FMO DATABASE

FMODB ID: NZ55Q

Calculation Name: 2DNU-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DNU

Chain ID: A

ChEMBL ID:

UniProt ID: Q5TCZ1

Base Structure: SolutionNMR

Registration Date: 2025-10-04

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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-397122.902355
FMO2-HF: Nuclear repulsion	370254.015001
FMO2-HF: Total energy	-26868.887355
FMO2-MP2: Total energy	-26949.184271

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.
-1.178	2.629	0.575	-2.153	-2.228	-0.027

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 : 0.854 / q_NPA : 0.919

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	-0.027	-0.020	2.456	-12.827	-9.219	0.576	-2.115	-2.068	-0.027
4	A	4	GLY	0	0.108	0.081	4.441	4.767	4.966	-0.001	-0.038	-0.160	0.000
5	A	5	SER	0	-0.064	-0.029	8.150	2.555	2.555	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.015	0.008	10.524	2.647	2.647	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.001	-0.006	13.417	-0.861	-0.861	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.927	-0.940	16.703	-14.938	-14.938	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.834	-0.920	20.338	-11.908	-11.908	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.851	0.921	14.458	20.499	20.499	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.040	-0.023	19.401	1.227	1.227	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.022	-0.012	19.651	-0.770	-0.770	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.025	0.003	20.268	0.671	0.671	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.004	-0.008	22.802	0.133	0.133	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.053	-0.036	25.815	0.505	0.505	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.014	0.020	23.807	-0.393	-0.393	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.046	-0.048	23.465	0.675	0.675	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.001	-0.006	23.309	-0.588	-0.588	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.003	0.014	22.111	0.067	0.067	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.003	0.002	24.326	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.015	-0.017	25.187	0.272	0.272	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.934	0.952	19.021	14.928	14.928	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.885	-0.920	20.808	-13.173	-13.173	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.840	-0.899	22.659	-11.831	-11.831	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.054	-0.039	15.619	-0.456	-0.456	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.004	0.017	20.208	0.441	0.441	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.048	-0.037	18.438	-1.033	-1.033	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.846	-0.919	18.548	-15.077	-15.077	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.873	0.942	21.125	10.980	10.980	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.013	0.009	21.744	0.043	0.043	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.021	0.007	16.413	-0.633	-0.633	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.018	-0.023	15.608	0.805	0.805	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.020	-0.012	15.399	-1.199	-1.199	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.808	-0.901	13.854	-19.775	-19.775	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.009	-0.007	16.795	0.082	0.082	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.060	-0.012	16.592	-0.156	-0.156	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.911	0.946	20.429	13.264	13.264	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.887	0.931	24.015	11.994	11.994	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.016	0.016	27.144	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.028	0.012	30.018	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.909	-0.949	32.674	-9.425	-9.425	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.018	-0.016	31.433	-0.131	-0.131	0.000	0.000	0.000	0.000
43	A	43	TRP	0	-0.002	0.020	25.974	-0.501	-0.501	0.000	0.000	0.000	0.000
44	A	44	TRP	0	0.029	-0.016	24.455	-0.086	-0.086	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.027	0.012	18.999	-0.460	-0.460	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.023	0.002	18.442	-0.154	-0.154	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.851	0.903	11.403	21.965	21.965	0.000	0.000	0.000	0.000
48	A	48	TYR	0	0.052	0.010	13.250	-0.188	-0.188	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.001	0.001	10.628	-0.471	-0.471	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.036	-0.012	8.716	-1.117	-1.117	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.922	0.963	9.546	19.428	19.428	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.785	-0.887	13.072	-21.004	-21.004	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.003	0.001	16.194	0.377	0.377	0.000	0.000	0.000	0.000
54	A	54	TRP	0	-0.027	-0.016	19.679	-0.139	-0.139	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.038	0.013	21.918	-0.053	-0.053	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.035	0.033	23.945	0.218	0.218	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.037	-0.001	26.788	-0.164	-0.164	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.006	-0.009	27.821	-0.070	-0.070	0.000	0.000	0.000	0.000
59	A	59	TYR	0	-0.042	-0.014	25.548	0.233	0.233	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.029	-0.013	22.033	-0.616	-0.616	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.944	0.983	24.793	11.936	11.936	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.964	0.989	24.359	11.895	11.895	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.012	0.003	21.738	0.365	0.365	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.904	0.937	23.747	11.019	11.019	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.875	-0.928	20.631	-14.666	-14.666	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.061	-0.037	23.898	0.584	0.584	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.033	0.006	25.062	-0.437	-0.437	0.000	0.000	0.000	0.000
68	A	68	PRO	0	-0.016	-0.013	26.140	0.238	0.238	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.033	-0.004	26.192	0.095	0.095	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.069	-0.032	28.253	0.346	0.346	0.000	0.000	0.000	0.000
71	A	71	GLY	-1	-0.886	-0.933	28.980	-11.074	-11.074	0.000	0.000	0.000	0.000

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