
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.
Apendix: None
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
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. |
1.05 | 3.729 | 0.136 | -0.983 | -1.831 | -0.004 |
Interaction energy analysis for fragmet #1(B:2:ASN)
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]. |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4 | B | 3 | THR | 0 | -0.036 | 0.073 | 4.414 | 1.327 | 1.621 | 0.000 | -0.108 | -0.186 | 0.000 |
5 | B | 4 | ASP | 0 | 0.180 | -0.104 | 3.842 | -2.147 | -0.731 | -0.001 | -0.735 | -0.679 | 0.000 |
6 | B | 4 | ASP | -1 | -0.975 | -0.818 | 5.069 | 1.152 | 1.152 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 5 | GLN | 0 | 0.120 | -0.086 | 3.938 | 0.677 | 0.884 | 0.000 | -0.052 | -0.154 | 0.000 |
8 | B | 5 | GLN | 0 | -0.069 | 0.107 | 3.294 | -2.316 | -2.466 | 0.055 | 0.285 | -0.190 | -0.002 |
9 | B | 6 | GLN | 0 | 0.031 | -0.103 | 4.432 | 0.290 | 0.430 | -0.002 | -0.066 | -0.073 | 0.000 |
10 | B | 6 | GLN | 0 | -0.058 | 0.088 | 2.853 | 1.128 | 1.900 | 0.084 | -0.307 | -0.549 | -0.002 |
11 | B | 7 | LYS | 0 | 0.146 | -0.051 | 6.300 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 7 | LYS | 1 | 0.861 | 1.064 | 8.051 | -0.482 | -0.482 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 8 | VAL | 0 | 0.084 | -0.091 | 8.318 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 8 | VAL | 0 | -0.089 | 0.106 | 8.586 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 9 | SER | 0 | 0.036 | -0.099 | 8.686 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 9 | SER | 0 | -0.067 | 0.051 | 7.745 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 10 | GLU | 0 | 0.102 | -0.095 | 10.256 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 10 | GLU | -1 | -1.038 | -0.850 | 11.152 | -0.251 | -0.251 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 11 | ILE | 0 | 0.091 | -0.090 | 12.339 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 11 | ILE | 0 | -0.090 | 0.097 | 12.586 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 12 | PHE | 0 | 0.051 | -0.105 | 13.285 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 12 | PHE | 0 | -0.080 | 0.083 | 12.886 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 13 | GLN | 0 | 0.041 | -0.108 | 14.322 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 13 | GLN | 0 | -0.056 | 0.104 | 13.803 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 14 | SER | 0 | 0.116 | -0.063 | 16.132 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 14 | SER | 0 | -0.062 | 0.073 | 16.354 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 15 | SER | 0 | 0.067 | -0.050 | 17.822 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 15 | SER | 0 | -0.068 | 0.050 | 18.282 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 16 | LYS | 0 | 0.066 | -0.090 | 18.960 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 16 | LYS | 1 | 0.803 | 1.020 | 16.330 | 0.566 | 0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 17 | GLU | 0 | 0.117 | -0.099 | 20.594 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 17 | GLU | -1 | -1.016 | -0.843 | 21.310 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 18 | LYS | 0 | 0.080 | -0.091 | 22.336 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 18 | LYS | 1 | 0.743 | 0.985 | 23.164 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 19 | LEU | 0 | 0.070 | -0.105 | 23.511 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 19 | LEU | 0 | -0.090 | 0.102 | 21.931 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 20 | GLN | 0 | 0.077 | -0.103 | 24.943 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 20 | GLN | 0 | -0.111 | 0.086 | 23.482 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 21 | GLY | 0 | -0.017 | -0.100 | 26.788 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 22 | ASP | 0 | 0.084 | -0.012 | 28.066 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 22 | ASP | -1 | -0.907 | -0.804 | 27.099 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 23 | ALA | 0 | 0.138 | -0.082 | 29.203 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 23 | ALA | 0 | -0.074 | 0.108 | 29.413 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 24 | LYS | 0 | 0.075 | -0.088 | 31.023 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 24 | LYS | 1 | 0.733 | 0.978 | 32.070 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 25 | VAL | 0 | 0.083 | -0.077 | 32.781 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 25 | VAL | 0 | -0.087 | 0.086 | 32.769 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 26 | VAL | 0 | 0.095 | -0.095 | 33.814 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 26 | VAL | 0 | -0.113 | 0.091 | 33.224 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 27 | SER | 0 | 0.074 | -0.080 | 35.146 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 27 | SER | 0 | -0.037 | 0.069 | 35.468 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 28 | ASP | 0 | 0.025 | -0.121 | 37.039 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 28 | ASP | -1 | -0.932 | -0.807 | 37.194 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 29 | ALA | 0 | 0.087 | -0.088 | 38.565 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 29 | ALA | 0 | -0.084 | 0.099 | 38.942 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 30 | PHE | 0 | 0.004 | -0.114 | 39.710 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 30 | PHE | 0 | -0.070 | 0.077 | 37.266 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 31 | MET | 0 | 0.024 | -0.076 | 41.247 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 31 | MET | 0 | -0.121 | 0.077 | 40.716 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 32 | MET | 0 | -0.075 | -0.159 | 43.067 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 32 | MET | 0 | 0.043 | 0.039 | 43.805 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |