FMO DATABASE

FMODB ID: QLNLY

Calculation Name: 2BDS-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BDS

Chain ID: A

ChEMBL ID:

UniProt ID: P11494

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	40
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-188713.853104
FMO2-HF: Nuclear repulsion	170905.747466
FMO2-HF: Total energy	-17808.105638
FMO2-MP2: Total energy	-17855.426951

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:ALA)

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

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.
26.26	26.968	14.76	-7.102	-8.366	-0.104

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.812 / q_NPA : 0.904

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	PRO	0	0.070	0.034	3.876	-6.168	-5.330	-0.009	-0.430	-0.399	0.000
12	A	12	ARG	1	0.755	0.860	2.100	67.284	68.211	1.763	-1.059	-1.630	-0.010
14	A	14	ASP	-1	-0.824	-0.899	1.860	-117.718	-118.375	12.977	-6.910	-5.411	-0.091
15	A	15	LEU	0	0.002	0.001	2.895	9.094	8.223	0.029	1.369	-0.527	-0.003
16	A	16	TRP	0	-0.021	-0.018	3.993	-1.570	-1.178	0.001	-0.068	-0.325	0.000
28	A	28	TYR	0	-0.034	-0.021	4.552	0.416	0.495	-0.001	-0.004	-0.074	0.000
4	A	4	CYS	0	-0.083	-0.020	6.009	3.760	3.760	0.000	0.000	0.000	0.000
5	A	5	PHE	0	0.049	0.034	7.810	-0.427	-0.427	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.075	-0.037	10.552	1.614	1.614	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.016	0.008	12.454	0.592	0.592	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.033	0.022	16.069	-0.097	-0.097	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.880	0.953	12.737	22.310	22.310	0.000	0.000	0.000	0.000
10	A	10	PRO	0	0.063	0.038	13.175	-1.430	-1.430	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.019	0.004	11.367	-1.049	-1.049	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.088	0.038	6.078	4.422	4.422	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.078	0.025	6.785	1.701	1.701	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.029	0.018	9.850	0.120	0.120	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.937	0.967	10.525	23.183	23.183	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.012	0.007	14.020	0.759	0.759	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.000	-0.004	13.460	0.334	0.334	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.046	-0.008	5.799	1.958	1.958	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.004	0.003	9.146	1.647	1.647	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.031	0.014	11.992	-1.097	-1.097	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.042	0.018	14.185	1.034	1.034	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.042	-0.030	8.744	-0.104	-0.104	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.035	0.030	10.545	-2.024	-2.024	0.000	0.000	0.000	0.000
29	A	29	THR	0	0.020	0.005	11.272	1.522	1.522	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.001	0.012	13.271	0.502	0.502	0.000	0.000	0.000	0.000
31	A	31	ASN	0	0.022	-0.014	10.495	-0.887	-0.887	0.000	0.000	0.000	0.000
32	A	33	TYR	0	0.021	0.003	11.034	-1.986	-1.986	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.884	0.938	11.471	22.831	22.831	0.000	0.000	0.000	0.000
34	A	35	TRP	0	0.064	0.045	13.812	-0.593	-0.593	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.003	0.012	15.393	0.361	0.361	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.002	-0.016	10.088	-1.215	-1.215	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.009	0.002	8.506	1.378	1.378	0.000	0.000	0.000	0.000
38	A	41	TYR	0	0.060	0.021	6.545	-3.340	-3.340	0.000	0.000	0.000	0.000
39	A	42	PRO	0	-0.014	-0.019	9.161	0.422	0.422	0.000	0.000	0.000	0.000
40	A	43	HIS	0	0.041	0.028	5.958	-1.279	-1.279	0.000	0.000	0.000	0.000

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