FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 2LR3R

Calculation Name: 1DP5-B-Xray540

Preferred Name: Saccharopepesin

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | beta-d-mannopyranose | alpha-d-mannopyranose

Ligand 3-letter code: NAG | BMA | MAN

Ligand of Interest (LOI):

PDB ID: 1DP5

Chain ID: B

ChEMBL ID: CHEMBL4451

UniProt ID: P07267

Base Structure: X-ray

Registration Date: 2025-07-07

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

DOI:

Apendix: None


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 61
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -98944.031311
FMO2-HF: Nuclear repulsion 86301.205031
FMO2-HF: Total energy -12642.826279
FMO2-MP2: Total energy -12678.104812


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/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.
1.053.7290.136-0.983-1.831-0.004
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 : 0.162 / q_NPA : 0.071
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   
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].
4B3THR0-0.0360.0734.4141.3271.6210.000-0.108-0.1860.000
5B4ASP00.180-0.1043.842-2.147-0.731-0.001-0.735-0.6790.000
6B4ASP-1-0.975-0.8185.0691.1521.1520.0000.0000.0000.000
7B5GLN00.120-0.0863.9380.6770.8840.000-0.052-0.1540.000
8B5GLN0-0.0690.1073.294-2.316-2.4660.0550.285-0.190-0.002
9B6GLN00.031-0.1034.4320.2900.430-0.002-0.066-0.0730.000
10B6GLN0-0.0580.0882.8531.1281.9000.084-0.307-0.549-0.002
11B7LYS00.146-0.0516.3000.2740.2740.0000.0000.0000.000
12B7LYS10.8611.0648.051-0.482-0.4820.0000.0000.0000.000
13B8VAL00.084-0.0918.3180.2170.2170.0000.0000.0000.000
14B8VAL0-0.0890.1068.586-0.006-0.0060.0000.0000.0000.000
15B9SER00.036-0.0998.6860.2540.2540.0000.0000.0000.000
16B9SER0-0.0670.0517.745-0.053-0.0530.0000.0000.0000.000
17B10GLU00.102-0.09510.2560.1110.1110.0000.0000.0000.000
18B10GLU-1-1.038-0.85011.152-0.251-0.2510.0000.0000.0000.000
19B11ILE00.091-0.09012.3390.0990.0990.0000.0000.0000.000
20B11ILE0-0.0900.09712.5860.0120.0120.0000.0000.0000.000
21B12PHE00.051-0.10513.2850.1030.1030.0000.0000.0000.000
22B12PHE0-0.0800.08312.886-0.018-0.0180.0000.0000.0000.000
23B13GLN00.041-0.10814.3220.0590.0590.0000.0000.0000.000
24B13GLN0-0.0560.10413.803-0.017-0.0170.0000.0000.0000.000
25B14SER00.116-0.06316.1320.0340.0340.0000.0000.0000.000
26B14SER0-0.0620.07316.3540.0230.0230.0000.0000.0000.000
27B15SER00.067-0.05017.8220.0500.0500.0000.0000.0000.000
28B15SER0-0.0680.05018.2820.0090.0090.0000.0000.0000.000
29B16LYS00.066-0.09018.9600.0410.0410.0000.0000.0000.000
30B16LYS10.8031.02016.3300.5660.5660.0000.0000.0000.000
31B17GLU00.117-0.09920.5940.0220.0220.0000.0000.0000.000
32B17GLU-1-1.016-0.84321.310-0.241-0.2410.0000.0000.0000.000
33B18LYS00.080-0.09122.3360.0220.0220.0000.0000.0000.000
34B18LYS10.7430.98523.1640.1410.1410.0000.0000.0000.000
35B19LEU00.070-0.10523.5110.0260.0260.0000.0000.0000.000
36B19LEU0-0.0900.10221.931-0.002-0.0020.0000.0000.0000.000
37B20GLN00.077-0.10324.9430.0170.0170.0000.0000.0000.000
38B20GLN0-0.1110.08623.482-0.023-0.0230.0000.0000.0000.000
39B21GLY0-0.017-0.10026.7880.0140.0140.0000.0000.0000.000
40B22ASP00.084-0.01228.0660.0150.0150.0000.0000.0000.000
41B22ASP-1-0.907-0.80427.099-0.145-0.1450.0000.0000.0000.000
42B23ALA00.138-0.08229.2030.0160.0160.0000.0000.0000.000
43B23ALA0-0.0740.10829.413-0.003-0.0030.0000.0000.0000.000
44B24LYS00.075-0.08831.0230.0070.0070.0000.0000.0000.000
45B24LYS10.7330.97832.0700.1050.1050.0000.0000.0000.000
46B25VAL00.083-0.07732.7810.0060.0060.0000.0000.0000.000
47B25VAL0-0.0870.08632.7690.0010.0010.0000.0000.0000.000
48B26VAL00.095-0.09533.8140.0100.0100.0000.0000.0000.000
49B26VAL0-0.1130.09133.2240.0000.0000.0000.0000.0000.000
50B27SER00.074-0.08035.1460.0070.0070.0000.0000.0000.000
51B27SER0-0.0370.06935.468-0.003-0.0030.0000.0000.0000.000
52B28ASP00.025-0.12137.0390.0040.0040.0000.0000.0000.000
53B28ASP-1-0.932-0.80737.194-0.099-0.0990.0000.0000.0000.000
54B29ALA00.087-0.08838.5650.0060.0060.0000.0000.0000.000
55B29ALA0-0.0840.09938.9420.0000.0000.0000.0000.0000.000
56B30PHE00.004-0.11439.7100.0060.0060.0000.0000.0000.000
57B30PHE0-0.0700.07737.266-0.001-0.0010.0000.0000.0000.000
58B31MET00.024-0.07641.2470.0040.0040.0000.0000.0000.000
59B31MET0-0.1210.07740.716-0.001-0.0010.0000.0000.0000.000
60B32MET0-0.075-0.15943.0670.0020.0020.0000.0000.0000.000
61B32MET00.0430.03943.8050.0010.0010.0000.0000.0000.000