![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: K9743
Calculation Name: 4ME7-E-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4ME7
Chain ID: E
UniProt ID: P96621
Base Structure: X-ray
Registration Date: 2023-06-21
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 | 78 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -386703.950513 |
---|---|
FMO2-HF: Nuclear repulsion | 353878.937329 |
FMO2-HF: Total energy | -32825.013184 |
FMO2-MP2: Total energy | -32916.522066 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024293/ligand_interaction/ligand_F024293.png)
Ligand Interaction
![ligand interaction](./Kdata/F024293/ligand_interaction/ligand_interaction_F024293.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(E:6:ALA)
Summations of interaction energy for
fragment #1(E:6:ALA)
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. |
-6.509 | -4.181 | -0.023 | -1.152 | -1.151 | -0.002 |
Interaction energy analysis for fragmet #1(E:6:ALA)
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 | E | 8 | THR | 0 | 0.003 | 0.013 | 3.823 | -2.522 | -0.355 | -0.021 | -1.135 | -1.010 | -0.002 |
4 | E | 9 | GLU | -1 | -0.893 | -0.948 | 4.619 | -1.920 | -1.892 | -0.001 | -0.015 | -0.012 | 0.000 |
5 | E | 10 | MET | 0 | -0.026 | -0.013 | 6.807 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 11 | LYS | 1 | 0.942 | 0.970 | 9.673 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 12 | ILE | 0 | 0.010 | 0.006 | 11.500 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 13 | SER | 0 | 0.008 | -0.026 | 14.413 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 14 | LEU | 0 | -0.028 | 0.012 | 14.652 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 15 | PRO | 0 | 0.043 | 0.017 | 18.521 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 16 | GLU | -1 | -0.857 | -0.940 | 21.129 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 17 | ASN | 0 | 0.021 | 0.003 | 22.830 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 18 | LEU | 0 | 0.014 | 0.013 | 18.929 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 19 | VAL | 0 | -0.026 | -0.010 | 17.237 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 20 | ALA | 0 | 0.035 | 0.021 | 19.025 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 21 | GLU | -1 | -0.949 | -0.961 | 21.838 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 22 | LEU | 0 | -0.065 | -0.029 | 14.057 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 23 | ASP | -1 | -0.773 | -0.905 | 17.094 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 24 | GLY | 0 | 0.015 | 0.025 | 18.643 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 25 | VAL | 0 | -0.071 | -0.051 | 17.363 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 26 | ALA | 0 | 0.010 | 0.013 | 15.632 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 27 | MET | 0 | -0.017 | -0.016 | 17.222 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 28 | ARG | 1 | 0.928 | 0.976 | 20.070 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 29 | GLU | -1 | -0.932 | -0.960 | 17.316 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 30 | LYS | 1 | 0.906 | 0.963 | 17.383 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 31 | ARG | 1 | 0.883 | 0.946 | 12.308 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 32 | SER | 0 | 0.047 | 0.022 | 9.682 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 33 | ARG | 1 | 0.918 | 0.927 | 11.547 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | E | 34 | ASN | 0 | -0.016 | -0.001 | 4.774 | -0.251 | -0.118 | -0.001 | -0.002 | -0.129 | 0.000 |
30 | E | 35 | GLU | -1 | -0.861 | -0.931 | 7.336 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | E | 36 | LEU | 0 | 0.010 | 0.005 | 8.305 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | E | 37 | ILE | 0 | -0.004 | -0.013 | 9.382 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | E | 38 | SER | 0 | -0.024 | -0.009 | 5.583 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | E | 39 | GLN | 0 | 0.027 | 0.007 | 7.936 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | E | 40 | ALA | 0 | 0.004 | 0.007 | 10.598 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | E | 41 | VAL | 0 | 0.003 | -0.003 | 10.163 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | E | 42 | ARG | 1 | 0.957 | 0.985 | 6.258 | -1.923 | -1.923 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | E | 43 | ALA | 0 | 0.036 | 0.020 | 11.957 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | E | 44 | TYR | 0 | 0.042 | 0.038 | 15.311 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | E | 45 | VAL | 0 | 0.043 | 0.008 | 12.977 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | E | 46 | SER | 0 | 0.000 | 0.001 | 14.318 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | E | 47 | GLU | -1 | -0.895 | -0.933 | 16.540 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | E | 48 | ARG | 1 | 0.874 | 0.923 | 18.720 | -0.330 | -0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | E | 49 | THR | 0 | 0.004 | 0.003 | 16.978 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | E | 50 | THR | 0 | -0.003 | -0.006 | 19.608 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | E | 51 | ARG | 1 | 0.879 | 0.928 | 21.830 | -0.269 | -0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | E | 52 | HIS | 0 | 0.023 | 0.030 | 22.553 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | E | 53 | ASN | 0 | 0.047 | 0.009 | 20.785 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | E | 54 | ARG | 1 | 0.919 | 0.953 | 24.889 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | E | 55 | ASP | -1 | -0.815 | -0.863 | 27.478 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | E | 56 | LEU | 0 | 0.009 | -0.001 | 25.644 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | E | 57 | MET | 0 | -0.025 | -0.006 | 28.062 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | E | 58 | ARG | 1 | 0.874 | 0.923 | 30.619 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | E | 59 | ARG | 1 | 0.873 | 0.918 | 31.085 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | E | 60 | GLY | 0 | 0.079 | 0.044 | 33.125 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | E | 61 | TYR | 0 | 0.018 | -0.006 | 33.221 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | E | 62 | MET | 0 | -0.077 | -0.041 | 36.631 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | E | 63 | GLU | -1 | -0.952 | -0.962 | 36.365 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | E | 64 | MET | 0 | -0.014 | -0.002 | 37.165 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | E | 65 | ALA | 0 | 0.000 | 0.012 | 40.064 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | E | 66 | LYS | 1 | 0.968 | 0.976 | 42.747 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | E | 67 | ILE | 0 | 0.008 | 0.002 | 41.526 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | E | 68 | ASN | 0 | 0.018 | -0.015 | 39.858 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | E | 69 | LEU | 0 | 0.013 | 0.022 | 43.438 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | E | 70 | ASN | 0 | -0.035 | -0.014 | 46.619 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | E | 71 | ILE | 0 | 0.072 | 0.021 | 43.495 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | E | 72 | SER | 0 | -0.044 | -0.007 | 45.840 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | E | 73 | SER | 0 | -0.034 | -0.015 | 47.572 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | E | 74 | GLU | -1 | -1.004 | -1.008 | 50.333 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | E | 75 | ALA | 0 | -0.006 | 0.007 | 48.986 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | E | 76 | HIS | 0 | -0.017 | 0.000 | 51.120 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | E | 77 | PHE | 0 | -0.001 | -0.015 | 52.470 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | E | 78 | ALA | 0 | -0.002 | -0.004 | 51.877 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | E | 79 | GLU | -1 | -0.945 | -0.978 | 47.778 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | E | 80 | CYS | 0 | -0.098 | -0.049 | 51.608 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | E | 81 | GLU | -1 | -0.887 | -0.931 | 54.726 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | E | 82 | ALA | 0 | -0.107 | -0.035 | 51.727 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | E | 83 | GLU | -1 | -1.021 | -1.007 | 52.633 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |