FMO DATABASE

FMODB ID: VN371

Calculation Name: 6K0A-E-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6K0A

Chain ID: E

ChEMBL ID:

UniProt ID: P54066

Base Structure: ElectronMicroscopy

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-695934.354019
FMO2-HF: Nuclear repulsion	658308.841913
FMO2-HF: Total energy	-37625.512106
FMO2-MP2: Total energy	-37736.044312

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.
115.573	117.36	0.004	-0.645	-1.147	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 : 0.860 / q_NPA : 0.920

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	3	THR	0	0.022	0.006	3.639	2.199	3.641	0.000	-0.557	-0.886	-0.001
66	A	66	LYS	1	0.968	0.970	4.132	37.964	38.309	0.004	-0.088	-0.261	0.001
4	A	4	PRO	0	0.058	0.008	6.047	1.180	1.180	0.000	0.000	0.000	0.000
5	A	5	HIS	0	-0.018	0.008	9.059	3.674	3.674	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.012	-0.006	4.966	6.665	6.665	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.007	0.014	8.406	-0.514	-0.514	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.022	0.018	9.879	1.165	1.165	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.914	0.945	9.650	27.115	27.115	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.054	-0.032	5.442	-8.047	-8.047	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.849	-0.916	8.896	-19.832	-19.832	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.016	-0.015	10.600	-1.509	-1.509	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.025	0.026	13.272	0.208	0.208	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.011	0.006	12.640	-1.375	-1.375	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.077	-0.033	8.322	-1.474	-1.474	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.920	0.959	12.352	19.391	19.391	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.024	-0.018	14.382	-1.084	-1.084	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.860	-0.917	16.885	-13.417	-13.417	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.018	0.017	20.070	-0.559	-0.559	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.053	-0.013	22.008	0.376	0.376	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.841	-0.929	24.469	-10.979	-10.979	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.028	-0.002	25.948	-0.414	-0.414	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.955	0.991	28.566	9.300	9.300	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.030	-0.016	31.334	0.178	0.178	0.000	0.000	0.000	0.000
25	A	25	LYS	1	1.030	0.991	31.244	8.696	8.696	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.014	0.011	31.997	-0.109	-0.109	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.013	-0.005	27.351	-0.157	-0.157	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.020	0.004	26.683	-0.430	-0.430	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.001	0.003	25.852	0.299	0.299	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.052	-0.010	24.613	-0.073	-0.073	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.887	0.913	21.017	12.671	12.671	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.102	0.037	19.801	0.610	0.610	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.900	0.953	15.296	16.713	16.713	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.007	0.014	15.878	0.889	0.889	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.010	-0.001	16.787	-1.109	-1.109	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.853	-0.933	19.251	-14.202	-14.202	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.811	-0.892	16.196	-18.549	-18.549	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.055	0.027	20.024	0.337	0.337	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.949	0.953	21.539	11.188	11.188	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.014	-0.024	22.675	-0.525	-0.525	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.018	0.025	23.972	0.363	0.363	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.019	0.001	18.292	-0.456	-0.456	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.057	0.038	21.531	0.642	0.642	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.027	-0.022	19.884	-0.872	-0.872	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.868	-0.925	21.314	-12.473	-12.473	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.724	0.850	21.878	11.005	11.005	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.867	-0.944	23.171	-12.587	-12.587	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.886	-0.933	24.421	-10.614	-10.614	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.019	0.017	26.325	0.348	0.348	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.911	0.957	27.422	9.660	9.660	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.864	-0.931	25.735	-11.714	-11.714	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.069	-0.043	25.797	0.528	0.528	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.021	0.017	25.376	-0.545	-0.545	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.003	-0.006	23.551	0.333	0.333	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.004	0.008	24.554	-0.479	-0.479	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.801	0.888	19.051	15.565	15.565	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.888	-0.966	23.737	-11.909	-11.909	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.048	-0.017	25.813	0.215	0.215	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.016	0.005	24.418	0.412	0.412	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.004	0.015	20.648	-0.505	-0.505	0.000	0.000	0.000	0.000
61	A	61	PHE	0	0.006	0.004	17.926	0.237	0.237	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.048	-0.026	16.162	-0.589	-0.589	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.043	0.012	12.135	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	64	GLN	0	-0.024	-0.026	12.449	-0.273	-0.273	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.008	0.003	6.498	-1.914	-1.914	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.023	0.026	8.141	-0.383	-0.383	0.000	0.000	0.000	0.000
68	A	68	CYS	0	-0.013	-0.009	8.597	1.551	1.551	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.966	0.979	10.668	16.299	16.299	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.002	0.001	10.270	-0.056	-0.056	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.971	0.998	13.427	14.595	14.595	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.001	-0.006	14.502	-0.359	-0.359	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.835	-0.915	17.639	-13.533	-13.533	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.023	-0.007	19.910	-0.740	-0.740	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.931	0.966	21.571	11.320	11.320	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.048	-0.023	18.235	0.167	0.167	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.049	0.003	15.676	-0.855	-0.855	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.005	0.006	18.891	0.413	0.413	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.067	-0.033	20.140	-0.442	-0.442	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.878	0.904	20.186	12.985	12.985	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.087	0.053	16.032	-0.230	-0.230	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.873	-0.936	15.881	-16.997	-16.997	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.876	-0.937	17.385	-14.598	-14.598	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.776	0.870	14.581	18.749	18.749	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.026	0.025	10.131	-0.829	-0.829	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.924	0.986	13.595	13.876	13.876	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.950	0.952	16.122	15.838	15.838	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.922	0.981	16.838	15.712	15.712	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.014	0.009	17.185	-1.037	-1.037	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.924	0.968	19.514	13.085	13.085	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.037	0.024	21.363	-0.533	-0.533	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.027	-0.024	24.063	0.326	0.326	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.019	0.005	25.696	-0.264	-0.264	0.000	0.000	0.000	0.000
94	A	94	PRO	0	-0.050	-0.016	27.308	0.056	0.056	0.000	0.000	0.000	0.000
95	A	95	TYR	-1	-0.900	-0.941	29.624	-9.365	-9.365	0.000	0.000	0.000	0.000

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