FMO DATABASE

FMODB ID: 9GLV2

Calculation Name: 1DP5-B-Xray372

Preferred Name: Saccharopepesin

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 1DP5

Chain ID: B

ChEMBL ID: CHEMBL4451

UniProt ID: P07267

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	31
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-98950.487598
FMO2-HF: Nuclear repulsion	86301.205031
FMO2-HF: Total energy	-12649.282567
FMO2-MP2: Total energy	-12684.731876

3D Structure

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:2:ASN)

Summations of interaction energy for fragment #1(B:2:ASN)

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.
-28.982	-29.842	18.391	-7.599	-9.932	-0.008

Interaction energy analysis for fragmet #1(B:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : -0.002

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	B	4	ASP	-1	-0.846	-0.913	3.842	-2.434	-0.510	-0.009	-0.841	-1.074	0.000
4	B	5	GLN	0	0.023	0.015	1.855	-15.704	-16.885	9.545	-3.770	-4.594	-0.037
5	B	6	GLN	0	-0.030	-0.008	1.871	-10.588	-12.343	8.856	-2.978	-4.123	0.029
6	B	7	LYS	1	1.001	1.007	5.362	-2.246	-2.094	-0.001	-0.010	-0.141	0.000
7	B	8	VAL	0	-0.001	0.008	7.740	0.021	0.021	0.000	0.000	0.000	0.000
8	B	9	SER	0	-0.032	-0.025	6.089	-0.063	-0.063	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.944	-0.972	8.553	1.006	1.006	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.016	0.015	10.806	0.045	0.045	0.000	0.000	0.000	0.000
11	B	12	PHE	0	-0.013	-0.021	11.093	0.008	0.008	0.000	0.000	0.000	0.000
12	B	13	GLN	0	-0.022	-0.008	11.404	-0.088	-0.088	0.000	0.000	0.000	0.000
13	B	14	SER	0	0.047	0.013	13.962	0.038	0.038	0.000	0.000	0.000	0.000
14	B	15	SER	0	-0.012	-0.002	16.262	0.055	0.055	0.000	0.000	0.000	0.000
15	B	16	LYS	1	0.883	0.937	13.772	0.921	0.921	0.000	0.000	0.000	0.000
16	B	17	GLU	-1	-0.920	-0.948	18.479	-0.056	-0.056	0.000	0.000	0.000	0.000
17	B	18	LYS	1	0.831	0.896	20.435	0.195	0.195	0.000	0.000	0.000	0.000
18	B	19	LEU	0	0.007	0.005	20.305	0.014	0.014	0.000	0.000	0.000	0.000
19	B	20	GLN	0	-0.034	-0.019	21.015	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	21	GLY	0	0.013	0.018	24.698	0.021	0.021	0.000	0.000	0.000	0.000
21	B	22	ASP	-1	-0.825	-0.912	25.663	-0.174	-0.174	0.000	0.000	0.000	0.000
22	B	23	ALA	0	-0.002	-0.006	27.322	0.011	0.011	0.000	0.000	0.000	0.000
23	B	24	LYS	1	0.814	0.898	29.076	0.114	0.114	0.000	0.000	0.000	0.000
24	B	25	VAL	0	0.018	0.011	30.859	0.011	0.011	0.000	0.000	0.000	0.000
25	B	26	VAL	0	-0.012	-0.006	31.664	0.008	0.008	0.000	0.000	0.000	0.000
26	B	27	SER	0	0.009	0.002	33.190	0.003	0.003	0.000	0.000	0.000	0.000
27	B	28	ASP	-1	-0.860	-0.920	35.021	-0.098	-0.098	0.000	0.000	0.000	0.000
28	B	29	ALA	0	-0.036	-0.014	36.712	0.008	0.008	0.000	0.000	0.000	0.000
29	B	30	PHE	0	-0.026	-0.020	35.479	0.001	0.001	0.000	0.000	0.000	0.000
30	B	31	MET	0	-0.063	-0.012	38.554	0.001	0.001	0.000	0.000	0.000	0.000
31	B	32	MET	0	-0.045	-0.014	40.968	0.009	0.009	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:2:ASN)