FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-05-02
All entries: 37386
Number of unique PDB entries: 7781
FMODB ID: G6991
Calculation Name: 2NPS-D-Xray372
Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2NPS
Chain ID: D
ChEMBL ID:
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UniProt ID: G3V7P1
Base Structure: X-ray
Registration Date: 2023-09-20
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptH |
| 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 | 63 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -255102.313228 |
|---|---|
| FMO2-HF: Nuclear repulsion | 229473.51209 |
| FMO2-HF: Total energy | -25628.801138 |
| FMO2-MP2: Total energy | -25700.867551 |
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(D:170:ASP)
Summations of interaction energy for
fragment #1(D:170:ASP)
| 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. |
| 2.947 | 5.649 | 0.036 | -0.93 | -1.809 | 0.002 |
Interaction energy analysis for fragmet #1(D:170:ASP)
| 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 | D | 172 | GLN | 0 | -0.059 | 0.003 | 3.386 | -1.942 | 0.568 | 0.037 | -0.915 | -1.633 | 0.002 |
| 4 | D | 173 | LEU | 0 | 0.035 | -0.012 | 4.548 | -4.593 | -4.401 | -0.001 | -0.015 | -0.176 | 0.000 |
| 5 | D | 174 | GLU | -1 | -0.882 | -0.921 | 6.795 | 20.774 | 20.774 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 175 | LEU | 0 | -0.018 | -0.027 | 6.566 | -2.407 | -2.407 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | D | 176 | VAL | 0 | -0.031 | -0.005 | 8.952 | -2.257 | -2.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | D | 177 | SER | 0 | 0.023 | -0.004 | 10.747 | -2.516 | -2.516 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 178 | GLY | 0 | 0.058 | 0.028 | 12.127 | -1.508 | -1.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 179 | SER | 0 | -0.052 | -0.027 | 13.259 | -1.839 | -1.839 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 180 | ILE | 0 | 0.020 | 0.015 | 14.804 | -1.213 | -1.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 181 | GLY | 0 | 0.041 | 0.028 | 16.469 | -1.086 | -1.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 182 | VAL | 0 | 0.024 | 0.007 | 18.247 | -0.997 | -0.997 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 183 | LEU | 0 | 0.009 | 0.033 | 18.535 | -0.886 | -0.886 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 184 | LYS | 1 | 0.918 | 0.959 | 20.741 | -13.272 | -13.272 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 185 | ASN | 0 | -0.036 | -0.019 | 22.456 | -0.653 | -0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 186 | MET | 0 | -0.046 | -0.055 | 22.933 | -0.501 | -0.501 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 187 | SER | 0 | -0.002 | 0.003 | 24.972 | -0.525 | -0.525 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 188 | GLN | 0 | 0.025 | 0.001 | 26.341 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 189 | ARG | 1 | 0.921 | 0.963 | 26.557 | -11.094 | -11.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 190 | ILE | 0 | -0.004 | 0.022 | 28.052 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 191 | GLY | 0 | 0.017 | 0.007 | 31.278 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 192 | GLY | 0 | -0.014 | -0.009 | 32.982 | -0.250 | -0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 193 | GLU | -1 | -0.834 | -0.919 | 34.466 | 7.992 | 7.992 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 194 | LEU | 0 | -0.049 | -0.036 | 34.141 | -0.193 | -0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 195 | GLU | -1 | -0.957 | -0.971 | 37.252 | 7.458 | 7.458 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 196 | GLU | -1 | -0.933 | -0.971 | 38.897 | 7.679 | 7.679 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | D | 197 | GLN | 0 | -0.106 | -0.061 | 38.703 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | D | 198 | ALA | 0 | 0.003 | 0.011 | 41.522 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | D | 199 | VAL | 0 | 0.023 | 0.015 | 43.342 | -0.181 | -0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | D | 200 | MET | 0 | 0.001 | 0.003 | 43.245 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | D | 201 | LEU | 0 | -0.056 | -0.038 | 43.531 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | D | 202 | GLU | -1 | -0.938 | -0.962 | 47.354 | 6.110 | 6.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | D | 203 | ASP | -1 | -0.892 | -0.937 | 49.322 | 6.138 | 6.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | D | 204 | PHE | 0 | -0.042 | -0.027 | 49.340 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | D | 205 | SER | 0 | 0.000 | -0.008 | 51.327 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | D | 206 | HIS | 0 | 0.012 | 0.009 | 53.101 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | D | 207 | GLU | -1 | -0.966 | -0.979 | 53.310 | 5.748 | 5.748 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | D | 208 | LEU | 0 | -0.057 | -0.026 | 53.941 | -0.160 | -0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | D | 209 | GLU | -1 | -0.892 | -0.947 | 56.969 | 5.380 | 5.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | D | 210 | SER | 0 | -0.038 | 0.001 | 59.369 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | D | 211 | THR | 0 | -0.058 | -0.055 | 59.524 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | D | 212 | GLN | 0 | 0.055 | 0.022 | 61.076 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | D | 213 | SER | 0 | 0.020 | 0.028 | 63.160 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | D | 214 | ARG | 1 | 0.849 | 0.919 | 62.061 | -5.136 | -5.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | D | 215 | LEU | 0 | 0.019 | 0.006 | 64.509 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | D | 216 | ASP | -1 | -0.848 | -0.916 | 66.977 | 4.684 | 4.684 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | D | 217 | ASN | 0 | -0.066 | -0.047 | 69.309 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | D | 218 | VAL | 0 | -0.060 | -0.030 | 69.981 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | D | 219 | MET | 0 | 0.015 | 0.002 | 67.966 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | D | 220 | LYS | 1 | 0.965 | 0.994 | 72.786 | -4.452 | -4.452 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | D | 221 | LYS | 1 | 0.928 | 0.955 | 74.637 | -4.267 | -4.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | D | 222 | LEU | 0 | 0.006 | 0.015 | 74.051 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | D | 223 | ALA | 0 | 0.055 | 0.028 | 76.952 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | D | 224 | LYS | 1 | 0.962 | 0.982 | 78.807 | -3.965 | -3.965 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | D | 225 | VAL | 0 | -0.035 | -0.018 | 80.097 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | D | 226 | SER | 0 | -0.033 | -0.034 | 80.762 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | D | 227 | HIS | 0 | -0.005 | 0.015 | 82.469 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | D | 228 | MET | 0 | -0.068 | -0.051 | 84.701 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | D | 229 | THR | 0 | -0.029 | -0.009 | 85.664 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | D | 230 | SER | 0 | -0.002 | 0.002 | 86.524 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | D | 231 | ASP | -1 | -0.936 | -0.966 | 87.883 | 3.645 | 3.645 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | D | 232 | ARG | 1 | 0.891 | 0.970 | 89.984 | -3.553 | -3.553 | 0.000 | 0.000 | 0.000 | 0.000 |