FMO DATABASE

FMODB ID: LRLL9

Calculation Name: 2AD6-B-Xray547

Preferred Name:

Target Type:

Ligand Name: pyrroloquinoline quinone

Ligand 3-letter code: PQQ

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2AD6

Chain ID: B

ChEMBL ID:

UniProt ID: P38539

Base Structure: X-ray

Registration Date: 2025-10-06

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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-304387.437908
FMO2-HF: Nuclear repulsion	276761.994939
FMO2-HF: Total energy	-27625.442969
FMO2-MP2: Total energy	-27704.572583

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(B:1:TYR)

Summations of interaction energy for fragment #1(B:1:TYR)

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.
-58.414	-40.752	19.193	-16.265	-20.589	-0.096

Interaction energy analysis for fragmet #1(B:1:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.790 / q_NPA : 0.884

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	B	3	GLY	0	-0.029	0.002	2.862	9.412	13.274	0.288	-1.712	-2.438	0.001
4	B	4	GLN	0	-0.033	-0.024	4.016	9.007	9.282	0.012	0.007	-0.294	0.000
5	B	5	ASN	0	-0.052	-0.024	4.730	11.282	11.383	-0.001	-0.013	-0.087	0.000
6	B	6	CYS	0	-0.035	-0.029	4.639	-1.125	-0.844	-0.002	-0.048	-0.231	0.000
12	B	13	TRP	0	-0.019	0.003	2.152	-15.952	-11.946	2.730	-2.871	-3.864	-0.016
13	B	14	GLU	-1	-0.828	-0.922	2.096	-117.964	-114.108	15.436	-9.534	-9.758	-0.082
14	B	15	ASN	0	-0.020	-0.003	3.434	-1.586	-0.303	0.270	-0.404	-1.149	-0.004
15	B	16	LYS	1	0.951	0.975	2.780	23.044	26.896	0.461	-1.669	-2.643	0.005
16	B	17	PRO	0	0.051	0.018	4.232	4.292	4.438	-0.001	-0.021	-0.125	0.000
7	B	7	LYS	1	0.938	0.986	7.120	33.507	33.507	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.845	-0.914	9.756	-18.670	-18.670	0.000	0.000	0.000	0.000
9	B	9	PRO	0	-0.008	-0.020	10.166	-1.607	-1.607	0.000	0.000	0.000	0.000
10	B	10	GLY	0	0.026	0.023	9.778	1.020	1.020	0.000	0.000	0.000	0.000
11	B	11	ASN	0	-0.098	-0.052	7.530	-2.605	-2.605	0.000	0.000	0.000	0.000
17	B	18	GLY	0	0.032	0.009	7.141	2.295	2.295	0.000	0.000	0.000	0.000
18	B	19	TYR	0	-0.074	-0.030	7.464	2.751	2.751	0.000	0.000	0.000	0.000
19	B	20	PRO	0	-0.001	0.008	8.701	-1.965	-1.965	0.000	0.000	0.000	0.000
20	B	21	GLU	-1	-0.910	-0.964	8.588	-27.944	-27.944	0.000	0.000	0.000	0.000
21	B	22	LYS	1	0.941	0.965	9.727	19.334	19.334	0.000	0.000	0.000	0.000
22	B	23	ILE	0	0.033	0.019	12.119	0.220	0.220	0.000	0.000	0.000	0.000
23	B	24	ALA	0	0.035	0.038	14.472	0.744	0.744	0.000	0.000	0.000	0.000
24	B	25	GLY	0	0.006	0.001	17.811	-0.325	-0.325	0.000	0.000	0.000	0.000
25	B	26	SER	0	-0.048	-0.034	15.612	-0.331	-0.331	0.000	0.000	0.000	0.000
26	B	27	LYS	1	0.917	0.946	14.822	19.167	19.167	0.000	0.000	0.000	0.000
27	B	28	TYR	0	-0.003	-0.018	12.855	-0.219	-0.219	0.000	0.000	0.000	0.000
28	B	29	ASP	-1	-0.828	-0.903	15.839	-14.593	-14.593	0.000	0.000	0.000	0.000
29	B	30	PRO	0	-0.035	-0.017	16.321	0.486	0.486	0.000	0.000	0.000	0.000
30	B	31	LYS	1	0.906	0.950	18.854	13.061	13.061	0.000	0.000	0.000	0.000
31	B	32	HIS	0	0.022	0.018	16.854	0.811	0.811	0.000	0.000	0.000	0.000
32	B	33	ASP	-1	-0.791	-0.894	22.094	-9.874	-9.874	0.000	0.000	0.000	0.000
33	B	34	PRO	0	-0.003	-0.015	24.910	-0.059	-0.059	0.000	0.000	0.000	0.000
34	B	35	VAL	0	-0.010	-0.001	25.925	0.097	0.097	0.000	0.000	0.000	0.000
35	B	36	GLU	-1	-0.923	-0.977	25.616	-9.430	-9.430	0.000	0.000	0.000	0.000
36	B	37	LEU	0	-0.042	-0.021	20.231	-0.076	-0.076	0.000	0.000	0.000	0.000
37	B	38	ASN	0	0.024	0.011	23.826	-0.306	-0.306	0.000	0.000	0.000	0.000
38	B	39	LYS	1	0.889	0.960	26.368	9.300	9.300	0.000	0.000	0.000	0.000
39	B	40	GLN	0	-0.020	-0.013	21.118	0.291	0.291	0.000	0.000	0.000	0.000
40	B	41	GLU	-1	-0.904	-0.939	26.385	-9.511	-9.511	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.830	-0.912	27.828	-8.082	-8.082	0.000	0.000	0.000	0.000
42	B	43	SER	0	-0.052	-0.026	29.573	0.383	0.383	0.000	0.000	0.000	0.000
43	B	44	ILE	0	0.013	0.008	26.238	0.240	0.240	0.000	0.000	0.000	0.000
44	B	45	LYS	1	0.919	0.960	30.665	8.375	8.375	0.000	0.000	0.000	0.000
45	B	46	ALA	0	-0.020	-0.018	33.167	0.265	0.265	0.000	0.000	0.000	0.000
46	B	47	MET	0	-0.079	-0.044	30.697	0.270	0.270	0.000	0.000	0.000	0.000
47	B	48	ASP	-1	-0.853	-0.934	32.274	-8.067	-8.067	0.000	0.000	0.000	0.000
48	B	49	ALA	0	-0.033	-0.010	35.522	0.205	0.205	0.000	0.000	0.000	0.000
49	B	50	ARG	1	0.914	0.961	35.201	7.646	7.646	0.000	0.000	0.000	0.000
50	B	51	ASN	0	0.012	0.001	35.164	0.303	0.303	0.000	0.000	0.000	0.000
51	B	52	ALA	0	0.027	0.011	39.019	0.135	0.135	0.000	0.000	0.000	0.000
52	B	53	LYS	1	0.865	0.943	40.589	6.196	6.196	0.000	0.000	0.000	0.000
53	B	54	ARG	1	0.852	0.933	38.849	6.933	6.933	0.000	0.000	0.000	0.000
54	B	55	ILE	0	0.009	0.010	40.486	0.134	0.134	0.000	0.000	0.000	0.000
55	B	56	ALA	0	-0.001	0.004	43.765	0.126	0.126	0.000	0.000	0.000	0.000
56	B	57	ASN	0	0.004	-0.001	46.394	0.063	0.063	0.000	0.000	0.000	0.000
57	B	58	ALA	0	0.028	0.034	46.352	0.115	0.115	0.000	0.000	0.000	0.000
58	B	59	LYS	1	0.924	0.961	47.065	6.077	6.077	0.000	0.000	0.000	0.000
59	B	60	SER	0	-0.073	-0.057	49.162	0.101	0.101	0.000	0.000	0.000	0.000
60	B	61	SER	0	-0.018	-0.015	51.476	0.107	0.107	0.000	0.000	0.000	0.000
61	B	62	GLY	0	0.008	0.021	52.044	0.093	0.093	0.000	0.000	0.000	0.000
62	B	63	ASN	0	-0.035	-0.026	51.410	0.019	0.019	0.000	0.000	0.000	0.000
63	B	64	PHE	0	0.008	-0.004	42.006	-0.056	-0.056	0.000	0.000	0.000	0.000
64	B	65	VAL	0	0.018	0.008	47.267	0.053	0.053	0.000	0.000	0.000	0.000
65	B	66	PHE	0	0.009	0.005	39.104	-0.117	-0.117	0.000	0.000	0.000	0.000
66	B	67	ASP	-1	-0.884	-0.942	44.148	-6.362	-6.362	0.000	0.000	0.000	0.000
67	B	68	VAL	0	-0.004	0.007	45.915	0.136	0.136	0.000	0.000	0.000	0.000
68	B	69	LYS	0	0.063	0.033	45.896	0.316	0.316	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:TYR)