FMO DATABASE

FMODB ID: KV263

Calculation Name: 2D8Y-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D8Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UHB6

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-529689.317213
FMO2-HF: Nuclear repulsion	492881.900336
FMO2-HF: Total energy	-36807.416877
FMO2-MP2: Total energy	-36908.972277

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:GLY)

Summations of interaction energy for fragment #1(A:1: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.
41.644	42.658	-0.013	-0.417	-0.584	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / 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

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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	3	SER	0	0.030	0.003	3.845	4.428	5.442	-0.013	-0.417	-0.584	-0.002
4	A	4	GLY	0	0.055	0.032	6.747	-0.093	-0.093	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.012	0.006	10.311	2.852	2.852	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.015	-0.011	11.515	-1.426	-1.426	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.010	0.025	14.271	0.983	0.983	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.017	-0.010	17.419	-0.409	-0.409	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.940	0.955	18.915	13.958	13.958	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.005	0.006	17.163	-0.521	-0.521	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.044	0.032	18.632	-0.823	-0.823	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.053	0.038	17.724	0.026	0.026	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.026	-0.008	19.320	0.154	0.154	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.054	0.022	22.839	0.012	0.012	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.875	0.931	25.371	12.049	12.049	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.816	-0.910	25.614	-11.700	-11.700	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.014	-0.024	24.220	0.340	0.340	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.100	-0.015	26.974	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.016	0.001	25.597	-0.203	-0.203	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.921	-0.967	27.435	-9.762	-9.762	0.000	0.000	0.000	0.000
21	A	21	CYS	0	-0.052	-0.033	29.461	0.060	0.060	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.011	0.012	22.660	0.230	0.230	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.945	0.981	26.425	9.297	9.297	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.018	0.001	28.511	-0.208	-0.208	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.045	-0.009	29.376	0.330	0.330	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.039	0.026	32.087	-0.142	-0.142	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.010	-0.021	34.982	0.040	0.040	0.000	0.000	0.000	0.000
28	A	28	MET	0	0.004	0.010	36.767	0.097	0.097	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.865	-0.941	35.869	-8.548	-8.548	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.862	0.922	30.284	9.713	9.713	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.003	0.009	35.548	0.176	0.176	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.013	-0.004	31.658	-0.278	-0.278	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.018	0.002	33.342	0.303	0.303	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.003	0.004	30.170	-0.061	-0.061	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.013	-0.010	29.385	-0.617	-0.617	0.000	0.000	0.000	0.000
36	A	36	GLN	0	0.035	0.026	25.734	-0.794	-0.794	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.031	0.012	28.822	0.469	0.469	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.025	0.003	30.096	-0.222	-0.222	0.000	0.000	0.000	0.000
39	A	39	HIS	0	0.019	-0.004	32.921	-0.098	-0.098	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.012	0.003	35.516	0.037	0.037	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.038	-0.022	38.697	0.181	0.181	0.000	0.000	0.000	0.000
42	A	42	CYS	0	0.005	-0.008	34.224	0.036	0.036	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.026	0.027	35.305	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.937	0.964	35.640	8.693	8.693	0.000	0.000	0.000	0.000
45	A	45	CYS	-1	-0.829	-0.731	36.830	-8.139	-8.139	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.009	-0.003	33.703	-0.096	-0.096	0.000	0.000	0.000	0.000
47	A	47	TYR	0	0.014	-0.030	35.762	-0.051	-0.051	0.000	0.000	0.000	0.000
48	A	48	CYS	0	-0.074	-0.084	38.648	0.179	0.179	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.019	0.019	38.243	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	50	ASN	0	0.050	0.009	39.945	0.161	0.161	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.939	0.964	41.393	7.150	7.150	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.049	0.001	38.977	0.170	0.170	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.022	-0.006	41.925	0.070	0.070	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.008	0.007	38.142	-0.043	-0.043	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.038	0.013	41.728	0.090	0.090	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.006	0.004	44.080	-0.053	-0.053	0.000	0.000	0.000	0.000
57	A	57	TYR	0	0.032	0.021	35.800	-0.061	-0.061	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.005	0.001	38.601	0.152	0.152	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.021	0.004	33.056	0.029	0.029	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.011	0.008	32.708	0.135	0.135	0.000	0.000	0.000	0.000
61	A	61	HIS	0	0.040	0.032	28.161	-0.306	-0.306	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.008	-0.001	27.960	-0.312	-0.312	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.941	0.972	28.296	10.703	10.703	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.001	0.009	31.248	0.190	0.190	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.055	0.010	33.946	-0.063	-0.063	0.000	0.000	0.000	0.000
66	A	66	CYS	0	-0.055	-0.088	38.062	0.120	0.120	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.906	0.932	41.775	7.410	7.410	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.015	0.009	44.039	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	69	HIS	1	0.936	0.940	40.939	7.373	7.373	0.000	0.000	0.000	0.000
70	A	70	PHE	0	0.028	0.019	38.337	-0.053	-0.053	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.046	-0.042	41.013	-0.043	-0.043	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.004	0.006	43.892	-0.028	-0.028	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.029	-0.002	38.426	0.016	0.016	0.000	0.000	0.000	0.000
74	A	74	PHE	0	0.002	0.005	35.899	-0.137	-0.137	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.940	0.980	40.404	6.630	6.630	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.025	0.018	42.698	0.087	0.087	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.900	0.930	45.326	6.465	6.465	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.032	0.022	46.408	-0.129	-0.129	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.031	-0.022	43.917	0.262	0.262	0.000	0.000	0.000	0.000
80	A	80	TYR	0	-0.053	-0.032	41.255	-0.119	-0.119	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.824	-0.888	42.033	-7.276	-7.276	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.964	-0.991	42.715	-7.079	-7.079	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.016	-0.002	40.009	-0.045	-0.045	0.000	0.000	0.000	0.000
84	A	84	PHE	0	-0.073	-0.038	35.230	-0.261	-0.261	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.042	0.017	37.599	0.253	0.253	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.063	-0.037	35.970	-0.327	-0.327	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.028	0.014	36.720	0.306	0.306	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.025	-0.002	36.366	-0.254	-0.254	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.008	-0.002	33.259	0.045	0.045	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.053	-0.024	34.915	0.073	0.073	0.000	0.000	0.000	0.000
91	A	91	GLY	-1	-0.930	-0.954	31.956	-10.014	-10.014	0.000	0.000	0.000	0.000

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