FMO DATABASE

FMODB ID: RLY38

Calculation Name: 2DID-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DID

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HCM9

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	53
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-217241.68516
FMO2-HF: Nuclear repulsion	197041.136749
FMO2-HF: Total energy	-20200.548411
FMO2-MP2: Total energy	-20256.398666

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.
-77.64	-73.354	1.12	-2.941	-2.464	-0.038

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 : 0.831 / q_NPA : 0.909

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	0.028	0.021	3.481	7.677	8.572	0.006	-0.348	-0.552	-0.001
4	A	4	GLY	0	-0.011	-0.014	2.284	-34.781	-31.489	1.115	-2.581	-1.826	-0.037
5	A	5	SER	0	-0.004	-0.020	4.378	3.973	4.072	-0.001	-0.012	-0.086	0.000
6	A	6	SER	0	-0.010	0.006	7.792	0.588	0.588	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.030	0.037	9.483	0.962	0.962	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.909	-0.950	12.874	-19.367	-19.367	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.021	-0.012	14.148	-1.308	-1.308	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.005	0.001	16.106	0.921	0.921	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.025	-0.013	18.395	-0.039	-0.039	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.035	0.012	20.857	0.056	0.056	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.035	-0.016	21.760	0.345	0.345	0.000	0.000	0.000	0.000
14	A	14	HIS	1	0.817	0.855	24.045	12.053	12.053	0.000	0.000	0.000	0.000
15	A	15	HIS	0	0.003	0.008	19.322	-0.131	-0.131	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.850	-0.930	20.583	-13.520	-13.520	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.013	0.007	19.660	-0.248	-0.248	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.053	-0.030	19.175	0.809	0.809	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.022	0.011	20.941	-0.380	-0.380	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.050	-0.015	23.348	0.491	0.491	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.024	0.014	25.087	-0.508	-0.508	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.096	-0.040	27.281	0.602	0.602	0.000	0.000	0.000	0.000
23	A	23	TYR	0	0.024	0.000	30.205	-0.077	-0.077	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.988	-0.992	32.515	-8.468	-8.468	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.821	-0.924	30.821	-9.753	-9.753	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.034	-0.004	28.762	-0.318	-0.318	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.874	-0.935	24.798	-13.265	-13.265	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.014	-0.001	22.464	0.223	0.223	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.033	-0.018	24.427	0.063	0.063	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.076	-0.090	23.798	-0.195	-0.195	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.048	0.006	24.553	0.514	0.514	0.000	0.000	0.000	0.000
32	A	32	ILE	0	0.030	0.000	27.194	0.459	0.459	0.000	0.000	0.000	0.000
33	A	33	CYS	-1	-0.784	-0.802	27.367	-11.547	-11.547	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.022	0.021	29.840	0.378	0.378	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.034	-0.007	31.859	0.382	0.382	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.023	-0.003	32.325	0.213	0.213	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.014	-0.026	34.164	0.070	0.070	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.046	-0.018	32.111	0.138	0.138	0.000	0.000	0.000	0.000
39	A	39	HIS	0	0.085	0.029	29.918	0.270	0.270	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.922	0.984	34.418	8.000	8.000	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.051	-0.034	37.248	0.151	0.151	0.000	0.000	0.000	0.000
42	A	42	HIS	1	0.835	0.922	33.997	9.298	9.298	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.055	0.027	35.379	0.023	0.023	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.005	0.008	30.189	-0.246	-0.246	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.018	-0.005	29.391	0.303	0.303	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.006	-0.001	27.839	-0.343	-0.343	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.013	-0.001	22.253	0.097	0.097	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.037	-0.028	23.417	-0.597	-0.597	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.021	0.002	25.547	0.453	0.453	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.008	0.007	26.663	-0.355	-0.355	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.084	-0.034	25.757	0.165	0.165	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.025	-0.024	22.143	-0.333	-0.333	0.000	0.000	0.000	0.000
53	A	53	GLY	-1	-0.910	-0.940	24.341	-11.538	-11.538	0.000	0.000	0.000	0.000

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