FMODB ID: MN2QZ
Calculation Name: 2DST-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2DST
Chain ID: A
UniProt ID: Q5SI36
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 122 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -986774.748304 |
---|---|
FMO2-HF: Nuclear repulsion | 941316.326404 |
FMO2-HF: Total energy | -45458.4219 |
FMO2-MP2: Total energy | -45592.893107 |
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:2:ARG)
Summations of interaction energy for
fragment #1(A:2:ARG)
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. |
-203.934 | -193.585 | 23.892 | -15.01 | -19.232 | -0.132 |
Interaction energy analysis for fragmet #1(A:2:ARG)
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 | 4 | ALA | 0 | 0.079 | 0.038 | 3.800 | -1.534 | 0.714 | -0.027 | -1.105 | -1.116 | 0.006 |
4 | A | 5 | GLY | 0 | -0.045 | -0.022 | 6.046 | 2.367 | 2.367 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 6 | TYR | 0 | -0.022 | -0.017 | 9.131 | -0.401 | -0.401 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | LEU | 0 | 0.011 | 0.011 | 12.298 | 0.623 | 0.623 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | HIS | 0 | -0.058 | -0.035 | 15.086 | 0.359 | 0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | LEU | 0 | -0.013 | -0.014 | 17.755 | 0.356 | 0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | TYR | 0 | -0.002 | -0.009 | 20.010 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | GLY | 0 | 0.014 | 0.009 | 23.225 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | LEU | 0 | -0.007 | 0.013 | 19.270 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | ASN | 0 | 0.008 | 0.015 | 16.409 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | LEU | 0 | 0.015 | 0.012 | 12.051 | -0.427 | -0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | VAL | 0 | 0.025 | 0.005 | 8.951 | -0.328 | -0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | PHE | 0 | -0.035 | -0.018 | 7.498 | -0.546 | -0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | ASP | -1 | -0.759 | -0.856 | 2.265 | -47.811 | -47.119 | 0.885 | -0.460 | -1.117 | -0.002 |
17 | A | 18 | ARG | 1 | 0.819 | 0.918 | 3.630 | 27.962 | 28.527 | 0.007 | -0.174 | -0.398 | -0.001 |
18 | A | 19 | VAL | 0 | 0.009 | -0.011 | 2.209 | -4.778 | -3.852 | 7.681 | -3.909 | -4.699 | -0.024 |
19 | A | 20 | GLY | 0 | 0.072 | 0.065 | 3.785 | 0.651 | 0.844 | 0.010 | -0.088 | -0.115 | 0.000 |
20 | A | 21 | LYS | 1 | 0.924 | 0.941 | 7.280 | 20.700 | 20.700 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | GLY | 0 | 0.067 | 0.047 | 10.633 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | PRO | 0 | 0.011 | -0.005 | 13.324 | -0.387 | -0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | PRO | 0 | 0.003 | 0.014 | 12.346 | -1.552 | -1.552 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | VAL | 0 | -0.022 | -0.011 | 10.941 | 0.977 | 0.977 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | LEU | 0 | -0.001 | 0.007 | 10.295 | -2.553 | -2.553 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | LEU | 0 | -0.026 | 0.002 | 5.567 | 0.817 | 0.817 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | VAL | 0 | 0.012 | -0.016 | 8.958 | -1.076 | -1.076 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | ALA | 0 | 0.057 | 0.023 | 8.802 | 1.191 | 1.191 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | GLU | -1 | -0.779 | -0.873 | 10.787 | -22.690 | -22.690 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | GLU | -1 | -0.829 | -0.906 | 8.179 | -31.469 | -31.469 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | ALA | 0 | 0.018 | 0.014 | 3.985 | -1.674 | -1.569 | -0.001 | -0.013 | -0.091 | 0.000 |
32 | A | 33 | SER | 0 | -0.066 | -0.054 | 3.735 | -11.829 | -11.437 | 0.003 | -0.144 | -0.251 | -0.001 |
33 | A | 34 | ARG | 1 | 0.808 | 0.903 | 5.220 | 26.273 | 26.323 | -0.001 | 0.000 | -0.049 | 0.000 |
34 | A | 35 | TRP | 0 | -0.016 | -0.007 | 2.858 | 5.206 | 6.123 | 0.059 | -0.368 | -0.608 | -0.001 |
35 | A | 36 | PRO | 0 | 0.010 | 0.002 | 1.916 | -49.347 | -49.708 | 11.308 | -5.928 | -5.019 | -0.085 |
36 | A | 37 | GLU | -1 | -0.707 | -0.815 | 3.419 | -47.205 | -46.511 | 0.034 | -0.267 | -0.461 | -0.002 |
37 | A | 38 | ALA | 0 | -0.011 | -0.004 | 2.543 | -24.161 | -21.830 | 1.294 | -1.692 | -1.933 | -0.023 |
38 | A | 39 | LEU | 0 | -0.050 | -0.031 | 2.768 | 4.984 | 6.305 | 0.344 | -0.376 | -1.289 | 0.002 |
39 | A | 40 | PRO | 0 | -0.003 | 0.010 | 5.073 | 2.307 | 2.336 | -0.001 | 0.000 | -0.028 | 0.000 |
40 | A | 41 | GLU | -1 | -0.910 | -0.963 | 8.765 | -23.359 | -23.359 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | GLY | 0 | -0.008 | -0.011 | 10.766 | 1.017 | 1.017 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | TYR | 0 | 0.014 | -0.002 | 10.153 | 1.469 | 1.469 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | ALA | 0 | -0.110 | -0.039 | 8.681 | -1.859 | -1.859 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | PHE | 0 | 0.080 | 0.019 | 5.769 | 0.586 | 0.586 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | TYR | 0 | -0.017 | -0.023 | 6.678 | -1.165 | -1.165 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | LEU | 0 | -0.026 | -0.007 | 2.546 | -0.631 | -0.384 | 2.297 | -0.486 | -2.058 | -0.001 |
47 | A | 48 | LEU | 0 | 0.028 | 0.010 | 6.633 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | ASP | -1 | -0.707 | -0.799 | 8.235 | -33.546 | -33.546 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | LEU | 0 | -0.009 | 0.004 | 10.580 | 1.897 | 1.897 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | PRO | 0 | 0.046 | 0.007 | 13.947 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | GLY | 0 | -0.034 | 0.007 | 17.165 | 0.416 | 0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | TYR | 0 | -0.045 | -0.038 | 13.589 | 0.813 | 0.813 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | GLY | 0 | 0.027 | 0.018 | 11.410 | -0.720 | -0.720 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | ARG | 1 | 0.697 | 0.779 | 5.893 | 36.930 | 36.930 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | THR | 0 | -0.026 | -0.014 | 13.038 | 0.763 | 0.763 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | GLU | -1 | -0.930 | -0.948 | 15.146 | -13.728 | -13.728 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | GLY | 0 | 0.033 | -0.003 | 18.811 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | PRO | 0 | -0.019 | 0.003 | 20.661 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | ARG | 1 | 0.872 | 0.918 | 17.882 | 15.361 | 15.361 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | MET | 0 | -0.033 | -0.005 | 21.566 | 0.389 | 0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | ALA | 0 | 0.010 | 0.009 | 22.230 | -0.440 | -0.440 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | PRO | 0 | 0.037 | 0.003 | 21.012 | -0.415 | -0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | GLU | -1 | -0.823 | -0.931 | 21.708 | -12.476 | -12.476 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | GLU | -1 | -0.900 | -0.949 | 23.823 | -11.984 | -11.984 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | LEU | 0 | -0.001 | -0.009 | 17.729 | -0.403 | -0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ALA | 0 | -0.003 | -0.005 | 19.014 | -0.763 | -0.763 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | HIS | 0 | 0.052 | 0.018 | 20.459 | -0.345 | -0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | PHE | 0 | -0.003 | 0.008 | 17.837 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | VAL | 0 | -0.008 | 0.006 | 15.195 | -0.551 | -0.551 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | ALA | 0 | 0.019 | 0.009 | 17.306 | -0.340 | -0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | GLY | 0 | 0.000 | -0.008 | 20.152 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | PHE | 0 | -0.010 | -0.022 | 10.929 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | ALA | 0 | 0.025 | 0.007 | 16.439 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | VAL | 0 | -0.011 | 0.006 | 17.393 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | MET | 0 | -0.019 | 0.005 | 18.105 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | MET | 0 | -0.062 | -0.028 | 11.752 | 0.290 | 0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | ASN | 0 | -0.077 | -0.039 | 15.943 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | LEU | 0 | -0.024 | -0.021 | 13.159 | -0.293 | -0.293 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | GLY | 0 | -0.007 | 0.009 | 16.994 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 81 | ALA | 0 | 0.000 | -0.009 | 20.457 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 82 | PRO | 0 | -0.038 | -0.003 | 15.164 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 83 | TRP | 0 | 0.018 | -0.002 | 15.634 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 84 | VAL | 0 | 0.015 | -0.003 | 13.837 | -1.323 | -1.323 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 85 | LEU | 0 | -0.019 | -0.003 | 9.808 | 1.012 | 1.012 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 86 | LEU | 0 | -0.049 | -0.020 | 11.748 | -0.938 | -0.938 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 87 | ARG | 1 | 0.807 | 0.864 | 6.441 | 34.443 | 34.443 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | GLY | 0 | -0.002 | -0.010 | 12.021 | -0.305 | -0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | LEU | 0 | -0.031 | -0.025 | 13.843 | 1.111 | 1.111 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | GLY | 0 | 0.023 | 0.011 | 13.757 | 0.970 | 0.970 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | LEU | 0 | -0.011 | -0.007 | 14.722 | 0.836 | 0.836 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 92 | ALA | 0 | -0.028 | -0.013 | 16.997 | 0.880 | 0.880 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | LEU | 0 | -0.027 | -0.013 | 16.194 | 0.716 | 0.716 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | GLY | 0 | 0.023 | 0.012 | 19.033 | 0.387 | 0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | PRO | 0 | 0.004 | -0.006 | 20.063 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | HIS | 0 | 0.041 | 0.024 | 22.818 | 0.379 | 0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | LEU | 0 | -0.009 | -0.001 | 17.145 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | GLU | -1 | -0.781 | -0.869 | 21.592 | -13.608 | -13.608 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | ALA | 0 | -0.061 | -0.023 | 23.699 | 0.388 | 0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | LEU | 0 | -0.045 | -0.014 | 22.966 | 0.412 | 0.412 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | GLY | 0 | -0.059 | -0.027 | 25.072 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | LEU | 0 | -0.044 | -0.016 | 18.299 | -0.207 | -0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ARG | 1 | 0.818 | 0.904 | 20.239 | 13.229 | 13.229 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | ALA | 0 | 0.009 | 0.007 | 17.381 | -1.109 | -1.109 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | LEU | 0 | -0.052 | -0.033 | 15.349 | 0.888 | 0.888 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | PRO | 0 | 0.004 | 0.008 | 14.829 | -1.391 | -1.391 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | ALA | 0 | 0.014 | -0.007 | 10.829 | 0.312 | 0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | GLU | -1 | -0.851 | -0.921 | 11.508 | -23.349 | -23.349 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | GLY | 0 | -0.011 | -0.007 | 12.840 | -0.754 | -0.754 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | VAL | 0 | -0.035 | -0.004 | 12.602 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 111 | GLU | -1 | -0.856 | -0.919 | 8.246 | -32.944 | -32.944 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 112 | VAL | 0 | 0.007 | -0.024 | 6.664 | 2.643 | 2.643 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 113 | ALA | 0 | 0.004 | -0.003 | 8.801 | 2.373 | 2.373 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 114 | GLU | -1 | -0.894 | -0.924 | 10.523 | -17.028 | -17.028 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 115 | VAL | 0 | 0.012 | 0.015 | 12.085 | 1.732 | 1.732 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 116 | LEU | 0 | -0.013 | -0.014 | 11.037 | 1.594 | 1.594 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 117 | SER | 0 | -0.010 | -0.013 | 14.421 | 1.630 | 1.630 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 118 | SER | 0 | 0.018 | 0.000 | 16.332 | 1.571 | 1.571 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 119 | LYS | 1 | 0.887 | 0.949 | 17.404 | 15.776 | 15.776 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 120 | LEU | 0 | -0.062 | -0.031 | 16.659 | 0.716 | 0.716 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 121 | SER | 0 | -0.045 | -0.019 | 19.687 | 0.731 | 0.731 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 122 | TYR | 0 | -0.043 | -0.017 | 20.150 | 0.940 | 0.940 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 123 | GLY | 0 | -0.031 | -0.004 | 23.489 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |