![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: G62Q1
Calculation Name: 1H2V-Z-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1H2V
Chain ID: Z
UniProt ID: Q09161
Base Structure: X-ray
Registration Date: 2023-09-19
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 | 92 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -689907.648185 |
---|---|
FMO2-HF: Nuclear repulsion | 651456.439214 |
FMO2-HF: Total energy | -38451.208971 |
FMO2-MP2: Total energy | -38560.33753 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F029022/ligand_interaction/ligand_F029022.png)
Ligand Interaction
![ligand interaction](./Kdata/F029022/ligand_interaction/ligand_interaction_F029022.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(Z:33:GLU)
Summations of interaction energy for
fragment #1(Z:33:GLU)
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. |
-138.152 | -131.733 | 2.985 | -4.168 | -5.237 | 0.026 |
Interaction energy analysis for fragmet #1(Z:33:GLU)
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 | Z | 35 | LEU | 0 | 0.086 | 0.013 | 3.222 | -10.041 | -6.996 | 0.064 | -1.561 | -1.548 | 0.011 |
4 | Z | 36 | LEU | 0 | 0.067 | 0.030 | 2.476 | -5.356 | -4.012 | 0.701 | -0.644 | -1.402 | -0.001 |
5 | Z | 37 | LYS | 1 | 0.929 | 0.964 | 1.983 | -76.770 | -74.740 | 2.220 | -1.963 | -2.287 | 0.016 |
6 | Z | 38 | LYS | 1 | 0.846 | 0.931 | 6.214 | -37.517 | -37.517 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | Z | 39 | SER | 0 | -0.027 | -0.016 | 8.030 | -2.859 | -2.859 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | Z | 40 | CYS | 0 | 0.051 | 0.041 | 9.774 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | Z | 41 | THR | 0 | -0.010 | -0.003 | 11.615 | -1.663 | -1.663 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | Z | 42 | LEU | 0 | -0.026 | -0.006 | 11.256 | 1.822 | 1.822 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | Z | 43 | TYR | 0 | -0.022 | 0.009 | 12.606 | -1.253 | -1.253 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | Z | 44 | VAL | 0 | 0.037 | -0.005 | 14.163 | 0.516 | 0.516 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | Z | 45 | GLY | 0 | 0.024 | 0.002 | 17.222 | -0.519 | -0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | Z | 46 | ASN | 0 | -0.079 | -0.067 | 18.893 | -0.341 | -0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | Z | 47 | LEU | 0 | 0.017 | 0.041 | 21.621 | -0.421 | -0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | Z | 48 | SER | 0 | -0.036 | -0.067 | 24.169 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | Z | 49 | PHE | 0 | -0.015 | -0.033 | 26.268 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | Z | 50 | TYR | 0 | -0.034 | -0.020 | 29.382 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | Z | 51 | THR | 0 | -0.033 | -0.009 | 25.981 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | Z | 52 | THR | 0 | -0.030 | -0.020 | 28.389 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | Z | 53 | GLU | -1 | -0.884 | -0.966 | 26.154 | 10.824 | 10.824 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | Z | 54 | GLU | -1 | -0.852 | -0.936 | 27.035 | 9.718 | 9.718 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | Z | 55 | GLN | 0 | 0.012 | 0.020 | 28.535 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | Z | 56 | ILE | 0 | 0.004 | -0.009 | 22.351 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | Z | 57 | TYR | 0 | 0.017 | 0.002 | 24.352 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | Z | 58 | GLU | -1 | -0.928 | -0.951 | 26.142 | 9.852 | 9.852 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | Z | 59 | LEU | 0 | -0.053 | -0.032 | 23.644 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | Z | 60 | PHE | 0 | 0.004 | -0.026 | 18.208 | 0.311 | 0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | Z | 61 | SER | 0 | 0.041 | 0.040 | 22.329 | 0.444 | 0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | Z | 62 | LYS | 1 | 0.862 | 0.946 | 24.862 | -10.600 | -10.600 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | Z | 63 | SER | 0 | -0.058 | -0.025 | 19.623 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | Z | 64 | GLY | 0 | 0.010 | 0.004 | 21.584 | 0.453 | 0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | Z | 65 | ASP | -1 | -0.895 | -0.935 | 22.866 | 11.347 | 11.347 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | Z | 66 | ILE | 0 | -0.038 | -0.030 | 21.184 | 0.653 | 0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | Z | 67 | LYS | 1 | 0.857 | 0.942 | 19.357 | -14.417 | -14.417 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | Z | 68 | LYS | 1 | 0.933 | 0.951 | 20.964 | -12.708 | -12.708 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | Z | 69 | ILE | 0 | 0.045 | 0.031 | 20.466 | 0.723 | 0.723 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | Z | 70 | ILE | 0 | -0.063 | -0.019 | 19.297 | -0.474 | -0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | Z | 71 | MET | 0 | 0.027 | 0.018 | 21.023 | 0.668 | 0.668 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | Z | 72 | GLY | 0 | 0.022 | 0.012 | 22.122 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | Z | 73 | LEU | 0 | -0.058 | -0.046 | 22.751 | -0.454 | -0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | Z | 74 | ASP | -1 | -0.857 | -0.938 | 24.999 | 10.011 | 10.011 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | Z | 75 | LYS | 1 | 0.955 | 0.969 | 25.472 | -10.542 | -10.542 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | Z | 76 | MET | 0 | -0.068 | -0.042 | 27.408 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | Z | 77 | LYS | 1 | 0.961 | 0.983 | 31.211 | -8.943 | -8.943 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | Z | 78 | LYS | 1 | 0.957 | 0.988 | 28.864 | -9.452 | -9.452 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | Z | 79 | THR | 0 | 0.029 | 0.011 | 30.165 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | Z | 80 | ALA | 0 | 0.044 | 0.017 | 26.907 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | Z | 81 | CYS | 0 | -0.034 | -0.005 | 24.053 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | Z | 82 | GLY | 0 | 0.030 | 0.022 | 24.063 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | Z | 83 | PHE | 0 | -0.060 | -0.039 | 18.689 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | Z | 84 | CYS | 0 | 0.009 | 0.017 | 19.093 | -0.660 | -0.660 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | Z | 85 | PHE | 0 | -0.048 | -0.009 | 13.715 | 0.891 | 0.891 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | Z | 86 | VAL | 0 | 0.040 | 0.017 | 16.403 | -0.812 | -0.812 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | Z | 87 | GLU | -1 | -0.918 | -0.955 | 15.863 | 16.205 | 16.205 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | Z | 88 | TYR | 0 | 0.025 | -0.007 | 16.290 | -0.429 | -0.429 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | Z | 89 | TYR | 0 | 0.012 | -0.001 | 17.507 | 0.477 | 0.477 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | Z | 90 | SER | 0 | -0.004 | -0.001 | 17.630 | 0.535 | 0.535 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | Z | 91 | ARG | 1 | 0.858 | 0.906 | 8.078 | -26.905 | -26.905 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | Z | 92 | ALA | 0 | 0.013 | -0.001 | 14.691 | 0.615 | 0.615 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | Z | 93 | ASP | -1 | -0.803 | -0.899 | 16.991 | 14.206 | 14.206 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | Z | 94 | ALA | 0 | -0.005 | 0.000 | 13.618 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | Z | 95 | GLU | -1 | -0.939 | -0.989 | 11.827 | 23.437 | 23.437 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | Z | 96 | ASN | 0 | 0.038 | 0.016 | 14.575 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | Z | 97 | ALA | 0 | 0.016 | 0.030 | 16.592 | -0.489 | -0.489 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | Z | 98 | MET | 0 | -0.047 | -0.011 | 10.729 | -0.423 | -0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | Z | 99 | ARG | 1 | 0.823 | 0.914 | 14.788 | -18.440 | -18.440 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | Z | 100 | TYR | 0 | -0.014 | -0.023 | 17.043 | -0.293 | -0.293 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | Z | 101 | ILE | 0 | 0.021 | 0.046 | 19.420 | -0.603 | -0.603 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | Z | 102 | ASN | 0 | 0.023 | 0.022 | 15.072 | -0.926 | -0.926 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | Z | 103 | GLY | 0 | -0.012 | 0.003 | 18.333 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | Z | 104 | THR | 0 | -0.046 | -0.031 | 20.563 | -0.824 | -0.824 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | Z | 105 | ARG | 1 | 0.876 | 0.916 | 23.841 | -10.348 | -10.348 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | Z | 106 | LEU | 0 | 0.036 | 0.026 | 24.666 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | Z | 107 | ASP | -1 | -0.825 | -0.859 | 27.276 | 9.625 | 9.625 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | Z | 108 | ASP | -1 | -0.892 | -0.952 | 30.328 | 9.532 | 9.532 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | Z | 109 | ARG | 1 | 0.827 | 0.918 | 25.552 | -11.124 | -11.124 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | Z | 110 | ILE | 0 | -0.008 | 0.003 | 21.969 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | Z | 111 | ILE | 0 | 0.006 | 0.029 | 20.475 | 0.236 | 0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | Z | 112 | ARG | 1 | 0.940 | 0.967 | 16.471 | -15.685 | -15.685 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | Z | 113 | THR | 0 | 0.033 | 0.013 | 14.523 | -0.606 | -0.606 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | Z | 114 | ASP | -1 | -0.905 | -0.953 | 10.072 | 23.594 | 23.594 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | Z | 115 | TRP | 0 | 0.009 | -0.007 | 6.874 | -0.381 | -0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | Z | 116 | ASP | -1 | -0.738 | -0.855 | 8.411 | 22.062 | 22.062 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | Z | 117 | ALA | 0 | -0.068 | -0.028 | 6.548 | 0.304 | 0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | Z | 118 | GLY | 0 | 0.037 | 0.023 | 8.061 | -0.435 | -0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | Z | 119 | PHE | 0 | 0.024 | 0.030 | 11.827 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | Z | 120 | LYS | 1 | 0.931 | 0.961 | 11.440 | -18.936 | -18.936 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | Z | 121 | GLU | -1 | -0.829 | -0.917 | 16.258 | 11.677 | 11.677 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | Z | 122 | GLY | 0 | -0.019 | -0.007 | 19.250 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | Z | 123 | ARG | 1 | 0.694 | 0.808 | 11.768 | -18.951 | -18.951 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | Z | 124 | GLN | 0 | 0.054 | 0.060 | 18.020 | 0.488 | 0.488 | 0.000 | 0.000 | 0.000 | 0.000 |