FMO DATABASE

FMODB ID: G7GG1

Calculation Name: 1L8D-A-Xray549

Preferred Name:

Target Type:

Ligand Name: citric acid | phosphate ion | mercury (ii) ion

Ligand 3-letter code: CIT | PO4 | HG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1L8D

Chain ID: A

ChEMBL ID:

UniProt ID: P58301

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-711655.651264
FMO2-HF: Nuclear repulsion	669058.186698
FMO2-HF: Total energy	-42597.464566
FMO2-MP2: Total energy	-42721.887192

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:396:LYS)

Summations of interaction energy for fragment #1(A:396:LYS)

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.
-228.631	-217.528	1.465	-5.894	-6.675	-0.063

Interaction energy analysis for fragmet #1(A:396:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.819 / q_NPA : 1.899

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	398	LEU	0	0.044	0.024	3.456	5.284	7.689	0.004	-1.018	-1.391	-0.004
4	A	399	LEU	0	-0.008	0.013	3.034	6.398	7.901	0.085	-0.575	-1.013	-0.003
5	A	400	GLU	-1	-0.824	-0.922	2.562	-122.445	-115.382	1.377	-4.297	-4.144	-0.056
103	A	498	LEU	-1	-0.943	-0.953	4.623	-71.914	-71.782	-0.001	-0.004	-0.127	0.000
6	A	401	GLU	-1	-0.868	-0.913	5.965	-50.287	-50.287	0.000	0.000	0.000	0.000
7	A	402	LEU	0	0.003	0.003	7.326	6.501	6.501	0.000	0.000	0.000	0.000
8	A	403	GLU	-1	-0.879	-0.951	6.646	-67.252	-67.252	0.000	0.000	0.000	0.000
9	A	404	THR	0	-0.006	-0.001	9.460	5.280	5.280	0.000	0.000	0.000	0.000
10	A	405	LYS	1	0.871	0.952	11.907	37.284	37.284	0.000	0.000	0.000	0.000
11	A	406	LYS	1	0.821	0.883	13.012	40.357	40.357	0.000	0.000	0.000	0.000
12	A	407	THR	0	-0.013	-0.007	13.654	2.649	2.649	0.000	0.000	0.000	0.000
13	A	408	THR	0	0.007	0.001	15.907	2.323	2.323	0.000	0.000	0.000	0.000
14	A	409	ILE	0	-0.060	-0.029	17.687	2.100	2.100	0.000	0.000	0.000	0.000
15	A	410	GLU	-1	-0.884	-0.948	17.680	-31.606	-31.606	0.000	0.000	0.000	0.000
16	A	411	GLU	-1	-0.930	-0.965	19.062	-29.904	-29.904	0.000	0.000	0.000	0.000
17	A	412	GLU	-1	-0.854	-0.936	22.172	-25.971	-25.971	0.000	0.000	0.000	0.000
18	A	413	ARG	1	0.911	0.962	22.349	27.528	27.528	0.000	0.000	0.000	0.000
19	A	414	ASN	0	-0.011	0.002	23.585	1.691	1.691	0.000	0.000	0.000	0.000
20	A	415	GLU	-1	-0.779	-0.863	26.506	-20.589	-20.589	0.000	0.000	0.000	0.000
21	A	416	ILE	0	-0.005	-0.004	28.054	1.146	1.146	0.000	0.000	0.000	0.000
22	A	417	THR	0	-0.056	-0.049	28.402	0.953	0.953	0.000	0.000	0.000	0.000
23	A	418	GLN	0	-0.015	0.011	30.806	0.176	0.176	0.000	0.000	0.000	0.000
24	A	419	ARG	1	0.874	0.910	30.833	20.536	20.536	0.000	0.000	0.000	0.000
25	A	420	ILE	0	-0.044	-0.023	32.262	0.812	0.812	0.000	0.000	0.000	0.000
26	A	421	GLY	0	-0.028	-0.011	35.716	0.553	0.553	0.000	0.000	0.000	0.000
27	A	422	GLU	-1	-0.883	-0.949	35.827	-17.330	-17.330	0.000	0.000	0.000	0.000
28	A	423	LEU	0	-0.006	-0.015	37.147	0.570	0.570	0.000	0.000	0.000	0.000
29	A	424	LYS	1	0.890	0.951	37.780	16.902	16.902	0.000	0.000	0.000	0.000
30	A	425	ASN	0	0.016	0.017	41.144	0.491	0.491	0.000	0.000	0.000	0.000
31	A	426	LYS	1	0.916	0.960	43.203	14.839	14.839	0.000	0.000	0.000	0.000
32	A	427	ILE	0	-0.048	-0.034	42.750	0.411	0.411	0.000	0.000	0.000	0.000
33	A	428	GLY	0	-0.024	-0.009	46.212	0.335	0.335	0.000	0.000	0.000	0.000
34	A	429	ASP	-1	-0.860	-0.929	47.007	-13.219	-13.219	0.000	0.000	0.000	0.000
35	A	430	LEU	0	-0.044	-0.027	47.218	0.328	0.328	0.000	0.000	0.000	0.000
36	A	431	LYS	1	0.898	0.950	48.199	13.370	13.370	0.000	0.000	0.000	0.000
37	A	432	THR	0	0.018	0.007	52.065	0.270	0.270	0.000	0.000	0.000	0.000
38	A	433	ALA	0	0.020	0.018	53.560	0.264	0.264	0.000	0.000	0.000	0.000
39	A	434	ILE	0	-0.044	-0.038	52.967	0.259	0.259	0.000	0.000	0.000	0.000
40	A	435	GLU	-1	-0.934	-0.953	56.460	-10.685	-10.685	0.000	0.000	0.000	0.000
41	A	436	GLU	-1	-0.813	-0.912	58.436	-10.308	-10.308	0.000	0.000	0.000	0.000
42	A	437	LEU	0	-0.026	-0.005	58.260	0.206	0.206	0.000	0.000	0.000	0.000
43	A	438	LYS	1	0.882	0.942	57.801	11.185	11.185	0.000	0.000	0.000	0.000
44	A	439	LYS	1	0.790	0.890	61.750	10.612	10.612	0.000	0.000	0.000	0.000
45	A	440	ALA	0	-0.003	0.017	63.992	0.163	0.163	0.000	0.000	0.000	0.000
46	A	441	LYS	1	0.942	0.964	65.896	9.147	9.147	0.000	0.000	0.000	0.000
47	A	442	GLY	0	0.055	0.046	68.940	0.126	0.126	0.000	0.000	0.000	0.000
48	A	443	LYS	1	0.887	0.939	67.862	9.235	9.235	0.000	0.000	0.000	0.000
49	A	444	CYS	0	-0.020	-0.027	61.881	-0.109	-0.109	0.000	0.000	0.000	0.000
50	A	445	PRO	0	-0.021	-0.007	62.545	0.114	0.114	0.000	0.000	0.000	0.000
51	A	446	VAL	0	0.015	0.001	58.545	0.021	0.021	0.000	0.000	0.000	0.000
52	A	447	CYS	-1	-0.801	-0.782	61.228	-10.414	-10.414	0.000	0.000	0.000	0.000
53	A	448	GLY	0	0.029	0.028	63.214	0.118	0.118	0.000	0.000	0.000	0.000
54	A	449	ARG	1	0.829	0.810	59.994	10.649	10.649	0.000	0.000	0.000	0.000
55	A	450	GLU	-1	-0.954	-0.977	66.734	-9.152	-9.152	0.000	0.000	0.000	0.000
56	A	451	LEU	0	-0.046	-0.025	61.657	-0.183	-0.183	0.000	0.000	0.000	0.000
57	A	452	THR	0	0.052	0.024	65.853	0.011	0.011	0.000	0.000	0.000	0.000
58	A	453	ASP	-1	-0.810	-0.924	65.954	-9.487	-9.487	0.000	0.000	0.000	0.000
59	A	454	GLU	-1	-0.937	-0.963	65.741	-9.577	-9.577	0.000	0.000	0.000	0.000
60	A	455	HIS	0	0.044	0.022	59.980	-0.122	-0.122	0.000	0.000	0.000	0.000
61	A	456	ARG	1	0.750	0.858	61.289	9.552	9.552	0.000	0.000	0.000	0.000
62	A	457	GLU	-1	-0.806	-0.898	61.060	-10.325	-10.325	0.000	0.000	0.000	0.000
63	A	458	GLU	-1	-0.951	-0.948	58.181	-11.128	-11.128	0.000	0.000	0.000	0.000
64	A	459	LEU	0	-0.011	-0.015	56.794	-0.314	-0.314	0.000	0.000	0.000	0.000
65	A	460	LEU	0	-0.001	0.001	56.115	-0.304	-0.304	0.000	0.000	0.000	0.000
66	A	461	SER	0	-0.018	-0.005	56.129	-0.213	-0.213	0.000	0.000	0.000	0.000
67	A	462	LYS	1	0.952	0.977	51.314	12.053	12.053	0.000	0.000	0.000	0.000
68	A	463	TYR	0	0.017	-0.002	51.840	-0.402	-0.402	0.000	0.000	0.000	0.000
69	A	464	HIS	0	0.004	-0.024	51.223	-0.257	-0.257	0.000	0.000	0.000	0.000
70	A	465	LEU	0	0.001	0.005	49.402	-0.265	-0.265	0.000	0.000	0.000	0.000
71	A	466	ASP	-1	-0.788	-0.886	46.093	-14.261	-14.261	0.000	0.000	0.000	0.000
72	A	467	LEU	0	-0.004	0.026	46.417	-0.400	-0.400	0.000	0.000	0.000	0.000
73	A	468	ASN	0	0.000	-0.025	46.437	-0.373	-0.373	0.000	0.000	0.000	0.000
74	A	469	ASN	0	0.016	0.008	43.226	-0.533	-0.533	0.000	0.000	0.000	0.000
75	A	470	SER	0	0.017	0.010	42.269	-0.528	-0.528	0.000	0.000	0.000	0.000
76	A	471	LYS	1	0.900	0.953	41.459	12.867	12.867	0.000	0.000	0.000	0.000
77	A	472	ASN	0	-0.008	-0.006	41.209	-0.318	-0.318	0.000	0.000	0.000	0.000
78	A	473	THR	0	-0.017	-0.005	37.233	-0.431	-0.431	0.000	0.000	0.000	0.000
79	A	474	LEU	0	0.005	-0.002	36.916	-0.457	-0.457	0.000	0.000	0.000	0.000
80	A	475	ALA	0	0.004	-0.002	36.625	-0.422	-0.422	0.000	0.000	0.000	0.000
81	A	476	LYS	1	0.954	0.970	34.405	15.926	15.926	0.000	0.000	0.000	0.000
82	A	477	LEU	0	0.015	0.016	32.416	-0.622	-0.622	0.000	0.000	0.000	0.000
83	A	478	ILE	0	-0.030	-0.009	31.819	-0.577	-0.577	0.000	0.000	0.000	0.000
84	A	479	ASP	-1	-0.906	-0.945	31.676	-18.355	-18.355	0.000	0.000	0.000	0.000
85	A	480	ARG	1	0.798	0.879	23.063	24.123	24.123	0.000	0.000	0.000	0.000
86	A	481	LYS	1	0.913	0.953	27.271	20.317	20.317	0.000	0.000	0.000	0.000
87	A	482	SER	0	0.005	-0.001	27.024	-0.953	-0.953	0.000	0.000	0.000	0.000
88	A	483	GLU	-1	-0.952	-0.970	24.659	-23.242	-23.242	0.000	0.000	0.000	0.000
89	A	484	LEU	0	0.012	0.015	22.693	-0.974	-0.974	0.000	0.000	0.000	0.000
90	A	485	GLU	-1	-0.831	-0.942	22.203	-24.322	-24.322	0.000	0.000	0.000	0.000
91	A	486	ARG	1	0.856	0.934	22.494	21.172	21.172	0.000	0.000	0.000	0.000
92	A	487	GLU	-1	-0.873	-0.942	19.211	-29.558	-29.558	0.000	0.000	0.000	0.000
93	A	488	LEU	0	0.001	0.015	17.440	-1.504	-1.504	0.000	0.000	0.000	0.000
94	A	489	ARG	1	0.917	0.940	17.556	26.572	26.572	0.000	0.000	0.000	0.000
95	A	490	ARG	1	0.874	0.960	16.328	28.937	28.937	0.000	0.000	0.000	0.000
96	A	491	ILE	0	0.081	0.043	12.372	-1.217	-1.217	0.000	0.000	0.000	0.000
97	A	492	ASP	-1	-0.784	-0.884	12.603	-38.893	-38.893	0.000	0.000	0.000	0.000
98	A	493	MET	0	-0.107	-0.047	13.694	-0.408	-0.408	0.000	0.000	0.000	0.000
99	A	494	GLU	-1	-0.960	-0.990	10.664	-40.829	-40.829	0.000	0.000	0.000	0.000
100	A	495	ILE	0	0.018	0.003	8.868	-3.264	-3.264	0.000	0.000	0.000	0.000
101	A	496	LYS	1	0.917	0.959	9.250	31.008	31.008	0.000	0.000	0.000	0.000
102	A	497	ARG	1	0.881	0.948	9.988	43.848	43.848	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:396:LYS)