FMO DATABASE

FMODB ID: ML82Z

Calculation Name: 2K8D-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2K8D

Chain ID: A

ChEMBL ID:

UniProt ID: O26807

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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1433578.050975
FMO2-HF: Nuclear repulsion	1371010.940647
FMO2-HF: Total energy	-62567.110328
FMO2-MP2: Total energy	-62743.256274

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:4:MET)

Summations of interaction energy for fragment #1(A:4: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.
-145.114	-136.033	4.146	-5.951	-7.276	-0.056

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.836 / q_NPA : 0.911

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	6	ASP	-1	-0.827	-0.904	2.544	-73.111	-66.129	3.116	-4.808	-5.290	-0.045
4	A	7	ARG	1	0.769	0.850	5.014	39.698	39.767	-0.001	-0.012	-0.056	0.000
20	A	23	ARG	1	0.815	0.906	2.300	59.876	61.906	1.031	-1.131	-1.930	-0.011
5	A	8	ILE	0	0.013	0.012	7.802	-0.685	-0.685	0.000	0.000	0.000	0.000
6	A	9	PRO	0	0.004	0.007	10.232	1.627	1.627	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.003	0.005	13.679	-0.905	-0.905	0.000	0.000	0.000	0.000
8	A	11	PHE	0	0.018	0.002	16.466	0.619	0.619	0.000	0.000	0.000	0.000
9	A	12	SER	0	0.009	-0.005	19.356	0.231	0.231	0.000	0.000	0.000	0.000
10	A	13	VAL	0	0.007	-0.005	22.464	0.639	0.639	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.014	0.005	24.130	0.435	0.435	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.800	0.903	23.251	13.795	13.795	0.000	0.000	0.000	0.000
13	A	16	ASN	0	-0.080	-0.028	26.076	0.152	0.152	0.000	0.000	0.000	0.000
14	A	17	ARG	1	0.795	0.872	22.810	13.605	13.605	0.000	0.000	0.000	0.000
15	A	18	VAL	0	-0.021	-0.019	18.560	-0.426	-0.426	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.755	-0.838	18.856	-14.329	-14.329	0.000	0.000	0.000	0.000
17	A	20	MET	0	-0.058	-0.031	12.500	-0.976	-0.976	0.000	0.000	0.000	0.000
18	A	21	VAL	0	0.021	0.019	12.066	0.916	0.916	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.858	-0.936	9.448	-27.164	-27.164	0.000	0.000	0.000	0.000
21	A	24	ILE	0	-0.027	0.004	5.958	4.416	4.416	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.861	-0.925	5.109	-55.776	-55.776	0.000	0.000	0.000	0.000
23	A	26	LEU	0	0.018	0.015	7.396	2.974	2.974	0.000	0.000	0.000	0.000
24	A	27	SER	0	0.025	0.014	10.192	-1.458	-1.458	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.891	-0.961	12.990	-20.535	-20.535	0.000	0.000	0.000	0.000
26	A	29	ASP	-1	-0.847	-0.917	15.267	-14.473	-14.473	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.864	-0.925	13.657	-19.069	-19.069	0.000	0.000	0.000	0.000
28	A	31	TRP	0	-0.054	-0.035	10.493	0.932	0.932	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.748	0.843	16.734	15.506	15.506	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.983	-0.982	19.606	-13.633	-13.633	0.000	0.000	0.000	0.000
31	A	34	ILE	0	0.023	0.021	14.612	0.380	0.380	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.032	-0.012	16.328	-0.361	-0.361	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.782	-0.854	19.278	-14.180	-14.180	0.000	0.000	0.000	0.000
34	A	37	PRO	0	0.044	0.014	22.303	-0.125	-0.125	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.901	-0.951	23.824	-11.403	-11.403	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.051	0.018	18.773	0.042	0.042	0.000	0.000	0.000	0.000
37	A	40	PHE	0	0.046	0.038	20.428	-0.102	-0.102	0.000	0.000	0.000	0.000
38	A	41	ARG	1	0.765	0.877	21.842	11.817	11.817	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.005	-0.007	19.823	0.132	0.132	0.000	0.000	0.000	0.000
40	A	43	ALA	0	0.028	0.009	18.010	-0.063	-0.063	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.860	0.928	19.393	11.501	11.501	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.761	0.877	22.099	12.044	12.044	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.011	0.018	20.524	0.279	0.279	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.035	0.014	21.532	0.058	0.058	0.000	0.000	0.000	0.000
45	A	48	THR	0	-0.069	-0.060	23.826	0.384	0.384	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.764	-0.858	27.324	-11.211	-11.211	0.000	0.000	0.000	0.000
47	A	50	PRO	0	-0.010	0.009	29.449	0.141	0.141	0.000	0.000	0.000	0.000
48	A	51	PRO	0	0.023	0.011	30.905	-0.276	-0.276	0.000	0.000	0.000	0.000
49	A	52	PHE	0	-0.021	-0.017	31.451	-0.094	-0.094	0.000	0.000	0.000	0.000
50	A	53	THR	0	0.024	0.002	31.198	0.158	0.158	0.000	0.000	0.000	0.000
51	A	54	GLY	0	0.021	0.016	33.893	0.138	0.138	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.867	0.917	35.243	8.470	8.470	0.000	0.000	0.000	0.000
53	A	56	TYR	0	-0.004	0.018	32.776	0.227	0.227	0.000	0.000	0.000	0.000
54	A	57	HIS	0	-0.003	-0.002	30.664	-0.666	-0.666	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.887	-0.936	34.244	-8.406	-8.406	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.039	-0.015	30.136	-0.084	-0.084	0.000	0.000	0.000	0.000
57	A	60	HIS	0	-0.050	-0.042	33.199	0.532	0.532	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.873	-0.914	30.836	-10.658	-10.658	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.886	-0.946	30.950	-9.647	-9.647	0.000	0.000	0.000	0.000
60	A	63	GLY	0	0.028	0.016	27.918	-0.202	-0.202	0.000	0.000	0.000	0.000
61	A	64	ILE	0	-0.037	-0.007	21.486	0.010	0.010	0.000	0.000	0.000	0.000
62	A	65	TYR	0	0.006	-0.004	20.442	0.053	0.053	0.000	0.000	0.000	0.000
63	A	66	ARG	1	0.803	0.873	17.824	16.118	16.118	0.000	0.000	0.000	0.000
64	A	67	CYS	0	-0.024	0.004	13.163	0.392	0.392	0.000	0.000	0.000	0.000
65	A	68	ILE	0	0.033	0.007	15.703	-0.926	-0.926	0.000	0.000	0.000	0.000
66	A	69	CYS	0	-0.068	-0.030	13.865	0.336	0.336	0.000	0.000	0.000	0.000
67	A	70	CYS	0	-0.023	-0.017	10.653	-1.871	-1.871	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.022	0.029	12.549	-0.382	-0.382	0.000	0.000	0.000	0.000
69	A	72	THR	0	0.008	0.012	12.706	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.867	-0.940	14.799	-17.099	-17.099	0.000	0.000	0.000	0.000
71	A	74	LEU	0	-0.014	-0.034	14.970	-1.299	-1.299	0.000	0.000	0.000	0.000
72	A	75	PHE	0	-0.007	-0.001	18.069	0.371	0.371	0.000	0.000	0.000	0.000
73	A	76	ASP	-1	-0.695	-0.841	21.457	-12.641	-12.641	0.000	0.000	0.000	0.000
74	A	77	SER	0	0.010	0.019	24.517	-0.151	-0.151	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.730	-0.839	27.250	-11.151	-11.151	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.159	-0.095	24.009	-0.083	-0.083	0.000	0.000	0.000	0.000
77	A	80	LYS	1	0.807	0.906	24.936	10.507	10.507	0.000	0.000	0.000	0.000
78	A	81	PHE	0	0.014	0.011	27.246	0.432	0.432	0.000	0.000	0.000	0.000
79	A	82	ASP	-1	-0.771	-0.897	30.065	-10.234	-10.234	0.000	0.000	0.000	0.000
80	A	83	SER	0	0.074	0.013	32.590	0.108	0.108	0.000	0.000	0.000	0.000
81	A	84	GLY	0	-0.041	-0.014	35.498	-0.122	-0.122	0.000	0.000	0.000	0.000
82	A	85	THR	0	-0.069	-0.052	32.398	0.099	0.099	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.010	0.024	31.327	-0.104	-0.104	0.000	0.000	0.000	0.000
84	A	87	TRP	0	-0.029	-0.002	28.887	-0.305	-0.305	0.000	0.000	0.000	0.000
85	A	88	PRO	0	0.036	0.030	23.350	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	89	SER	0	-0.008	-0.027	23.928	-0.716	-0.716	0.000	0.000	0.000	0.000
87	A	90	PHE	0	-0.019	-0.001	20.337	0.306	0.306	0.000	0.000	0.000	0.000
88	A	91	TYR	0	0.005	-0.006	26.076	-0.103	-0.103	0.000	0.000	0.000	0.000
89	A	92	ASP	-1	-0.849	-0.915	23.884	-12.435	-12.435	0.000	0.000	0.000	0.000
90	A	93	VAL	0	-0.029	-0.017	19.222	-0.208	-0.208	0.000	0.000	0.000	0.000
91	A	94	VAL	0	0.013	0.027	18.563	0.257	0.257	0.000	0.000	0.000	0.000
92	A	95	SER	0	0.025	-0.002	16.944	0.131	0.131	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.820	-0.895	13.108	-21.435	-21.435	0.000	0.000	0.000	0.000
94	A	97	HIS	0	-0.065	-0.035	12.778	-0.048	-0.048	0.000	0.000	0.000	0.000
95	A	98	ASN	0	0.037	0.002	11.226	-4.468	-4.468	0.000	0.000	0.000	0.000
96	A	99	ILE	0	-0.038	-0.011	12.444	-0.181	-0.181	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.825	0.897	8.937	23.330	23.330	0.000	0.000	0.000	0.000
98	A	101	LEU	0	0.015	0.020	12.343	0.702	0.702	0.000	0.000	0.000	0.000
99	A	102	ARG	1	0.836	0.900	7.569	25.529	25.529	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.911	-0.981	14.168	-13.006	-13.006	0.000	0.000	0.000	0.000
101	A	104	ASP	-1	-0.757	-0.836	17.507	-13.578	-13.578	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.966	0.969	20.225	12.674	12.674	0.000	0.000	0.000	0.000
103	A	106	SER	0	0.007	-0.015	22.650	0.723	0.723	0.000	0.000	0.000	0.000
104	A	107	LEU	0	-0.117	-0.066	24.952	-0.016	-0.016	0.000	0.000	0.000	0.000
105	A	108	GLY	0	-0.011	0.007	27.963	0.370	0.370	0.000	0.000	0.000	0.000
106	A	109	MET	0	-0.031	-0.014	28.284	0.351	0.351	0.000	0.000	0.000	0.000
107	A	110	VAL	0	0.000	0.005	22.538	-0.261	-0.261	0.000	0.000	0.000	0.000
108	A	111	ARG	1	0.801	0.871	22.784	12.275	12.275	0.000	0.000	0.000	0.000
109	A	112	CYS	0	0.016	0.034	17.826	-0.097	-0.097	0.000	0.000	0.000	0.000
110	A	113	GLU	-1	-0.802	-0.882	12.525	-21.727	-21.727	0.000	0.000	0.000	0.000
111	A	114	VAL	0	-0.014	-0.018	16.130	-0.052	-0.052	0.000	0.000	0.000	0.000
112	A	115	LEU	0	0.006	0.016	11.457	0.326	0.326	0.000	0.000	0.000	0.000
113	A	116	CYS	0	0.017	0.017	11.562	-0.129	-0.129	0.000	0.000	0.000	0.000
114	A	117	ALA	0	0.046	0.030	8.630	-2.378	-2.378	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.832	0.880	6.567	22.703	22.703	0.000	0.000	0.000	0.000
116	A	119	CYS	0	-0.043	-0.030	7.010	-1.377	-1.377	0.000	0.000	0.000	0.000
117	A	120	ASP	-1	-0.893	-0.927	7.099	-33.247	-33.247	0.000	0.000	0.000	0.000
118	A	121	ALA	0	-0.046	-0.033	9.869	1.406	1.406	0.000	0.000	0.000	0.000
119	A	122	HIS	0	-0.047	-0.040	12.496	1.482	1.482	0.000	0.000	0.000	0.000
120	A	123	LEU	0	-0.013	-0.003	14.291	0.125	0.125	0.000	0.000	0.000	0.000
121	A	124	GLY	0	0.029	0.024	16.908	1.176	1.176	0.000	0.000	0.000	0.000
122	A	125	HIS	0	-0.018	0.008	18.263	-0.114	-0.114	0.000	0.000	0.000	0.000
123	A	126	VAL	0	0.011	0.009	20.149	0.373	0.373	0.000	0.000	0.000	0.000
124	A	127	PHE	0	-0.027	-0.020	22.577	-0.026	-0.026	0.000	0.000	0.000	0.000
125	A	128	ASP	-1	-0.934	-0.962	25.693	-10.347	-10.347	0.000	0.000	0.000	0.000
126	A	129	ASP	-1	-0.832	-0.907	28.088	-9.726	-9.726	0.000	0.000	0.000	0.000
127	A	130	GLY	0	-0.009	0.002	31.253	0.227	0.227	0.000	0.000	0.000	0.000
128	A	131	PRO	0	-0.050	-0.016	32.778	0.119	0.119	0.000	0.000	0.000	0.000
129	A	132	ARG	1	0.987	1.001	32.743	7.857	7.857	0.000	0.000	0.000	0.000
130	A	133	PRO	0	-0.012	-0.021	30.941	0.252	0.252	0.000	0.000	0.000	0.000
131	A	134	THR	0	-0.013	-0.007	28.222	-0.158	-0.158	0.000	0.000	0.000	0.000
132	A	135	GLY	0	0.024	0.018	29.834	0.045	0.045	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.874	0.922	23.675	12.265	12.265	0.000	0.000	0.000	0.000
134	A	137	ARG	1	0.832	0.904	26.794	10.331	10.331	0.000	0.000	0.000	0.000
135	A	138	TYR	0	0.033	0.004	19.101	-0.095	-0.095	0.000	0.000	0.000	0.000
136	A	139	CYS	0	-0.048	-0.017	22.662	0.572	0.572	0.000	0.000	0.000	0.000
137	A	140	MET	0	-0.051	0.003	19.074	-1.013	-1.013	0.000	0.000	0.000	0.000
138	A	141	ASN	0	0.008	-0.021	20.515	0.855	0.855	0.000	0.000	0.000	0.000
139	A	142	SER	0	-0.001	-0.005	17.935	-0.803	-0.803	0.000	0.000	0.000	0.000
140	A	143	ALA	0	0.056	0.012	18.889	0.435	0.435	0.000	0.000	0.000	0.000
141	A	144	ALA	0	-0.001	-0.011	16.363	0.208	0.208	0.000	0.000	0.000	0.000
142	A	145	LEU	0	-0.037	-0.004	18.110	-0.127	-0.127	0.000	0.000	0.000	0.000
143	A	146	LYS	1	0.894	0.948	20.803	14.145	14.145	0.000	0.000	0.000	0.000
144	A	147	PHE	0	0.052	0.019	22.160	-0.381	-0.381	0.000	0.000	0.000	0.000
145	A	148	ILE	0	-0.057	-0.026	21.809	-0.104	-0.104	0.000	0.000	0.000	0.000
146	A	149	PRO	0	0.098	0.049	25.298	0.100	0.100	0.000	0.000	0.000	0.000
147	A	150	ARG	1	0.731	0.831	26.014	10.852	10.852	0.000	0.000	0.000	0.000
148	A	151	ASP	-1	-0.746	-0.882	24.493	-12.372	-12.372	0.000	0.000	0.000	0.000
149	A	152	GLN	0	-0.119	-0.064	25.019	-0.344	-0.344	0.000	0.000	0.000	0.000
150	A	153	ILE	0	-0.083	-0.024	27.637	0.306	0.306	0.000	0.000	0.000	0.000
151	A	154	GLY	-1	-0.894	-0.940	28.963	-10.604	-10.604	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)