0.031	20.710	-0.090	-0.090	0.000	0.000	0.000	0.000
107	A	110	VAL	0	-0.016	-0.012	21.130	0.048	0.048	0.000	0.000	0.000	0.000
108	A	111	LEU	0	0.026	0.015	18.394	0.028	0.028	0.000	0.000	0.000	0.000
109	A	112	ASP	-1	-0.813	-0.881	16.748	-1.911	-1.911	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.019	0.005	16.459	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.818	0.898	18.041	0.941	0.941	0.000	0.000	0.000	0.000
112	A	115	LEU	0	-0.002	-0.010	14.141	0.007	0.007	0.000	0.000	0.000	0.000
113	A	116	THR	0	-0.038	-0.034	13.121	-0.149	-0.149	0.000	0.000	0.000	0.000
114	A	117	ALA	0	0.001	0.003	13.844	0.105	0.105	0.000	0.000	0.000	0.000
115	A	118	ILE	0	-0.038	-0.009	15.864	0.127	0.127	0.000	0.000	0.000	0.000
116	A	119	LEU	0	-0.080	-0.040	10.363	-0.096	-0.096	0.000	0.000	0.000	0.000
117	A	120	ARG	0	-0.033	-0.003	11.459	0.816	0.816	0.000	0.000	0.000	0.000

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