FMO DATABASE

FMODB ID: QLN9Y

Calculation Name: 2DIP-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DIP

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NEG5

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-649716.698662
FMO2-HF: Nuclear repulsion	609055.135735
FMO2-HF: Total energy	-40661.562928
FMO2-MP2: Total energy	-40774.317591

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.
43.789	44.815	-0.014	-0.418	-0.595	-0.001

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 : 0.885 / q_NPA : 0.930

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	SER	0	0.026	0.025	3.847	2.315	3.341	-0.014	-0.418	-0.595	-0.001
4	A	4	GLY	0	0.051	0.009	6.932	0.368	0.368	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.060	-0.024	9.198	1.020	1.020	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.036	0.025	12.721	-0.169	-0.169	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.025	-0.014	14.979	0.114	0.114	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.050	-0.012	18.352	0.412	0.412	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.901	-0.940	20.184	-11.412	-11.412	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.976	-0.984	22.040	-14.115	-14.115	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.036	0.005	24.231	0.663	0.663	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.876	0.935	25.911	11.050	11.050	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.003	0.013	24.910	-0.645	-0.645	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.022	0.009	26.446	0.402	0.402	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.028	0.016	28.324	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.931	0.956	31.155	9.708	9.708	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.015	0.012	32.484	0.333	0.333	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.000	0.001	33.177	-0.259	-0.259	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.005	0.008	31.857	0.099	0.099	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.007	-0.001	33.839	0.181	0.181	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.037	0.013	32.670	-0.304	-0.304	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.879	-0.937	32.044	-9.671	-9.671	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.861	0.921	29.638	10.358	10.358	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.923	-0.966	29.943	-10.205	-10.205	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.876	0.932	24.294	12.294	12.294	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.072	0.053	26.630	-0.073	-0.073	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.846	-0.929	23.314	-14.014	-14.014	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.869	0.914	19.220	14.280	14.280	0.000	0.000	0.000	0.000
29	A	29	HIS	0	-0.068	-0.026	18.670	-2.016	-2.016	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.033	-0.007	19.775	-0.273	-0.273	0.000	0.000	0.000	0.000
31	A	31	GLY	0	-0.043	-0.017	16.227	-0.034	-0.034	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.004	-0.004	13.341	-0.476	-0.476	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.013	0.018	17.813	0.201	0.201	0.000	0.000	0.000	0.000
34	A	34	CYS	0	-0.069	-0.005	20.268	-0.579	-0.579	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.035	-0.012	19.755	0.122	0.122	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.021	-0.026	22.719	0.516	0.516	0.000	0.000	0.000	0.000
37	A	37	CYS	0	0.024	0.018	25.706	0.077	0.077	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.911	0.968	25.322	12.425	12.425	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.000	-0.004	25.638	-0.271	-0.271	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.031	0.000	20.905	-0.651	-0.651	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.004	-0.004	24.168	0.482	0.482	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.004	0.005	19.992	0.243	0.243	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.851	-0.923	22.616	-12.511	-12.511	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.006	0.007	24.112	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.917	0.953	18.497	15.507	15.507	0.000	0.000	0.000	0.000
46	A	46	CYS	0	0.016	0.017	16.265	0.266	0.266	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.017	-0.030	15.915	-1.298	-1.298	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.855	0.935	9.547	29.694	29.694	0.000	0.000	0.000	0.000
49	A	49	CYS	0	-0.007	0.013	14.321	-0.316	-0.316	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.110	-0.086	10.605	-2.055	-2.055	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.750	-0.863	12.550	-18.147	-18.147	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.054	-0.008	15.298	1.463	1.463	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.032	0.013	14.628	-1.603	-1.603	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.943	-0.966	14.833	-17.466	-17.466	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.030	0.025	15.759	1.403	1.403	0.000	0.000	0.000	0.000
56	A	56	HIS	0	-0.017	-0.021	13.035	-1.529	-1.529	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.003	-0.011	17.735	1.111	1.111	0.000	0.000	0.000	0.000
58	A	58	CYS	0	0.025	0.032	19.581	-0.680	-0.680	0.000	0.000	0.000	0.000
59	A	59	GLN	0	0.021	0.000	22.273	-0.258	-0.258	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.843	-0.917	23.681	-10.822	-10.822	0.000	0.000	0.000	0.000
61	A	61	CYS	0	0.013	-0.011	24.379	0.272	0.272	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.046	-0.021	19.398	-0.097	-0.097	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.918	-0.957	23.817	-11.026	-11.026	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.005	0.005	27.102	0.399	0.399	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.008	0.000	24.759	-0.057	-0.057	0.000	0.000	0.000	0.000
66	A	66	CYS	0	0.014	0.025	25.773	-0.270	-0.270	0.000	0.000	0.000	0.000
67	A	67	HIS	1	0.804	0.885	20.563	14.754	14.754	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.016	0.003	20.553	-0.855	-0.855	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.000	0.014	21.797	-0.078	-0.078	0.000	0.000	0.000	0.000
70	A	70	HIS	0	0.016	0.016	18.116	-0.237	-0.237	0.000	0.000	0.000	0.000
71	A	71	THR	0	0.012	-0.010	14.147	0.036	0.036	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.020	0.007	15.028	-1.342	-1.342	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.061	-0.023	10.482	-1.403	-1.403	0.000	0.000	0.000	0.000
74	A	74	PHE	0	0.035	0.018	13.449	0.407	0.407	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.953	0.982	10.738	22.914	22.914	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.862	-0.929	13.808	-16.236	-16.236	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.947	0.976	15.286	15.667	15.667	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.973	0.970	15.102	17.809	17.809	0.000	0.000	0.000	0.000
79	A	79	ASN	0	0.028	0.013	13.660	0.036	0.036	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.025	0.002	12.358	0.548	0.548	0.000	0.000	0.000	0.000
81	A	81	LYS	0	0.013	0.000	5.816	-1.244	-1.244	0.000	0.000	0.000	0.000
82	A	82	TRP	0	-0.030	-0.025	7.382	3.141	3.141	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.882	0.944	9.958	18.830	18.830	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.032	0.003	12.480	-0.424	-0.424	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.026	-0.003	14.062	0.732	0.732	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.894	-0.946	17.619	-14.883	-14.883	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.932	0.973	20.360	14.672	14.672	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.917	0.952	22.841	13.178	13.178	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.043	0.009	25.307	-0.296	-0.296	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.938	-0.943	27.631	-9.386	-9.386	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.881	-0.941	29.418	-10.510	-10.510	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.052	-0.039	32.036	-0.114	-0.114	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.035	-0.032	33.636	0.095	0.095	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.016	0.026	35.717	0.160	0.160	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.010	-0.001	36.643	0.142	0.142	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.067	-0.045	36.742	0.117	0.117	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.068	-0.029	39.755	0.090	0.090	0.000	0.000	0.000	0.000
98	A	98	GLY	-1	-0.912	-0.936	42.865	-6.980	-6.980	0.000	0.000	0.000	0.000

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