FMO DATABASE

FMODB ID: KK143

Calculation Name: 2KFT-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KFT

Chain ID: A

ChEMBL ID:

UniProt ID: O43918

Base Structure: SolutionNMR

Registration Date: 2025-10-04

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	-271306.315121
FMO2-HF: Nuclear repulsion	248208.005154
FMO2-HF: Total energy	-23098.309967
FMO2-MP2: Total energy	-23158.696715

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:-2:GLY)

Summations of interaction energy for fragment #1(A:-2:GLY)

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.
-95.591	-94.511	-0.015	-0.306	-0.76	0

Interaction energy analysis for fragmet #1(A:-2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.903 / q_NPA : 0.943

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	294	LYS	1	0.986	1.006	3.837	33.206	33.989	-0.014	-0.276	-0.494
5	A	296	GLU	-1	-0.922	-0.949	4.256	-51.625	-51.328	-0.001	-0.030	-0.266
4	A	295	ASN	0	0.000	-0.013	5.780	5.044	5.044	0.000	0.000	0.000
6	A	297	ASP	-1	-0.966	-0.977	5.619	-40.223	-40.223	0.000	0.000	0.000
7	A	298	GLU	-1	-0.849	-0.908	8.277	-20.908	-20.908	0.000	0.000	0.000
8	A	299	CYS	-1	-0.863	-0.864	11.465	-17.000	-17.000	0.000	0.000	0.000
9	A	300	ALA	0	-0.016	-0.027	14.182	0.303	0.303	0.000	0.000	0.000
10	A	301	VAL	0	-0.073	-0.071	15.382	0.790	0.790	0.000	0.000	0.000
11	A	302	CYS	0	-0.051	-0.049	17.828	0.925	0.925	0.000	0.000	0.000
12	A	303	ARG	1	0.849	0.924	13.712	19.883	19.883	0.000	0.000	0.000
13	A	304	ASP	-1	-0.880	-0.921	14.930	-16.542	-16.542	0.000	0.000	0.000
14	A	305	GLY	0	0.066	0.028	13.617	-1.122	-1.122	0.000	0.000	0.000
15	A	306	GLY	0	-0.045	-0.042	14.504	1.382	1.382	0.000	0.000	0.000
16	A	307	GLU	-1	-0.916	-0.961	14.990	-16.616	-16.616	0.000	0.000	0.000
17	A	308	LEU	0	-0.040	-0.023	12.008	0.826	0.826	0.000	0.000	0.000
18	A	309	ILE	0	0.001	0.014	14.226	-0.726	-0.726	0.000	0.000	0.000
19	A	310	CYS	0	-0.012	-0.021	10.226	-0.654	-0.654	0.000	0.000	0.000
20	A	311	CYS	0	-0.111	0.016	12.109	1.839	1.839	0.000	0.000	0.000
21	A	312	ASP	-1	-0.757	-0.885	11.543	-23.187	-23.187	0.000	0.000	0.000
22	A	313	GLY	0	-0.018	-0.022	12.815	-0.175	-0.175	0.000	0.000	0.000
23	A	314	CYS	0	-0.105	-0.037	11.119	0.992	0.992	0.000	0.000	0.000
24	A	315	PRO	0	0.052	0.020	6.360	0.283	0.283	0.000	0.000	0.000
25	A	316	ARG	1	0.913	0.923	8.347	18.587	18.587	0.000	0.000	0.000
26	A	317	ALA	0	0.047	0.033	11.145	0.057	0.057	0.000	0.000	0.000
27	A	318	PHE	0	0.056	0.011	12.626	0.981	0.981	0.000	0.000	0.000
28	A	319	HIS	1	0.879	0.928	16.236	16.597	16.597	0.000	0.000	0.000
29	A	320	LEU	0	0.004	0.006	18.364	0.966	0.966	0.000	0.000	0.000
30	A	321	ALA	0	-0.030	-0.035	20.733	0.481	0.481	0.000	0.000	0.000
31	A	322	CYS	0	-0.021	-0.003	20.327	0.372	0.372	0.000	0.000	0.000
32	A	323	LEU	0	-0.039	0.003	18.920	-0.238	-0.238	0.000	0.000	0.000
33	A	324	SER	0	-0.022	-0.006	22.296	0.487	0.487	0.000	0.000	0.000
34	A	325	PRO	0	-0.002	0.004	23.791	0.432	0.432	0.000	0.000	0.000
35	A	326	PRO	0	-0.036	-0.015	24.382	-0.481	-0.481	0.000	0.000	0.000
36	A	327	LEU	0	0.032	0.007	19.967	0.327	0.327	0.000	0.000	0.000
37	A	328	ARG	1	0.898	0.957	24.383	11.306	11.306	0.000	0.000	0.000
38	A	329	GLU	-1	-0.929	-0.960	25.030	-10.976	-10.976	0.000	0.000	0.000
39	A	330	ILE	0	-0.015	-0.019	18.980	-0.194	-0.194	0.000	0.000	0.000
40	A	331	PRO	0	0.004	-0.005	20.257	0.336	0.336	0.000	0.000	0.000
41	A	332	SER	0	0.002	0.008	21.526	-0.321	-0.321	0.000	0.000	0.000
42	A	333	GLY	0	-0.010	-0.005	20.080	0.357	0.357	0.000	0.000	0.000
43	A	334	THR	0	-0.035	-0.008	16.232	-0.520	-0.520	0.000	0.000	0.000
44	A	335	TRP	0	0.032	-0.001	15.265	0.857	0.857	0.000	0.000	0.000
45	A	336	ARG	1	0.883	0.911	16.132	15.036	15.036	0.000	0.000	0.000
46	A	337	CYS	0	0.004	0.004	15.594	0.744	0.744	0.000	0.000	0.000
47	A	338	SER	0	0.066	0.007	18.240	0.110	0.110	0.000	0.000	0.000
48	A	339	SER	0	0.007	0.006	18.758	0.057	0.057	0.000	0.000	0.000
49	A	340	CYS	0	-0.017	-0.009	16.303	-0.024	-0.024	0.000	0.000	0.000
50	A	341	LEU	0	0.015	0.021	18.958	0.228	0.228	0.000	0.000	0.000
51	A	342	GLN	0	-0.005	-0.010	22.239	0.233	0.233	0.000	0.000	0.000
52	A	343	ALA	0	-0.051	-0.018	21.364	0.452	0.452	0.000	0.000	0.000
53	A	344	THR	0	-0.070	-0.034	23.343	0.272	0.272	0.000	0.000	0.000
54	A	345	VAL	0	-0.054	-0.019	20.625	0.149	0.149	0.000	0.000	0.000
55	A	346	GLN	0	-0.057	-0.039	22.195	0.420	0.420	0.000	0.000	0.000
56	A	347	GLU	-2	-1.712	-1.814	18.617	-29.376	-29.376	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:GLY)