![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6YYGZ
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 | 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 | 95 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -720769.804822 |
---|---|
FMO2-HF: Nuclear repulsion | 682136.995735 |
FMO2-HF: Total energy | -38632.809087 |
FMO2-MP2: Total energy | -38745.224101 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033492/ligand_interaction/ligand_F033492.png)
Ligand Interaction
![ligand interaction](./Kdata/F033492/ligand_interaction/ligand_interaction_F033492.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. |
-21.107 | -9.422 | 9.452 | -6.951 | -14.19 | -0.07 |
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 | 0.879 | 0.929 | 2.593 | -0.110 | 2.629 | 2.325 | -1.246 | -3.818 | -0.001 |
4 | A | 4 | VAL | 0 | -0.011 | -0.013 | 4.231 | -1.031 | -1.131 | 0.032 | 0.240 | -0.173 | 0.000 |
5 | A | 5 | ILE | 0 | -0.004 | 0.007 | 8.039 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | ALA | 0 | 0.011 | 0.008 | 10.420 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | GLN | 0 | -0.025 | -0.007 | 14.081 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ASP | -1 | -0.738 | -0.826 | 17.352 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | PHE | 0 | -0.023 | -0.034 | 20.402 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ILE | 0 | 0.000 | 0.011 | 24.084 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LYS | 1 | 0.897 | 0.941 | 26.554 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | PRO | 0 | 0.009 | -0.006 | 30.193 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | GLU | -1 | -0.901 | -0.961 | 31.406 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | ALA | 0 | 0.010 | 0.001 | 30.933 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ILE | 0 | -0.004 | 0.010 | 27.044 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | ASP | -1 | -0.899 | -0.964 | 28.361 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ILE | 0 | -0.060 | -0.020 | 30.825 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | VAL | 0 | 0.026 | 0.017 | 25.704 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | LEU | 0 | -0.006 | 0.008 | 24.392 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | PRO | 0 | -0.063 | -0.037 | 25.161 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LEU | 0 | 0.030 | 0.023 | 24.786 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | TYR | 0 | 0.007 | -0.041 | 20.371 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.898 | 0.955 | 20.644 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.757 | -0.838 | 21.264 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | 0.048 | 0.030 | 17.708 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | -0.023 | -0.001 | 15.847 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | GLU | -1 | -0.882 | -0.921 | 16.682 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | LYS | 1 | 0.838 | 0.887 | 18.302 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | THR | 0 | -0.011 | -0.011 | 12.398 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ARG | 1 | 0.809 | 0.882 | 13.403 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | GLN | 0 | -0.109 | -0.045 | 14.480 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | GLU | -1 | -0.750 | -0.861 | 12.536 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | PRO | 0 | -0.042 | -0.035 | 12.290 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LEU | 0 | -0.033 | -0.009 | 9.057 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | CSO | 0 | -0.034 | -0.013 | 7.635 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LEU | 0 | -0.031 | -0.007 | 2.669 | -0.634 | 0.004 | 0.416 | -0.217 | -0.838 | -0.001 |
37 | A | 37 | ALA | 0 | 0.002 | -0.006 | 6.488 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | TYR | 0 | -0.028 | -0.045 | 8.302 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ASP | -1 | -0.895 | -0.923 | 10.293 | -0.312 | -0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | LEU | 0 | -0.018 | -0.008 | 12.770 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | PHE | 0 | -0.035 | -0.010 | 12.215 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | VAL | 0 | 0.023 | 0.009 | 17.394 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASP | -1 | -0.810 | -0.880 | 20.428 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | GLN | 0 | -0.003 | -0.016 | 21.732 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LYS | 1 | 0.830 | 0.914 | 22.321 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASP | -1 | -0.774 | -0.865 | 24.602 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | PRO | 0 | 0.028 | 0.008 | 24.445 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLY | 0 | 0.051 | 0.040 | 25.567 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | HIS | 1 | 0.742 | 0.869 | 18.613 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PHE | 0 | 0.029 | 0.010 | 19.630 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | VAL | 0 | -0.027 | -0.023 | 13.660 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | PHE | 0 | 0.040 | 0.022 | 13.287 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ILE | 0 | -0.047 | -0.031 | 7.736 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | GLU | -1 | -0.737 | -0.850 | 8.568 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLU | -1 | -0.866 | -0.927 | 2.537 | -10.616 | -7.669 | 4.383 | -2.553 | -4.777 | -0.034 |
56 | A | 56 | TRP | 0 | 0.024 | 0.017 | 3.617 | -1.078 | -0.648 | 0.004 | -0.102 | -0.332 | 0.000 |
57 | A | 57 | PRO | 0 | 0.018 | 0.000 | 2.601 | -3.574 | -1.377 | 1.166 | -1.434 | -1.929 | -0.017 |
58 | A | 58 | ASP | -1 | -0.790 | -0.902 | 2.604 | -3.380 | -1.536 | 1.026 | -1.461 | -1.410 | -0.017 |
59 | A | 59 | ARG | 1 | 0.842 | 0.887 | 4.920 | 0.348 | 0.395 | -0.001 | -0.003 | -0.043 | 0.000 |
60 | A | 60 | ALA | 0 | 0.008 | 0.001 | 8.357 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ALA | 0 | -0.025 | -0.014 | 7.143 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | 0.008 | 0.015 | 8.396 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ASP | -1 | -0.766 | -0.853 | 9.896 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ILE | 0 | -0.042 | -0.020 | 12.126 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | HIS | 1 | 0.825 | 0.900 | 11.592 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | CSO | 0 | -0.100 | -0.061 | 13.449 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ALA | 0 | -0.008 | 0.003 | 15.867 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | THR | 0 | -0.043 | -0.012 | 15.809 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | GLU | -1 | -0.830 | -0.878 | 18.634 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | HIS | 0 | 0.051 | 0.010 | 15.804 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | PHE | 0 | 0.004 | 0.010 | 15.533 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | THR | 0 | -0.041 | -0.050 | 19.206 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ARG | 1 | 0.711 | 0.803 | 22.185 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.042 | -0.027 | 21.379 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | VAL | 0 | 0.029 | 0.025 | 18.786 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | PRO | 0 | -0.008 | -0.003 | 22.171 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | LEU | 0 | -0.041 | -0.018 | 25.511 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ILE | 0 | -0.002 | 0.005 | 22.098 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ASN | 0 | -0.006 | -0.024 | 22.200 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ALA | 0 | -0.010 | 0.014 | 25.849 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | HIS | 0 | -0.030 | -0.023 | 28.442 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | GLN | 0 | -0.005 | 0.011 | 25.130 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | ARG | 1 | 0.737 | 0.826 | 26.376 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | GLN | 0 | -0.047 | -0.022 | 24.767 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | ASP | -1 | -0.875 | -0.935 | 24.190 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | GLY | 0 | 0.033 | 0.022 | 20.980 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | THR | 0 | -0.071 | -0.038 | 17.403 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | VAL | 0 | 0.036 | 0.003 | 13.028 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | VAL | 0 | -0.026 | -0.009 | 10.972 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | LEU | 0 | 0.009 | 0.008 | 8.852 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | MET | 0 | -0.054 | -0.035 | 6.362 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | ASP | -1 | -0.858 | -0.920 | 5.086 | 0.174 | 0.423 | 0.000 | -0.035 | -0.214 | 0.000 |
93 | A | 93 | ALA | 0 | -0.031 | -0.015 | 2.845 | -0.549 | 0.068 | 0.102 | -0.131 | -0.589 | 0.000 |
94 | A | 94 | VAL | 0 | 0.002 | -0.005 | 4.857 | -0.278 | -0.201 | -0.001 | -0.009 | -0.067 | 0.000 |
95 | A | 95 | PRO | 0 | -0.036 | -0.008 | 8.251 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |