FMODB ID: M3R2Z
Calculation Name: 1B35-D-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1B35
Chain ID: D
UniProt ID: P13418
Base Structure: X-ray
Registration Date: 2023-03-13
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 | -206182.141698 |
---|---|
FMO2-HF: Nuclear repulsion | 185869.246003 |
FMO2-HF: Total energy | -20312.895695 |
FMO2-MP2: Total energy | -20373.581073 |
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:1:ALA)
Summations of interaction energy for
fragment #1(D:1:ALA)
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. |
-10.668 | -5.744 | 0.416 | -1.825 | -3.51 | 0.002 |
Interaction energy analysis for fragmet #1(D:1:ALA)
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 | 3 | SER | 0 | -0.006 | -0.016 | 3.361 | -3.826 | -1.828 | 0.032 | -0.941 | -1.089 | 0.005 |
4 | D | 4 | GLU | -1 | -0.879 | -0.941 | 2.723 | -5.319 | -3.936 | 0.304 | -0.452 | -1.234 | -0.002 |
5 | D | 5 | LEU | 0 | -0.012 | -0.006 | 2.984 | 0.191 | 1.059 | 0.074 | -0.297 | -0.645 | -0.001 |
6 | D | 6 | LYS | 1 | 0.955 | 0.985 | 5.851 | 0.497 | 0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | D | 7 | GLN | 0 | -0.006 | -0.018 | 7.679 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | D | 8 | LEU | 0 | -0.014 | 0.004 | 8.231 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | D | 9 | GLU | -1 | -0.971 | -0.977 | 9.908 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | D | 10 | THR | 0 | -0.080 | -0.040 | 12.271 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | D | 11 | ASN | 0 | -0.006 | 0.001 | 12.528 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | D | 12 | ASN | 0 | -0.022 | -0.003 | 14.167 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | D | 13 | SER | 0 | 0.011 | -0.018 | 13.151 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | D | 14 | PRO | 0 | 0.009 | 0.005 | 10.325 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | D | 15 | SER | 0 | -0.045 | -0.013 | 11.277 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | D | 16 | THR | 0 | 0.008 | 0.003 | 11.360 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | D | 17 | ALA | 0 | -0.018 | -0.012 | 13.696 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | D | 18 | LEU | 0 | 0.007 | 0.015 | 17.358 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | D | 19 | GLY | 0 | -0.003 | 0.002 | 20.670 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | D | 20 | GLN | 0 | -0.008 | -0.013 | 22.322 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | D | 21 | ILE | 0 | 0.000 | 0.006 | 24.613 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | D | 22 | SER | 0 | 0.024 | -0.002 | 26.115 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | D | 23 | GLU | -1 | -0.908 | -0.960 | 27.076 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | D | 24 | GLY | 0 | -0.049 | -0.013 | 29.106 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | D | 25 | LEU | 0 | -0.001 | 0.010 | 21.506 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | D | 26 | THR | 0 | -0.026 | -0.019 | 25.475 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | D | 27 | THR | 0 | -0.018 | -0.012 | 20.099 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | D | 28 | LEU | 0 | 0.019 | 0.003 | 22.782 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | D | 29 | SER | 0 | -0.013 | -0.007 | 25.327 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | D | 30 | HIS | 0 | -0.007 | 0.004 | 16.058 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | D | 31 | ILE | 0 | 0.023 | 0.012 | 20.360 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | D | 32 | PRO | 0 | -0.054 | -0.008 | 15.270 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | D | 33 | VAL | 0 | 0.042 | 0.016 | 14.912 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | D | 34 | LEU | 0 | 0.049 | 0.022 | 12.939 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | D | 35 | GLY | 0 | 0.016 | 0.036 | 11.278 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | D | 36 | ASN | 0 | -0.078 | -0.078 | 9.171 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | D | 37 | ILE | 0 | 0.026 | 0.007 | 7.119 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | D | 38 | PHE | 0 | 0.008 | 0.001 | 3.309 | 0.197 | 0.497 | 0.008 | -0.070 | -0.237 | 0.000 |
39 | D | 39 | SER | 0 | -0.022 | -0.013 | 4.296 | -0.553 | -0.437 | -0.001 | -0.015 | -0.099 | 0.000 |
40 | D | 40 | THR | 0 | -0.018 | 0.002 | 6.388 | -0.106 | -0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | D | 41 | PRO | 0 | -0.014 | -0.003 | 4.148 | 1.057 | 1.228 | 0.000 | -0.040 | -0.130 | 0.000 |
42 | D | 42 | ALA | 0 | 0.033 | -0.011 | 4.722 | -1.311 | -1.223 | -0.001 | -0.010 | -0.076 | 0.000 |
43 | D | 43 | TRP | 0 | 0.011 | 0.016 | 5.628 | -0.618 | -0.618 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | D | 44 | ILE | 0 | -0.022 | 0.007 | 8.258 | -0.391 | -0.391 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | D | 45 | SER | 0 | -0.060 | -0.033 | 10.693 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | D | 46 | ALA | 0 | 0.061 | 0.020 | 13.279 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | D | 47 | LYS | 1 | 0.944 | 0.982 | 13.923 | -0.760 | -0.760 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | D | 48 | ALA | 0 | 0.049 | 0.016 | 17.207 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | D | 49 | ALA | 0 | -0.001 | -0.011 | 16.585 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | D | 50 | ASP | -1 | -0.862 | -0.932 | 12.322 | 0.863 | 0.863 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | D | 51 | LEU | 0 | 0.014 | 0.008 | 14.840 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | D | 52 | ALA | 0 | 0.013 | 0.016 | 17.420 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | D | 53 | LYS | 1 | 0.962 | 0.965 | 13.500 | -0.492 | -0.492 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | D | 54 | LEU | 0 | -0.022 | 0.010 | 13.726 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | D | 55 | PHE | 0 | -0.068 | -0.042 | 15.818 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | D | 56 | GLY | 0 | 0.008 | 0.013 | 18.101 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | D | 57 | PHE | 0 | -0.072 | -0.019 | 19.146 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |