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: N955Q
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 | 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 | 63 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -254234.205315 |
|---|---|
| FMO2-HF: Nuclear repulsion | 228604.432373 |
| FMO2-HF: Total energy | -25629.772943 |
| FMO2-MP2: Total energy | -25701.67126 |
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. |
| -1.801 | 1.772 | 0.111 | -1.729 | -1.955 | 0.004 |
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 | -0.057 | -0.037 | 3.008 | -5.317 | -1.927 | 0.111 | -1.704 | -1.797 | 0.004 |
| 4 | D | 173 | LEU | 0 | 0.019 | 0.001 | 4.453 | -5.025 | -4.842 | 0.000 | -0.025 | -0.158 | 0.000 |
| 5 | D | 174 | GLU | -1 | -0.819 | -0.910 | 7.136 | 19.694 | 19.694 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 175 | LEU | 0 | -0.039 | -0.020 | 6.820 | -2.389 | -2.389 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | D | 176 | VAL | 0 | -0.034 | -0.016 | 9.134 | -2.290 | -2.290 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | D | 177 | SER | 0 | -0.040 | -0.004 | 11.149 | -2.430 | -2.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 178 | GLY | 0 | 0.064 | 0.026 | 12.511 | -1.462 | -1.462 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 179 | SER | 0 | -0.051 | -0.020 | 13.570 | -1.768 | -1.768 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 180 | ILE | 0 | 0.017 | -0.006 | 15.257 | -1.218 | -1.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 181 | GLY | 0 | 0.032 | 0.022 | 16.795 | -0.994 | -0.994 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 182 | VAL | 0 | -0.023 | -0.016 | 18.304 | -0.985 | -0.985 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 183 | LEU | 0 | 0.032 | 0.018 | 18.730 | -0.813 | -0.813 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 184 | LYS | 1 | 0.925 | 0.978 | 21.142 | -12.817 | -12.817 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 185 | ASN | 0 | -0.013 | -0.001 | 22.715 | -0.721 | -0.721 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 186 | MET | 0 | -0.016 | -0.017 | 23.227 | -0.462 | -0.462 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 187 | SER | 0 | 0.003 | -0.012 | 24.913 | -0.464 | -0.464 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 188 | GLN | 0 | 0.017 | 0.010 | 26.843 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 189 | ARG | 1 | 0.885 | 0.941 | 26.244 | -11.085 | -11.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 190 | ILE | 0 | 0.007 | 0.010 | 28.489 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 191 | GLY | 0 | 0.002 | 0.002 | 31.421 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 192 | GLY | 0 | 0.005 | 0.002 | 33.253 | -0.242 | -0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 193 | GLU | -1 | -0.862 | -0.916 | 34.680 | 7.941 | 7.941 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 194 | LEU | 0 | -0.030 | -0.026 | 34.425 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 195 | GLU | -1 | -0.942 | -0.956 | 37.609 | 7.412 | 7.412 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 196 | GLU | -1 | -0.943 | -0.976 | 39.192 | 7.502 | 7.502 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | D | 197 | GLN | 0 | -0.104 | -0.076 | 38.736 | -0.267 | -0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | D | 198 | ALA | 0 | -0.022 | -0.006 | 41.653 | -0.185 | -0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | D | 199 | VAL | 0 | 0.001 | 0.001 | 43.478 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | D | 200 | MET | 0 | 0.004 | 0.009 | 43.755 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | D | 201 | LEU | 0 | -0.041 | -0.028 | 44.013 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | D | 202 | GLU | -1 | -0.887 | -0.923 | 47.635 | 6.004 | 6.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | D | 203 | ASP | -1 | -0.907 | -0.955 | 49.336 | 6.084 | 6.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | D | 204 | PHE | 0 | -0.026 | -0.019 | 50.275 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | D | 205 | SER | 0 | -0.028 | -0.021 | 51.892 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | D | 206 | HIS | 0 | -0.009 | -0.018 | 53.341 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | D | 207 | GLU | -1 | -0.952 | -0.976 | 53.704 | 5.670 | 5.670 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | D | 208 | LEU | 0 | -0.022 | 0.007 | 53.802 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | D | 209 | GLU | -1 | -0.869 | -0.917 | 56.376 | 5.388 | 5.388 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | D | 210 | SER | 0 | 0.017 | 0.023 | 59.571 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | D | 211 | THR | 0 | -0.082 | -0.060 | 59.501 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | D | 212 | GLN | 0 | 0.013 | -0.001 | 61.117 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | D | 213 | SER | 0 | -0.015 | -0.015 | 63.407 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | D | 214 | ARG | 1 | 0.839 | 0.915 | 62.419 | -5.112 | -5.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | D | 215 | LEU | 0 | 0.026 | 0.009 | 64.300 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | D | 216 | ASP | -1 | -0.767 | -0.876 | 67.376 | 4.478 | 4.478 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | D | 217 | ASN | 0 | -0.008 | -0.010 | 69.244 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | D | 218 | VAL | 0 | -0.043 | -0.018 | 70.044 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | D | 219 | MET | 0 | 0.009 | 0.011 | 68.780 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | D | 220 | LYS | 1 | 0.816 | 0.898 | 70.822 | -4.532 | -4.532 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | D | 221 | LYS | 1 | 0.910 | 0.954 | 74.400 | -4.263 | -4.263 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | D | 222 | LEU | 0 | 0.009 | 0.015 | 74.754 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | D | 223 | ALA | 0 | 0.065 | 0.029 | 77.237 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | D | 224 | LYS | 1 | 0.967 | 0.991 | 79.086 | -3.907 | -3.907 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | D | 225 | VAL | 0 | -0.027 | -0.021 | 80.472 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | D | 226 | SER | 0 | 0.030 | 0.018 | 81.243 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | D | 227 | HIS | 0 | -0.033 | -0.011 | 82.108 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | D | 228 | MET | 0 | -0.093 | -0.059 | 84.734 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | D | 229 | THR | 0 | -0.064 | -0.042 | 85.592 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | D | 230 | SER | 0 | -0.005 | -0.009 | 86.495 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | D | 231 | ASP | -1 | -0.883 | -0.928 | 87.971 | 3.599 | 3.599 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | D | 232 | ARG | 1 | 0.860 | 0.953 | 89.913 | -3.545 | -3.545 | 0.000 | 0.000 | 0.000 | 0.000 |