FMODB ID: GNZ81
Calculation Name: 1L2W-I-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1L2W
Chain ID: I
UniProt ID: P08008
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 | 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 | 57 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -187247.095136 |
---|---|
FMO2-HF: Nuclear repulsion | 165437.698851 |
FMO2-HF: Total energy | -21809.396285 |
FMO2-MP2: Total energy | -21871.902575 |
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(I:22:SER)
Summations of interaction energy for
fragment #1(I:22:SER)
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. |
-8.849 | -5.797 | 0.053 | -1.539 | -1.565 | -0.004 |
Interaction energy analysis for fragmet #1(I:22:SER)
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 | I | 24 | GLY | 0 | 0.021 | 0.007 | 3.430 | -2.850 | -1.374 | 0.009 | -0.811 | -0.675 | 0.001 |
4 | I | 25 | GLU | -1 | -0.937 | -0.973 | 3.377 | -9.295 | -7.744 | 0.045 | -0.725 | -0.870 | -0.005 |
5 | I | 26 | MET | 0 | 0.013 | 0.004 | 5.376 | 0.549 | 0.574 | -0.001 | -0.003 | -0.020 | 0.000 |
6 | I | 27 | SER | 0 | -0.034 | -0.020 | 7.312 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | I | 28 | GLY | 0 | -0.016 | -0.007 | 6.299 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | I | 29 | ARG | 1 | 0.927 | 0.973 | 7.333 | 1.715 | 1.715 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | I | 30 | SER | 0 | 0.058 | 0.036 | 6.589 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | I | 31 | VAL | 0 | -0.028 | -0.012 | 7.478 | 0.616 | 0.616 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | I | 32 | SER | 0 | -0.014 | -0.010 | 9.625 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | I | 33 | GLN | 0 | 0.008 | 0.010 | 12.389 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | I | 34 | GLN | 0 | -0.011 | -0.010 | 15.844 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | I | 35 | THR | 0 | -0.017 | -0.011 | 18.813 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | I | 36 | SER | 0 | 0.003 | 0.008 | 22.485 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | I | 37 | ASP | -1 | -0.812 | -0.897 | 24.405 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | I | 38 | GLN | 0 | 0.011 | -0.016 | 27.316 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | I | 39 | TYR | 0 | 0.015 | 0.011 | 28.592 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | I | 40 | ALA | 0 | 0.028 | 0.010 | 25.842 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | I | 41 | ASN | 0 | -0.037 | -0.037 | 27.834 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | I | 42 | ASN | 0 | -0.029 | -0.006 | 29.636 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | I | 43 | LEU | 0 | -0.047 | -0.020 | 28.642 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | I | 44 | ALA | 0 | -0.009 | -0.009 | 28.109 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | I | 45 | GLY | 0 | -0.001 | 0.014 | 29.973 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | I | 46 | ARG | 1 | 0.837 | 0.919 | 33.186 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | I | 47 | THR | 0 | -0.036 | -0.012 | 35.130 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | I | 48 | GLU | -1 | -0.866 | -0.940 | 38.102 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | I | 49 | SER | 0 | -0.041 | -0.006 | 40.786 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | I | 50 | PRO | 0 | 0.024 | -0.003 | 43.727 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | I | 51 | GLN | 0 | -0.007 | 0.005 | 45.314 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | I | 52 | GLY | 0 | 0.003 | 0.005 | 47.924 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | I | 53 | SER | 0 | -0.023 | -0.016 | 50.477 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | I | 54 | SER | 0 | 0.055 | 0.004 | 50.467 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | I | 55 | LEU | 0 | -0.011 | -0.004 | 49.040 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | I | 56 | ALA | 0 | 0.041 | 0.013 | 52.455 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | I | 57 | SER | 0 | -0.023 | 0.003 | 55.651 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | I | 58 | ARG | 1 | 0.923 | 0.952 | 50.686 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | I | 59 | ILE | 0 | 0.040 | 0.028 | 56.921 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | I | 60 | ILE | 0 | -0.029 | 0.000 | 52.858 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | I | 61 | GLU | -1 | -0.918 | -0.961 | 54.907 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | I | 62 | ARG | 1 | 0.919 | 0.963 | 53.217 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | I | 63 | LEU | 0 | 0.014 | -0.003 | 49.612 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | I | 64 | SER | 0 | 0.008 | 0.010 | 53.548 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | I | 65 | SER | 0 | -0.020 | -0.007 | 54.079 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | I | 66 | VAL | 0 | 0.017 | 0.002 | 47.702 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | I | 67 | ALA | 0 | 0.029 | 0.016 | 49.054 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | I | 68 | HIS | 0 | 0.068 | 0.025 | 49.073 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | I | 69 | SER | 0 | 0.010 | -0.007 | 45.587 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | I | 70 | VAL | 0 | 0.007 | 0.001 | 44.477 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | I | 71 | ILE | 0 | 0.053 | 0.043 | 44.167 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | I | 72 | GLY | 0 | 0.026 | 0.017 | 43.860 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | I | 73 | PHE | 0 | -0.034 | -0.020 | 37.165 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | I | 74 | ILE | 0 | 0.040 | -0.003 | 39.592 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | I | 75 | GLN | 0 | -0.019 | -0.025 | 40.036 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | I | 76 | ARG | 1 | 0.879 | 0.966 | 37.043 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | I | 77 | MET | 0 | -0.031 | -0.020 | 34.008 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | I | 78 | PHE | 0 | -0.035 | 0.015 | 35.653 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |