![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: LNZ19
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 | 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 | 120 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1002478.72292 |
---|---|
FMO2-HF: Nuclear repulsion | 956299.721751 |
FMO2-HF: Total energy | -46179.001168 |
FMO2-MP2: Total energy | -46314.829322 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033317/ligand_interaction/ligand_F033317.png)
Ligand Interaction
![ligand interaction](./Kdata/F033317/ligand_interaction/ligand_interaction_F033317.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. |
-97.417 | -90.313 | 4.196 | -4.269 | -7.03 | -0.03 |
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 | -0.052 | -0.015 | 3.550 | -11.305 | -9.429 | 0.002 | -0.904 | -0.974 | -0.001 |
4 | A | 71 | VAL | 0 | 0.027 | 0.017 | 6.113 | 4.407 | 4.407 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 72 | LEU | 0 | -0.015 | -0.002 | 9.051 | -1.033 | -1.033 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 73 | VAL | 0 | -0.018 | -0.018 | 11.263 | 1.157 | 1.157 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 74 | VAL | 0 | -0.003 | -0.015 | 13.852 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 75 | ASP | -1 | -0.823 | -0.942 | 17.514 | -14.610 | -14.610 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 76 | ASP | -1 | -0.787 | -0.875 | 20.026 | -13.027 | -13.027 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 77 | ASN | 0 | -0.019 | 0.002 | 22.114 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 78 | ALA | 0 | 0.024 | -0.010 | 19.620 | -0.738 | -0.738 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 79 | VAL | 0 | 0.001 | 0.002 | 18.588 | -0.832 | -0.832 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 80 | ASN | 0 | -0.028 | -0.016 | 18.564 | -0.565 | -0.565 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 81 | ARG | 1 | 0.901 | 0.958 | 15.390 | 16.163 | 16.163 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 82 | GLU | -1 | -0.945 | -0.979 | 13.909 | -22.784 | -22.784 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 83 | ALA | 0 | -0.012 | 0.004 | 13.433 | -1.397 | -1.397 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 84 | LEU | 0 | -0.012 | -0.002 | 12.623 | -0.952 | -0.952 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 85 | ILE | 0 | 0.038 | 0.014 | 8.879 | -2.403 | -2.403 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 86 | LEU | 0 | -0.027 | -0.008 | 8.750 | -3.664 | -3.664 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 87 | TYR | 0 | 0.059 | 0.018 | 9.335 | -2.113 | -2.113 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 88 | LEU | 0 | 0.052 | 0.025 | 7.275 | -1.143 | -1.143 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 89 | LYS | 1 | 0.951 | 0.997 | 4.757 | 32.920 | 33.005 | -0.001 | -0.003 | -0.080 | 0.000 |
23 | A | 90 | SER | 0 | -0.112 | -0.057 | 5.503 | -2.350 | -2.350 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 91 | ARG | 1 | 0.876 | 0.932 | 7.552 | 26.491 | 26.491 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 92 | GLY | 0 | -0.012 | 0.005 | 4.373 | 1.656 | 1.723 | -0.001 | -0.014 | -0.052 | 0.000 |
26 | A | 93 | ILE | 0 | -0.050 | -0.018 | 2.923 | -16.904 | -14.662 | 0.132 | -1.280 | -1.094 | -0.014 |
27 | A | 94 | ASP | -1 | -0.912 | -0.973 | 2.464 | -62.441 | -61.420 | 3.710 | -1.475 | -3.256 | -0.011 |
28 | A | 95 | ALA | 0 | 0.005 | -0.007 | 3.519 | 5.498 | 5.612 | 0.063 | 0.030 | -0.207 | 0.000 |
29 | A | 96 | VAL | 0 | -0.021 | -0.006 | 7.302 | -0.453 | -0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 97 | GLY | 0 | 0.024 | 0.005 | 10.577 | 0.543 | 0.543 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 98 | ALA | 0 | -0.044 | -0.023 | 14.109 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 99 | ASP | -1 | -0.967 | -0.995 | 17.473 | -14.344 | -14.344 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 100 | GLY | 0 | 0.114 | 0.036 | 20.684 | 0.778 | 0.778 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 101 | ALA | 0 | -0.005 | -0.007 | 21.408 | -0.684 | -0.684 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 102 | GLU | -1 | -0.948 | -0.970 | 22.170 | -12.435 | -12.435 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 103 | GLU | -1 | -0.813 | -0.897 | 18.362 | -16.971 | -16.971 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 104 | ALA | 0 | -0.011 | -0.004 | 17.609 | -0.956 | -0.956 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 105 | ARG | 1 | 0.806 | 0.852 | 17.315 | 11.681 | 11.681 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 106 | LEU | 0 | 0.021 | 0.024 | 17.931 | -0.354 | -0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 107 | TYR | 0 | 0.030 | 0.001 | 11.910 | -1.463 | -1.463 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 108 | LEU | 0 | -0.034 | -0.016 | 13.375 | -1.069 | -1.069 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 109 | HIS | 0 | -0.014 | 0.009 | 13.978 | -0.528 | -0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 110 | TYR | 0 | -0.015 | -0.023 | 12.996 | -0.652 | -0.652 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 111 | GLN | 0 | -0.025 | 0.003 | 7.809 | -1.323 | -1.323 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 112 | LYS | 1 | 0.972 | 0.960 | 9.134 | 16.615 | 16.615 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 113 | ARG | 1 | 0.839 | 0.926 | 2.642 | 49.660 | 51.359 | 0.291 | -0.623 | -1.367 | -0.004 |
47 | A | 114 | ILE | 0 | -0.037 | -0.002 | 5.964 | -2.653 | -2.653 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 115 | GLY | 0 | 0.011 | 0.016 | 8.412 | 2.526 | 2.526 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 116 | LEU | 0 | -0.027 | -0.005 | 9.597 | 1.251 | 1.251 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 117 | MET | 0 | 0.001 | 0.017 | 11.739 | -1.471 | -1.471 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 118 | ILE | 0 | -0.019 | -0.005 | 12.101 | 0.620 | 0.620 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 119 | THR | 0 | 0.001 | -0.012 | 15.545 | -0.336 | -0.336 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 120 | ASP | -1 | -0.745 | -0.862 | 18.838 | -12.789 | -12.789 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 121 | LEU | 0 | -0.064 | -0.046 | 21.776 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 122 | ARG | 1 | 0.812 | 0.852 | 25.262 | 11.276 | 11.276 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 123 | MET | 0 | -0.080 | 0.007 | 22.271 | -0.614 | -0.614 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 124 | GLN | 0 | -0.042 | 0.006 | 26.457 | 0.685 | 0.685 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 125 | PRO | 0 | -0.028 | -0.028 | 27.456 | -0.323 | -0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 126 | GLU | -1 | -0.763 | -0.870 | 27.193 | -11.352 | -11.352 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 127 | SER | 0 | 0.022 | 0.022 | 26.832 | -0.492 | -0.492 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 128 | GLY | 0 | 0.050 | 0.011 | 24.122 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 129 | LEU | 0 | 0.008 | 0.000 | 24.858 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 130 | ASP | -1 | -0.894 | -0.952 | 27.303 | -10.311 | -10.311 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 131 | LEU | 0 | 0.004 | 0.006 | 20.412 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 132 | ILE | 0 | 0.004 | 0.002 | 22.101 | -0.265 | -0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 133 | ARG | 1 | 0.963 | 0.985 | 23.822 | 10.040 | 10.040 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 134 | THR | 0 | -0.047 | -0.017 | 24.215 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 135 | ILE | 0 | 0.008 | 0.004 | 19.150 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 136 | ARG | 1 | 0.802 | 0.881 | 19.427 | 13.733 | 13.733 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 137 | ALA | 0 | -0.053 | -0.012 | 23.861 | 0.278 | 0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 138 | SER | 0 | -0.038 | -0.014 | 20.863 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 139 | GLU | -1 | -0.892 | -0.962 | 18.187 | -13.362 | -13.362 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 140 | ARG | 1 | 0.766 | 0.869 | 10.871 | 19.197 | 19.197 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 141 | ALA | 0 | 0.055 | 0.035 | 17.926 | -0.445 | -0.445 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 142 | ALA | 0 | -0.026 | -0.016 | 17.543 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 143 | LEU | 0 | -0.050 | 0.001 | 13.538 | -0.596 | -0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 144 | SER | 0 | 0.031 | 0.002 | 14.088 | 0.762 | 0.762 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 145 | ILE | 0 | -0.017 | -0.019 | 15.328 | -1.040 | -1.040 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 146 | ILE | 0 | -0.011 | 0.000 | 14.424 | 0.606 | 0.606 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 147 | VAL | 0 | 0.051 | 0.032 | 18.095 | -0.434 | -0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 148 | VAL | 0 | -0.053 | -0.028 | 17.383 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 149 | SER | 0 | 0.044 | 0.026 | 20.558 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 150 | GLY | 0 | -0.048 | -0.045 | 23.874 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 151 | ASP | -1 | -0.965 | -0.968 | 26.094 | -9.729 | -9.729 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 152 | THR | 0 | 0.013 | 0.007 | 28.101 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 153 | ASP | -1 | -0.866 | -0.924 | 30.640 | -8.963 | -8.963 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 154 | VAL | 0 | -0.003 | -0.014 | 32.373 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 155 | GLU | -1 | -0.930 | -0.974 | 33.632 | -8.214 | -8.214 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 156 | GLU | -1 | -0.757 | -0.843 | 29.166 | -10.763 | -10.763 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 157 | ALA | 0 | -0.017 | -0.013 | 29.027 | -0.324 | -0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 158 | VAL | 0 | -0.022 | -0.017 | 29.601 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 159 | ASP | -1 | -0.922 | -0.955 | 31.435 | -9.428 | -9.428 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 160 | VAL | 0 | -0.035 | -0.032 | 25.250 | -0.256 | -0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 161 | MET | 0 | -0.046 | -0.020 | 25.323 | -0.524 | -0.524 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 162 | HIS | 0 | -0.018 | -0.006 | 27.907 | -0.201 | -0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 163 | LEU | 0 | -0.083 | -0.025 | 25.685 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 164 | GLY | 0 | 0.010 | 0.011 | 24.441 | -0.424 | -0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 165 | VAL | 0 | -0.075 | -0.029 | 21.421 | -0.596 | -0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 166 | VAL | 0 | -0.049 | -0.022 | 17.005 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 167 | ASP | -1 | -0.829 | -0.938 | 20.293 | -13.266 | -13.266 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 168 | PHE | 0 | 0.005 | 0.001 | 21.349 | -0.444 | -0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 169 | LEU | 0 | -0.075 | -0.039 | 18.524 | 0.368 | 0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 170 | LEU | 0 | 0.054 | 0.021 | 22.506 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 171 | LYS | 1 | 0.904 | 0.961 | 20.982 | 13.530 | 13.530 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 172 | PRO | 0 | -0.010 | -0.013 | 23.013 | 0.424 | 0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 173 | VAL | 0 | 0.029 | 0.019 | 17.628 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 174 | ASP | -1 | -0.863 | -0.928 | 20.144 | -14.645 | -14.645 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 175 | LEU | 0 | -0.006 | -0.023 | 14.491 | -0.581 | -0.581 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 176 | GLY | 0 | -0.004 | 0.007 | 15.370 | -1.195 | -1.195 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 177 | LYS | 1 | 1.020 | 1.020 | 16.582 | 12.687 | 12.687 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 178 | LEU | 0 | 0.004 | -0.001 | 13.606 | -0.531 | -0.531 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 179 | LEU | 0 | -0.020 | -0.019 | 9.598 | -1.149 | -1.149 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 180 | GLU | -1 | -0.970 | -0.968 | 12.438 | -17.093 | -17.093 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 181 | LEU | 0 | -0.029 | -0.018 | 14.855 | -0.445 | -0.445 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 182 | VAL | 0 | -0.001 | 0.001 | 9.168 | -0.473 | -0.473 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 183 | ASN | 0 | -0.003 | -0.016 | 9.514 | -3.515 | -3.515 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 184 | LYS | 1 | 0.953 | 0.989 | 11.309 | 15.878 | 15.878 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 185 | GLU | -1 | -0.928 | -0.961 | 13.014 | -17.344 | -17.344 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 186 | LEU | 0 | -0.028 | -0.015 | 6.440 | -0.597 | -0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 187 | LYS | 1 | 0.856 | 0.949 | 8.469 | 18.707 | 18.707 | 0.000 | 0.000 | 0.000 | 0.000 |