![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R9Q18
Calculation Name: 4XVV-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4XVV
Chain ID: A
UniProt ID: A6TE95
Base Structure: X-ray
Registration Date: 2023-06-22
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 | 76 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -490832.386137 |
---|---|
FMO2-HF: Nuclear repulsion | 459042.798527 |
FMO2-HF: Total energy | -31789.58761 |
FMO2-MP2: Total energy | -31877.462798 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F026415/ligand_interaction/ligand_F026415.png)
Ligand Interaction
![ligand interaction](./Kdata/F026415/ligand_interaction/ligand_interaction_F026415.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:0:GLY)
Summations of interaction energy for
fragment #1(A:0:GLY)
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. |
-13.914 | -9.76 | 4.611 | -4.389 | -4.377 | -0.03 |
Interaction energy analysis for fragmet #1(A:0:GLY)
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 | 27 | GLU | -1 | -0.878 | -0.925 | 3.320 | -2.538 | -0.080 | 0.013 | -1.286 | -1.185 | 0.006 |
4 | A | 28 | GLU | -1 | -0.897 | -0.943 | 2.154 | -14.159 | -12.585 | 4.599 | -3.093 | -3.081 | -0.036 |
5 | A | 29 | THR | 0 | -0.107 | -0.049 | 5.183 | 1.330 | 1.452 | -0.001 | -0.010 | -0.111 | 0.000 |
6 | A | 30 | THR | 0 | -0.086 | -0.046 | 7.882 | 0.873 | 0.873 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 31 | PRO | 0 | 0.050 | -0.002 | 9.491 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 32 | GLN | 0 | 0.013 | 0.028 | 9.333 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 33 | ASN | 0 | -0.034 | -0.056 | 7.839 | 0.469 | 0.469 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 34 | MET | 0 | 0.011 | 0.044 | 11.324 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 35 | THR | 0 | -0.025 | -0.047 | 13.642 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 36 | CYS | 0 | -0.047 | -0.034 | 17.029 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 37 | GLN | 0 | -0.055 | -0.041 | 20.387 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 38 | GLU | -1 | -0.794 | -0.870 | 14.980 | -0.777 | -0.777 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 39 | PHE | 0 | -0.014 | -0.025 | 18.835 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 40 | MET | 0 | -0.090 | -0.043 | 19.929 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 41 | ASP | -1 | -0.849 | -0.894 | 21.486 | -0.337 | -0.337 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 42 | MET | 0 | -0.081 | -0.010 | 18.442 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 43 | ASN | 0 | -0.005 | -0.015 | 21.181 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 44 | PRO | 0 | 0.095 | 0.013 | 22.606 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 45 | LYS | 1 | 0.915 | 0.959 | 23.970 | 0.298 | 0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 46 | SER | 0 | 0.014 | 0.013 | 18.844 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 47 | MET | 0 | -0.032 | 0.005 | 20.140 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 48 | THR | 0 | 0.027 | -0.021 | 21.852 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 49 | PRO | 0 | -0.011 | -0.006 | 18.952 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 50 | VAL | 0 | 0.006 | 0.010 | 16.105 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 51 | ALA | 0 | 0.044 | 0.004 | 18.208 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 52 | PHE | 0 | 0.017 | 0.007 | 19.360 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 53 | TRP | 0 | 0.010 | 0.010 | 11.272 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 54 | VAL | 0 | 0.000 | -0.001 | 17.076 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 55 | VAL | 0 | -0.029 | -0.009 | 18.353 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 56 | ASN | 0 | -0.019 | -0.022 | 19.704 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 57 | ARG | 1 | 0.834 | 0.934 | 12.213 | 0.539 | 0.539 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 58 | ASN | 0 | -0.069 | -0.039 | 15.447 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 59 | THR | 0 | -0.023 | -0.006 | 17.424 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 60 | ASP | -1 | -0.808 | -0.892 | 20.923 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 61 | PHE | 0 | -0.015 | -0.028 | 18.594 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 62 | SER | 0 | -0.073 | -0.042 | 23.889 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 63 | GLY | 0 | -0.022 | -0.005 | 26.494 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 64 | GLY | 0 | -0.037 | -0.015 | 28.004 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 65 | ASP | -1 | -0.958 | -0.956 | 26.471 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 66 | TYR | 0 | -0.095 | -0.062 | 23.812 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 67 | VAL | 0 | -0.025 | 0.007 | 24.716 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 68 | ASP | -1 | -0.784 | -0.899 | 25.229 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 69 | TRP | 0 | 0.045 | 0.001 | 20.534 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 70 | HIS | 0 | 0.026 | 0.023 | 26.954 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 71 | GLU | -1 | -0.892 | -0.938 | 29.038 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 72 | VAL | 0 | -0.029 | -0.018 | 23.369 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 73 | GLU | -1 | -0.871 | -0.925 | 26.686 | -0.273 | -0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 74 | THR | 0 | -0.068 | -0.056 | 28.201 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 75 | VAL | 0 | -0.023 | 0.001 | 30.095 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 76 | SER | 0 | -0.010 | -0.012 | 25.090 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 77 | VAL | 0 | 0.014 | 0.016 | 24.374 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 78 | PRO | 0 | 0.008 | 0.001 | 26.396 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 79 | LYS | 1 | 0.829 | 0.931 | 27.820 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 80 | MET | 0 | 0.016 | 0.006 | 19.787 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 81 | LEU | 0 | 0.012 | 0.012 | 25.078 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 82 | GLN | 0 | -0.005 | 0.014 | 26.760 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 83 | GLU | -1 | -0.855 | -0.930 | 25.392 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 85 | HIS | 0 | -0.002 | -0.023 | 24.771 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 86 | LYS | 1 | 0.734 | 0.872 | 28.027 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 87 | ASN | 0 | -0.024 | -0.021 | 23.922 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 88 | PRO | 0 | 0.077 | 0.035 | 23.245 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 89 | ALA | 0 | -0.003 | 0.002 | 20.598 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 90 | ALA | 0 | -0.044 | -0.003 | 19.341 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 91 | LYS | 1 | 0.904 | 0.940 | 13.573 | 0.388 | 0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 92 | LEU | 0 | 0.046 | 0.000 | 15.549 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 93 | GLY | 0 | -0.034 | -0.003 | 14.067 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 94 | ASP | -1 | -0.882 | -0.922 | 14.953 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 95 | LEU | 0 | -0.028 | -0.019 | 18.240 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 96 | SER | 0 | 0.002 | -0.021 | 18.551 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 97 | ALA | 0 | 0.004 | -0.001 | 20.787 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 98 | VAL | 0 | -0.002 | 0.000 | 23.751 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 99 | ILE | 0 | 0.016 | 0.004 | 22.942 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 100 | LYS | 1 | 0.988 | 1.018 | 22.751 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 101 | LYS | 1 | 0.923 | 0.981 | 26.216 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |