FMODB ID: 39G6L
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 | 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 | 108 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -781753.28933 |
---|---|
FMO2-HF: Nuclear repulsion | 740038.921458 |
FMO2-HF: Total energy | -41714.367872 |
FMO2-MP2: Total energy | -41836.083958 |
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. |
-13.494 | -12.106 | 20.355 | -8.805 | -12.936 | -0.042 |
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 | -0.021 | -0.001 | 3.847 | -1.480 | 1.735 | -0.023 | -1.825 | -1.367 | 0.003 |
4 | A | 4 | ASN | 0 | 0.035 | 0.026 | 6.171 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | TYR | 0 | -0.045 | -0.033 | 7.875 | 0.237 | 0.237 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | LEU | 0 | 0.035 | 0.027 | 6.388 | -0.494 | -0.494 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | LEU | 0 | -0.008 | -0.015 | 8.880 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | SER | 0 | -0.007 | -0.004 | 11.959 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | GLY | 0 | -0.011 | -0.001 | 14.120 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLN | 0 | -0.014 | 0.003 | 8.544 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | THR | 0 | -0.014 | -0.027 | 7.826 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | LEU | 0 | -0.049 | -0.006 | 2.077 | -0.985 | -1.362 | 2.500 | -0.845 | -1.278 | -0.002 |
13 | A | 13 | ASP | -1 | -0.793 | -0.896 | 4.523 | 0.782 | 0.885 | -0.001 | -0.004 | -0.098 | 0.000 |
14 | A | 14 | THR | 0 | 0.004 | -0.029 | 5.869 | 0.810 | 0.810 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLU | -1 | -0.882 | -0.933 | 5.278 | 1.559 | 1.559 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | -0.025 | 0.010 | 2.349 | 0.859 | 1.612 | 3.075 | -1.879 | -1.948 | 0.000 |
17 | A | 17 | HIS | 0 | -0.078 | -0.073 | 2.062 | -7.995 | -12.227 | 11.582 | -1.682 | -5.668 | -0.008 |
18 | A | 18 | LEU | 0 | -0.018 | -0.010 | 2.307 | -7.813 | -5.967 | 3.223 | -2.567 | -2.501 | -0.035 |
19 | A | 19 | LYS | 1 | 0.844 | 0.915 | 5.069 | 0.414 | 0.494 | -0.001 | -0.003 | -0.076 | 0.000 |
20 | A | 20 | ASN | 0 | -0.055 | -0.055 | 7.671 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLY | 0 | 0.027 | 0.027 | 11.271 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ASP | -1 | -0.907 | -0.959 | 12.243 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | PHE | 0 | -0.038 | 0.015 | 12.600 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ASP | -1 | -0.773 | -0.878 | 7.406 | 0.408 | 0.408 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | -0.045 | -0.014 | 7.465 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | 0.042 | 0.009 | 5.973 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | MET | 0 | -0.048 | -0.007 | 6.332 | -0.670 | -0.670 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLN | 0 | 0.018 | 0.013 | 8.045 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASP | -1 | -0.879 | -0.959 | 9.852 | 0.467 | 0.467 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ASP | -1 | -0.874 | -0.949 | 11.481 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | CYS | 0 | -0.115 | -0.014 | 12.626 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASN | 0 | -0.003 | 0.010 | 14.124 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | LEU | 0 | 0.019 | 0.016 | 8.748 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | VAL | 0 | -0.010 | -0.011 | 10.901 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LEU | 0 | -0.016 | -0.002 | 10.794 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | TYR | 0 | -0.001 | -0.025 | 9.686 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ASN | 0 | -0.032 | -0.048 | 13.654 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLY | 0 | 0.041 | 0.022 | 15.603 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ASN | 0 | -0.105 | -0.049 | 16.878 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | TRP | 0 | 0.035 | 0.029 | 12.880 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLN | 0 | 0.032 | 0.009 | 15.001 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | SER | 0 | 0.006 | -0.001 | 14.895 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASN | 0 | -0.060 | -0.029 | 16.554 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | THR | 0 | -0.015 | -0.012 | 15.307 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ALA | 0 | 0.032 | 0.020 | 17.282 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASN | 0 | -0.029 | -0.014 | 17.746 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | ASN | 0 | -0.065 | -0.025 | 18.670 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLY | 0 | 0.031 | 0.006 | 18.371 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | ARG | 1 | 0.848 | 0.926 | 15.136 | -0.341 | -0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ASP | -1 | -0.822 | -0.915 | 12.466 | 0.310 | 0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | LYS | 1 | 0.858 | 0.940 | 9.133 | -0.229 | -0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | LEU | 0 | 0.030 | 0.012 | 7.909 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | THR | 0 | -0.062 | -0.030 | 9.154 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | LEU | 0 | 0.012 | 0.012 | 11.540 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | THR | 0 | -0.016 | -0.016 | 13.570 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | ASP | -1 | -0.859 | -0.927 | 17.231 | -0.262 | -0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | TYR | 0 | 0.014 | -0.007 | 19.821 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | GLY | 0 | 0.048 | 0.020 | 17.974 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | GLU | -1 | -0.841 | -0.906 | 17.647 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | LEU | 0 | 0.036 | 0.012 | 11.563 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | VAL | 0 | -0.041 | -0.034 | 13.940 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | ILE | 0 | 0.042 | 0.030 | 12.164 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | LYS | 1 | 0.887 | 0.943 | 13.500 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | ASN | 0 | 0.052 | 0.009 | 13.893 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | GLY | 0 | 0.027 | 0.026 | 15.201 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ASP | -1 | -0.890 | -0.923 | 16.157 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | GLY | 0 | -0.031 | -0.010 | 16.741 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | SER | 0 | -0.070 | -0.047 | 17.790 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | THR | 0 | -0.047 | -0.049 | 18.281 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | VAL | 0 | 0.024 | 0.019 | 16.872 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | TRP | 0 | 0.038 | 0.012 | 14.885 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | LYS | 1 | 0.905 | 0.951 | 17.341 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | SER | 0 | 0.028 | 0.020 | 16.879 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | GLY | 0 | -0.013 | 0.011 | 18.742 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | ALA | 0 | -0.031 | -0.018 | 21.135 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | GLN | 0 | -0.073 | -0.045 | 21.125 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | SER | 0 | 0.000 | 0.007 | 23.282 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | VAL | 0 | 0.027 | 0.007 | 24.804 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | LYS | 1 | 0.881 | 0.945 | 22.609 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 81 | GLY | 0 | -0.026 | -0.013 | 22.624 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 82 | ASN | 0 | -0.042 | -0.019 | 18.443 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 83 | TYR | 0 | -0.010 | -0.022 | 16.991 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 84 | ALA | 0 | 0.002 | -0.002 | 13.684 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 85 | ALA | 0 | 0.008 | 0.019 | 11.175 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 86 | VAL | 0 | -0.016 | -0.026 | 11.181 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 87 | VAL | 0 | 0.045 | 0.030 | 8.981 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | HIS | 0 | -0.003 | 0.002 | 11.889 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | PRO | 0 | 0.018 | -0.009 | 15.527 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | ASP | -1 | -0.833 | -0.899 | 16.687 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | GLY | 0 | 0.012 | 0.009 | 16.089 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 92 | ARG | 1 | 0.795 | 0.880 | 16.459 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | LEU | 0 | 0.022 | 0.019 | 11.239 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | VAL | 0 | -0.055 | -0.025 | 14.320 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | VAL | 0 | 0.011 | -0.002 | 14.659 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | PHE | 0 | -0.026 | -0.006 | 16.406 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | GLY | 0 | 0.016 | 0.006 | 18.199 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | PRO | 0 | 0.021 | 0.018 | 20.952 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | SER | 0 | -0.035 | -0.038 | 20.567 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | VAL | 0 | 0.005 | 0.019 | 22.284 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | PHE | 0 | -0.001 | -0.008 | 24.353 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | LYS | 1 | 0.876 | 0.927 | 21.229 | 0.261 | 0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ILE | 0 | 0.019 | 0.023 | 23.546 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | ASP | -1 | -0.833 | -0.927 | 22.912 | -0.302 | -0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | PRO | 0 | -0.013 | 0.004 | 21.434 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | TRP | 0 | -0.007 | 0.000 | 18.084 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | VAL | 0 | 0.011 | 0.010 | 24.432 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | ARG | 1 | 0.921 | 0.964 | 27.945 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | GLY | 0 | 0.008 | 0.007 | 30.514 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |