FMODB ID: YYJ42
Calculation Name: 1YOD-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1YOD
Chain ID: A
Base Structure: X-ray
Registration Date: 2023-06-19
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 | 30 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -111637.768323 |
---|---|
FMO2-HF: Nuclear repulsion | 98160.195163 |
FMO2-HF: Total energy | -13477.57316 |
FMO2-MP2: Total energy | -13514.741638 |
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:22:GLN)
Summations of interaction energy for
fragment #1(A:22:GLN)
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. |
-2.163 | 0.505 | 0.039 | -0.974 | -1.733 | 0.002 |
Interaction energy analysis for fragmet #1(A:22:GLN)
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 | 24 | ALA | 0 | 0.006 | 0.009 | 3.558 | -1.600 | 0.168 | 0.006 | -0.766 | -1.008 | 0.002 |
4 | A | 25 | ARG | 1 | 0.997 | 0.999 | 3.255 | -2.162 | -1.541 | 0.034 | -0.153 | -0.502 | 0.000 |
5 | A | 26 | GLN | 0 | -0.010 | -0.003 | 4.568 | 0.728 | 1.007 | -0.001 | -0.055 | -0.223 | 0.000 |
6 | A | 27 | ASN | 0 | 0.022 | -0.007 | 6.332 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 28 | LEU | 0 | 0.013 | 0.014 | 8.241 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 29 | GLN | 0 | 0.027 | 0.018 | 8.911 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 30 | ASN | 0 | 0.024 | 0.006 | 9.120 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 31 | LEU | 0 | -0.017 | -0.007 | 12.381 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 32 | TYR | 0 | 0.011 | 0.010 | 13.592 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 33 | ILE | 0 | 0.065 | 0.029 | 13.239 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 34 | ASN | 0 | -0.013 | 0.001 | 16.556 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 35 | ARG | 1 | 0.840 | 0.913 | 18.239 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 36 | CYS | 0 | 0.040 | 0.015 | 18.514 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 37 | LEU | 0 | 0.016 | 0.010 | 19.462 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 38 | ARG | 1 | 0.882 | 0.941 | 21.629 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 39 | GLU | -1 | -0.846 | -0.916 | 23.171 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 40 | ILE | 0 | 0.081 | 0.047 | 23.470 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 41 | CYS | 0 | -0.068 | -0.047 | 25.789 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 42 | GLN | 0 | -0.109 | -0.057 | 28.394 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 43 | GLU | -1 | -0.840 | -0.922 | 28.850 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 44 | LEU | 0 | -0.004 | -0.008 | 29.058 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 45 | LYS | 1 | 0.822 | 0.906 | 30.118 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 46 | GLU | -1 | -0.828 | -0.896 | 34.418 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 47 | ILE | 0 | 0.023 | 0.007 | 33.707 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 48 | ARG | 1 | 0.905 | 0.948 | 33.997 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 49 | ALA | 0 | -0.039 | -0.011 | 38.465 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 50 | MET | 0 | -0.032 | -0.008 | 38.413 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 51 | LEU | 0 | -0.088 | -0.030 | 39.290 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |