![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: QYK8Y
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 | 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 | 76 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -492935.75475 |
---|---|
FMO2-HF: Nuclear repulsion | 461146.092259 |
FMO2-HF: Total energy | -31789.662491 |
FMO2-MP2: Total energy | -31877.561156 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F026414/ligand_interaction/ligand_F026414.png)
Ligand Interaction
![ligand interaction](./Kdata/F026414/ligand_interaction/ligand_interaction_F026414.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. |
-16.59 | -15.953 | 11.233 | -6.719 | -5.15 | -0.06 |
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 | -0.871 | -0.914 | 3.658 | -2.441 | -0.264 | 0.000 | -1.111 | -1.065 | 0.004 |
4 | A | 28 | GLU | -1 | -0.863 | -0.919 | 1.827 | -17.185 | -18.863 | 11.234 | -5.595 | -3.961 | -0.064 |
5 | A | 29 | THR | 0 | -0.114 | -0.060 | 5.226 | 1.427 | 1.565 | -0.001 | -0.013 | -0.124 | 0.000 |
6 | A | 30 | THR | 0 | -0.057 | -0.040 | 7.738 | 0.878 | 0.878 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 31 | PRO | 0 | 0.030 | -0.004 | 9.528 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 32 | GLN | 0 | -0.006 | 0.007 | 8.639 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 33 | ASN | 0 | -0.030 | -0.057 | 7.698 | 0.487 | 0.487 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 34 | MET | 0 | 0.014 | 0.045 | 11.131 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 35 | THR | 0 | -0.022 | -0.048 | 13.419 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 36 | CYS | 0 | -0.040 | -0.029 | 16.831 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 37 | GLN | 0 | -0.049 | -0.035 | 20.089 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 38 | GLU | -1 | -0.787 | -0.862 | 14.786 | -0.801 | -0.801 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 39 | PHE | 0 | -0.023 | -0.030 | 18.761 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 40 | MET | 0 | -0.075 | -0.034 | 19.858 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 41 | ASP | -1 | -0.858 | -0.906 | 21.241 | -0.348 | -0.348 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 42 | MET | 0 | -0.079 | -0.013 | 18.475 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 43 | ASN | 0 | 0.002 | -0.016 | 21.076 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 44 | PRO | 0 | 0.073 | 0.008 | 22.578 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 45 | LYS | 1 | 0.920 | 0.968 | 24.017 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 46 | SER | 0 | 0.023 | 0.011 | 18.847 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 47 | MET | 0 | -0.040 | 0.005 | 20.032 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 48 | THR | 0 | 0.039 | -0.025 | 21.506 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 49 | PRO | 0 | -0.017 | -0.012 | 18.792 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 50 | VAL | 0 | 0.006 | 0.009 | 15.919 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 51 | ALA | 0 | 0.040 | 0.004 | 17.789 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 52 | PHE | 0 | 0.020 | 0.008 | 19.398 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 53 | TRP | 0 | 0.018 | 0.010 | 11.102 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 54 | VAL | 0 | -0.002 | -0.003 | 16.794 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 55 | VAL | 0 | -0.027 | -0.007 | 17.994 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 56 | ASN | 0 | 0.003 | -0.011 | 19.750 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 57 | ARG | 1 | 0.781 | 0.892 | 12.415 | 0.633 | 0.633 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 58 | ASN | 0 | -0.058 | -0.032 | 15.520 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 59 | THR | 0 | -0.018 | -0.006 | 17.877 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 60 | ASP | -1 | -0.812 | -0.883 | 21.520 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 61 | PHE | 0 | -0.015 | -0.027 | 19.161 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 62 | SER | 0 | -0.085 | -0.052 | 24.549 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 63 | GLY | 0 | -0.021 | -0.009 | 26.753 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 64 | GLY | 0 | -0.019 | -0.004 | 27.888 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 65 | ASP | -1 | -0.872 | -0.929 | 25.901 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 66 | TYR | 0 | -0.092 | -0.050 | 23.881 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 67 | VAL | 0 | 0.008 | 0.020 | 24.948 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 68 | ASP | -1 | -0.765 | -0.879 | 25.411 | -0.219 | -0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 69 | TRP | 0 | 0.024 | -0.003 | 20.465 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 70 | HIS | 0 | 0.031 | 0.027 | 26.823 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 71 | GLU | -1 | -0.889 | -0.934 | 29.221 | -0.178 | -0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 72 | VAL | 0 | -0.034 | -0.027 | 23.299 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 73 | GLU | -1 | -0.864 | -0.901 | 26.468 | -0.273 | -0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 74 | THR | 0 | -0.061 | -0.060 | 28.025 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 75 | VAL | 0 | -0.028 | -0.002 | 29.757 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 76 | SER | 0 | -0.016 | -0.011 | 24.923 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 77 | VAL | 0 | 0.010 | 0.017 | 23.893 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 78 | PRO | 0 | 0.005 | 0.000 | 25.910 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 79 | LYS | 1 | 0.817 | 0.920 | 27.326 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 80 | MET | 0 | 0.007 | 0.006 | 19.476 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 81 | LEU | 0 | 0.025 | 0.014 | 24.662 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 82 | GLN | 0 | -0.002 | 0.018 | 26.427 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 83 | GLU | -1 | -0.854 | -0.926 | 24.724 | -0.201 | -0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 85 | HIS | 0 | 0.004 | -0.016 | 24.572 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 86 | LYS | 1 | 0.729 | 0.860 | 27.805 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 87 | ASN | 0 | -0.020 | -0.024 | 23.214 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 88 | PRO | 0 | 0.057 | 0.031 | 23.036 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 89 | ALA | 0 | -0.001 | 0.001 | 20.315 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 90 | ALA | 0 | -0.036 | 0.001 | 19.212 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 91 | LYS | 1 | 0.903 | 0.950 | 12.926 | 0.546 | 0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 92 | LEU | 0 | 0.029 | -0.003 | 15.218 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 93 | GLY | 0 | -0.023 | 0.006 | 13.269 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 94 | ASP | -1 | -0.889 | -0.929 | 14.163 | -0.395 | -0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 95 | LEU | 0 | -0.024 | -0.015 | 17.400 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 96 | SER | 0 | 0.008 | -0.013 | 18.118 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 97 | ALA | 0 | 0.000 | 0.005 | 20.305 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 98 | VAL | 0 | -0.007 | -0.001 | 23.126 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 99 | ILE | 0 | 0.002 | -0.008 | 22.397 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 100 | LYS | 1 | 0.908 | 0.966 | 23.212 | 0.216 | 0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 101 | LYS | 1 | 0.911 | 0.978 | 25.842 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |