FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: LQ889
Calculation Name: 2DNH-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2DNH
Chain ID: A
UniProt ID: Q8N6W0
Base Structure: SolutionNMR
Registration Date: 2025-10-04
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
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 | 105 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -651343.53548 |
|---|---|
| FMO2-HF: Nuclear repulsion | 612371.217885 |
| FMO2-HF: Total energy | -38972.317596 |
| FMO2-MP2: Total energy | -39083.893805 |
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(A:119:GLY)
Summations of interaction energy for
fragment #1(A:119:GLY)
| 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. |
| -17.047 | -16.359 | -0.005 | -0.175 | -0.508 | 0 |
Interaction energy analysis for fragmet #1(A:119:GLY)
| 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 | 121 | SER | 0 | 0.026 | 0.028 | 3.821 | 1.895 | 2.583 | -0.005 | -0.175 | -0.508 | 0.000 |
| 4 | A | 122 | GLY | 0 | 0.029 | 0.017 | 6.368 | 4.480 | 4.480 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 123 | SER | 0 | -0.031 | -0.018 | 7.996 | -2.415 | -2.415 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 124 | SER | 0 | -0.022 | -0.029 | 10.539 | 1.725 | 1.725 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 125 | GLY | 0 | 0.003 | 0.002 | 14.028 | -0.764 | -0.764 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 126 | SER | 0 | 0.007 | 0.009 | 16.673 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 127 | GLU | -1 | -0.915 | -0.941 | 20.108 | -14.957 | -14.957 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 128 | SER | 0 | 0.011 | 0.012 | 22.270 | 0.483 | 0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 129 | ARG | 1 | 0.895 | 0.937 | 25.426 | 11.155 | 11.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 130 | GLY | 0 | 0.094 | 0.041 | 28.228 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 131 | GLY | 0 | -0.019 | 0.009 | 27.018 | 0.325 | 0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 132 | ARG | 1 | 0.940 | 0.957 | 19.490 | 14.514 | 14.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 133 | ASP | -1 | -0.757 | -0.877 | 25.942 | -10.216 | -10.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 134 | ARG | 1 | 0.835 | 0.922 | 25.868 | 11.280 | 11.280 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 135 | LYS | 1 | 0.869 | 0.942 | 27.528 | 9.846 | 9.846 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 136 | LEU | 0 | -0.020 | -0.002 | 25.622 | -0.305 | -0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 137 | PHE | 0 | -0.020 | -0.017 | 29.407 | 0.437 | 0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 138 | VAL | 0 | 0.032 | 0.012 | 30.603 | -0.321 | -0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 139 | GLY | 0 | 0.031 | 0.002 | 32.904 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 140 | MET | 0 | -0.015 | -0.001 | 34.582 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 141 | LEU | 0 | 0.008 | 0.019 | 35.999 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 142 | ASN | 0 | 0.015 | 0.001 | 38.695 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 143 | LYS | 1 | 0.932 | 0.943 | 42.394 | 6.451 | 6.451 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 144 | GLN | 0 | -0.043 | -0.022 | 44.429 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 145 | GLN | 0 | 0.012 | 0.020 | 37.586 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 146 | SER | 0 | -0.034 | -0.041 | 42.370 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 147 | GLU | -1 | -0.852 | -0.961 | 39.560 | -7.765 | -7.765 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 148 | GLU | -1 | -0.913 | -0.955 | 38.810 | -7.607 | -7.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 149 | ASP | -1 | -0.857 | -0.893 | 39.031 | -7.809 | -7.809 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 150 | VAL | 0 | 0.014 | 0.008 | 34.269 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 151 | LEU | 0 | 0.024 | 0.003 | 34.604 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 152 | ARG | 1 | 0.901 | 0.944 | 34.723 | 7.766 | 7.766 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 153 | LEU | 0 | -0.019 | 0.001 | 32.277 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 154 | PHE | 0 | 0.014 | -0.018 | 30.185 | -0.374 | -0.374 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 155 | GLN | 0 | -0.001 | 0.004 | 29.757 | -0.450 | -0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 156 | PRO | 0 | -0.067 | -0.032 | 30.258 | -0.206 | -0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 157 | PHE | 0 | -0.034 | -0.014 | 25.111 | -0.373 | -0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 158 | GLY | 0 | 0.049 | 0.029 | 25.488 | -0.570 | -0.570 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 159 | VAL | 0 | -0.030 | -0.017 | 27.653 | 0.428 | 0.428 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 160 | ILE | 0 | -0.060 | -0.034 | 29.957 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 161 | ASP | -1 | -0.848 | -0.910 | 31.989 | -9.950 | -9.950 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 162 | GLU | -1 | -0.928 | -0.967 | 33.989 | -8.248 | -8.248 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 163 | CYS | 0 | -0.071 | -0.027 | 34.660 | -0.310 | -0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 164 | THR | 0 | 0.025 | 0.025 | 36.887 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 165 | VAL | 0 | 0.017 | 0.009 | 38.316 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 166 | LEU | 0 | -0.035 | -0.010 | 37.826 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 167 | ARG | 1 | 0.940 | 0.963 | 41.634 | 6.907 | 6.907 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 168 | GLY | 0 | -0.031 | -0.010 | 45.227 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 169 | PRO | 0 | 0.000 | -0.001 | 47.774 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 170 | ASP | -1 | -0.881 | -0.943 | 51.158 | -5.943 | -5.943 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 171 | GLY | 0 | 0.018 | 0.018 | 50.166 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 172 | SER | 0 | -0.042 | -0.024 | 48.468 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 173 | SER | 0 | -0.001 | -0.005 | 42.813 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 174 | LYS | 1 | 0.932 | 0.951 | 41.659 | 7.278 | 7.278 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 175 | GLY | 0 | 0.063 | 0.049 | 40.658 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 176 | CYS | 0 | -0.091 | -0.043 | 37.102 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 177 | ALA | 0 | 0.003 | 0.005 | 36.134 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 178 | PHE | 0 | -0.009 | -0.010 | 33.250 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 179 | VAL | 0 | 0.035 | 0.017 | 31.328 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 180 | LYS | 1 | 0.838 | 0.910 | 30.675 | 9.794 | 9.794 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 181 | PHE | 0 | 0.046 | 0.023 | 27.211 | 0.157 | 0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 182 | SER | 0 | 0.064 | 0.051 | 28.485 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 183 | SER | 0 | -0.048 | -0.039 | 23.004 | -0.371 | -0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 184 | HIS | 0 | 0.022 | -0.007 | 19.598 | -0.382 | -0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 185 | THR | 0 | -0.001 | -0.001 | 18.170 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 186 | GLU | -1 | -0.837 | -0.908 | 20.562 | -13.094 | -13.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 187 | ALA | 0 | 0.000 | 0.004 | 23.812 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 188 | GLN | 0 | 0.038 | 0.005 | 17.457 | 0.616 | 0.616 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 189 | ALA | 0 | 0.006 | 0.019 | 21.186 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 190 | ALA | 0 | 0.029 | 0.008 | 21.951 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 191 | ILE | 0 | -0.029 | -0.013 | 22.808 | 0.380 | 0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 192 | HIS | 0 | -0.099 | -0.069 | 19.378 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 193 | ALA | 0 | 0.000 | 0.027 | 22.304 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 194 | LEU | 0 | -0.015 | -0.001 | 24.866 | 0.465 | 0.465 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 195 | HIS | 0 | -0.001 | -0.003 | 23.874 | 0.739 | 0.739 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 196 | GLY | 0 | -0.012 | -0.009 | 26.706 | -0.240 | -0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 197 | SER | 0 | -0.050 | -0.028 | 27.473 | 0.375 | 0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 198 | GLN | 0 | 0.037 | 0.017 | 29.461 | 0.340 | 0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 199 | THR | 0 | 0.012 | 0.004 | 33.099 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 200 | MET | 0 | -0.010 | 0.021 | 35.100 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 201 | PRO | 0 | 0.023 | -0.006 | 38.726 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 202 | GLY | 0 | -0.017 | -0.011 | 42.383 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 203 | ALA | 0 | -0.013 | 0.007 | 39.239 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 204 | SER | 0 | -0.002 | -0.007 | 40.067 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 205 | SER | 0 | -0.029 | -0.016 | 35.574 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 206 | SER | 0 | -0.003 | -0.011 | 31.602 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 207 | LEU | 0 | -0.032 | -0.011 | 31.300 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 208 | VAL | 0 | -0.019 | -0.005 | 30.008 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 209 | VAL | 0 | 0.009 | 0.007 | 27.365 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 210 | LYS | 1 | 0.966 | 0.988 | 25.872 | 9.861 | 9.861 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 211 | PHE | 0 | 0.058 | 0.023 | 21.402 | 0.383 | 0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 212 | ALA | 0 | -0.039 | -0.014 | 26.862 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 213 | ASP | -1 | -0.893 | -0.968 | 29.123 | -9.775 | -9.775 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 214 | THR | 0 | -0.082 | -0.049 | 25.619 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 215 | ASP | -1 | -0.892 | -0.942 | 24.710 | -12.228 | -12.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 216 | LYS | 1 | 0.842 | 0.935 | 26.730 | 10.739 | 10.739 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 217 | GLU | -1 | -0.897 | -0.937 | 24.735 | -12.378 | -12.378 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 218 | SER | 0 | -0.045 | -0.021 | 29.290 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 219 | GLY | 0 | 0.032 | 0.003 | 31.752 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 220 | PRO | 0 | -0.046 | -0.006 | 31.786 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 221 | SER | 0 | 0.000 | -0.011 | 27.484 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 222 | SER | 0 | -0.072 | -0.033 | 28.799 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 223 | GLY | -1 | -0.915 | -0.946 | 31.290 | -8.759 | -8.759 | 0.000 | 0.000 | 0.000 | 0.000 |