![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 766MK
Calculation Name: 4HL9-A-Xray372
Preferred Name:
Target Type:
Ligand Name: s-hydroxycysteine
ligand 3-letter code: CSO
PDB ID: 4HL9
Chain ID: A
UniProt ID: Q2RXF1
Base Structure: X-ray
Registration Date: 2023-09-21
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 | 95 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -717499.501776 |
---|---|
FMO2-HF: Nuclear repulsion | 678867.086353 |
FMO2-HF: Total energy | -38632.415422 |
FMO2-MP2: Total energy | -38744.786361 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033494/ligand_interaction/ligand_F033494.png)
Ligand Interaction
![ligand interaction](./Kdata/F033494/ligand_interaction/ligand_interaction_F033494.png)
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. |
-22.331 | -9.756 | 8.905 | -7.545 | -13.936 | -0.071 |
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 | LYS | 1 | 0.961 | 0.974 | 2.623 | -1.452 | 1.608 | 2.272 | -1.284 | -4.048 | 0.000 |
4 | A | 4 | VAL | 0 | -0.014 | -0.010 | 4.279 | -1.048 | -1.086 | 0.029 | 0.165 | -0.156 | 0.000 |
5 | A | 5 | ILE | 0 | -0.006 | 0.003 | 8.087 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | ALA | 0 | 0.036 | 0.026 | 10.564 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | GLN | 0 | -0.031 | 0.005 | 14.191 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ASP | -1 | -0.721 | -0.822 | 17.242 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | PHE | 0 | -0.021 | -0.029 | 20.465 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ILE | 0 | 0.032 | 0.029 | 23.927 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LYS | 1 | 0.922 | 0.960 | 26.549 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | PRO | 0 | 0.032 | 0.010 | 30.285 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | GLU | -1 | -0.904 | -0.970 | 31.288 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | ALA | 0 | -0.010 | -0.001 | 30.423 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ILE | 0 | -0.003 | 0.013 | 27.485 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | ASP | -1 | -0.891 | -0.961 | 28.739 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.056 | -0.020 | 30.415 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | VAL | 0 | 0.021 | 0.006 | 25.961 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | LEU | 0 | -0.006 | 0.013 | 24.629 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | PRO | 0 | -0.048 | -0.028 | 25.148 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LEU | 0 | 0.026 | 0.021 | 24.793 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | TYR | 0 | -0.002 | -0.046 | 20.200 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.900 | 0.949 | 20.596 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.789 | -0.876 | 21.357 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.020 | 0.010 | 17.579 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | -0.020 | -0.012 | 16.252 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.974 | -0.987 | 16.632 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | LYS | 1 | 0.904 | 0.947 | 18.245 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | THR | 0 | -0.021 | -0.010 | 12.571 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ARG | 1 | 0.848 | 0.913 | 13.216 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | GLN | 0 | -0.060 | -0.015 | 14.257 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLU | -1 | -0.763 | -0.862 | 12.849 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | PRO | 0 | -0.023 | -0.022 | 12.832 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LEU | 0 | -0.016 | -0.014 | 8.903 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | CSO | 0 | -0.038 | 0.003 | 7.991 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LEU | 0 | -0.035 | -0.005 | 3.300 | -0.342 | 0.058 | 0.037 | -0.084 | -0.353 | 0.000 |
37 | A | 37 | ALA | 0 | 0.021 | 0.005 | 7.105 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | TYR | 0 | 0.034 | 0.008 | 8.533 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ASP | -1 | -0.917 | -0.945 | 11.151 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | LEU | 0 | -0.003 | 0.002 | 13.311 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | PHE | 0 | -0.047 | -0.025 | 12.380 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | VAL | 0 | 0.006 | 0.000 | 17.391 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASP | -1 | -0.836 | -0.897 | 20.373 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | GLN | 0 | -0.018 | -0.029 | 21.296 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LYS | 1 | 0.883 | 0.935 | 23.341 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASP | -1 | -0.779 | -0.849 | 24.330 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | PRO | 0 | 0.037 | 0.010 | 24.347 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLY | 0 | 0.025 | 0.020 | 25.706 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | HIS | 1 | 0.767 | 0.891 | 18.654 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PHE | 0 | 0.011 | 0.001 | 19.554 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | VAL | 0 | -0.014 | -0.020 | 13.428 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | PHE | 0 | 0.023 | 0.019 | 13.238 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ILE | 0 | -0.030 | -0.021 | 7.747 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | GLU | -1 | -0.868 | -0.945 | 8.426 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLU | -1 | -0.945 | -0.977 | 2.385 | -10.356 | -6.745 | 4.049 | -3.107 | -4.553 | -0.041 |
56 | A | 56 | TRP | 0 | -0.020 | -0.019 | 3.683 | -0.869 | -0.510 | 0.002 | -0.078 | -0.283 | 0.000 |
57 | A | 57 | PRO | 0 | 0.018 | 0.001 | 2.780 | -3.938 | -1.678 | 1.024 | -1.435 | -1.849 | -0.016 |
58 | A | 58 | ASP | -1 | -0.858 | -0.940 | 2.685 | -4.293 | -2.552 | 0.831 | -1.322 | -1.250 | -0.015 |
59 | A | 59 | ARG | 1 | 0.921 | 0.959 | 4.869 | 0.750 | 0.811 | -0.001 | -0.003 | -0.057 | 0.000 |
60 | A | 60 | ALA | 0 | 0.055 | 0.036 | 8.225 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ALA | 0 | 0.009 | 0.000 | 7.234 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | 0.006 | 0.006 | 8.672 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ASP | -1 | -0.890 | -0.959 | 10.165 | -0.189 | -0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ILE | 0 | -0.054 | -0.021 | 12.104 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | HIS | 1 | 0.873 | 0.930 | 12.071 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | CSO | 0 | -0.060 | -0.039 | 13.982 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ALA | 0 | 0.000 | 0.017 | 16.332 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | THR | 0 | -0.058 | -0.020 | 16.349 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | GLU | -1 | -0.819 | -0.897 | 19.236 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | HIS | 0 | 0.023 | -0.007 | 16.274 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | PHE | 0 | 0.030 | 0.017 | 15.866 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | THR | 0 | -0.043 | -0.039 | 19.566 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ARG | 1 | 0.755 | 0.865 | 22.523 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.046 | -0.036 | 21.579 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | VAL | 0 | 0.026 | 0.022 | 18.941 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | PRO | 0 | -0.009 | -0.002 | 22.347 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | LEU | 0 | -0.036 | -0.017 | 25.622 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ILE | 0 | -0.014 | 0.000 | 22.050 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ASN | 0 | 0.026 | -0.003 | 22.155 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ALA | 0 | -0.051 | -0.003 | 26.001 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | HIS | 0 | -0.024 | -0.016 | 28.749 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | GLN | 0 | -0.003 | 0.013 | 25.383 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | ARG | 1 | 0.717 | 0.790 | 26.764 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | GLN | 0 | -0.055 | -0.041 | 24.606 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | ASP | -1 | -0.898 | -0.930 | 23.667 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLY | 0 | 0.026 | 0.017 | 20.654 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | THR | 0 | -0.078 | -0.041 | 17.255 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | VAL | 0 | 0.050 | 0.013 | 12.874 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | VAL | 0 | -0.052 | -0.021 | 10.634 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | LEU | 0 | 0.007 | -0.004 | 8.752 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | MET | 0 | -0.064 | -0.037 | 5.798 | -0.279 | -0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | ASP | -1 | -0.842 | -0.903 | 4.838 | 0.520 | 0.872 | 0.005 | -0.079 | -0.278 | 0.000 |
93 | A | 93 | ALA | 0 | -0.037 | -0.026 | 2.346 | -0.923 | -0.269 | 0.655 | -0.287 | -1.023 | 0.001 |
94 | A | 94 | VAL | 0 | 0.008 | -0.002 | 4.285 | -0.367 | -0.252 | 0.002 | -0.031 | -0.086 | 0.000 |
95 | A | 95 | PRO | 0 | -0.037 | -0.009 | 7.752 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |