FMODB ID: 2JK1R
Calculation Name: 2BO3-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2BO3
Chain ID: A
UniProt ID: O25025
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 | 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 | 92 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -594697.867852 |
---|---|
FMO2-HF: Nuclear repulsion | 557005.752336 |
FMO2-HF: Total energy | -37692.115515 |
FMO2-MP2: Total energy | -37803.044889 |
3D Structure
Ligand structure
Ligand Interaction
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:1:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
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. |
-7.826 | -2.578 | 1.971 | -2.935 | -4.285 | -0.012 |
Interaction energy analysis for fragmet #1(A:1:MET)
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 | 3 | ASP | -1 | -0.895 | -0.947 | 2.793 | -7.038 | -2.671 | 0.334 | -2.447 | -2.255 | -0.008 |
4 | A | 4 | TYR | 0 | -0.007 | -0.019 | 2.384 | -0.059 | 0.822 | 1.637 | -0.488 | -2.030 | -0.004 |
5 | A | 5 | SER | 0 | -0.029 | -0.030 | 6.642 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | GLU | -1 | -0.834 | -0.915 | 8.498 | -0.977 | -0.977 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | LEU | 0 | -0.084 | -0.032 | 7.991 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | GLU | -1 | -0.825 | -0.881 | 10.287 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ILE | 0 | -0.028 | -0.008 | 10.951 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | PHE | 0 | -0.052 | -0.031 | 12.316 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLU | -1 | -0.920 | -0.949 | 16.432 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLY | 0 | 0.051 | 0.036 | 19.218 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | ASN | 0 | -0.026 | -0.037 | 20.463 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | PRO | 0 | 0.010 | -0.011 | 23.881 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | LEU | 0 | 0.025 | 0.003 | 25.310 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | ASP | -1 | -0.826 | -0.896 | 24.480 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LYS | 1 | 0.844 | 0.900 | 18.537 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | TRP | 0 | -0.002 | -0.016 | 24.137 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | ASN | 0 | 0.029 | 0.012 | 27.268 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ASP | -1 | -0.878 | -0.931 | 23.424 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | ILE | 0 | -0.033 | -0.024 | 22.036 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ILE | 0 | -0.031 | -0.016 | 25.986 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | PHE | 0 | -0.066 | -0.038 | 29.057 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | HIS | 0 | -0.067 | -0.028 | 24.000 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | -0.010 | 0.022 | 26.883 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | SER | 0 | 0.004 | -0.010 | 27.870 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | LYS | 1 | 0.966 | 0.967 | 30.473 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | LYS | 1 | 0.936 | 0.977 | 33.764 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | LEU | 0 | -0.023 | -0.015 | 29.515 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | SER | 0 | 0.072 | 0.042 | 31.560 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LYS | 1 | 0.810 | 0.891 | 33.265 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | LYS | 1 | 0.974 | 0.986 | 35.537 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | GLU | -1 | -0.743 | -0.821 | 32.489 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LEU | 0 | 0.033 | 0.008 | 34.469 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | GLU | -1 | -0.809 | -0.883 | 37.474 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | ARG | 1 | 0.848 | 0.916 | 34.458 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | LEU | 0 | -0.045 | -0.029 | 34.739 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | LEU | 0 | 0.017 | 0.018 | 39.366 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | GLU | -1 | -0.946 | -0.971 | 42.532 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | LEU | 0 | -0.026 | -0.012 | 39.772 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | LEU | 0 | -0.014 | -0.003 | 42.593 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | ALA | 0 | 0.073 | 0.038 | 44.262 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | LEU | 0 | -0.044 | -0.014 | 46.320 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | LEU | 0 | -0.051 | -0.034 | 42.812 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLU | -1 | -0.941 | -0.968 | 47.195 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | THR | 0 | 0.039 | 0.003 | 49.595 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | PHE | 0 | -0.104 | -0.048 | 49.818 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | ILE | 0 | -0.010 | -0.017 | 48.249 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLU | -1 | -0.892 | -0.928 | 52.509 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | LYS | 1 | 0.788 | 0.897 | 55.149 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | GLU | -1 | -0.967 | -0.972 | 54.675 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | ASP | -1 | -0.904 | -0.939 | 56.742 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | LEU | 0 | -0.115 | -0.069 | 53.063 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | GLU | -1 | -0.803 | -0.915 | 53.850 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLU | -1 | -0.886 | -0.939 | 53.858 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | LYS | 1 | 0.935 | 0.964 | 52.642 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | PHE | 0 | 0.000 | -0.009 | 45.794 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLU | -1 | -0.881 | -0.932 | 49.463 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | SER | 0 | -0.070 | -0.045 | 50.722 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | PHE | 0 | -0.032 | -0.022 | 43.561 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ALA | 0 | 0.009 | 0.007 | 45.803 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LYS | 1 | 0.861 | 0.926 | 46.132 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ALA | 0 | -0.073 | -0.022 | 47.872 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | LEU | 0 | 0.023 | 0.013 | 40.573 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | ARG | 1 | 0.903 | 0.948 | 42.670 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | ILE | 0 | -0.039 | -0.035 | 43.226 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ASP | -1 | -0.794 | -0.865 | 42.534 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | GLU | -1 | -0.931 | -0.972 | 38.869 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | GLU | -1 | -0.865 | -0.927 | 38.080 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | LEU | 0 | -0.034 | -0.017 | 38.533 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | GLN | 0 | -0.017 | -0.018 | 37.451 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | GLN | 0 | 0.049 | 0.023 | 30.716 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | LYS | 1 | 0.854 | 0.930 | 34.072 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ILE | 0 | -0.003 | -0.008 | 35.820 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLU | -1 | -0.798 | -0.888 | 31.274 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | SER | 0 | -0.040 | -0.037 | 31.262 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | ARG | 1 | 0.886 | 0.950 | 32.216 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | LYS | 1 | 0.832 | 0.901 | 32.653 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | THR | 0 | 0.009 | 0.012 | 27.196 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ASP | -1 | -0.850 | -0.915 | 29.182 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ILE | 0 | -0.038 | -0.025 | 31.040 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | VAL | 0 | 0.001 | 0.010 | 26.965 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | ILE | 0 | 0.019 | 0.000 | 25.551 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | GLN | 0 | -0.011 | -0.007 | 27.863 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | SER | 0 | -0.043 | -0.038 | 30.201 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | MET | 0 | -0.023 | -0.018 | 23.957 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | ALA | 0 | 0.029 | 0.020 | 26.834 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | ASN | 0 | -0.045 | -0.028 | 27.842 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | ILE | 0 | -0.055 | -0.030 | 27.302 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | LEU | 0 | -0.015 | -0.008 | 22.212 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | SER | 0 | -0.093 | -0.019 | 26.390 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | GLY | 0 | -0.076 | -0.038 | 29.149 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |