FMO DATABASE

FMODB ID: Y93G2

Calculation Name: 2A8N-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A8N

Chain ID: A

ChEMBL ID:

UniProt ID: A9CK16

Base Structure: X-ray

Registration Date: 2025-10-03

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1096492.29363
FMO2-HF: Nuclear repulsion	1046113.78291
FMO2-HF: Total energy	-50378.51072
FMO2-MP2: Total energy	-50522.329424

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:ALA)

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

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.
12.78	15.81	0.294	-1.354	-1.97	-0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.914

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	4	ARG	1	0.948	0.972	2.639	55.095	57.790	0.289	-1.246	-1.739	-0.007
6	A	7	PHE	0	-0.018	-0.017	3.561	1.361	1.653	0.007	-0.100	-0.199	-0.001
33	A	34	GLY	0	-0.044	-0.019	4.750	-2.934	-2.893	-0.001	-0.005	-0.034	0.000
34	A	35	ARG	1	0.861	0.912	4.952	25.297	25.299	-0.001	-0.003	0.002	0.000
4	A	5	THR	0	0.046	0.022	5.959	3.326	3.326	0.000	0.000	0.000	0.000
5	A	6	HIS	0	0.029	0.027	6.541	5.134	5.134	0.000	0.000	0.000	0.000
7	A	8	MET	0	0.032	0.014	8.888	2.762	2.762	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.821	-0.890	11.449	-17.481	-17.481	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.027	-0.018	10.516	2.067	2.067	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.022	0.015	13.144	1.635	1.635	0.000	0.000	0.000	0.000
11	A	12	LEU	0	0.028	0.003	14.991	1.691	1.691	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.057	-0.023	16.478	1.265	1.265	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.886	-0.940	17.194	-15.236	-15.236	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.024	-0.010	19.108	0.903	0.903	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.841	0.900	18.065	17.440	17.440	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.002	-0.019	21.604	0.754	0.754	0.000	0.000	0.000	0.000
17	A	18	ALA	0	-0.033	-0.010	23.601	0.474	0.474	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.015	0.011	25.359	0.490	0.490	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.958	-0.978	26.945	-10.653	-10.653	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.796	0.904	23.560	12.875	12.875	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.852	-0.917	30.387	-9.093	-9.093	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.785	-0.866	27.492	-10.618	-10.618	0.000	0.000	0.000	0.000
23	A	24	VAL	0	0.003	-0.009	26.048	-0.080	-0.080	0.000	0.000	0.000	0.000
24	A	25	PRO	0	0.021	0.015	24.581	-0.403	-0.403	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.044	-0.028	20.442	-0.441	-0.441	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.023	0.002	18.758	0.451	0.451	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.020	-0.008	15.368	-0.562	-0.562	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.023	-0.020	10.460	0.103	0.103	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.005	0.018	12.127	-0.872	-0.872	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.008	-0.014	5.932	-0.434	-0.434	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.055	0.019	9.434	0.988	0.988	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.842	-0.905	8.687	-31.675	-31.675	0.000	0.000	0.000	0.000
35	A	36	VAL	0	-0.015	-0.008	7.767	1.726	1.726	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.026	-0.008	10.215	1.044	1.044	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.003	0.018	13.610	1.630	1.630	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.922	0.953	13.557	18.982	18.982	0.000	0.000	0.000	0.000
39	A	40	SER	0	0.017	-0.006	16.469	1.074	1.074	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.051	0.035	19.210	-0.525	-0.525	0.000	0.000	0.000	0.000
41	A	42	ASN	0	0.009	0.012	21.678	-0.360	-0.360	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.822	0.877	24.466	12.053	12.053	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.074	-0.033	27.413	0.306	0.306	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.813	0.891	30.008	9.549	9.549	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.841	-0.880	28.394	-11.003	-11.003	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.033	-0.027	27.805	0.218	0.218	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.053	-0.016	32.180	0.348	0.348	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.794	-0.852	29.923	-10.346	-10.346	0.000	0.000	0.000	0.000
49	A	50	VAL	0	0.034	-0.005	30.299	-0.334	-0.334	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.047	-0.069	27.942	-0.378	-0.378	0.000	0.000	0.000	0.000
51	A	52	ALA	0	-0.008	0.015	26.001	-0.529	-0.529	0.000	0.000	0.000	0.000
52	A	53	HIS	0	-0.001	-0.028	23.461	0.003	0.003	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.017	0.024	19.400	-0.174	-0.174	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.776	-0.917	18.201	-15.136	-15.136	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.001	-0.005	19.216	-0.393	-0.393	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.005	0.009	21.520	0.115	0.115	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.012	-0.009	15.784	-0.125	-0.125	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.000	0.000	17.889	-0.479	-0.479	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.928	0.967	19.148	11.600	11.600	0.000	0.000	0.000	0.000
60	A	61	MET	0	0.016	0.010	19.394	0.140	0.140	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.001	0.004	16.355	-0.112	-0.112	0.000	0.000	0.000	0.000
62	A	63	CYS	0	-0.066	-0.036	18.191	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.969	-0.977	21.098	-12.071	-12.071	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.036	-0.024	18.961	0.214	0.214	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.067	-0.033	15.883	-0.377	-0.377	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.001	0.019	20.217	0.285	0.285	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.088	-0.053	18.482	0.357	0.357	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.943	-0.978	22.648	-11.709	-11.709	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.901	0.953	21.135	12.254	12.254	0.000	0.000	0.000	0.000
70	A	71	LEU	0	0.020	0.013	15.913	-0.358	-0.358	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.020	0.016	15.877	-0.884	-0.884	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.019	-0.023	13.434	-0.336	-0.336	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.025	-0.001	11.266	-2.164	-2.164	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.805	-0.886	7.249	-32.289	-32.289	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.003	-0.005	10.105	-0.525	-0.525	0.000	0.000	0.000	0.000
76	A	77	TYR	0	-0.012	-0.010	5.904	-2.775	-2.775	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.029	0.010	11.824	0.896	0.896	0.000	0.000	0.000	0.000
78	A	79	THR	0	0.036	0.008	15.362	-0.346	-0.346	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.034	-0.011	17.345	0.372	0.372	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.683	-0.804	18.950	-13.613	-13.613	0.000	0.000	0.000	0.000
81	A	82	PRO	0	0.004	0.007	18.453	0.636	0.636	0.000	0.000	0.000	0.000
82	A	83	CYS	0	0.029	0.033	21.331	0.336	0.336	0.000	0.000	0.000	0.000
83	A	84	THR	0	0.023	-0.012	24.581	-0.338	-0.338	0.000	0.000	0.000	0.000
84	A	85	MET	0	-0.024	0.010	26.571	0.062	0.062	0.000	0.000	0.000	0.000
85	A	86	CYS	0	-0.018	-0.013	21.454	0.027	0.027	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.023	0.014	21.640	-0.508	-0.508	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.009	0.006	22.717	-0.208	-0.208	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.010	0.002	22.792	-0.127	-0.127	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.011	0.000	17.404	-0.348	-0.348	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.038	-0.025	19.643	-0.252	-0.252	0.000	0.000	0.000	0.000
91	A	92	PHE	0	-0.053	-0.038	22.015	0.018	0.018	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.037	0.021	19.622	0.151	0.151	0.000	0.000	0.000	0.000
93	A	94	ARG	1	0.855	0.920	19.370	12.298	12.298	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.024	0.028	13.940	-0.619	-0.619	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.839	0.909	7.354	30.665	30.665	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.794	0.891	6.914	29.511	29.511	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.008	0.011	12.206	-0.129	-0.129	0.000	0.000	0.000	0.000
98	A	99	TYR	0	0.006	0.003	7.252	-2.771	-2.771	0.000	0.000	0.000	0.000
99	A	100	TYR	0	-0.014	-0.048	11.992	0.078	0.078	0.000	0.000	0.000	0.000
100	A	101	GLY	0	0.062	0.051	14.903	-0.134	-0.134	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.020	-0.002	16.427	0.450	0.450	0.000	0.000	0.000	0.000
102	A	103	GLN	0	0.033	0.007	19.758	0.033	0.033	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.800	-0.901	22.260	-11.262	-11.262	0.000	0.000	0.000	0.000
104	A	105	PRO	0	0.024	0.000	25.307	0.252	0.252	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.794	0.884	27.908	11.487	11.487	0.000	0.000	0.000	0.000
106	A	107	GLY	0	-0.006	-0.006	28.412	0.341	0.341	0.000	0.000	0.000	0.000
107	A	108	GLY	0	-0.008	0.012	24.764	-0.143	-0.143	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.060	-0.029	24.145	0.496	0.496	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.051	-0.019	18.872	-0.039	-0.039	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.806	-0.878	19.583	-14.647	-14.647	0.000	0.000	0.000	0.000
111	A	112	SER	0	-0.070	-0.050	23.118	0.762	0.762	0.000	0.000	0.000	0.000
112	A	113	GLY	0	0.035	0.010	26.092	-0.063	-0.063	0.000	0.000	0.000	0.000
113	A	114	VAL	0	-0.022	-0.025	28.162	0.131	0.131	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.866	0.955	25.122	11.437	11.437	0.000	0.000	0.000	0.000
115	A	116	PHE	0	0.065	0.035	24.538	0.056	0.056	0.000	0.000	0.000	0.000
116	A	117	PHE	0	0.016	-0.024	19.550	0.204	0.204	0.000	0.000	0.000	0.000
117	A	118	SER	0	-0.074	-0.034	23.616	-0.023	-0.023	0.000	0.000	0.000	0.000
118	A	119	GLN	0	-0.018	-0.008	25.987	0.661	0.661	0.000	0.000	0.000	0.000
119	A	120	PRO	0	0.013	-0.007	28.816	-0.169	-0.169	0.000	0.000	0.000	0.000
120	A	121	THR	0	-0.041	-0.018	31.159	0.030	0.030	0.000	0.000	0.000	0.000
121	A	122	CYS	0	-0.074	-0.003	24.899	-0.252	-0.252	0.000	0.000	0.000	0.000
122	A	123	HIS	0	0.014	0.000	26.879	-0.082	-0.082	0.000	0.000	0.000	0.000
123	A	124	HIS	0	-0.050	-0.029	18.068	0.617	0.617	0.000	0.000	0.000	0.000
124	A	125	ALA	0	0.051	0.037	20.327	0.163	0.163	0.000	0.000	0.000	0.000
125	A	126	PRO	0	-0.045	0.007	14.983	-0.206	-0.206	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.811	-0.899	11.825	-21.716	-21.716	0.000	0.000	0.000	0.000
127	A	128	VAL	0	-0.020	-0.023	13.880	-0.713	-0.713	0.000	0.000	0.000	0.000
128	A	129	TYR	0	-0.055	-0.038	10.446	-0.933	-0.933	0.000	0.000	0.000	0.000
129	A	130	SER	0	-0.026	-0.036	13.204	-0.747	-0.747	0.000	0.000	0.000	0.000
130	A	131	GLY	-1	-0.947	-0.959	14.077	-21.114	-21.114	0.000	0.000	0.000	0.000

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