![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: MNV5Z
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 | 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 | 120 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1009038.993616 |
---|---|
FMO2-HF: Nuclear repulsion | 962858.767994 |
FMO2-HF: Total energy | -46180.225622 |
FMO2-MP2: Total energy | -46316.082164 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033315/ligand_interaction/ligand_F033315.png)
Ligand Interaction
![ligand interaction](./Kdata/F033315/ligand_interaction/ligand_interaction_F033315.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. |
-118.33 | -110.171 | 12.081 | -8.806 | -11.436 | -0.085 |
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 | -0.039 | -0.016 | 2.640 | -14.702 | -11.045 | 0.639 | -2.138 | -2.158 | -0.014 |
4 | A | 71 | VAL | 0 | 0.028 | 0.017 | 5.417 | 4.097 | 4.097 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 72 | LEU | 0 | -0.003 | 0.007 | 8.729 | -1.148 | -1.148 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 73 | VAL | 0 | -0.012 | -0.009 | 12.025 | 1.038 | 1.038 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 74 | VAL | 0 | 0.015 | -0.009 | 14.745 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 75 | ASP | -1 | -0.755 | -0.902 | 18.286 | -14.752 | -14.752 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 76 | ASP | -1 | -0.768 | -0.874 | 20.769 | -12.887 | -12.887 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 77 | ASN | 0 | 0.002 | 0.009 | 23.053 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 78 | ALA | 0 | 0.035 | -0.003 | 19.544 | -0.687 | -0.687 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 79 | VAL | 0 | -0.032 | -0.011 | 18.535 | -0.910 | -0.910 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 80 | ASN | 0 | -0.060 | -0.033 | 18.773 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 81 | ARG | 1 | 0.802 | 0.921 | 15.575 | 16.547 | 16.547 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 82 | GLU | -1 | -0.814 | -0.914 | 13.898 | -22.651 | -22.651 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 83 | ALA | 0 | -0.011 | 0.009 | 13.119 | -1.577 | -1.577 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 84 | LEU | 0 | 0.011 | 0.008 | 12.742 | -1.205 | -1.205 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 85 | ILE | 0 | 0.005 | 0.004 | 9.263 | -2.759 | -2.759 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 86 | LEU | 0 | -0.020 | -0.008 | 8.478 | -3.997 | -3.997 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 87 | TYR | 0 | 0.023 | 0.010 | 8.926 | -2.443 | -2.443 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 88 | LEU | 0 | 0.031 | 0.016 | 7.373 | -1.589 | -1.589 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 89 | LYS | 1 | 0.876 | 0.959 | 4.281 | 36.414 | 36.565 | -0.001 | -0.009 | -0.141 | 0.000 |
23 | A | 90 | SER | 0 | -0.096 | -0.057 | 4.983 | -2.917 | -2.871 | -0.001 | 0.000 | -0.045 | 0.000 |
24 | A | 91 | ARG | 1 | 0.885 | 0.938 | 7.097 | 28.983 | 28.983 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 92 | GLY | 0 | 0.003 | 0.015 | 3.456 | 1.985 | 2.438 | 0.009 | -0.244 | -0.218 | -0.001 |
26 | A | 93 | ILE | 0 | -0.031 | -0.003 | 1.828 | -36.403 | -37.698 | 8.765 | -3.983 | -3.488 | -0.056 |
27 | A | 94 | ASP | -1 | -0.800 | -0.895 | 2.647 | -65.550 | -62.844 | 1.983 | -1.426 | -3.263 | -0.008 |
28 | A | 95 | ALA | 0 | 0.002 | -0.013 | 4.230 | 6.065 | 6.320 | 0.017 | -0.061 | -0.212 | 0.000 |
29 | A | 96 | VAL | 0 | -0.014 | -0.005 | 7.970 | -0.967 | -0.967 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 97 | GLY | 0 | 0.043 | 0.010 | 10.819 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 98 | ALA | 0 | -0.048 | -0.021 | 14.605 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 99 | ASP | -1 | -0.937 | -0.988 | 17.869 | -14.227 | -14.227 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 100 | GLY | 0 | 0.114 | 0.047 | 21.350 | 0.655 | 0.655 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 101 | ALA | 0 | -0.013 | -0.005 | 21.343 | -0.659 | -0.659 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 102 | GLU | -1 | -0.946 | -0.968 | 22.187 | -12.320 | -12.320 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 103 | GLU | -1 | -0.799 | -0.898 | 18.196 | -17.511 | -17.511 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 104 | ALA | 0 | 0.000 | -0.008 | 17.379 | -0.995 | -0.995 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 105 | ARG | 1 | 0.803 | 0.840 | 17.346 | 11.851 | 11.851 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 106 | LEU | 0 | 0.007 | 0.018 | 18.409 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 107 | TYR | 0 | -0.009 | -0.023 | 12.393 | -1.406 | -1.406 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 108 | LEU | 0 | -0.029 | -0.010 | 13.775 | -1.071 | -1.071 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 109 | HIS | 0 | 0.031 | 0.042 | 14.573 | -0.691 | -0.691 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 110 | TYR | 0 | 0.015 | -0.006 | 12.942 | -0.603 | -0.603 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 111 | GLN | 0 | 0.004 | 0.010 | 8.320 | -1.147 | -1.147 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 112 | LYS | 1 | 0.872 | 0.911 | 9.456 | 17.268 | 17.268 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 113 | ARG | 1 | 0.738 | 0.854 | 2.730 | 53.705 | 55.891 | 0.670 | -0.945 | -1.911 | -0.006 |
47 | A | 114 | ILE | 0 | -0.042 | -0.007 | 6.549 | -3.201 | -3.201 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 115 | GLY | 0 | 0.006 | 0.014 | 8.217 | 2.418 | 2.418 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 116 | LEU | 0 | -0.023 | -0.007 | 9.686 | 1.648 | 1.648 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 117 | MET | 0 | -0.009 | 0.004 | 11.229 | -1.430 | -1.430 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 118 | ILE | 0 | -0.019 | -0.009 | 12.347 | 0.557 | 0.557 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 119 | THR | 0 | 0.009 | -0.010 | 15.907 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 120 | ASP | -1 | -0.710 | -0.824 | 19.371 | -12.959 | -12.959 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 121 | LEU | 0 | -0.044 | -0.031 | 22.499 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 122 | ARG | 1 | 0.787 | 0.851 | 25.917 | 11.088 | 11.088 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 123 | MET | 0 | -0.072 | -0.003 | 22.066 | -0.553 | -0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 124 | GLN | 0 | -0.019 | -0.001 | 27.013 | 0.713 | 0.713 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 125 | PRO | 0 | -0.027 | -0.020 | 27.501 | -0.365 | -0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 126 | GLU | -1 | -0.799 | -0.873 | 26.769 | -11.518 | -11.518 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 127 | SER | 0 | 0.028 | 0.003 | 26.856 | -0.513 | -0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 128 | GLY | 0 | 0.029 | -0.001 | 23.741 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 129 | LEU | 0 | 0.011 | 0.011 | 24.102 | -0.384 | -0.384 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 130 | ASP | -1 | -0.839 | -0.887 | 26.537 | -10.529 | -10.529 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 131 | LEU | 0 | 0.021 | 0.034 | 19.700 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 132 | ILE | 0 | -0.013 | -0.006 | 21.494 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 133 | ARG | 1 | 0.816 | 0.884 | 23.293 | 10.200 | 10.200 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 134 | THR | 0 | -0.025 | -0.023 | 24.873 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 135 | ILE | 0 | -0.008 | 0.001 | 18.628 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 136 | ARG | 1 | 0.742 | 0.852 | 19.468 | 14.099 | 14.099 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 137 | ALA | 0 | -0.024 | 0.002 | 24.107 | 0.370 | 0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 138 | SER | 0 | -0.039 | -0.023 | 21.251 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 139 | GLU | -1 | -0.880 | -0.963 | 18.447 | -14.119 | -14.119 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 140 | ARG | 1 | 0.781 | 0.875 | 11.800 | 19.699 | 19.699 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 141 | ALA | 0 | 0.037 | 0.032 | 18.244 | -0.593 | -0.593 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 142 | ALA | 0 | -0.023 | -0.013 | 17.334 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 143 | LEU | 0 | -0.049 | -0.003 | 13.454 | -0.590 | -0.590 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 144 | SER | 0 | 0.021 | 0.007 | 13.814 | 1.155 | 1.155 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 145 | ILE | 0 | 0.009 | -0.004 | 14.813 | -1.211 | -1.211 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 146 | ILE | 0 | -0.022 | -0.003 | 14.922 | 0.619 | 0.619 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 147 | VAL | 0 | 0.036 | 0.024 | 18.164 | -0.424 | -0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 148 | VAL | 0 | -0.051 | -0.040 | 17.396 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 149 | SER | 0 | 0.032 | 0.009 | 20.732 | -0.185 | -0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 150 | GLY | 0 | -0.008 | -0.009 | 24.176 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 151 | ASP | -1 | -0.877 | -0.926 | 26.267 | -9.886 | -9.886 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 152 | THR | 0 | -0.046 | -0.021 | 28.649 | -0.399 | -0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 153 | ASP | -1 | -0.817 | -0.881 | 31.021 | -9.237 | -9.237 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 154 | VAL | 0 | -0.005 | -0.027 | 32.590 | -0.273 | -0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 155 | GLU | -1 | -0.950 | -0.968 | 33.838 | -8.333 | -8.333 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 156 | GLU | -1 | -0.770 | -0.869 | 29.587 | -10.892 | -10.892 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 157 | ALA | 0 | -0.005 | -0.009 | 29.163 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 158 | VAL | 0 | -0.022 | -0.012 | 29.374 | -0.261 | -0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 159 | ASP | -1 | -0.842 | -0.907 | 30.972 | -9.998 | -9.998 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 160 | VAL | 0 | 0.011 | -0.010 | 24.771 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 161 | MET | 0 | -0.057 | -0.024 | 25.129 | -0.537 | -0.537 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 162 | HIS | 0 | -0.019 | -0.005 | 27.682 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 163 | LEU | 0 | -0.043 | -0.006 | 25.550 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 164 | GLY | 0 | 0.004 | 0.012 | 24.470 | -0.476 | -0.476 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 165 | VAL | 0 | -0.028 | -0.003 | 21.132 | -0.668 | -0.668 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 166 | VAL | 0 | -0.068 | -0.039 | 16.853 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 167 | ASP | -1 | -0.799 | -0.910 | 20.061 | -13.852 | -13.852 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 168 | PHE | 0 | 0.037 | 0.011 | 21.519 | -0.338 | -0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 169 | LEU | 0 | -0.047 | -0.020 | 18.505 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 170 | LEU | 0 | 0.032 | 0.013 | 22.628 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 171 | LYS | 1 | 0.750 | 0.864 | 20.535 | 14.275 | 14.275 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 172 | PRO | 0 | -0.027 | -0.019 | 22.993 | 0.458 | 0.458 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 173 | VAL | 0 | 0.043 | 0.016 | 18.021 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 174 | ASP | -1 | -0.840 | -0.917 | 19.624 | -15.552 | -15.552 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 175 | LEU | 0 | -0.005 | -0.020 | 14.528 | -0.674 | -0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 176 | GLY | 0 | -0.007 | 0.009 | 14.800 | -1.368 | -1.368 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 177 | LYS | 1 | 0.907 | 0.945 | 15.935 | 13.201 | 13.201 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 178 | LEU | 0 | -0.004 | 0.001 | 13.557 | -0.557 | -0.557 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 179 | LEU | 0 | -0.015 | -0.014 | 9.703 | -1.639 | -1.639 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 180 | GLU | -1 | -0.967 | -0.962 | 12.311 | -17.388 | -17.388 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 181 | LEU | 0 | -0.012 | -0.005 | 14.701 | -0.516 | -0.516 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 182 | VAL | 0 | 0.022 | 0.002 | 9.165 | -0.541 | -0.541 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 183 | ASN | 0 | -0.051 | -0.037 | 9.111 | -3.797 | -3.797 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 184 | LYS | 1 | 0.900 | 0.961 | 11.235 | 16.636 | 16.636 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 185 | GLU | -1 | -0.821 | -0.922 | 12.785 | -17.871 | -17.871 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 186 | LEU | 0 | -0.023 | -0.002 | 5.772 | -0.448 | -0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 187 | LYS | 1 | 0.761 | 0.904 | 8.003 | 19.474 | 19.474 | 0.000 | 0.000 | 0.000 | 0.000 |