FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-04-05
All entries: 36946
Number of unique PDB entries: 7781
FMODB ID: 52LQZ
Calculation Name: 5C3I-D-Xray372
Preferred Name: Histone chaperone ASF1A
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 5C3I
Chain ID: D
ChEMBL ID: CHEMBL3392950
UniProt ID: Q9Y294
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 | -222368.628254 |
|---|---|
| FMO2-HF: Nuclear repulsion | 197568.976726 |
| FMO2-HF: Total energy | -24799.651528 |
| FMO2-MP2: Total energy | -24870.388622 |
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:68:ASP)
Summations of interaction energy for
fragment #1(D:68: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. |
| 140.014 | 142.652 | -0.023 | -1.339 | -1.276 | 0 |
Interaction energy analysis for fragmet #1(D:68: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 | 70 | GLU | -1 | -0.980 | -0.977 | 3.872 | 33.049 | 35.687 | -0.023 | -1.339 | -1.276 | 0.000 |
| 4 | D | 71 | GLU | -1 | -0.863 | -0.909 | 6.903 | 29.627 | 29.627 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | D | 72 | LEU | 0 | -0.052 | -0.041 | 8.462 | -1.926 | -1.926 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 73 | ILE | 0 | -0.055 | -0.046 | 12.011 | -2.532 | -2.532 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | D | 74 | GLY | 0 | 0.031 | 0.002 | 13.380 | 1.035 | 1.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | D | 75 | ASP | -1 | -0.965 | -0.986 | 15.334 | 16.247 | 16.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 76 | GLY | 0 | -0.008 | -0.010 | 15.886 | 0.950 | 0.950 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 77 | MET | 0 | 0.003 | 0.034 | 16.437 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 78 | GLU | -1 | -0.879 | -0.949 | 18.318 | 13.934 | 13.934 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 79 | ARG | 1 | 0.738 | 0.842 | 15.240 | -19.651 | -19.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 80 | ASP | -1 | -0.779 | -0.858 | 17.860 | 16.995 | 16.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 81 | TYR | 0 | -0.038 | -0.010 | 19.304 | -0.611 | -0.611 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 82 | ARG | 1 | 0.794 | 0.892 | 23.919 | -13.546 | -13.546 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 83 | ALA | 0 | 0.025 | 0.017 | 26.911 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 84 | ILE | 0 | -0.015 | -0.011 | 26.885 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 85 | PRO | 0 | 0.011 | 0.014 | 31.238 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 86 | GLU | -1 | -0.952 | -0.984 | 33.736 | 9.154 | 9.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 87 | LEU | 0 | -0.053 | -0.034 | 29.088 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 88 | ASP | -1 | -0.900 | -0.937 | 30.787 | 10.433 | 10.433 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 89 | ALA | 0 | -0.043 | -0.031 | 32.890 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 90 | TYR | 0 | -0.040 | -0.019 | 33.691 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 91 | GLU | -1 | -0.925 | -0.955 | 36.909 | 8.376 | 8.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 92 | ALA | 0 | 0.005 | -0.011 | 38.711 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 93 | GLU | -1 | -0.952 | -0.972 | 40.868 | 7.390 | 7.390 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 94 | GLY | 0 | -0.042 | -0.024 | 40.639 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | D | 95 | LEU | 0 | -0.052 | -0.014 | 39.451 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | D | 96 | ALA | 0 | -0.010 | -0.008 | 43.026 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | D | 97 | LEU | 0 | -0.044 | -0.029 | 46.521 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | D | 98 | ASP | -1 | -0.952 | -0.978 | 49.432 | 6.068 | 6.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | D | 99 | ASP | -1 | -0.970 | -0.993 | 49.532 | 6.247 | 6.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | D | 100 | GLU | -1 | -0.923 | -0.942 | 51.324 | 5.577 | 5.577 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | D | 101 | ASP | -1 | -0.965 | -0.987 | 52.181 | 5.924 | 5.924 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | D | 102 | VAL | 0 | -0.088 | -0.035 | 48.482 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | D | 103 | GLU | -1 | -0.990 | -0.995 | 51.859 | 5.676 | 5.676 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | D | 104 | GLU | -1 | -0.895 | -0.954 | 48.823 | 6.637 | 6.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | D | 105 | LEU | 0 | -0.063 | -0.019 | 45.679 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | D | 106 | THR | 0 | 0.013 | -0.004 | 50.150 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | D | 107 | ALA | 0 | 0.015 | -0.007 | 51.357 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | D | 108 | SER | 0 | -0.033 | -0.025 | 51.675 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | D | 109 | GLN | 0 | 0.077 | 0.044 | 50.284 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | D | 110 | ARG | 1 | 0.921 | 0.945 | 44.734 | -6.701 | -6.701 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | D | 111 | GLU | -1 | -0.789 | -0.853 | 47.305 | 6.446 | 6.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | D | 112 | ALA | 0 | -0.060 | -0.036 | 48.917 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | D | 113 | ALA | 0 | 0.041 | 0.021 | 45.304 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | D | 114 | GLU | -1 | -0.795 | -0.880 | 43.312 | 7.033 | 7.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | D | 115 | ARG | 1 | 0.862 | 0.919 | 44.206 | -5.988 | -5.988 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | D | 116 | ALA | 0 | 0.021 | 0.021 | 45.558 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | D | 117 | MET | 0 | -0.052 | -0.019 | 40.322 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | D | 118 | ARG | 1 | 0.844 | 0.875 | 41.019 | -6.648 | -6.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | D | 119 | GLN | 0 | -0.131 | -0.060 | 42.509 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | D | 120 | ARG | 1 | 0.940 | 0.932 | 37.891 | -7.823 | -7.823 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | D | 121 | ASP | -1 | -0.859 | -0.896 | 37.152 | 8.170 | 8.170 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | D | 122 | ARG | 1 | 0.834 | 0.929 | 37.692 | -6.759 | -6.759 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | D | 123 | GLU | -1 | -0.943 | -0.956 | 38.724 | 7.010 | 7.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | D | 134 | ALA | 0 | 0.028 | -0.005 | 44.667 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | D | 135 | ALA | 0 | -0.019 | 0.002 | 45.750 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | D | 136 | ALA | 0 | -0.009 | -0.007 | 43.809 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | D | 137 | ALA | 0 | 0.002 | 0.006 | 45.138 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | D | 138 | ALA | 0 | 0.001 | -0.001 | 45.253 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | D | 139 | ALA | 0 | -0.011 | -0.009 | 47.485 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | D | 140 | ALA | 0 | 0.007 | 0.015 | 49.336 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |