FMODB ID: 436JN
Calculation Name: 1YZE-A-Xray372
Preferred Name: Ubiquitin carboxyl-terminal hydrolase 7
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 1YZE
Chain ID: A
ChEMBL ID: CHEMBL2157850
UniProt ID: Q93009
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 | 107 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -900941.569292 |
---|---|
FMO2-HF: Nuclear repulsion | 856383.373098 |
FMO2-HF: Total energy | -44558.196195 |
FMO2-MP2: Total energy | -44686.838152 |
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(A:65:TRP)
Summations of interaction energy for
fragment #1(A:65:TRP)
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. |
-4.53 | -2.883 | 2.264 | 0.709 | -4.616 | -0.006 |
Interaction energy analysis for fragmet #1(A:65:TRP)
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 | 67 | SER | 0 | 0.050 | 0.003 | 3.066 | 1.022 | -0.573 | 0.012 | 2.788 | -1.205 | 0.003 |
4 | A | 68 | GLU | -1 | -0.872 | -0.927 | 5.304 | 0.843 | 0.969 | -0.001 | -0.002 | -0.122 | 0.000 |
5 | A | 69 | ALA | 0 | -0.027 | -0.024 | 7.556 | 0.707 | 0.707 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 70 | THR | 0 | 0.037 | 0.032 | 10.071 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 71 | PHE | 0 | -0.021 | -0.012 | 12.426 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 72 | GLN | 0 | 0.056 | 0.000 | 14.449 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 73 | PHE | 0 | -0.015 | -0.005 | 17.942 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 74 | THR | 0 | -0.026 | -0.025 | 19.976 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 75 | VAL | 0 | -0.018 | 0.014 | 23.541 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 76 | GLU | -1 | -0.776 | -0.935 | 26.031 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 77 | ARG | 1 | 0.832 | 0.915 | 29.044 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 78 | PHE | 0 | 0.069 | 0.042 | 28.039 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 79 | SER | 0 | -0.028 | -0.022 | 31.389 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 80 | ARG | 1 | 0.925 | 0.942 | 35.021 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 81 | LEU | 0 | 0.028 | 0.037 | 33.076 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 82 | SER | 0 | -0.048 | -0.037 | 32.309 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 83 | GLU | -1 | -0.838 | -0.919 | 27.544 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 84 | SER | 0 | -0.012 | 0.003 | 22.782 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 85 | VAL | 0 | 0.024 | 0.011 | 23.852 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 86 | LEU | 0 | 0.006 | 0.011 | 19.001 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 87 | SER | 0 | 0.022 | 0.022 | 16.219 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 88 | PRO | 0 | 0.002 | -0.012 | 15.208 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 89 | PRO | 0 | 0.010 | 0.010 | 10.930 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 90 | CYS | 0 | -0.053 | -0.015 | 9.645 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 91 | PHE | 0 | 0.036 | -0.004 | 4.815 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 92 | VAL | 0 | 0.011 | 0.016 | 4.640 | 2.114 | 2.290 | -0.001 | -0.018 | -0.156 | 0.000 |
29 | A | 93 | ARG | 1 | 0.878 | 0.956 | 3.039 | -2.612 | -1.977 | 0.124 | -0.189 | -0.569 | 0.000 |
30 | A | 94 | ASN | 0 | -0.026 | -0.035 | 2.194 | -5.253 | -3.079 | 2.121 | -1.805 | -2.490 | -0.009 |
31 | A | 95 | LEU | 0 | 0.034 | 0.048 | 4.011 | -1.165 | -1.034 | 0.009 | -0.065 | -0.074 | 0.000 |
32 | A | 96 | PRO | 0 | -0.010 | 0.022 | 7.449 | 0.805 | 0.805 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 97 | TRP | 0 | 0.065 | -0.006 | 7.483 | -0.644 | -0.644 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 98 | LYS | 1 | 0.813 | 0.912 | 11.794 | -0.931 | -0.931 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 99 | ILE | 0 | 0.015 | 0.019 | 15.101 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 100 | MET | 0 | -0.012 | 0.001 | 18.160 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 101 | VAL | 0 | -0.029 | -0.005 | 21.484 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 102 | MET | 0 | 0.024 | 0.014 | 24.808 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 103 | PRO | 0 | 0.040 | 0.030 | 28.299 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 104 | ARG | 1 | 0.995 | 0.998 | 30.268 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 115 | VAL | 0 | -0.030 | -0.018 | 28.223 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 116 | GLY | 0 | -0.022 | -0.032 | 27.813 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 117 | PHE | 0 | -0.032 | -0.034 | 20.042 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 118 | PHE | 0 | -0.040 | -0.026 | 21.357 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 119 | LEU | 0 | -0.011 | 0.009 | 13.714 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 120 | GLN | 0 | 0.070 | 0.021 | 16.326 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 121 | CYS | 0 | -0.061 | -0.023 | 10.984 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 122 | ASN | 0 | 0.045 | -0.007 | 11.774 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 123 | ALA | 0 | -0.014 | -0.008 | 13.143 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 124 | GLU | -1 | -0.937 | -0.955 | 14.614 | 0.497 | 0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 125 | SER | 0 | -0.071 | -0.027 | 14.274 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 126 | ASP | -1 | -0.879 | -0.918 | 16.205 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 127 | SER | 0 | -0.022 | -0.013 | 15.602 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 128 | THR | 0 | -0.015 | -0.052 | 17.915 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 129 | SER | 0 | -0.010 | 0.002 | 17.138 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 130 | TRP | 0 | -0.017 | 0.027 | 12.426 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 131 | SER | 0 | 0.029 | -0.008 | 13.237 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 132 | CYS | 0 | -0.070 | -0.022 | 9.597 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 133 | HIS | 0 | 0.011 | 0.018 | 12.019 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 134 | ALA | 0 | 0.031 | 0.023 | 11.602 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 135 | GLN | 0 | -0.014 | -0.001 | 13.379 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 136 | ALA | 0 | 0.018 | 0.001 | 14.867 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 137 | VAL | 0 | -0.043 | -0.013 | 16.585 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 138 | LEU | 0 | 0.003 | 0.007 | 18.550 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 139 | LYS | 1 | 0.930 | 0.951 | 20.677 | -0.595 | -0.595 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 140 | ILE | 0 | 0.015 | 0.042 | 22.489 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 141 | ILE | 0 | -0.047 | -0.032 | 24.060 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 150 | PHE | 0 | 0.072 | 0.017 | 23.711 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 151 | SER | 0 | -0.042 | -0.027 | 22.961 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 152 | ARG | 1 | 0.905 | 0.952 | 23.627 | -0.367 | -0.367 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 153 | ARG | 1 | 0.922 | 0.968 | 19.914 | -0.437 | -0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 154 | ILE | 0 | -0.013 | 0.000 | 17.789 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 155 | SER | 0 | 0.029 | -0.017 | 18.185 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 156 | HIS | 1 | 0.777 | 0.912 | 17.251 | -0.597 | -0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 157 | LEU | 0 | 0.100 | 0.067 | 15.386 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 158 | PHE | 0 | -0.067 | -0.018 | 14.112 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 159 | PHE | 0 | 0.084 | 0.004 | 15.250 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 160 | HIS | 0 | 0.001 | 0.007 | 16.979 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 161 | LYS | 1 | 0.954 | 0.976 | 19.283 | -0.240 | -0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 162 | GLU | -1 | -0.890 | -0.929 | 20.185 | 0.357 | 0.357 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 163 | ASN | 0 | 0.035 | 0.006 | 16.243 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 164 | ASP | -1 | -0.828 | -0.926 | 17.005 | 0.622 | 0.622 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 165 | TRP | 0 | -0.027 | -0.019 | 19.100 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 166 | GLY | 0 | 0.014 | -0.005 | 20.119 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 167 | PHE | 0 | -0.043 | -0.003 | 22.634 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 168 | SER | 0 | 0.081 | 0.035 | 26.223 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 169 | ASN | 0 | -0.031 | -0.018 | 28.813 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 170 | PHE | 0 | -0.050 | -0.013 | 24.206 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 171 | MET | 0 | 0.011 | -0.009 | 28.713 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 172 | ALA | 0 | 0.028 | 0.030 | 31.683 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 173 | TRP | 0 | -0.003 | 0.001 | 30.760 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 188 | LYS | 1 | 0.937 | 0.990 | 27.077 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 189 | VAL | 0 | -0.050 | -0.036 | 27.073 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 190 | THR | 0 | 0.034 | 0.039 | 22.116 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 191 | PHE | 0 | 0.008 | 0.028 | 21.378 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 192 | GLU | -1 | -0.913 | -0.967 | 17.950 | 0.693 | 0.693 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 193 | VAL | 0 | -0.006 | -0.001 | 14.725 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 194 | PHE | 0 | -0.017 | 0.013 | 11.501 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 195 | VAL | 0 | 0.010 | 0.004 | 9.994 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 196 | GLN | 0 | -0.025 | -0.026 | 10.540 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 197 | ALA | 0 | 0.009 | -0.006 | 8.130 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 198 | ASP | -1 | -0.864 | -0.938 | 9.367 | 0.641 | 0.641 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 199 | ALA | 0 | -0.057 | -0.052 | 7.642 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 200 | PRO | 0 | 0.012 | -0.003 | 6.934 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 201 | HIS | 0 | 0.012 | 0.004 | 9.750 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 202 | GLY | 0 | 0.038 | 0.027 | 12.397 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 203 | VAL | 0 | -0.042 | -0.013 | 9.108 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |