FMODB ID: JLK19
Calculation Name: 3R0E-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3R0E
Chain ID: A
UniProt ID: B5LYJ9
Base Structure: X-ray
Registration Date: 2023-06-26
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 | 108 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -781662.29167 |
---|---|
FMO2-HF: Nuclear repulsion | 739948.069903 |
FMO2-HF: Total energy | -41714.221768 |
FMO2-MP2: Total energy | -41835.940606 |
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:LEU)
Summations of interaction energy for
fragment #1(A:1: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. |
-6.856 | -3.048 | 10.071 | -4.506 | -9.376 | -0.02 |
Interaction energy analysis for fragmet #1(A:1: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 | A | 3 | THR | 0 | -0.019 | -0.003 | 3.802 | -1.849 | 1.566 | -0.030 | -1.895 | -1.491 | 0.003 |
4 | A | 4 | ASN | 0 | 0.046 | 0.038 | 6.529 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | TYR | 0 | -0.041 | -0.032 | 8.670 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | LEU | 0 | 0.017 | 0.026 | 6.524 | -0.361 | -0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | LEU | 0 | -0.003 | -0.010 | 9.274 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | SER | 0 | 0.017 | 0.010 | 11.709 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | GLY | 0 | -0.014 | -0.006 | 13.718 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLN | 0 | -0.019 | 0.001 | 8.446 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | THR | 0 | -0.018 | -0.024 | 7.657 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | LEU | 0 | -0.037 | -0.003 | 2.447 | -1.595 | -1.086 | 0.506 | -0.315 | -0.700 | -0.002 |
13 | A | 13 | ASP | -1 | -0.817 | -0.907 | 4.467 | 0.740 | 0.851 | -0.001 | -0.006 | -0.104 | 0.000 |
14 | A | 14 | THR | 0 | -0.008 | -0.041 | 5.212 | 0.890 | 0.890 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLU | -1 | -0.845 | -0.921 | 5.658 | 1.757 | 1.757 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | -0.023 | 0.011 | 2.505 | 2.440 | 2.382 | 3.940 | -2.158 | -1.725 | 0.001 |
17 | A | 17 | HIS | 0 | -0.088 | -0.075 | 2.155 | -5.933 | -7.697 | 5.262 | 1.025 | -4.523 | -0.011 |
18 | A | 18 | LEU | 0 | -0.031 | -0.008 | 2.956 | -4.525 | -2.930 | 0.394 | -1.157 | -0.833 | -0.011 |
19 | A | 19 | LYS | 1 | 0.832 | 0.908 | 5.698 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ASN | 0 | -0.067 | -0.062 | 7.980 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLY | 0 | 0.022 | 0.020 | 11.591 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ASP | -1 | -0.890 | -0.953 | 12.450 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | PHE | 0 | -0.052 | 0.007 | 12.770 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ASP | -1 | -0.740 | -0.864 | 7.381 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | -0.068 | -0.036 | 8.044 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | 0.062 | 0.022 | 6.223 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | MET | 0 | -0.055 | -0.004 | 6.495 | -0.501 | -0.501 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLN | 0 | 0.022 | 0.016 | 8.090 | 0.358 | 0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASP | -1 | -0.850 | -0.943 | 10.190 | 0.610 | 0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ASP | -1 | -0.952 | -0.969 | 11.767 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | CYS | 0 | -0.120 | -0.033 | 12.343 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASN | 0 | 0.024 | 0.022 | 14.242 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | LEU | 0 | 0.026 | 0.017 | 9.173 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | VAL | 0 | -0.008 | -0.009 | 11.246 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LEU | 0 | -0.003 | 0.010 | 11.255 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | TYR | 0 | 0.000 | -0.019 | 9.589 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ASN | 0 | -0.037 | -0.049 | 13.680 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLY | 0 | 0.047 | 0.018 | 16.005 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ASN | 0 | -0.113 | -0.046 | 17.269 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | TRP | 0 | 0.011 | 0.008 | 13.549 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLN | 0 | 0.031 | 0.018 | 15.533 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | SER | 0 | 0.007 | 0.000 | 15.233 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASN | 0 | -0.068 | -0.026 | 16.902 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | THR | 0 | -0.009 | -0.019 | 15.770 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ALA | 0 | 0.039 | 0.028 | 17.429 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASN | 0 | -0.080 | -0.042 | 18.082 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | ASN | 0 | -0.038 | -0.012 | 18.675 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLY | 0 | 0.030 | 0.005 | 17.821 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | ARG | 1 | 0.869 | 0.935 | 15.835 | -0.264 | -0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ASP | -1 | -0.813 | -0.919 | 12.530 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | LYS | 1 | 0.870 | 0.941 | 9.024 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | LEU | 0 | 0.025 | 0.007 | 8.077 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | THR | 0 | -0.061 | -0.020 | 8.949 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | LEU | 0 | 0.028 | 0.010 | 11.552 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | THR | 0 | 0.003 | -0.005 | 13.834 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | ASP | -1 | -0.838 | -0.915 | 17.365 | -0.270 | -0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | TYR | 0 | -0.015 | -0.021 | 19.926 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | GLY | 0 | 0.044 | 0.020 | 17.941 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | GLU | -1 | -0.850 | -0.914 | 18.279 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | LEU | 0 | 0.020 | 0.006 | 11.906 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | VAL | 0 | -0.044 | -0.034 | 13.985 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | ILE | 0 | 0.054 | 0.029 | 12.351 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | LYS | 1 | 0.910 | 0.960 | 13.414 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | ASN | 0 | 0.055 | 0.010 | 13.829 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | GLY | 0 | 0.025 | 0.023 | 15.100 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ASP | -1 | -0.887 | -0.923 | 16.107 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | GLY | 0 | -0.020 | 0.002 | 17.117 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | SER | 0 | -0.088 | -0.056 | 18.157 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | THR | 0 | -0.066 | -0.059 | 18.241 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | VAL | 0 | 0.029 | 0.015 | 16.736 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | TRP | 0 | 0.024 | 0.004 | 15.373 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | LYS | 1 | 0.903 | 0.963 | 17.258 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | SER | 0 | 0.041 | 0.022 | 17.275 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | GLY | 0 | -0.019 | 0.004 | 19.137 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | ALA | 0 | -0.035 | -0.014 | 21.526 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | GLN | 0 | -0.080 | -0.049 | 21.447 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | SER | 0 | 0.001 | 0.005 | 23.350 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | VAL | 0 | 0.021 | 0.002 | 24.987 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | LYS | 1 | 0.900 | 0.958 | 22.769 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 81 | GLY | 0 | -0.031 | -0.015 | 22.546 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 82 | ASN | 0 | -0.054 | -0.019 | 18.533 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 83 | TYR | 0 | 0.011 | -0.010 | 17.127 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 84 | ALA | 0 | -0.010 | -0.007 | 13.997 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 85 | ALA | 0 | -0.016 | 0.006 | 11.440 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 86 | VAL | 0 | 0.003 | -0.006 | 11.539 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 87 | VAL | 0 | 0.045 | 0.033 | 9.676 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | HIS | 0 | -0.006 | -0.002 | 12.763 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | PRO | 0 | 0.017 | 0.000 | 15.986 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | ASP | -1 | -0.852 | -0.911 | 17.003 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | GLY | 0 | -0.001 | -0.006 | 16.141 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 92 | ARG | 1 | 0.819 | 0.905 | 17.191 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | LEU | 0 | 0.023 | 0.014 | 11.682 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | VAL | 0 | -0.042 | -0.025 | 14.971 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | VAL | 0 | 0.015 | 0.010 | 15.164 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | PHE | 0 | -0.026 | -0.013 | 17.097 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | GLY | 0 | 0.006 | 0.003 | 18.643 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | PRO | 0 | 0.004 | 0.007 | 21.306 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | SER | 0 | -0.025 | -0.026 | 20.930 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | VAL | 0 | 0.010 | 0.004 | 22.578 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | PHE | 0 | -0.010 | -0.017 | 24.599 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | LYS | 1 | 0.880 | 0.936 | 21.331 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ILE | 0 | 0.013 | 0.018 | 23.607 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | ASP | -1 | -0.814 | -0.925 | 23.035 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | PRO | 0 | -0.032 | -0.004 | 21.465 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | TRP | 0 | -0.008 | 0.000 | 18.025 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | VAL | 0 | -0.008 | 0.006 | 24.334 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | ARG | 1 | 0.930 | 0.968 | 27.829 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | GLY | 0 | 0.029 | 0.017 | 31.322 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |