FMO DATABASE

FMODB ID: GVKQ1

Calculation Name: 5VMD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol | zinc ion

Ligand 3-letter code: EDO | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5VMD

Chain ID: A

ChEMBL ID:

UniProt ID: Q86XK2

Base Structure: X-ray

Registration Date: 2025-10-06

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	69
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-356437.443196
FMO2-HF: Nuclear repulsion	326206.817221
FMO2-HF: Total energy	-30230.625976
FMO2-MP2: Total energy	-30310.498988

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:834:GLN)

Summations of interaction energy for fragment #1(A:834: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.
20.913	22.304	8.567	-4.58	-5.378	0.025

Interaction energy analysis for fragmet #1(A:834:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.917

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	836	LEU	0	-0.005	-0.039	2.935	-2.459	0.434	0.212	-1.479	-1.626	-0.011
5	A	838	LYS	1	0.864	0.925	1.882	29.848	28.346	8.355	-3.101	-3.752	0.036
4	A	837	TYR	0	0.005	-0.021	5.788	5.090	5.090	0.000	0.000	0.000	0.000
6	A	839	ILE	0	0.070	0.024	6.761	1.429	1.429	0.000	0.000	0.000	0.000
7	A	840	SER	0	0.041	0.021	5.256	0.551	0.551	0.000	0.000	0.000	0.000
8	A	841	SER	0	-0.045	-0.028	7.469	0.825	0.825	0.000	0.000	0.000	0.000
9	A	842	TYR	0	-0.013	-0.014	9.198	1.054	1.054	0.000	0.000	0.000	0.000
10	A	843	THR	0	0.036	0.013	11.460	0.758	0.758	0.000	0.000	0.000	0.000
11	A	844	SER	0	-0.041	-0.027	10.353	0.953	0.953	0.000	0.000	0.000	0.000
12	A	845	TYR	0	-0.046	-0.018	13.007	0.845	0.845	0.000	0.000	0.000	0.000
13	A	846	PRO	0	-0.041	-0.013	15.126	0.674	0.674	0.000	0.000	0.000	0.000
14	A	847	MET	0	-0.017	0.007	16.618	0.622	0.622	0.000	0.000	0.000	0.000
15	A	848	HIS	0	-0.064	-0.030	19.252	-0.099	-0.099	0.000	0.000	0.000	0.000
16	A	849	ASP	-1	-0.854	-0.924	21.744	-12.955	-12.955	0.000	0.000	0.000	0.000
17	A	850	PHE	0	-0.041	-0.013	24.327	0.213	0.213	0.000	0.000	0.000	0.000
18	A	851	TYR	0	0.010	-0.004	27.911	-0.240	-0.240	0.000	0.000	0.000	0.000
19	A	852	ARG	1	0.915	0.960	30.834	8.855	8.855	0.000	0.000	0.000	0.000
20	A	853	CYS	0	-0.072	-0.012	34.067	0.013	0.013	0.000	0.000	0.000	0.000
21	A	854	HIS	0	0.005	0.006	35.049	0.312	0.312	0.000	0.000	0.000	0.000
22	A	855	THR	0	0.028	0.006	39.639	0.141	0.141	0.000	0.000	0.000	0.000
23	A	856	CYS	0	-0.057	-0.034	40.548	0.175	0.175	0.000	0.000	0.000	0.000
24	A	857	ASN	0	0.010	0.004	42.116	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	858	THR	0	-0.007	0.000	43.382	0.007	0.007	0.000	0.000	0.000	0.000
26	A	859	THR	0	-0.047	-0.013	40.533	0.065	0.065	0.000	0.000	0.000	0.000
27	A	860	ASP	-1	-0.807	-0.907	40.626	-7.594	-7.594	0.000	0.000	0.000	0.000
28	A	861	ARG	1	0.900	0.942	35.546	7.838	7.838	0.000	0.000	0.000	0.000
29	A	862	ASN	0	-0.007	0.010	35.879	-0.447	-0.447	0.000	0.000	0.000	0.000
30	A	863	ALA	0	0.054	0.030	31.987	-0.178	-0.178	0.000	0.000	0.000	0.000
31	A	864	ILE	0	-0.023	0.001	32.616	0.144	0.144	0.000	0.000	0.000	0.000
32	A	865	CYS	0	0.010	0.010	30.287	-0.254	-0.254	0.000	0.000	0.000	0.000
33	A	866	VAL	0	0.098	0.028	26.876	0.286	0.286	0.000	0.000	0.000	0.000
34	A	867	ASN	0	0.002	-0.010	29.700	-0.055	-0.055	0.000	0.000	0.000	0.000
35	A	868	CYS	0	0.015	0.001	32.296	0.277	0.277	0.000	0.000	0.000	0.000
36	A	869	ILE	0	0.035	0.023	31.332	0.211	0.211	0.000	0.000	0.000	0.000
37	A	870	LYS	1	0.905	0.956	28.334	10.605	10.605	0.000	0.000	0.000	0.000
38	A	871	LYS	1	0.899	0.948	34.615	8.667	8.667	0.000	0.000	0.000	0.000
39	A	872	CYS	0	-0.038	-0.015	37.857	0.188	0.188	0.000	0.000	0.000	0.000
40	A	873	HIS	0	0.036	0.020	37.016	0.014	0.014	0.000	0.000	0.000	0.000
41	A	874	GLN	0	0.005	0.011	37.977	-0.145	-0.145	0.000	0.000	0.000	0.000
42	A	875	GLY	0	-0.011	-0.013	38.359	0.196	0.196	0.000	0.000	0.000	0.000
43	A	876	HIS	0	0.007	-0.004	38.951	0.114	0.114	0.000	0.000	0.000	0.000
44	A	877	ASP	-1	-0.888	-0.939	37.857	-8.033	-8.033	0.000	0.000	0.000	0.000
45	A	878	VAL	0	-0.035	-0.038	33.494	0.007	0.007	0.000	0.000	0.000	0.000
46	A	879	GLU	-1	-0.852	-0.913	30.806	-9.093	-9.093	0.000	0.000	0.000	0.000
47	A	880	PHE	0	-0.083	-0.048	23.114	-0.085	-0.085	0.000	0.000	0.000	0.000
48	A	881	ILE	0	0.010	0.008	26.981	-0.044	-0.044	0.000	0.000	0.000	0.000
49	A	882	ARG	1	0.851	0.908	18.905	13.497	13.497	0.000	0.000	0.000	0.000
50	A	883	HIS	0	0.028	0.017	23.089	0.187	0.187	0.000	0.000	0.000	0.000
51	A	884	ASP	-1	-0.806	-0.916	18.792	-14.441	-14.441	0.000	0.000	0.000	0.000
52	A	885	ARG	1	0.901	0.956	21.225	12.332	12.332	0.000	0.000	0.000	0.000
53	A	886	PHE	0	-0.042	-0.048	19.153	0.422	0.422	0.000	0.000	0.000	0.000
54	A	887	PHE	0	-0.033	0.010	20.364	-0.147	-0.147	0.000	0.000	0.000	0.000
55	A	888	CYS	-1	-0.823	-0.823	22.298	-9.808	-9.808	0.000	0.000	0.000	0.000
56	A	889	ASP	-1	-0.797	-0.908	24.343	-10.651	-10.651	0.000	0.000	0.000	0.000
57	A	890	CYS	0	-0.071	-0.063	26.516	0.199	0.199	0.000	0.000	0.000	0.000
58	A	891	GLY	0	-0.015	-0.061	24.497	0.042	0.042	0.000	0.000	0.000	0.000
59	A	892	ALA	0	-0.056	-0.026	22.279	-0.247	-0.247	0.000	0.000	0.000	0.000
60	A	893	GLY	0	-0.028	-0.006	23.206	-0.104	-0.104	0.000	0.000	0.000	0.000
61	A	894	THR	0	-0.068	-0.041	25.514	0.065	0.065	0.000	0.000	0.000	0.000
62	A	895	LEU	0	-0.043	-0.018	27.345	0.340	0.340	0.000	0.000	0.000	0.000
63	A	896	SER	0	-0.019	-0.021	30.814	-0.092	-0.092	0.000	0.000	0.000	0.000
64	A	897	ASN	0	-0.047	-0.010	33.197	0.181	0.181	0.000	0.000	0.000	0.000
65	A	898	PRO	0	0.027	0.018	29.841	-0.160	-0.160	0.000	0.000	0.000	0.000
66	A	899	CYS	0	0.018	0.014	27.168	0.311	0.311	0.000	0.000	0.000	0.000
67	A	900	THR	0	-0.042	-0.031	29.673	-0.060	-0.060	0.000	0.000	0.000	0.000
68	A	901	LEU	0	-0.075	-0.055	29.086	0.176	0.176	0.000	0.000	0.000	0.000
69	A	902	ALA	-1	-0.917	-0.936	25.148	-10.414	-10.414	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:834:GLN)