![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 1JQJZ
Calculation Name: 3FX7-A-Xray312
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3FX7
Chain ID: A
UniProt ID: O24902
Base Structure: X-ray
Registration Date: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 86 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -552930.718039 |
---|---|
FMO2-HF: Nuclear repulsion | 516983.521591 |
FMO2-HF: Total energy | -35947.196447 |
FMO2-MP2: Total energy | -36053.682724 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015637/ligand_interaction/ligand_F015637.png)
Ligand Interaction
![ligand interaction](./Kdata/F015637/ligand_interaction/ligand_interaction_F015637.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:4:ACE )
Summations of interaction energy for
fragment #1(A:4:ACE )
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. |
-4.54 | -6.125 | 7.171 | -3.15 | -2.433 | -0.011 |
Interaction energy analysis for fragmet #1(A:4:ACE )
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 | 6 | MET | 0 | -0.021 | 0.011 | 3.724 | 0.710 | 2.133 | -0.004 | -0.669 | -0.749 | -0.002 |
4 | A | 7 | ASP | -1 | -0.826 | -0.899 | 5.745 | -0.766 | -0.766 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 8 | THR | 0 | -0.016 | -0.055 | 7.226 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 9 | GLH | 0 | -0.047 | -0.047 | 9.458 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 10 | GLU | -1 | -0.962 | -0.977 | 11.663 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 11 | VAL | 0 | -0.011 | -0.022 | 8.531 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 12 | ARG | 1 | 0.809 | 0.883 | 11.682 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 13 | GLU | -1 | -0.848 | -0.885 | 13.883 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 14 | PHE | 0 | -0.038 | -0.010 | 14.343 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 15 | VAL | 0 | -0.016 | -0.013 | 13.135 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 16 | GLY | 0 | 0.044 | 0.030 | 16.033 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 17 | HIS | 0 | -0.050 | -0.026 | 19.103 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 18 | LEU | 0 | -0.004 | 0.001 | 17.143 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 19 | GLU | -1 | -0.829 | -0.920 | 19.300 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 20 | ARG | 1 | 1.010 | 1.007 | 21.792 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 21 | PHE | 0 | -0.044 | -0.018 | 23.430 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 22 | LYS | 1 | 0.878 | 0.947 | 21.623 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 23 | GLU | -1 | -0.989 | -0.986 | 25.132 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 24 | LEU | 0 | 0.001 | -0.001 | 27.919 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 25 | LEU | 0 | 0.010 | 0.003 | 28.042 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 26 | ARG | 1 | 0.888 | 0.954 | 27.600 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 27 | GLU | -1 | -0.960 | -0.976 | 31.612 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 28 | GLU | -1 | -0.915 | -0.969 | 33.620 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 29 | VAL | 0 | -0.036 | -0.014 | 33.692 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 30 | ASN | 0 | -0.016 | -0.015 | 35.160 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 31 | SER | 0 | -0.022 | 0.004 | 37.637 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 32 | LEU | 0 | 0.027 | 0.009 | 39.117 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 33 | SER | 0 | 0.022 | 0.012 | 39.700 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 34 | ASN | 0 | -0.029 | -0.020 | 41.450 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 35 | HIS | 0 | -0.012 | -0.001 | 43.638 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 36 | PHE | 0 | -0.028 | -0.014 | 44.479 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 37 | HIS | 0 | -0.102 | -0.060 | 43.284 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 38 | ASN | 0 | 0.025 | 0.019 | 47.431 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 39 | LEU | 0 | -0.027 | 0.014 | 49.350 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 40 | GLU | -1 | -0.899 | -0.964 | 51.253 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 41 | SER | 0 | -0.073 | -0.042 | 54.737 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 42 | TRP | 0 | -0.040 | -0.008 | 48.019 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 43 | ARG | 1 | 0.926 | 0.947 | 51.887 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 44 | ASP | -1 | -0.824 | -0.907 | 53.764 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 45 | ALA | 0 | 0.078 | 0.029 | 53.340 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 46 | ARG | 1 | 0.918 | 0.956 | 50.814 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 47 | ARG | 1 | 0.928 | 0.988 | 48.456 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 48 | ASP | -1 | -0.877 | -0.946 | 48.365 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 49 | LYS | 1 | 0.863 | 0.927 | 45.089 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 50 | PHE | 0 | -0.006 | -0.014 | 41.993 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 51 | SER | 0 | 0.025 | 0.002 | 43.537 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 52 | GLU | -1 | -0.863 | -0.915 | 42.817 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 53 | VAL | 0 | -0.063 | -0.023 | 39.853 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 54 | LEU | 0 | -0.005 | -0.008 | 38.394 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 55 | ASP | -1 | -0.896 | -0.945 | 38.113 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 56 | ASN | 0 | -0.002 | -0.011 | 36.813 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 57 | LEU | 0 | -0.029 | -0.001 | 33.179 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 58 | LYS | 1 | 0.921 | 0.945 | 33.182 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 59 | SER | 0 | -0.023 | -0.006 | 32.797 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 60 | THR | 0 | 0.025 | 0.008 | 29.680 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 61 | PHE | 0 | -0.049 | -0.041 | 28.810 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 62 | ASN | 0 | -0.028 | -0.013 | 27.927 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 63 | GLU | -1 | -0.921 | -0.948 | 27.295 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 64 | PHE | 0 | -0.002 | -0.008 | 21.670 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 65 | ASP | -1 | -0.862 | -0.929 | 23.176 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 66 | GLU | -1 | -0.946 | -0.969 | 23.043 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 67 | ALA | 0 | 0.038 | 0.020 | 20.725 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 68 | ALA | 0 | -0.027 | -0.027 | 18.894 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 69 | GLN | 0 | 0.016 | -0.007 | 18.271 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 70 | GLU | -1 | -0.926 | -0.958 | 17.633 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 71 | GLN | 0 | -0.021 | -0.013 | 13.425 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 72 | ILE | 0 | -0.020 | -0.005 | 13.586 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 73 | ALA | 0 | -0.043 | -0.020 | 14.471 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 74 | TRP | 0 | 0.021 | 0.010 | 6.375 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 75 | LEU | 0 | 0.029 | -0.003 | 9.029 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 76 | LYS | 1 | 0.821 | 0.908 | 10.075 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 77 | GLU | -1 | -0.888 | -0.955 | 11.433 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 78 | ARG | 1 | 0.901 | 0.968 | 1.958 | -4.604 | -7.089 | 4.880 | -1.439 | -0.955 | -0.003 |
76 | A | 79 | ILE | 0 | 0.004 | -0.009 | 6.742 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 80 | ARG | 1 | 0.912 | 0.970 | 8.697 | -0.286 | -0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 81 | VAL | 0 | 0.024 | 0.022 | 6.101 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 82 | LEU | 0 | -0.042 | -0.024 | 2.317 | 0.353 | -0.170 | 2.295 | -1.042 | -0.729 | -0.006 |
80 | A | 83 | GLU | -1 | -0.773 | -0.859 | 6.234 | -0.469 | -0.469 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 84 | GLU | -1 | -0.965 | -0.983 | 9.709 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 85 | ASP | -1 | -0.922 | -0.962 | 6.129 | -0.834 | -0.834 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 86 | TYR | 0 | -0.077 | -0.038 | 8.024 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 87 | LEU | 0 | -0.089 | -0.049 | 9.533 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 88 | GLU | -1 | -1.008 | -0.990 | 12.058 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 89 | NME | 0 | -0.073 | -0.024 | 11.100 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |