FMO DATABASE

FMODB ID: 9L232

Calculation Name: 1IYM-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1IYM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9LRB7

Base Structure: SolutionNMR

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	55
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-260660.394501
FMO2-HF: Nuclear repulsion	237780.84716
FMO2-HF: Total energy	-22879.547341
FMO2-MP2: Total energy	-22939.451084

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:127:ALA)

Summations of interaction energy for fragment #1(A:127: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.
-308.316	-303.177	11.841	-9.991	-6.988	-0.12

Interaction energy analysis for fragmet #1(A:127:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.756 / q_NPA : 0.863

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	129	ASP	-1	-0.847	-0.905	1.760	-121.992	-118.860	11.770	-8.958	-5.943	-0.111
4	A	130	ASP	-1	-0.969	-0.993	4.533	-24.743	-24.538	-0.001	-0.031	-0.173	0.000
14	A	140	GLU	-1	-0.911	-0.971	3.166	-60.670	-58.868	0.072	-1.002	-0.872	-0.009
5	A	131	GLY	0	-0.009	0.006	8.122	1.563	1.563	0.000	0.000	0.000	0.000
6	A	132	VAL	0	-0.073	-0.032	9.206	3.473	3.473	0.000	0.000	0.000	0.000
7	A	133	GLU	-1	-0.824	-0.918	8.164	-34.098	-34.098	0.000	0.000	0.000	0.000
8	A	134	CYS	-1	-0.774	-0.768	10.683	-16.924	-16.924	0.000	0.000	0.000	0.000
9	A	135	ALA	0	-0.034	-0.027	13.630	-0.152	-0.152	0.000	0.000	0.000	0.000
10	A	136	VAL	0	-0.080	-0.031	15.819	0.844	0.844	0.000	0.000	0.000	0.000
11	A	137	CYS	0	-0.035	-0.057	14.411	0.126	0.126	0.000	0.000	0.000	0.000
12	A	138	LEU	0	-0.073	-0.036	11.495	-0.428	-0.428	0.000	0.000	0.000	0.000
13	A	139	ALA	0	0.023	0.018	9.437	-2.563	-2.563	0.000	0.000	0.000	0.000
15	A	141	LEU	0	-0.080	-0.040	7.849	2.529	2.529	0.000	0.000	0.000	0.000
16	A	142	GLU	-1	-0.928	-0.957	8.853	-29.420	-29.420	0.000	0.000	0.000	0.000
17	A	143	ASP	-1	-0.953	-0.984	11.473	-18.353	-18.353	0.000	0.000	0.000	0.000
18	A	144	GLY	0	-0.064	-0.036	14.412	0.100	0.100	0.000	0.000	0.000	0.000
19	A	145	GLU	-1	-0.842	-0.895	13.214	-20.166	-20.166	0.000	0.000	0.000	0.000
20	A	146	GLU	-1	-0.950	-0.982	17.256	-12.895	-12.895	0.000	0.000	0.000	0.000
21	A	147	ALA	0	0.002	0.001	15.809	0.127	0.127	0.000	0.000	0.000	0.000
22	A	148	ARG	1	0.821	0.911	17.906	13.281	13.281	0.000	0.000	0.000	0.000
23	A	149	PHE	0	0.050	0.027	15.520	-0.338	-0.338	0.000	0.000	0.000	0.000
24	A	150	LEU	0	0.006	0.001	20.591	0.852	0.852	0.000	0.000	0.000	0.000
25	A	151	PRO	0	0.034	0.009	23.407	-0.279	-0.279	0.000	0.000	0.000	0.000
26	A	152	ARG	1	0.881	0.937	25.997	10.390	10.390	0.000	0.000	0.000	0.000
27	A	153	CYS	0	-0.059	-0.025	21.708	0.016	0.016	0.000	0.000	0.000	0.000
28	A	154	GLY	0	0.027	0.028	20.402	-0.320	-0.320	0.000	0.000	0.000	0.000
29	A	155	HIS	0	0.009	-0.011	17.310	-0.937	-0.937	0.000	0.000	0.000	0.000
30	A	156	GLY	0	0.042	0.011	16.062	1.013	1.013	0.000	0.000	0.000	0.000
31	A	157	PHE	0	0.032	-0.004	15.345	-0.775	-0.775	0.000	0.000	0.000	0.000
32	A	158	HIS	1	0.852	0.845	12.503	21.260	21.260	0.000	0.000	0.000	0.000
33	A	159	ALA	0	-0.010	0.006	17.538	0.557	0.557	0.000	0.000	0.000	0.000
34	A	160	GLU	-1	-0.869	-0.941	19.498	-14.807	-14.807	0.000	0.000	0.000	0.000
35	A	161	CYS	0	-0.031	-0.030	16.514	0.564	0.564	0.000	0.000	0.000	0.000
36	A	162	VAL	0	-0.003	0.003	20.043	0.308	0.308	0.000	0.000	0.000	0.000
37	A	163	ASP	-1	-0.832	-0.925	21.777	-11.537	-11.537	0.000	0.000	0.000	0.000
38	A	164	MET	0	-0.076	-0.050	23.051	0.416	0.416	0.000	0.000	0.000	0.000
39	A	165	TRP	0	-0.014	0.005	21.822	0.141	0.141	0.000	0.000	0.000	0.000
40	A	166	LEU	0	-0.034	0.003	24.112	0.416	0.416	0.000	0.000	0.000	0.000
41	A	167	GLY	0	0.043	0.030	27.096	0.223	0.223	0.000	0.000	0.000	0.000
42	A	168	SER	0	-0.104	-0.076	29.717	0.466	0.466	0.000	0.000	0.000	0.000
43	A	169	HIS	0	-0.025	0.002	27.962	0.375	0.375	0.000	0.000	0.000	0.000
44	A	170	SER	0	0.024	0.017	28.292	-0.369	-0.369	0.000	0.000	0.000	0.000
45	A	171	THR	0	-0.078	-0.052	27.332	-0.036	-0.036	0.000	0.000	0.000	0.000
46	A	172	CYS	0	-0.019	0.009	21.676	-0.488	-0.488	0.000	0.000	0.000	0.000
47	A	173	PRO	0	0.015	0.021	19.646	0.237	0.237	0.000	0.000	0.000	0.000
48	A	174	LEU	0	0.038	0.031	16.141	0.280	0.280	0.000	0.000	0.000	0.000
49	A	175	CYS	0	-0.070	-0.026	19.997	0.228	0.228	0.000	0.000	0.000	0.000
50	A	176	ARG	1	0.949	0.972	23.195	12.575	12.575	0.000	0.000	0.000	0.000
51	A	177	LEU	0	-0.017	-0.015	24.525	0.581	0.581	0.000	0.000	0.000	0.000
52	A	178	THR	0	-0.030	-0.027	26.583	-0.320	-0.320	0.000	0.000	0.000	0.000
53	A	179	VAL	0	0.012	-0.001	26.273	-0.046	-0.046	0.000	0.000	0.000	0.000
54	A	180	VAL	0	-0.026	-0.002	28.708	0.126	0.126	0.000	0.000	0.000	0.000
55	A	181	VAL	-1	-0.919	-0.952	32.525	-8.727	-8.727	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:127:ALA)