![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2NNLR
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 | OptHSide |
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 | -718570.180074 |
---|---|
FMO2-HF: Nuclear repulsion | 679937.498256 |
FMO2-HF: Total energy | -38632.681817 |
FMO2-MP2: Total energy | -38745.08254 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033493/ligand_interaction/ligand_F033493.png)
Ligand Interaction
![ligand interaction](./Kdata/F033493/ligand_interaction/ligand_interaction_F033493.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. |
-21.729 | -9.73 | 9.11 | -7.262 | -13.845 | -0.068 |
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 | 0.874 | 0.918 | 2.582 | -0.987 | 2.237 | 1.682 | -1.268 | -3.638 | 0.000 |
4 | A | 4 | VAL | 0 | -0.013 | -0.013 | 4.419 | -1.076 | -1.037 | 0.020 | 0.068 | -0.127 | 0.000 |
5 | A | 5 | ILE | 0 | 0.003 | 0.011 | 8.215 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | ALA | 0 | 0.027 | 0.023 | 10.697 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | GLN | 0 | -0.026 | 0.002 | 14.301 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ASP | -1 | -0.726 | -0.828 | 17.360 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | PHE | 0 | -0.033 | -0.037 | 20.483 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ILE | 0 | 0.033 | 0.029 | 24.035 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LYS | 1 | 0.918 | 0.965 | 26.609 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | PRO | 0 | 0.036 | 0.010 | 30.353 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | GLU | -1 | -0.893 | -0.963 | 31.328 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | ALA | 0 | -0.007 | -0.004 | 30.490 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ILE | 0 | -0.010 | 0.009 | 27.432 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | ASP | -1 | -0.901 | -0.964 | 28.668 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.058 | -0.020 | 30.794 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | VAL | 0 | 0.027 | 0.011 | 25.940 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | LEU | 0 | -0.007 | 0.012 | 24.491 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | PRO | 0 | -0.050 | -0.033 | 25.150 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LEU | 0 | 0.034 | 0.026 | 24.809 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | TYR | 0 | 0.005 | -0.041 | 20.228 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.896 | 0.947 | 20.578 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.762 | -0.834 | 21.321 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.062 | 0.030 | 17.534 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | -0.022 | 0.003 | 16.179 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.930 | -0.955 | 16.575 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | LYS | 1 | 0.822 | 0.883 | 18.155 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | THR | 0 | -0.040 | -0.031 | 12.484 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ARG | 1 | 0.829 | 0.887 | 13.128 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | GLN | 0 | -0.056 | -0.012 | 14.145 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLU | -1 | -0.760 | -0.861 | 12.701 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | PRO | 0 | -0.021 | -0.023 | 12.662 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LEU | 0 | -0.026 | -0.016 | 8.926 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | CSO | 0 | -0.041 | 0.002 | 7.787 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LEU | 0 | -0.025 | -0.001 | 3.023 | -0.454 | 0.043 | 0.095 | -0.116 | -0.476 | 0.000 |
37 | A | 37 | ALA | 0 | 0.008 | -0.001 | 6.986 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | TYR | 0 | 0.006 | -0.021 | 8.531 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ASP | -1 | -0.904 | -0.924 | 10.837 | -0.150 | -0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | LEU | 0 | -0.003 | 0.003 | 13.131 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | PHE | 0 | -0.043 | -0.025 | 12.236 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | VAL | 0 | 0.010 | 0.003 | 17.307 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASP | -1 | -0.825 | -0.886 | 20.345 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | GLN | 0 | -0.026 | -0.030 | 21.338 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LYS | 1 | 0.884 | 0.936 | 23.026 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASP | -1 | -0.763 | -0.845 | 24.420 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | PRO | 0 | 0.029 | 0.007 | 24.392 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLY | 0 | 0.038 | 0.027 | 25.693 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | HIS | 1 | 0.757 | 0.880 | 18.769 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PHE | 0 | 0.008 | 0.000 | 19.621 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | VAL | 0 | -0.011 | -0.017 | 13.501 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | PHE | 0 | 0.023 | 0.018 | 13.196 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ILE | 0 | -0.045 | -0.027 | 7.688 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | GLU | -1 | -0.799 | -0.899 | 8.449 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLU | -1 | -0.876 | -0.926 | 2.455 | -9.928 | -6.933 | 4.238 | -2.547 | -4.686 | -0.032 |
56 | A | 56 | TRP | 0 | -0.003 | -0.010 | 3.630 | -1.005 | -0.602 | 0.003 | -0.095 | -0.310 | 0.000 |
57 | A | 57 | PRO | 0 | 0.023 | 0.004 | 2.574 | -3.781 | -1.710 | 1.512 | -1.460 | -2.124 | -0.018 |
58 | A | 58 | ASP | -1 | -0.807 | -0.919 | 2.543 | -4.010 | -2.250 | 1.392 | -1.630 | -1.522 | -0.019 |
59 | A | 59 | ARG | 1 | 0.848 | 0.899 | 4.750 | 0.635 | 0.698 | -0.001 | -0.005 | -0.056 | 0.000 |
60 | A | 60 | ALA | 0 | 0.024 | 0.016 | 8.129 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ALA | 0 | -0.022 | -0.013 | 7.180 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | 0.002 | 0.007 | 8.624 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ASP | -1 | -0.814 | -0.902 | 10.144 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ILE | 0 | -0.037 | -0.013 | 12.087 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | HIS | 1 | 0.866 | 0.924 | 11.861 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | CSO | 0 | -0.069 | -0.035 | 13.819 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ALA | 0 | 0.005 | 0.014 | 16.193 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | THR | 0 | -0.058 | -0.018 | 16.246 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | GLU | -1 | -0.814 | -0.880 | 19.065 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | HIS | 0 | 0.046 | 0.006 | 16.119 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | PHE | 0 | 0.006 | 0.011 | 15.715 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | THR | 0 | -0.035 | -0.040 | 19.453 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ARG | 1 | 0.714 | 0.815 | 22.399 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.041 | -0.033 | 21.439 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | VAL | 0 | 0.026 | 0.019 | 18.903 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | PRO | 0 | 0.009 | 0.011 | 22.286 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | LEU | 0 | -0.049 | -0.021 | 25.558 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ILE | 0 | -0.007 | 0.000 | 22.116 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ASN | 0 | -0.013 | -0.030 | 22.538 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ALA | 0 | -0.035 | 0.004 | 25.984 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | HIS | 0 | -0.039 | -0.022 | 28.746 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | GLN | 0 | -0.006 | 0.012 | 25.395 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | ARG | 1 | 0.716 | 0.791 | 26.505 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | GLN | 0 | -0.071 | -0.032 | 24.465 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | ASP | -1 | -0.864 | -0.923 | 24.016 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLY | 0 | 0.031 | 0.019 | 20.800 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | THR | 0 | -0.084 | -0.045 | 17.429 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | VAL | 0 | 0.043 | 0.006 | 12.903 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | VAL | 0 | -0.045 | -0.018 | 10.965 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | LEU | 0 | 0.017 | 0.004 | 8.944 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | MET | 0 | -0.058 | -0.034 | 6.223 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | ASP | -1 | -0.858 | -0.915 | 5.089 | 0.073 | 0.306 | 0.001 | -0.040 | -0.194 | 0.000 |
93 | A | 93 | ALA | 0 | -0.031 | -0.021 | 2.722 | -0.797 | -0.156 | 0.169 | -0.157 | -0.652 | 0.001 |
94 | A | 94 | VAL | 0 | 0.010 | 0.000 | 4.737 | -0.297 | -0.224 | -0.001 | -0.012 | -0.060 | 0.000 |
95 | A | 95 | PRO | 0 | -0.036 | -0.008 | 8.074 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |