![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 98432
Calculation Name: 3HDV-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3HDV
Chain ID: A
UniProt ID: Q88QX9
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 | 120 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1004905.646939 |
---|---|
FMO2-HF: Nuclear repulsion | 958725.751919 |
FMO2-HF: Total energy | -46179.895021 |
FMO2-MP2: Total energy | -46315.728368 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033316/ligand_interaction/ligand_F033316.png)
Ligand Interaction
![ligand interaction](./Kdata/F033316/ligand_interaction/ligand_interaction_F033316.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:68:ARG)
Summations of interaction energy for
fragment #1(A:68: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. |
-100.623 | -89.677 | 3.005 | -5.857 | -8.093 | -0.046 |
Interaction energy analysis for fragmet #1(A:68: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 | 70 | LEU | 0 | -0.057 | -0.021 | 3.060 | -11.555 | -8.153 | 0.103 | -1.856 | -1.649 | -0.006 |
4 | A | 71 | VAL | 0 | 0.017 | 0.013 | 5.526 | 4.048 | 4.048 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 72 | LEU | 0 | -0.011 | 0.001 | 8.748 | -0.946 | -0.946 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 73 | VAL | 0 | -0.019 | -0.020 | 11.810 | 1.115 | 1.115 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 74 | VAL | 0 | 0.015 | -0.007 | 14.551 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 75 | ASP | -1 | -0.818 | -0.944 | 18.013 | -14.653 | -14.653 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 76 | ASP | -1 | -0.779 | -0.872 | 20.621 | -12.941 | -12.941 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 77 | ASN | 0 | -0.010 | 0.007 | 22.514 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 78 | ALA | 0 | 0.033 | -0.004 | 19.972 | -0.757 | -0.757 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 79 | VAL | 0 | -0.003 | -0.002 | 18.906 | -0.836 | -0.836 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 80 | ASN | 0 | -0.025 | -0.011 | 18.780 | -0.479 | -0.479 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 81 | ARG | 1 | 0.824 | 0.927 | 15.637 | 16.537 | 16.537 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 82 | GLU | -1 | -0.856 | -0.933 | 14.406 | -22.329 | -22.329 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 83 | ALA | 0 | -0.013 | 0.005 | 13.667 | -1.400 | -1.400 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 84 | LEU | 0 | -0.008 | -0.003 | 13.115 | -0.981 | -0.981 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 85 | ILE | 0 | 0.017 | 0.010 | 9.437 | -2.588 | -2.588 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 86 | LEU | 0 | -0.024 | -0.006 | 8.900 | -3.601 | -3.601 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 87 | TYR | 0 | 0.056 | 0.022 | 9.346 | -2.234 | -2.234 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 88 | LEU | 0 | 0.049 | 0.029 | 7.647 | -1.339 | -1.339 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 89 | LYS | 1 | 0.898 | 0.975 | 4.729 | 33.827 | 33.915 | -0.001 | -0.003 | -0.084 | 0.000 |
23 | A | 90 | SER | 0 | -0.113 | -0.060 | 5.288 | -2.941 | -2.941 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 91 | ARG | 1 | 0.885 | 0.936 | 7.252 | 27.233 | 27.233 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 92 | GLY | 0 | -0.009 | 0.005 | 3.815 | 1.526 | 1.691 | 0.001 | -0.060 | -0.105 | 0.000 |
26 | A | 93 | ILE | 0 | -0.050 | -0.023 | 2.330 | -25.184 | -22.091 | 1.304 | -2.259 | -2.138 | -0.032 |
27 | A | 94 | ASP | -1 | -0.852 | -0.923 | 2.759 | -58.116 | -56.178 | 1.320 | -0.832 | -2.425 | -0.004 |
28 | A | 95 | ALA | 0 | 0.033 | 0.003 | 4.277 | 4.534 | 4.741 | 0.013 | -0.058 | -0.162 | 0.000 |
29 | A | 96 | VAL | 0 | 0.004 | -0.006 | 7.993 | -0.631 | -0.631 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 97 | GLY | 0 | 0.032 | 0.012 | 11.069 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 98 | ALA | 0 | -0.045 | -0.022 | 14.628 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 99 | ASP | -1 | -0.952 | -0.996 | 17.642 | -14.366 | -14.366 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 100 | GLY | 0 | 0.108 | 0.042 | 20.828 | 0.782 | 0.782 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 101 | ALA | 0 | -0.006 | -0.007 | 21.072 | -0.700 | -0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 102 | GLU | -1 | -0.941 | -0.966 | 21.932 | -12.395 | -12.395 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 103 | GLU | -1 | -0.829 | -0.909 | 18.294 | -17.322 | -17.322 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 104 | ALA | 0 | -0.003 | -0.004 | 17.341 | -0.981 | -0.981 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 105 | ARG | 1 | 0.800 | 0.833 | 17.287 | 11.847 | 11.847 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 106 | LEU | 0 | 0.012 | 0.021 | 17.987 | -0.385 | -0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 107 | TYR | 0 | 0.022 | -0.003 | 12.073 | -1.466 | -1.466 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 108 | LEU | 0 | -0.026 | -0.012 | 13.424 | -1.164 | -1.164 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 109 | HIS | 0 | -0.001 | 0.020 | 14.041 | -0.605 | -0.605 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 110 | TYR | 0 | -0.005 | -0.031 | 12.733 | -0.628 | -0.628 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 111 | GLN | 0 | 0.013 | 0.012 | 7.781 | -1.323 | -1.323 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 112 | LYS | 1 | 0.906 | 0.947 | 9.081 | 17.354 | 17.354 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 113 | ARG | 1 | 0.769 | 0.877 | 2.833 | 51.806 | 53.859 | 0.265 | -0.789 | -1.530 | -0.004 |
47 | A | 114 | ILE | 0 | -0.039 | -0.007 | 6.029 | -2.963 | -2.963 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 115 | GLY | 0 | 0.012 | 0.017 | 8.244 | 2.409 | 2.409 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 116 | LEU | 0 | -0.034 | -0.012 | 9.541 | 1.403 | 1.403 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 117 | MET | 0 | 0.007 | 0.018 | 11.271 | -1.471 | -1.471 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 118 | ILE | 0 | -0.020 | -0.008 | 12.346 | 0.647 | 0.647 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 119 | THR | 0 | 0.005 | -0.007 | 15.946 | -0.300 | -0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 120 | ASP | -1 | -0.745 | -0.845 | 19.283 | -13.057 | -13.057 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 121 | LEU | 0 | -0.027 | -0.029 | 22.327 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 122 | ARG | 1 | 0.739 | 0.836 | 25.809 | 11.127 | 11.127 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 123 | MET | 0 | -0.030 | 0.010 | 22.275 | -0.624 | -0.624 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 124 | GLN | 0 | -0.045 | -0.005 | 27.110 | 0.713 | 0.713 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 125 | PRO | 0 | -0.027 | -0.026 | 27.732 | -0.325 | -0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 126 | GLU | -1 | -0.778 | -0.863 | 26.620 | -11.560 | -11.560 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 127 | SER | 0 | 0.020 | -0.006 | 26.798 | -0.522 | -0.522 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 128 | GLY | 0 | 0.038 | 0.007 | 23.994 | -0.282 | -0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 129 | LEU | 0 | -0.001 | -0.001 | 24.490 | -0.342 | -0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 130 | ASP | -1 | -0.862 | -0.909 | 26.812 | -10.463 | -10.463 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 131 | LEU | 0 | 0.020 | 0.021 | 19.939 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 132 | ILE | 0 | -0.008 | -0.006 | 21.559 | -0.301 | -0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 133 | ARG | 1 | 0.854 | 0.921 | 23.397 | 10.179 | 10.179 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 134 | THR | 0 | -0.037 | -0.014 | 24.463 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 135 | ILE | 0 | 0.004 | 0.001 | 18.729 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 136 | ARG | 1 | 0.795 | 0.888 | 19.216 | 14.055 | 14.055 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 137 | ALA | 0 | -0.055 | -0.012 | 23.479 | 0.283 | 0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 138 | SER | 0 | -0.044 | -0.023 | 20.798 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 139 | GLU | -1 | -0.879 | -0.961 | 17.872 | -14.022 | -14.022 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 140 | ARG | 1 | 0.760 | 0.869 | 10.967 | 19.776 | 19.776 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 141 | ALA | 0 | 0.060 | 0.039 | 17.590 | -0.470 | -0.470 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 142 | ALA | 0 | -0.022 | -0.015 | 16.778 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 143 | LEU | 0 | -0.044 | 0.005 | 13.421 | -0.698 | -0.698 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 144 | SER | 0 | 0.006 | 0.001 | 13.850 | 0.997 | 0.997 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 145 | ILE | 0 | 0.005 | -0.010 | 14.990 | -1.083 | -1.083 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 146 | ILE | 0 | -0.015 | -0.004 | 14.687 | 0.640 | 0.640 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 147 | VAL | 0 | 0.050 | 0.031 | 18.223 | -0.421 | -0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 148 | VAL | 0 | -0.051 | -0.030 | 17.678 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 149 | SER | 0 | 0.054 | 0.017 | 20.912 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 150 | GLY | 0 | -0.022 | -0.023 | 24.282 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 151 | ASP | -1 | -0.931 | -0.967 | 26.507 | -9.860 | -9.860 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 152 | THR | 0 | -0.017 | 0.007 | 28.669 | -0.282 | -0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 153 | ASP | -1 | -0.828 | -0.894 | 31.046 | -9.078 | -9.078 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 154 | VAL | 0 | 0.004 | -0.015 | 32.702 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 155 | GLU | -1 | -0.936 | -0.965 | 33.909 | -8.322 | -8.322 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 156 | GLU | -1 | -0.775 | -0.866 | 29.569 | -10.870 | -10.870 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 157 | ALA | 0 | -0.010 | -0.012 | 29.326 | -0.325 | -0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 158 | VAL | 0 | -0.024 | -0.015 | 29.611 | -0.256 | -0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 159 | ASP | -1 | -0.853 | -0.919 | 31.130 | -9.856 | -9.856 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 160 | VAL | 0 | 0.009 | -0.011 | 25.156 | -0.270 | -0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 161 | MET | 0 | -0.058 | -0.022 | 25.196 | -0.545 | -0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 162 | HIS | 0 | -0.016 | -0.002 | 27.651 | -0.221 | -0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 163 | LEU | 0 | -0.060 | -0.013 | 25.511 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 164 | GLY | 0 | 0.019 | 0.014 | 24.407 | -0.458 | -0.458 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 165 | VAL | 0 | -0.072 | -0.030 | 21.144 | -0.647 | -0.647 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 166 | VAL | 0 | -0.049 | -0.024 | 16.761 | 0.253 | 0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 167 | ASP | -1 | -0.785 | -0.897 | 20.129 | -13.647 | -13.647 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 168 | PHE | 0 | 0.034 | 0.009 | 21.543 | -0.409 | -0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 169 | LEU | 0 | -0.068 | -0.032 | 18.488 | 0.366 | 0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 170 | LEU | 0 | 0.049 | 0.020 | 22.674 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 171 | LYS | 1 | 0.799 | 0.904 | 20.809 | 14.104 | 14.104 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 172 | PRO | 0 | -0.004 | -0.009 | 23.254 | 0.453 | 0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 173 | VAL | 0 | 0.021 | 0.014 | 17.834 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 174 | ASP | -1 | -0.838 | -0.914 | 20.006 | -15.069 | -15.069 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 175 | LEU | 0 | -0.020 | -0.027 | 14.803 | -0.645 | -0.645 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 176 | GLY | 0 | 0.000 | 0.007 | 15.234 | -1.259 | -1.259 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 177 | LYS | 1 | 0.926 | 0.955 | 16.299 | 13.263 | 13.263 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 178 | LEU | 0 | -0.002 | -0.002 | 13.648 | -0.608 | -0.608 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 179 | LEU | 0 | -0.028 | -0.022 | 9.817 | -1.283 | -1.283 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 180 | GLU | -1 | -0.962 | -0.962 | 12.139 | -17.571 | -17.571 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 181 | LEU | 0 | -0.018 | -0.013 | 14.517 | -0.454 | -0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 182 | VAL | 0 | -0.006 | -0.006 | 9.073 | -0.520 | -0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 183 | ASN | 0 | -0.003 | -0.017 | 9.009 | -3.732 | -3.732 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 184 | LYS | 1 | 0.910 | 0.972 | 10.916 | 16.493 | 16.493 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 185 | GLU | -1 | -0.856 | -0.937 | 13.144 | -17.946 | -17.946 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 186 | LEU | 0 | -0.007 | 0.013 | 6.387 | -0.495 | -0.495 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 187 | LYS | 1 | 0.783 | 0.903 | 8.475 | 20.017 | 20.017 | 0.000 | 0.000 | 0.000 | 0.000 |