FMO DATABASE

FMODB ID: VY8Z1

Calculation Name: 1HDL-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HDL

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NQ38

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	-290591.765763
FMO2-HF: Nuclear repulsion	266156.254468
FMO2-HF: Total energy	-24435.511295
FMO2-MP2: Total energy	-24500.371625

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:LYS)

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

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.
-169.918	-163.044	1.408	-4.181	-4.101	-0.044

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.799 / q_NPA : 1.885

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	GLU	-1	-0.898	-0.954	3.653	-68.503	-67.192	-0.001	-0.587	-0.723	0.000
5	A	5	GLN	0	-0.093	-0.043	3.240	6.608	7.048	0.007	-0.094	-0.353	-0.001
6	A	6	GLU	-1	-0.929	-0.972	2.370	-136.122	-131.101	1.403	-3.492	-2.932	-0.043
9	A	9	HIS	0	0.088	0.041	3.966	10.453	10.555	-0.001	-0.008	-0.093	0.000
4	A	4	ASP	-1	-0.895	-0.954	6.037	-55.362	-55.362	0.000	0.000	0.000	0.000
7	A	7	MET	0	0.009	0.016	5.615	2.593	2.593	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.093	-0.040	8.320	3.518	3.518	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.906	-0.954	8.318	-38.119	-38.119	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.001	-0.025	11.873	2.178	2.178	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.028	0.030	8.152	3.552	3.552	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.013	0.003	12.255	1.988	1.988	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.030	-0.029	14.983	2.310	2.310	0.000	0.000	0.000	0.000
15	A	15	MET	0	0.018	0.024	12.494	1.293	1.293	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.915	0.959	17.226	24.424	24.424	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.025	-0.032	19.295	1.524	1.524	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.117	0.071	17.668	0.681	0.681	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.900	0.962	18.712	24.446	24.446	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.029	0.015	15.820	0.312	0.312	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.073	-0.029	18.866	1.432	1.432	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.037	0.010	15.582	-0.451	-0.451	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.072	-0.034	20.408	0.087	0.087	0.000	0.000	0.000	0.000
24	A	24	GLN	0	0.047	0.024	21.016	0.625	0.625	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.822	-0.903	23.453	-20.592	-20.592	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.971	0.974	22.674	23.517	23.517	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.894	0.937	25.124	20.376	20.376	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.038	0.016	21.801	0.456	0.456	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.014	0.004	24.648	-0.364	-0.364	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.047	-0.017	25.859	0.558	0.558	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.005	0.000	24.579	0.397	0.397	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.024	0.025	20.484	-0.402	-0.402	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.824	-0.918	18.797	-29.544	-29.544	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.011	0.003	18.969	-1.242	-1.242	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.025	-0.010	21.383	-0.164	-0.164	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.002	0.000	16.001	0.087	0.087	0.000	0.000	0.000	0.000
37	A	37	PHE	0	0.023	0.014	16.538	-0.668	-0.668	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.032	-0.025	17.603	-0.294	-0.294	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.006	-0.009	19.008	0.904	0.904	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.917	0.976	9.036	50.697	50.697	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.026	-0.027	17.823	-0.191	-0.191	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.001	-0.005	15.073	0.544	0.544	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.895	0.917	14.742	24.907	24.907	0.000	0.000	0.000	0.000
44	A	46	MET	0	0.020	0.033	16.166	1.031	1.031	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.017	-0.006	11.497	0.376	0.376	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.067	0.031	14.016	0.141	0.141	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.880	-0.933	16.262	-25.264	-25.264	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.779	0.865	15.949	31.709	31.709	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.870	-0.934	13.575	-38.603	-38.603	0.000	0.000	0.000	0.000
50	A	52	ALA	0	0.006	0.003	17.282	0.767	0.767	0.000	0.000	0.000	0.000
51	A	53	LYS	1	0.873	0.940	20.184	26.875	26.875	0.000	0.000	0.000	0.000
52	A	54	SER	0	-0.068	-0.027	18.090	0.025	0.025	0.000	0.000	0.000	0.000
53	A	55	GLN	-1	-0.954	-0.958	19.163	-25.424	-25.424	0.000	0.000	0.000	0.000

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