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: 9QLG2
Calculation Name: 7PHC-p-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7PHC
Chain ID: p
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-06
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 | 114 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -781867.411153 |
|---|---|
| FMO2-HF: Nuclear repulsion | 735807.78572 |
| FMO2-HF: Total energy | -46059.625434 |
| FMO2-MP2: Total energy | -46196.746106 |
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:1:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
| 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. |
| 241.745 | 244.656 | 0.834 | -0.858 | -2.886 | 0 |
Interaction energy analysis for fragmet #1(A:1:MET)
| 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 | 3 | ILE | 0 | 0.093 | 0.053 | 2.349 | 6.118 | 8.874 | 0.834 | -0.831 | -2.758 | 0.000 |
| 4 | A | 4 | LYS | 1 | 0.926 | 0.960 | 4.512 | 36.102 | 36.257 | 0.000 | -0.027 | -0.128 | 0.000 |
| 5 | A | 5 | GLY | 0 | 0.085 | 0.043 | 8.205 | 1.115 | 1.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | GLY | 0 | 0.019 | 0.019 | 10.836 | 1.541 | 1.541 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | LYS | 1 | 1.037 | 1.007 | 14.022 | 17.669 | 17.669 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLN | 0 | 0.096 | 0.062 | 12.491 | 1.616 | 1.616 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | THR | 0 | 0.015 | -0.012 | 13.628 | 1.185 | 1.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | ARG | 1 | 0.971 | 0.985 | 16.173 | 14.186 | 14.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | VAL | 0 | 0.014 | 0.015 | 18.262 | 0.786 | 0.786 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ARG | 1 | 0.932 | 0.954 | 15.119 | 17.067 | 17.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ARG | 1 | 0.947 | 0.969 | 16.773 | 15.838 | 15.838 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | LYS | 1 | 0.984 | 0.992 | 22.097 | 12.031 | 12.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | LYS | 1 | 0.974 | 0.986 | 22.697 | 11.852 | 11.852 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | TRP | 0 | -0.006 | -0.004 | 21.119 | 0.467 | 0.467 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LEU | 0 | -0.002 | 0.007 | 25.773 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LYS | 1 | 0.939 | 0.983 | 27.880 | 9.384 | 9.384 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLN | 0 | -0.054 | -0.037 | 28.339 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ALA | 0 | 0.002 | 0.017 | 31.961 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | SER | 0 | -0.016 | -0.027 | 33.814 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | GLY | 0 | 0.036 | 0.025 | 36.623 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | SER | 0 | -0.065 | -0.032 | 38.279 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | PHE | 0 | 0.059 | 0.013 | 40.599 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | GLY | 0 | 0.061 | 0.037 | 41.232 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | THR | 0 | -0.035 | -0.029 | 35.523 | -0.201 | -0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ARG | 1 | 0.974 | 0.990 | 36.125 | 7.300 | 7.300 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | HIS | 0 | 0.086 | 0.055 | 33.581 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ALA | 0 | 0.011 | 0.020 | 31.557 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | SER | 0 | 0.019 | -0.010 | 29.414 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | TYR | 0 | -0.006 | -0.017 | 23.586 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | LYS | 1 | 0.983 | 0.978 | 26.238 | 11.095 | 11.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | VAL | 0 | 0.059 | 0.042 | 30.133 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | ALA | 0 | 0.075 | 0.057 | 30.403 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | LYS | 1 | 0.964 | 0.973 | 26.172 | 10.914 | 10.914 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | GLN | 0 | 0.001 | 0.019 | 31.281 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | THR | 0 | -0.002 | -0.013 | 34.710 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | VAL | 0 | 0.018 | 0.007 | 31.616 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | ILE | 0 | 0.012 | 0.005 | 33.167 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | GLN | 0 | 0.018 | 0.007 | 35.254 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | ALA | 0 | 0.049 | 0.030 | 37.468 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | ALA | 0 | 0.000 | -0.001 | 35.673 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | LYS | 1 | 0.898 | 0.938 | 37.578 | 8.067 | 8.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | TYR | 0 | -0.021 | -0.007 | 40.212 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | ALA | 0 | 0.134 | 0.064 | 40.369 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | TYR | 0 | -0.042 | -0.010 | 40.422 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | ARG | 1 | 0.939 | 0.971 | 42.442 | 6.680 | 6.680 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | ASP | -1 | -0.871 | -0.936 | 45.544 | -6.416 | -6.416 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ARG | 1 | 0.884 | 0.924 | 40.036 | 7.418 | 7.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | ARG | 1 | 0.898 | 0.962 | 43.811 | 6.845 | 6.845 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | ASN | 0 | -0.032 | -0.014 | 48.003 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | LYS | 1 | 1.043 | 1.027 | 49.311 | 6.251 | 6.251 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | LYS | 1 | 0.968 | 0.981 | 51.153 | 5.979 | 5.979 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | ARG | 1 | 0.912 | 0.962 | 52.222 | 5.921 | 5.921 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ASP | -1 | -0.824 | -0.901 | 53.134 | -5.662 | -5.662 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | PHE | 0 | 0.012 | -0.007 | 53.386 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | ARG | 1 | 0.932 | 0.973 | 57.772 | 5.323 | 5.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | SER | 0 | -0.019 | -0.031 | 59.366 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | LEU | 0 | 0.024 | 0.028 | 59.954 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | TRP | 0 | 0.012 | -0.006 | 57.929 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | ILE | 0 | -0.050 | -0.015 | 63.151 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | LEU | 0 | 0.006 | 0.013 | 64.929 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ARG | 1 | 0.911 | 0.940 | 64.837 | 4.819 | 4.819 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | LEU | 0 | -0.003 | 0.003 | 67.768 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | ASN | 0 | 0.001 | -0.012 | 69.581 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ALA | 0 | -0.015 | 0.010 | 70.783 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | ALA | 0 | 0.087 | 0.045 | 71.879 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | LEU | 0 | -0.034 | -0.028 | 73.010 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | ARG | 1 | 0.907 | 0.962 | 75.362 | 4.124 | 4.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | GLU | -1 | -0.935 | -0.969 | 73.998 | -4.183 | -4.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | GLN | 0 | -0.072 | -0.037 | 77.059 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | GLY | 0 | 0.033 | 0.036 | 80.098 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | MET | 0 | -0.054 | -0.026 | 77.594 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | THR | 0 | 0.019 | 0.003 | 75.117 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | TYR | 0 | 0.061 | 0.003 | 66.946 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | SER | 0 | -0.001 | -0.012 | 73.187 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | VAL | 0 | 0.035 | 0.024 | 74.109 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | PHE | 0 | 0.039 | 0.018 | 71.496 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ILE | 0 | -0.032 | -0.029 | 69.892 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | ASN | 0 | 0.018 | 0.012 | 73.084 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | LEU | 0 | -0.011 | -0.002 | 75.855 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | LEU | 0 | -0.031 | -0.006 | 70.972 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | LYS | 1 | 0.837 | 0.929 | 69.794 | 4.388 | 4.388 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | LYS | 1 | 0.911 | 0.956 | 74.528 | 3.916 | 3.916 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | HIS | 0 | 0.031 | 0.033 | 77.990 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | ASN | 0 | -0.044 | -0.020 | 76.969 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | ILE | 0 | 0.058 | 0.027 | 73.077 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | GLU | -1 | -0.859 | -0.935 | 73.258 | -4.130 | -4.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | ILE | 0 | -0.012 | -0.019 | 67.076 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | ASN | 0 | 0.051 | 0.025 | 67.816 | -0.106 | -0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | ARG | 1 | 0.878 | 0.936 | 61.942 | 4.797 | 4.797 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | LYS | 1 | 0.949 | 0.984 | 63.899 | 4.734 | 4.734 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | VAL | 0 | 0.078 | 0.030 | 60.913 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | LEU | 0 | 0.040 | 0.013 | 62.940 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | SER | 0 | -0.023 | -0.015 | 66.076 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | GLU | -1 | -0.786 | -0.896 | 64.750 | -4.758 | -4.758 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | LEU | 0 | -0.032 | -0.014 | 63.482 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | ALA | 0 | 0.049 | 0.022 | 68.145 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | ILE | 0 | -0.035 | -0.022 | 71.239 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | LYS | 1 | 0.838 | 0.915 | 68.422 | 4.539 | 4.539 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | GLU | -1 | -0.819 | -0.889 | 71.345 | -4.260 | -4.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | PRO | 0 | 0.039 | 0.022 | 73.657 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | SER | 0 | 0.036 | 0.002 | 77.502 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | LYS | 1 | 0.827 | 0.924 | 73.988 | 4.160 | 4.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 105 | PHE | 0 | 0.026 | 0.014 | 74.118 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 106 | ASN | 0 | 0.024 | 0.006 | 75.747 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 107 | LEU | 0 | 0.049 | 0.039 | 77.589 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 108 | A | 108 | ILE | 0 | -0.008 | -0.015 | 73.896 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 109 | A | 109 | VAL | 0 | -0.015 | -0.001 | 77.319 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 110 | A | 110 | GLN | 0 | -0.001 | -0.010 | 79.630 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 111 | A | 111 | LYS | 1 | 0.931 | 0.979 | 79.133 | 3.908 | 3.908 | 0.000 | 0.000 | 0.000 | 0.000 |
| 112 | A | 112 | VAL | 0 | -0.028 | 0.004 | 75.889 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 113 | A | 113 | LYS | 1 | 0.817 | 0.894 | 78.930 | 3.869 | 3.869 | 0.000 | 0.000 | 0.000 | 0.000 |
| 114 | A | 114 | SER | -1 | -0.825 | -0.905 | 81.560 | -3.768 | -3.768 | 0.000 | 0.000 | 0.000 | 0.000 |