FMO DATABASE

FMODB ID: ZZLKN

Calculation Name: 2KPI-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KPI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KZL7

Base Structure: SolutionNMR

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	56
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-250957.516129
FMO2-HF: Nuclear repulsion	228799.043019
FMO2-HF: Total energy	-22158.47311
FMO2-MP2: Total energy	-22219.361531

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:1:MET)

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

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.
-93.546	-92.077	-0.009	-0.57	-0.89	0

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.902

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].
3	A	3	LEU	0	0.045	0.021	3.853	-1.900	-0.431	-0.009	-0.570	-0.890
4	A	4	GLU	-1	-0.944	-0.964	6.499	-25.976	-25.976	0.000	0.000	0.000
5	A	5	ALA	0	-0.013	-0.020	8.990	0.806	0.806	0.000	0.000	0.000
6	A	6	GLY	0	-0.007	-0.005	12.216	1.355	1.355	0.000	0.000	0.000
7	A	7	LEU	0	0.006	0.005	14.653	1.024	1.024	0.000	0.000	0.000
8	A	8	LEU	0	0.010	-0.002	16.863	0.245	0.245	0.000	0.000	0.000
9	A	9	GLU	-1	-0.942	-0.966	18.146	-13.393	-13.393	0.000	0.000	0.000
10	A	10	ILE	0	-0.061	-0.017	17.964	0.796	0.796	0.000	0.000	0.000
11	A	11	LEU	0	0.012	0.010	21.225	-0.220	-0.220	0.000	0.000	0.000
12	A	12	ALA	0	-0.004	-0.002	20.293	0.175	0.175	0.000	0.000	0.000
13	A	13	CYS	0	-0.024	0.018	22.321	0.079	0.079	0.000	0.000	0.000
14	A	14	PRO	0	0.003	0.009	20.581	-0.582	-0.582	0.000	0.000	0.000
15	A	15	ALA	0	-0.008	-0.001	19.209	-0.701	-0.701	0.000	0.000	0.000
16	A	16	CYS	0	-0.037	-0.009	20.123	-0.257	-0.257	0.000	0.000	0.000
17	A	17	HIS	0	0.000	-0.007	18.361	0.030	0.030	0.000	0.000	0.000
18	A	18	ALA	0	-0.023	-0.014	21.269	0.183	0.183	0.000	0.000	0.000
19	A	19	PRO	0	0.078	0.020	24.467	-0.263	-0.263	0.000	0.000	0.000
20	A	20	LEU	0	-0.010	-0.001	24.863	0.171	0.171	0.000	0.000	0.000
21	A	21	GLU	-1	-0.926	-0.949	28.583	-9.224	-9.224	0.000	0.000	0.000
22	A	22	GLU	-1	-0.958	-0.981	32.244	-9.828	-9.828	0.000	0.000	0.000
23	A	23	ARG	1	0.924	0.943	33.733	8.500	8.500	0.000	0.000	0.000
24	A	24	ASP	-1	-0.913	-0.948	37.102	-7.838	-7.838	0.000	0.000	0.000
25	A	25	ALA	0	-0.034	-0.001	36.659	-0.135	-0.135	0.000	0.000	0.000
26	A	26	GLU	-1	-0.922	-0.980	34.289	-8.556	-8.556	0.000	0.000	0.000
27	A	27	LEU	0	0.000	0.009	28.384	-0.077	-0.077	0.000	0.000	0.000
28	A	28	ILE	0	-0.008	-0.015	31.969	0.108	0.108	0.000	0.000	0.000
29	A	29	CYS	0	-0.058	-0.045	26.693	-0.288	-0.288	0.000	0.000	0.000
30	A	30	THR	0	-0.017	-0.028	28.985	0.434	0.434	0.000	0.000	0.000
31	A	31	GLY	0	0.067	0.012	28.376	-0.436	-0.436	0.000	0.000	0.000
32	A	32	GLN	0	-0.056	-0.028	27.372	0.043	0.043	0.000	0.000	0.000
33	A	33	ASP	-1	-0.920	-0.946	26.763	-10.478	-10.478	0.000	0.000	0.000
34	A	34	CYS	0	-0.125	-0.054	27.560	-0.311	-0.311	0.000	0.000	0.000
35	A	35	GLY	0	0.041	0.020	29.671	0.296	0.296	0.000	0.000	0.000
36	A	36	LEU	0	-0.059	-0.021	27.785	0.213	0.213	0.000	0.000	0.000
37	A	37	ALA	0	0.048	0.023	31.542	-0.122	-0.122	0.000	0.000	0.000
38	A	38	TYR	0	-0.037	-0.032	26.931	-0.150	-0.150	0.000	0.000	0.000
39	A	39	PRO	0	0.034	0.025	31.515	0.005	0.005	0.000	0.000	0.000
40	A	40	VAL	0	0.010	0.008	31.915	-0.352	-0.352	0.000	0.000	0.000
41	A	41	ARG	1	0.849	0.928	31.371	10.105	10.105	0.000	0.000	0.000
42	A	42	ASP	-1	-0.920	-0.963	32.633	-9.281	-9.281	0.000	0.000	0.000
43	A	43	GLY	0	-0.018	-0.010	33.660	-0.068	-0.068	0.000	0.000	0.000
44	A	44	ILE	0	-0.030	-0.014	27.492	-0.289	-0.289	0.000	0.000	0.000
45	A	45	PRO	0	0.029	0.022	26.676	0.265	0.265	0.000	0.000	0.000
46	A	46	VAL	0	-0.011	-0.002	27.325	-0.412	-0.412	0.000	0.000	0.000
47	A	47	LEU	0	0.025	0.003	22.250	-0.093	-0.093	0.000	0.000	0.000
48	A	48	LEU	0	0.000	0.000	22.773	-0.513	-0.513	0.000	0.000	0.000
49	A	49	VAL	0	0.041	0.007	23.597	0.434	0.434	0.000	0.000	0.000
50	A	50	ASP	-1	-0.937	-0.970	26.283	-10.907	-10.907	0.000	0.000	0.000
51	A	51	GLU	-1	-0.952	-0.992	28.344	-10.235	-10.235	0.000	0.000	0.000
52	A	52	ALA	0	0.003	0.023	28.625	0.286	0.286	0.000	0.000	0.000
53	A	53	ARG	1	0.876	0.943	30.603	9.425	9.425	0.000	0.000	0.000
54	A	54	ARG	1	0.883	0.936	30.253	9.469	9.469	0.000	0.000	0.000
55	A	55	PRO	0	-0.018	-0.018	34.874	0.055	0.055	0.000	0.000	0.000
56	A	56	GLU	-2	-1.896	-1.922	37.839	-15.163	-15.163	0.000	0.000	0.000

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