FMODB ID: YVML2
Calculation Name: 2II7-F-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2II7
Chain ID: F
UniProt ID: Q8YSC3
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 91 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -622957.433929 |
---|---|
FMO2-HF: Nuclear repulsion | 587571.764391 |
FMO2-HF: Total energy | -35385.669538 |
FMO2-MP2: Total energy | -35489.77496 |
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(F:2:LEU)
Summations of interaction energy for
fragment #1(F:2:LEU)
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. |
-5.339 | -1.451 | 0.921 | -1.868 | -2.939 | -0.014 |
Interaction energy analysis for fragmet #1(F:2:LEU)
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 | F | 4 | ILE | 0 | 0.001 | -0.009 | 3.872 | 1.168 | 2.665 | -0.018 | -0.721 | -0.758 | 0.002 |
4 | F | 5 | GLY | 0 | 0.014 | 0.013 | 6.796 | -0.371 | -0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | F | 6 | ARG | 1 | 0.859 | 0.925 | 10.316 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | F | 7 | THR | 0 | 0.054 | 0.031 | 11.148 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | F | 8 | CYS | 0 | 0.001 | 0.013 | 13.362 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | F | 9 | TRP | 0 | -0.054 | -0.034 | 13.408 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | F | 10 | ALA | 0 | 0.037 | 0.015 | 19.143 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | F | 11 | ILE | 0 | -0.048 | -0.015 | 22.567 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | F | 12 | ALA | 0 | -0.039 | -0.023 | 25.358 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | F | 13 | GLU | -1 | -0.883 | -0.938 | 28.615 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | F | 14 | GLY | 0 | 0.001 | -0.008 | 29.133 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | F | 15 | TYR | 0 | -0.009 | -0.032 | 31.391 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | F | 16 | ILE | 0 | -0.025 | -0.001 | 32.246 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | F | 17 | PRO | 0 | 0.019 | 0.003 | 35.197 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | F | 18 | PRO | 0 | -0.060 | -0.011 | 38.414 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | F | 31 | GLU | -1 | -0.789 | -0.880 | 28.413 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | F | 32 | THR | 0 | -0.057 | -0.053 | 22.806 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | F | 33 | VAL | 0 | 0.031 | 0.030 | 20.053 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | F | 34 | CYS | 0 | -0.028 | -0.009 | 18.644 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | F | 35 | ILE | 0 | 0.030 | 0.012 | 14.310 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | F | 36 | LEU | 0 | -0.018 | -0.008 | 9.795 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | F | 37 | ASN | 0 | -0.014 | -0.010 | 8.657 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | F | 38 | ALA | 0 | -0.019 | -0.024 | 5.374 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | F | 39 | GLY | 0 | 0.055 | 0.034 | 4.035 | -1.089 | -0.873 | 0.000 | -0.053 | -0.162 | 0.000 |
27 | F | 40 | ASP | -1 | -0.842 | -0.929 | 2.536 | -7.304 | -5.321 | 0.941 | -1.087 | -1.837 | -0.016 |
28 | F | 41 | GLU | -1 | -0.895 | -0.933 | 5.378 | -0.340 | -0.271 | -0.001 | -0.001 | -0.066 | 0.000 |
29 | F | 42 | ASP | -1 | -0.855 | -0.930 | 8.803 | -0.803 | -0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | F | 43 | ALA | 0 | 0.014 | 0.025 | 11.597 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | F | 44 | HIS | 0 | 0.024 | 0.002 | 13.006 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | F | 45 | VAL | 0 | -0.029 | -0.010 | 15.977 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | F | 46 | GLU | -1 | -0.823 | -0.885 | 18.057 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | F | 47 | ILE | 0 | -0.006 | -0.015 | 21.019 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | F | 48 | THR | 0 | -0.073 | -0.021 | 23.484 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | F | 49 | ILE | 0 | 0.018 | 0.011 | 26.655 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | F | 50 | TYR | 0 | -0.004 | -0.007 | 26.901 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | F | 51 | TYR | 0 | 0.040 | 0.008 | 31.909 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | F | 52 | SER | 0 | 0.015 | 0.011 | 35.454 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | F | 53 | ASP | -1 | -0.821 | -0.894 | 38.240 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | F | 54 | LYS | 1 | 0.769 | 0.870 | 37.615 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | F | 55 | GLU | -1 | -0.889 | -0.952 | 35.536 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | F | 56 | PRO | 0 | -0.036 | -0.018 | 30.699 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | F | 57 | VAL | 0 | -0.025 | 0.004 | 31.584 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | F | 58 | GLY | 0 | 0.013 | -0.008 | 29.436 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | F | 59 | PRO | 0 | -0.027 | -0.033 | 24.829 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | F | 60 | TYR | 0 | 0.054 | 0.028 | 25.852 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | F | 61 | ARG | 1 | 0.814 | 0.882 | 22.822 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | F | 62 | LEU | 0 | -0.024 | -0.018 | 18.907 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | F | 63 | THR | 0 | 0.018 | 0.014 | 15.787 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | F | 64 | VAL | 0 | -0.042 | -0.026 | 13.168 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | F | 65 | PRO | 0 | 0.025 | 0.002 | 12.968 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | F | 66 | ALA | 0 | 0.020 | 0.019 | 7.721 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | F | 67 | ARG | 1 | 0.755 | 0.875 | 4.606 | 2.439 | 2.562 | -0.001 | -0.006 | -0.116 | 0.000 |
55 | F | 68 | ARG | 1 | 0.889 | 0.953 | 8.101 | 1.021 | 1.021 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | F | 69 | THR | 0 | -0.017 | -0.013 | 11.580 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | F | 70 | LYS | 1 | 0.877 | 0.926 | 14.051 | 0.289 | 0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | F | 71 | HIS | 0 | 0.035 | 0.020 | 17.436 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | F | 72 | VAL | 0 | -0.008 | -0.008 | 20.197 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | F | 73 | ARG | 1 | 0.869 | 0.929 | 22.954 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | F | 74 | PHE | 0 | 0.040 | 0.005 | 25.779 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | F | 75 | ASN | 0 | -0.066 | -0.022 | 28.578 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | F | 76 | ASP | -1 | -0.792 | -0.884 | 28.021 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | F | 77 | LEU | 0 | -0.059 | -0.012 | 25.318 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | F | 78 | ASN | 0 | -0.053 | -0.052 | 29.322 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | F | 79 | ASP | -1 | -0.886 | -0.926 | 29.245 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | F | 80 | PRO | 0 | -0.009 | -0.015 | 29.063 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | F | 81 | ALA | 0 | 0.002 | -0.003 | 32.205 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | F | 82 | PRO | 0 | -0.018 | 0.000 | 33.128 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | F | 83 | ILE | 0 | 0.003 | 0.027 | 30.142 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | F | 84 | PRO | 0 | -0.042 | -0.020 | 34.280 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | F | 85 | HIS | 0 | -0.016 | -0.022 | 35.813 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | F | 86 | ASP | -1 | -0.891 | -0.929 | 38.456 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | F | 87 | THR | 0 | -0.062 | -0.028 | 37.620 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | F | 88 | ASP | -1 | -0.900 | -0.943 | 36.123 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | F | 89 | PHE | 0 | -0.097 | -0.050 | 29.457 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | F | 90 | ALA | 0 | 0.024 | 0.032 | 29.418 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | F | 91 | SER | 0 | -0.004 | -0.016 | 25.661 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | F | 92 | VAL | 0 | -0.003 | 0.002 | 22.303 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | F | 93 | ILE | 0 | -0.005 | -0.002 | 18.252 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | F | 94 | GLN | 0 | -0.006 | -0.015 | 17.520 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | F | 95 | SER | 0 | -0.001 | -0.011 | 12.398 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | F | 96 | ASN | 0 | -0.007 | -0.009 | 12.293 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | F | 97 | VAL | 0 | 0.008 | 0.013 | 8.110 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | F | 98 | PRO | 0 | -0.049 | -0.032 | 6.941 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | F | 99 | ILE | 0 | 0.014 | 0.025 | 8.682 | -0.310 | -0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | F | 100 | VAL | 0 | 0.012 | -0.006 | 10.349 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | F | 101 | VAL | 0 | -0.008 | -0.006 | 12.938 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | F | 102 | GLN | 0 | -0.037 | -0.017 | 16.748 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | F | 103 | HIS | 0 | 0.000 | 0.005 | 19.664 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | F | 104 | THR | 0 | 0.021 | 0.012 | 23.153 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |