FMO DATABASE

FMODB ID: QLY2Y

Calculation Name: 1VGL-B-Xray547

Preferred Name:

Target Type:

Ligand Name: mercury (ii) ion

Ligand 3-letter code: HG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VGL

Chain ID: B

ChEMBL ID:

UniProt ID: Q79V61

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-807026.911812
FMO2-HF: Nuclear repulsion	766814.484513
FMO2-HF: Total energy	-40212.427299
FMO2-MP2: Total energy	-40332.446442

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.
-213.956	-213.844	20.826	-10.029	-10.906	-0.098

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 : 0.837 / q_NPA : 0.911

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	LYS	1	0.948	1.006	3.646	32.636	34.044	-0.019	-0.522	-0.866	0.000
93	A	96	GLU	-1	-0.916	-0.986	2.731	-51.486	-49.415	1.058	-1.232	-1.897	-0.013
94	A	97	ILE	0	0.041	0.026	3.945	-0.903	0.122	0.004	-0.386	-0.642	-0.001
95	A	98	GLY	0	-0.097	-0.085	2.114	-45.198	-46.913	19.478	-11.078	-6.685	-0.078
96	A	99	ASP	-1	-0.872	-0.911	2.922	-35.336	-38.031	0.306	3.194	-0.804	-0.006
97	A	100	GLN	0	-0.041	-0.025	5.063	2.402	2.420	-0.001	-0.005	-0.012	0.000
4	A	7	THR	0	-0.046	-0.019	5.850	2.368	2.368	0.000	0.000	0.000	0.000
5	A	8	TYR	0	-0.007	-0.008	9.191	1.319	1.319	0.000	0.000	0.000	0.000
6	A	9	VAL	0	0.057	0.032	9.690	0.447	0.447	0.000	0.000	0.000	0.000
7	A	10	LEU	0	-0.040	-0.028	12.218	2.008	2.008	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.880	0.955	13.449	20.589	20.589	0.000	0.000	0.000	0.000
9	A	12	LEU	0	-0.037	-0.031	16.735	1.322	1.322	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.014	-0.030	18.272	-0.124	-0.124	0.000	0.000	0.000	0.000
11	A	14	VAL	0	0.002	-0.012	22.242	0.635	0.635	0.000	0.000	0.000	0.000
12	A	15	ALA	0	0.012	0.011	24.525	-0.133	-0.133	0.000	0.000	0.000	0.000
13	A	16	GLY	0	0.021	0.023	26.393	0.472	0.472	0.000	0.000	0.000	0.000
14	A	17	ASN	0	-0.096	-0.053	24.739	-0.213	-0.213	0.000	0.000	0.000	0.000
15	A	18	THR	0	0.045	0.009	26.826	0.263	0.263	0.000	0.000	0.000	0.000
16	A	19	PRO	0	0.044	0.006	27.134	-0.409	-0.409	0.000	0.000	0.000	0.000
17	A	20	ASN	0	-0.049	-0.023	27.451	-0.363	-0.363	0.000	0.000	0.000	0.000
18	A	21	SER	0	0.044	0.002	25.376	-0.485	-0.485	0.000	0.000	0.000	0.000
19	A	22	VAL	0	0.057	0.027	22.072	-0.583	-0.583	0.000	0.000	0.000	0.000
20	A	23	ARG	1	0.911	0.958	22.077	10.457	10.457	0.000	0.000	0.000	0.000
21	A	24	ALA	0	-0.006	0.006	22.941	-0.417	-0.417	0.000	0.000	0.000	0.000
22	A	25	LEU	0	0.028	0.009	19.384	-0.377	-0.377	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.867	0.925	18.072	14.785	14.785	0.000	0.000	0.000	0.000
24	A	27	THR	0	-0.087	-0.052	18.288	-0.484	-0.484	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.030	-0.020	17.694	-0.171	-0.171	0.000	0.000	0.000	0.000
26	A	29	ASN	0	0.023	0.018	12.607	-1.377	-1.377	0.000	0.000	0.000	0.000
27	A	30	ASN	0	-0.005	-0.001	14.461	-1.348	-1.348	0.000	0.000	0.000	0.000
28	A	31	ILE	0	-0.046	-0.032	16.220	-0.262	-0.262	0.000	0.000	0.000	0.000
29	A	32	LEU	0	-0.004	-0.003	13.747	0.194	0.194	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.742	-0.855	8.688	-33.446	-33.446	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.896	0.954	12.704	16.744	16.744	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.949	-0.996	15.988	-14.563	-14.563	0.000	0.000	0.000	0.000
33	A	36	PHE	0	-0.037	-0.030	14.702	0.524	0.524	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.905	0.961	11.321	17.577	17.577	0.000	0.000	0.000	0.000
35	A	38	GLY	0	0.009	0.011	8.214	-0.172	-0.172	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.022	-0.010	9.267	-1.327	-1.327	0.000	0.000	0.000	0.000
37	A	40	TYR	0	-0.024	-0.022	11.946	0.764	0.764	0.000	0.000	0.000	0.000
38	A	41	ALA	0	0.060	0.033	8.446	-2.374	-2.374	0.000	0.000	0.000	0.000
39	A	42	LEU	0	-0.042	-0.014	10.571	2.037	2.037	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.915	0.954	11.804	22.410	22.410	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.004	-0.001	13.871	1.530	1.530	0.000	0.000	0.000	0.000
42	A	45	ILE	0	0.021	0.020	16.707	-0.157	-0.157	0.000	0.000	0.000	0.000
43	A	46	ASP	-1	-0.810	-0.926	19.388	-12.083	-12.083	0.000	0.000	0.000	0.000
44	A	47	VAL	0	0.018	0.001	22.527	0.070	0.070	0.000	0.000	0.000	0.000
45	A	48	LEU	0	-0.038	-0.029	25.066	0.420	0.420	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.857	0.943	21.485	14.479	14.479	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.029	-0.020	20.941	-0.460	-0.460	0.000	0.000	0.000	0.000
48	A	51	PRO	0	0.009	0.012	24.197	-0.126	-0.126	0.000	0.000	0.000	0.000
49	A	52	GLN	0	-0.042	-0.018	25.039	0.402	0.402	0.000	0.000	0.000	0.000
50	A	53	LEU	0	-0.003	-0.005	20.992	-0.435	-0.435	0.000	0.000	0.000	0.000
51	A	54	ALA	0	0.015	0.013	17.642	0.400	0.400	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.941	-0.968	19.463	-13.091	-13.091	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.921	-0.970	14.557	-17.464	-17.464	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.841	-0.888	16.275	-18.972	-18.972	0.000	0.000	0.000	0.000
55	A	58	LYS	1	0.815	0.889	18.640	16.315	16.315	0.000	0.000	0.000	0.000
56	A	59	ILE	0	-0.004	0.010	21.123	-0.406	-0.406	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.030	-0.010	23.060	0.640	0.640	0.000	0.000	0.000	0.000
58	A	61	ALA	0	0.036	0.008	25.572	-0.042	-0.042	0.000	0.000	0.000	0.000
59	A	62	THR	0	0.066	0.008	25.801	-0.229	-0.229	0.000	0.000	0.000	0.000
60	A	63	PRO	0	-0.028	-0.021	27.148	-0.184	-0.184	0.000	0.000	0.000	0.000
61	A	64	CYS	0	-0.031	-0.001	26.770	0.134	0.134	0.000	0.000	0.000	0.000
62	A	65	LEU	0	0.059	0.025	20.985	0.070	0.070	0.000	0.000	0.000	0.000
63	A	66	ALA	0	0.068	0.027	23.578	-0.425	-0.425	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.888	0.937	24.694	9.971	9.971	0.000	0.000	0.000	0.000
65	A	68	VAL	0	0.008	0.009	22.074	0.269	0.269	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.021	0.038	18.930	-0.642	-0.642	0.000	0.000	0.000	0.000
67	A	70	PRO	0	0.055	0.022	19.261	0.870	0.870	0.000	0.000	0.000	0.000
68	A	71	PRO	0	0.037	0.008	22.483	0.159	0.159	0.000	0.000	0.000	0.000
69	A	72	PRO	0	-0.041	-0.013	21.976	0.532	0.532	0.000	0.000	0.000	0.000
70	A	73	VAL	0	0.082	0.048	19.183	0.247	0.247	0.000	0.000	0.000	0.000
71	A	74	ARG	1	0.900	0.959	22.159	11.827	11.827	0.000	0.000	0.000	0.000
72	A	75	ARG	1	0.880	0.936	25.382	11.705	11.705	0.000	0.000	0.000	0.000
73	A	76	ILE	0	0.017	0.023	22.173	0.419	0.419	0.000	0.000	0.000	0.000
74	A	77	ILE	0	0.053	0.026	21.064	0.266	0.266	0.000	0.000	0.000	0.000
75	A	78	GLY	0	-0.002	0.014	25.056	0.315	0.315	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.854	-0.916	27.683	-10.347	-10.347	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.046	0.017	22.923	0.331	0.331	0.000	0.000	0.000	0.000
78	A	81	SER	0	-0.040	-0.018	27.372	0.230	0.230	0.000	0.000	0.000	0.000
79	A	82	ASN	0	-0.087	-0.060	29.458	0.510	0.510	0.000	0.000	0.000	0.000
80	A	83	ARG	1	0.805	0.892	31.631	10.041	10.041	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.790	-0.875	28.974	-10.015	-10.015	0.000	0.000	0.000	0.000
82	A	85	LYS	1	0.895	0.957	31.140	9.402	9.402	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.039	0.037	25.995	0.063	0.063	0.000	0.000	0.000	0.000
84	A	87	LEU	0	-0.076	-0.031	23.079	-0.235	-0.235	0.000	0.000	0.000	0.000
85	A	88	ILE	0	-0.018	-0.005	25.790	0.452	0.452	0.000	0.000	0.000	0.000
86	A	89	GLY	0	-0.019	-0.018	25.246	0.446	0.446	0.000	0.000	0.000	0.000
87	A	90	LEU	0	-0.066	-0.024	20.825	-0.393	-0.393	0.000	0.000	0.000	0.000
88	A	91	ASP	-1	-0.742	-0.863	18.748	-15.466	-15.466	0.000	0.000	0.000	0.000
89	A	92	LEU	0	-0.067	-0.034	15.760	-0.545	-0.545	0.000	0.000	0.000	0.000
90	A	93	LEU	0	0.015	0.022	13.714	0.863	0.863	0.000	0.000	0.000	0.000
91	A	94	TYR	0	-0.054	-0.024	9.185	-1.346	-1.346	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.847	-0.933	8.850	-24.098	-24.098	0.000	0.000	0.000	0.000
98	A	101	ALA	0	0.013	0.021	5.982	-5.735	-5.735	0.000	0.000	0.000	0.000
99	A	102	GLU	-1	-0.960	-0.992	5.358	-48.683	-48.683	0.000	0.000	0.000	0.000
100	A	103	ASP	-1	-0.834	-0.915	9.002	-19.647	-19.647	0.000	0.000	0.000	0.000
101	A	104	ASP	-1	-0.836	-0.908	12.750	-17.207	-17.207	0.000	0.000	0.000	0.000
102	A	105	LEU	0	-0.099	-0.072	15.314	1.163	1.163	0.000	0.000	0.000	0.000
103	A	106	GLY	0	-0.055	-0.020	11.814	0.630	0.630	0.000	0.000	0.000	0.000
104	A	107	LEU	0	-0.019	-0.006	6.639	-1.584	-1.584	0.000	0.000	0.000	0.000
105	A	108	GLU	-2	-1.744	-1.853	10.461	-47.512	-47.512	0.000	0.000	0.000	0.000

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