![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2JVJR
Calculation Name: 2F51-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2F51
Chain ID: A
UniProt ID: Q8IEV4
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 111 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -859379.656876 |
---|---|
FMO2-HF: Nuclear repulsion | 817359.196301 |
FMO2-HF: Total energy | -42020.460574 |
FMO2-MP2: Total energy | -42144.903824 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F029853/ligand_interaction/ligand_F029853.png)
Ligand Interaction
![ligand interaction](./Kdata/F029853/ligand_interaction/ligand_interaction_F029853.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:2:SER)
Summations of interaction energy for
fragment #1(A:2:SER)
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. |
-0.214 | 2.089 | -0.002 | -1.065 | -1.236 | 0.003 |
Interaction energy analysis for fragmet #1(A:2:SER)
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 | 4 | PRO | 0 | -0.031 | -0.002 | 3.665 | -2.163 | 0.015 | -0.001 | -1.055 | -1.122 | 0.003 |
4 | A | 5 | ILE | 0 | -0.051 | -0.017 | 4.691 | 1.699 | 1.824 | -0.001 | -0.010 | -0.114 | 0.000 |
5 | A | 6 | VAL | 0 | -0.010 | -0.002 | 7.806 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | HIS | 0 | -0.042 | -0.037 | 8.518 | 0.664 | 0.664 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | PHE | 0 | -0.010 | -0.002 | 11.999 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | ASN | 0 | -0.047 | -0.034 | 14.354 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | GLY | 0 | 0.034 | 0.020 | 17.257 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | THR | 0 | 0.018 | 0.008 | 20.260 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | HIS | 0 | 0.144 | 0.054 | 22.378 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | GLU | -1 | -0.826 | -0.916 | 23.455 | -0.236 | -0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | ALA | 0 | -0.031 | -0.010 | 19.895 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | LEU | 0 | 0.018 | 0.017 | 17.900 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | LEU | 0 | 0.004 | 0.000 | 19.270 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | ASN | 0 | -0.043 | -0.033 | 20.619 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | ARG | 1 | 0.987 | 1.008 | 10.222 | 0.749 | 0.749 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | ILE | 0 | -0.022 | -0.011 | 15.904 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | LYS | 1 | 0.840 | 0.916 | 17.650 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | GLU | -1 | -0.914 | -0.963 | 14.958 | -0.320 | -0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | ALA | 0 | -0.067 | -0.014 | 13.919 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | PRO | 0 | 0.001 | 0.006 | 12.628 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | GLY | 0 | 0.014 | -0.006 | 15.298 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | LEU | 0 | -0.090 | -0.028 | 16.705 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | VAL | 0 | 0.040 | 0.019 | 14.861 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | LEU | 0 | -0.032 | 0.002 | 15.113 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | VAL | 0 | 0.004 | 0.003 | 15.402 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | ASP | -1 | -0.842 | -0.953 | 16.652 | -0.726 | -0.726 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | PHE | 0 | -0.003 | 0.004 | 18.280 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | PHE | 0 | 0.033 | -0.011 | 16.969 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | ALA | 0 | 0.116 | 0.055 | 21.599 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | THR | 0 | 0.016 | -0.001 | 19.487 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | TRP | 0 | 0.004 | 0.001 | 22.013 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | CYS | 0 | 0.001 | 0.041 | 24.666 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | GLY | 0 | 0.044 | 0.021 | 24.102 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | PRO | 0 | -0.012 | -0.029 | 24.155 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | CYS | 0 | 0.016 | 0.020 | 21.550 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | GLN | 0 | -0.029 | -0.015 | 20.054 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | ARG | 1 | 0.935 | 0.964 | 19.346 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | LEU | 0 | 0.028 | 0.017 | 18.246 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | GLY | 0 | -0.011 | -0.018 | 16.127 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | GLN | 0 | -0.028 | -0.005 | 14.590 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | ILE | 0 | -0.016 | -0.017 | 14.368 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | LEU | 0 | 0.005 | 0.002 | 13.230 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | PRO | 0 | 0.033 | 0.020 | 8.719 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | SER | 0 | 0.004 | 0.016 | 9.146 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 48 | ILE | 0 | -0.019 | -0.015 | 11.138 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | ALA | 0 | 0.019 | 0.009 | 8.735 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | GLU | -1 | -0.988 | -0.988 | 5.603 | -2.515 | -2.515 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | ALA | 0 | -0.047 | -0.029 | 8.258 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | ASN | 0 | -0.058 | -0.030 | 11.017 | 0.352 | 0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | LYS | 1 | 0.987 | 0.985 | 5.049 | 1.205 | 1.205 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | ASP | -1 | -0.939 | -0.963 | 9.469 | -0.491 | -0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | VAL | 0 | -0.065 | -0.020 | 11.909 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | THR | 0 | -0.031 | -0.013 | 10.503 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | PHE | 0 | 0.028 | 0.010 | 10.322 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | ILE | 0 | 0.001 | -0.003 | 10.984 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | LYS | 1 | 0.880 | 0.974 | 13.019 | 1.153 | 1.153 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | VAL | 0 | -0.007 | -0.014 | 15.109 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | ASP | -1 | -0.855 | -0.929 | 18.164 | -0.501 | -0.501 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | VAL | 0 | 0.030 | -0.021 | 19.847 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | ASP | -1 | -0.852 | -0.909 | 23.182 | -0.327 | -0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | LYS | 1 | 0.826 | 0.918 | 17.449 | 0.535 | 0.535 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | ASN | 0 | -0.075 | -0.036 | 18.340 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | GLY | 0 | 0.097 | 0.055 | 22.629 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ASN | 0 | 0.022 | 0.003 | 26.234 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | ALA | 0 | -0.021 | -0.013 | 22.647 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | ALA | 0 | 0.016 | 0.003 | 24.153 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | ASP | -1 | -0.891 | -0.940 | 25.364 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | ALA | 0 | -0.081 | -0.045 | 27.563 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | TYR | 0 | -0.065 | -0.038 | 22.816 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | GLY | 0 | -0.007 | 0.014 | 26.956 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | VAL | 0 | -0.074 | -0.035 | 24.603 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | SER | 0 | 0.045 | 0.019 | 28.028 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | SER | 0 | -0.049 | -0.019 | 29.420 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | ILE | 0 | 0.003 | 0.015 | 24.878 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | PRO | 0 | -0.006 | -0.033 | 22.100 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | ALA | 0 | -0.015 | -0.002 | 23.212 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | LEU | 0 | -0.008 | 0.006 | 19.412 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 81 | PHE | 0 | 0.023 | -0.001 | 20.843 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 82 | PHE | 0 | 0.014 | 0.015 | 18.021 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 83 | VAL | 0 | 0.008 | -0.005 | 19.580 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 84 | LYS | 1 | 0.975 | 0.976 | 19.641 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 85 | LYS | 1 | 0.890 | 0.961 | 20.203 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 86 | GLU | -1 | -0.908 | -0.971 | 22.214 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 87 | GLY | 0 | 0.026 | 0.024 | 25.778 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | ASN | 0 | -0.065 | -0.041 | 25.447 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | GLU | -1 | -0.930 | -0.961 | 27.019 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | ILE | 0 | -0.017 | -0.007 | 22.283 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | LYS | 1 | 0.953 | 0.995 | 24.591 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 92 | THR | 0 | 0.031 | -0.005 | 24.189 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | LEU | 0 | -0.142 | -0.069 | 22.640 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | ASP | -1 | -0.737 | -0.823 | 24.503 | -0.317 | -0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | GLN | 0 | -0.011 | 0.000 | 24.533 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | PHE | 0 | -0.041 | -0.019 | 22.577 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | VAL | 0 | 0.056 | 0.031 | 25.533 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | GLY | 0 | 0.005 | 0.008 | 25.799 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | ALA | 0 | -0.018 | -0.014 | 23.034 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | ASP | -1 | -0.891 | -0.942 | 24.045 | -0.360 | -0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | VAL | 0 | 0.036 | -0.005 | 19.639 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | SER | 0 | -0.001 | -0.005 | 21.757 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ARG | 1 | 0.873 | 0.931 | 24.101 | 0.332 | 0.332 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | ILE | 0 | -0.012 | -0.005 | 18.049 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | LYS | 1 | 0.955 | 0.970 | 17.907 | 0.553 | 0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | ALA | 0 | 0.054 | 0.037 | 20.597 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | ASH | 0 | -0.092 | -0.088 | 21.996 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | ILE | 0 | -0.027 | -0.012 | 15.994 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | GLU | -1 | -0.953 | -0.974 | 19.551 | -0.345 | -0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | LYS | 1 | 0.916 | 0.973 | 21.687 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 111 | PHE | 0 | -0.049 | -0.040 | 21.184 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 112 | LYS | 1 | 0.940 | 0.996 | 18.392 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |