FMO DATABASE

FMODB ID: VY8G1

Calculation Name: 1IML-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1IML

Chain ID: A

ChEMBL ID:

UniProt ID: P63255

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	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-433193.4114
FMO2-HF: Nuclear repulsion	402063.454472
FMO2-HF: Total energy	-31129.956928
FMO2-MP2: Total energy	-31214.974114

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:PRO)

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

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.
-9.209	-3.592	15.438	-10.479	-10.575	-0.1

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.883 / q_NPA : 0.915

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	CYS	0	-0.058	0.017	3.878	1.290	2.969	-0.021	-0.848	-0.810	-0.001
9	A	9	GLU	-1	-0.837	-0.892	4.315	-47.397	-47.260	-0.001	-0.029	-0.108	0.000
10	A	10	VAL	0	-0.075	-0.024	2.545	3.325	4.355	0.639	-0.448	-1.220	-0.003
11	A	11	TYR	0	0.056	0.022	2.590	-13.271	-11.228	1.151	-1.350	-1.844	-0.016
12	A	12	PHE	0	0.019	-0.003	4.391	-1.786	-1.489	-0.001	-0.031	-0.266	0.000
15	A	15	ARG	1	0.826	0.922	4.680	46.645	46.791	-0.001	-0.010	-0.135	0.000
21	A	21	LYS	1	0.926	0.965	2.987	49.055	49.559	0.040	-0.117	-0.427	0.000
22	A	22	ASP	-1	-0.799	-0.884	1.862	-98.268	-98.460	13.633	-7.628	-5.812	-0.080
23	A	23	TRP	0	0.030	-0.014	4.178	0.827	0.800	-0.001	-0.018	0.047	0.000
4	A	4	PRO	0	0.034	0.020	6.518	2.895	2.895	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.844	0.901	9.527	21.286	21.286	0.000	0.000	0.000	0.000
6	A	6	CYS	0	0.014	0.006	10.552	0.846	0.846	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.836	-0.902	10.121	-24.645	-24.645	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.889	0.933	8.567	26.605	26.605	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.017	0.014	6.114	0.382	0.382	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.861	-0.945	8.248	-23.377	-23.377	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.013	-0.008	6.952	3.996	3.996	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.020	-0.019	6.498	-3.533	-3.533	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.013	-0.025	8.096	3.859	3.859	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.068	0.039	8.892	-2.929	-2.929	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.023	0.028	8.232	-0.296	-0.296	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.040	-0.004	6.500	-1.641	-1.641	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.942	0.970	8.621	23.390	23.390	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.001	0.006	11.606	1.055	1.055	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.036	-0.020	10.790	0.809	0.809	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.021	0.028	10.897	0.727	0.727	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.888	0.930	13.278	16.674	16.674	0.000	0.000	0.000	0.000
30	A	30	CYS	-1	-0.807	-0.716	17.061	-14.043	-14.043	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.822	-0.881	19.083	-15.664	-15.664	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.946	0.935	20.896	11.782	11.782	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.096	-0.124	23.461	0.533	0.533	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.057	0.048	22.162	0.319	0.319	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.972	0.975	22.032	12.049	12.049	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.009	-0.021	16.546	-0.344	-0.344	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.028	0.008	15.992	0.709	0.709	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.014	-0.003	16.890	-0.067	-0.067	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.018	-0.004	14.887	-0.773	-0.773	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.037	0.031	15.461	0.873	0.873	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.013	0.010	17.411	0.859	0.859	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.092	-0.045	13.185	-0.486	-0.486	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.034	0.029	17.277	-0.062	-0.062	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.986	-1.004	13.526	-21.820	-21.820	0.000	0.000	0.000	0.000
45	A	45	HIS	1	0.942	0.988	16.365	16.248	16.248	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.817	-0.923	15.898	-17.038	-17.038	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.042	0.037	14.145	0.849	0.849	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.786	0.880	15.154	16.988	16.988	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.010	0.024	13.237	0.346	0.346	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.039	-0.008	15.856	0.799	0.799	0.000	0.000	0.000	0.000
51	A	51	CYS	0	0.030	-0.045	18.914	-0.454	-0.454	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.013	0.010	20.424	0.423	0.423	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.037	0.030	21.797	0.805	0.805	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.017	0.003	25.353	-0.181	-0.181	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.086	-0.078	23.464	0.213	0.213	0.000	0.000	0.000	0.000
56	A	56	TYR	0	0.061	0.037	20.162	0.047	0.047	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.009	-0.013	23.482	0.190	0.190	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.013	0.015	26.827	0.273	0.273	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.092	-0.042	25.152	0.456	0.456	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.053	-0.038	22.506	-0.071	-0.071	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.074	0.051	25.191	-0.348	-0.348	0.000	0.000	0.000	0.000
62	A	62	PRO	0	-0.066	-0.021	27.996	0.238	0.238	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.990	0.990	31.426	9.937	9.937	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.026	0.007	34.362	0.146	0.146	0.000	0.000	0.000	0.000
65	A	65	PHE	0	-0.027	-0.015	37.993	-0.126	-0.126	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.077	0.029	38.729	-0.065	-0.065	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.888	0.962	38.937	8.017	8.017	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.024	-0.008	37.508	-0.095	-0.095	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.008	-0.009	37.585	0.195	0.195	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.008	0.003	38.799	-0.127	-0.127	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.915	-0.954	38.983	-7.452	-7.452	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.005	0.015	36.762	-0.269	-0.269	0.000	0.000	0.000	0.000
73	A	73	HIS	0	-0.076	-0.042	32.388	0.056	0.056	0.000	0.000	0.000	0.000
74	A	74	THR	0	0.041	0.001	35.299	0.032	0.032	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.045	-0.019	33.167	-0.297	-0.297	0.000	0.000	0.000	0.000
76	A	76	LYS	0	0.070	0.046	32.276	0.668	0.668	0.000	0.000	0.000	0.000

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