FMODB ID: GNG91
Calculation Name: 2Z5E-A-Xray372
Preferred Name: Proteasome assembly chaperone 3
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2Z5E
Chain ID: A
ChEMBL ID: CHEMBL1075137
UniProt ID: Q9BT73
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 122 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -941968.602604 |
---|---|
FMO2-HF: Nuclear repulsion | 895653.036585 |
FMO2-HF: Total energy | -46315.566019 |
FMO2-MP2: Total energy | -46448.776533 |
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: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. |
-7.069 | -4.436 | 3.594 | -2.271 | -3.956 | -0.02 |
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 | ASP | -1 | -0.945 | -0.952 | 2.308 | -7.514 | -6.067 | 3.317 | -2.039 | -2.725 | -0.021 |
4 | A | 4 | THR | 0 | -0.034 | -0.026 | 3.663 | 1.187 | 1.488 | 0.000 | -0.041 | -0.260 | 0.000 |
5 | A | 5 | PRO | 0 | -0.003 | -0.010 | 4.814 | 0.416 | 0.549 | -0.001 | -0.004 | -0.128 | 0.000 |
6 | A | 6 | LEU | 0 | 0.038 | 0.022 | 2.853 | -1.126 | -0.374 | 0.278 | -0.187 | -0.843 | 0.001 |
7 | A | 7 | VAL | 0 | -0.055 | -0.019 | 6.608 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ILE | 0 | -0.014 | 0.005 | 10.350 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | SER | 0 | 0.014 | -0.016 | 13.007 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LYS | 1 | 0.912 | 0.971 | 15.710 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLN | 0 | 0.017 | 0.002 | 18.736 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | LYS | 1 | 0.951 | 0.978 | 21.467 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | THR | 0 | 0.004 | -0.001 | 24.984 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLU | -1 | -0.929 | -0.968 | 27.923 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | VAL | 0 | -0.001 | 0.007 | 31.332 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | VAL | 0 | 0.016 | 0.006 | 33.278 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | CYS | 0 | -0.044 | -0.015 | 36.169 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | GLY | 0 | 0.051 | 0.026 | 39.334 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | -0.014 | 0.003 | 35.545 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | PRO | 0 | -0.014 | -0.003 | 33.341 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | THR | 0 | -0.024 | -0.005 | 30.188 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | GLN | 0 | -0.023 | -0.003 | 26.001 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | VAL | 0 | 0.005 | -0.006 | 24.826 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | VAL | 0 | 0.034 | 0.011 | 19.275 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | CYS | 0 | -0.058 | -0.007 | 20.595 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | THR | 0 | 0.055 | 0.024 | 14.690 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ALA | 0 | -0.033 | -0.001 | 15.289 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | PHE | 0 | 0.026 | -0.001 | 13.558 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | SER | 0 | -0.005 | 0.000 | 14.423 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | SER | 0 | 0.035 | -0.004 | 15.882 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | HIS | 0 | 0.021 | 0.021 | 18.569 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ILE | 0 | -0.007 | 0.012 | 18.584 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | LEU | 0 | -0.016 | 0.003 | 18.815 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | VAL | 0 | 0.023 | -0.001 | 20.905 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | VAL | 0 | 0.003 | 0.002 | 22.464 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | VAL | 0 | 0.007 | -0.006 | 25.041 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | THR | 0 | -0.021 | -0.009 | 26.813 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLN | 0 | 0.110 | 0.034 | 29.618 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | PHE | 0 | -0.037 | -0.046 | 32.872 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLY | 0 | 0.063 | 0.037 | 29.913 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | LYS | 1 | 0.904 | 0.964 | 29.676 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | MET | 0 | 0.056 | 0.031 | 26.198 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLY | 0 | -0.022 | -0.015 | 28.836 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | THR | 0 | -0.043 | -0.016 | 31.216 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LEU | 0 | 0.009 | 0.013 | 25.329 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | VAL | 0 | 0.013 | -0.011 | 29.068 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | SER | 0 | 0.040 | 0.031 | 27.796 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | LEU | 0 | -0.075 | -0.050 | 27.975 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLU | -1 | -0.887 | -0.948 | 27.858 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PRO | 0 | 0.020 | 0.011 | 28.495 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | SER | 0 | -0.033 | -0.023 | 31.623 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | SER | 0 | 0.061 | 0.018 | 33.945 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | VAL | 0 | -0.016 | 0.005 | 35.399 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | ALA | 0 | -0.086 | -0.041 | 35.970 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | SER | 0 | 0.078 | 0.038 | 36.335 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ASP | -1 | -0.961 | -0.972 | 37.567 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | VAL | 0 | -0.047 | 0.002 | 38.596 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | SER | 0 | 0.009 | -0.020 | 35.978 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | LYS | 1 | 0.867 | 0.955 | 33.973 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | PRO | 0 | 0.108 | 0.053 | 32.124 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | VAL | 0 | -0.024 | -0.009 | 35.012 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | -0.010 | -0.008 | 30.901 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | THR | 0 | 0.006 | 0.002 | 33.365 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | THR | 0 | -0.021 | -0.001 | 32.635 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | LYS | 1 | 0.961 | 0.988 | 31.554 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | VAL | 0 | 0.012 | 0.011 | 32.091 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | LEU | 0 | -0.057 | -0.032 | 27.508 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | LEU | 0 | 0.043 | 0.014 | 27.837 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | GLY | 0 | 0.021 | 0.010 | 31.878 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | GLN | 0 | -0.021 | -0.016 | 34.767 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ASP | -1 | -0.843 | -0.911 | 37.756 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | GLU | -1 | -0.766 | -0.886 | 38.867 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | PRO | 0 | 0.039 | 0.007 | 40.195 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.002 | -0.006 | 40.862 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | ILE | 0 | -0.018 | -0.006 | 35.235 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | HIS | 1 | 0.808 | 0.882 | 36.167 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | VAL | 0 | 0.007 | 0.006 | 36.618 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | PHE | 0 | -0.008 | -0.014 | 34.246 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ALA | 0 | 0.032 | 0.023 | 32.232 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | LYS | 1 | 1.006 | 0.983 | 32.692 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ASN | 0 | -0.061 | -0.023 | 34.014 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | LEU | 0 | -0.030 | -0.013 | 30.762 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | VAL | 0 | 0.030 | 0.002 | 27.769 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | ALA | 0 | 0.033 | 0.020 | 29.211 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | PHE | 0 | -0.075 | -0.045 | 28.162 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | VAL | 0 | 0.048 | 0.039 | 24.249 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | SER | 0 | 0.010 | 0.008 | 25.634 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | GLN | 0 | -0.025 | -0.026 | 26.782 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | GLU | -1 | -0.743 | -0.811 | 26.265 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | ALA | 0 | -0.050 | -0.011 | 22.101 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | GLY | 0 | 0.002 | -0.003 | 22.204 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | ASN | 0 | -0.046 | -0.036 | 24.332 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | ARG | 1 | 0.882 | 0.959 | 16.371 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | ALA | 0 | 0.057 | 0.043 | 23.430 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 95 | VAL | 0 | -0.016 | -0.024 | 23.387 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 96 | LEU | 0 | -0.002 | 0.011 | 22.291 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 97 | LEU | 0 | -0.013 | -0.015 | 24.329 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 98 | ALA | 0 | 0.027 | 0.027 | 25.800 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 99 | VAL | 0 | 0.005 | 0.002 | 27.456 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 100 | ALA | 0 | -0.005 | -0.005 | 30.600 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 101 | VAL | 0 | 0.006 | 0.004 | 32.833 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 102 | LYS | 1 | 0.873 | 0.949 | 35.545 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 103 | ASP | -1 | -0.860 | -0.927 | 38.822 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 104 | LYS | 1 | 0.856 | 0.932 | 37.226 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 105 | SER | 0 | 0.095 | 0.044 | 40.090 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 106 | MET | 0 | 0.029 | 0.020 | 40.244 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 107 | GLU | -1 | -0.883 | -0.958 | 40.425 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 108 | GLY | 0 | 0.033 | -0.004 | 38.271 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 109 | LEU | 0 | -0.045 | -0.019 | 35.135 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 110 | LYS | 1 | 0.925 | 0.950 | 35.189 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 111 | ALA | 0 | 0.078 | 0.040 | 35.246 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 112 | LEU | 0 | -0.021 | -0.010 | 31.944 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 113 | ARG | 1 | 0.854 | 0.929 | 30.751 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 114 | GLU | -1 | -0.893 | -0.939 | 30.294 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 115 | VAL | 0 | -0.001 | 0.002 | 27.490 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 116 | ILE | 0 | -0.003 | -0.012 | 25.701 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 117 | ARG | 1 | 0.770 | 0.844 | 25.346 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 118 | VAL | 0 | -0.007 | -0.003 | 25.150 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 119 | CYS | 0 | -0.100 | -0.037 | 22.109 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 120 | GLN | 0 | 0.016 | 0.018 | 21.459 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 121 | VAL | 0 | -0.034 | -0.027 | 17.162 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 122 | TRP | 0 | 0.011 | -0.006 | 18.027 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |