FMODB ID: 6N3YZ
Calculation Name: 5JAA-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5JAA
Chain ID: A
UniProt ID: Q9KMA5
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 | OptH |
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 | 102 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -625229.668926 |
---|---|
FMO2-HF: Nuclear repulsion | 585487.273851 |
FMO2-HF: Total energy | -39742.395075 |
FMO2-MP2: Total energy | -39860.426009 |
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:3:ASN)
Summations of interaction energy for
fragment #1(A:3:ASN)
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. |
-0.052 | 2.574 | -0.027 | -1.272 | -1.326 | 0 |
Interaction energy analysis for fragmet #1(A:3:ASN)
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 | 5 | ASP | -1 | -0.845 | -0.916 | 3.805 | 3.112 | 5.738 | -0.027 | -1.272 | -1.326 | 0.000 |
4 | A | 6 | LEU | 0 | 0.059 | 0.032 | 6.654 | -0.975 | -0.975 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 7 | PHE | 0 | 0.035 | 0.017 | 10.113 | -0.435 | -0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | ALA | 0 | 0.025 | 0.025 | 9.322 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | GLU | -1 | -0.847 | -0.919 | 8.697 | -1.233 | -1.233 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | LEU | 0 | -0.003 | -0.009 | 11.822 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | SER | 0 | -0.023 | -0.032 | 14.625 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | SER | 0 | 0.002 | -0.005 | 13.978 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | ALA | 0 | 0.028 | 0.016 | 15.378 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | LEU | 0 | -0.009 | -0.002 | 17.024 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | VAL | 0 | -0.059 | -0.015 | 18.577 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | GLU | -1 | -0.908 | -0.962 | 16.619 | -0.751 | -0.751 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | ALA | 0 | -0.003 | -0.003 | 20.648 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | LYS | 1 | 0.970 | 0.995 | 22.729 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | GLN | 0 | -0.012 | 0.014 | 22.671 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | HIS | 0 | -0.019 | -0.007 | 24.190 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | SER | 0 | -0.063 | -0.059 | 26.042 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | GLU | -1 | -0.906 | -0.950 | 28.574 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | GLY | 0 | -0.006 | 0.009 | 29.532 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 24 | LYS | 1 | 0.767 | 0.874 | 28.067 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 25 | LEU | 0 | 0.007 | 0.003 | 21.190 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 26 | THR | 0 | -0.002 | 0.005 | 24.784 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | LEU | 0 | 0.051 | 0.025 | 19.765 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | LYS | 1 | 0.931 | 0.986 | 20.474 | 0.605 | 0.605 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | THR | 0 | -0.004 | -0.025 | 22.553 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | HIS | 0 | -0.045 | -0.026 | 21.606 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | HIS | 0 | 0.020 | 0.011 | 26.697 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | VAL | 0 | -0.003 | -0.009 | 28.463 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | ASN | 0 | -0.029 | -0.014 | 31.398 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | ASP | -1 | -0.921 | -0.949 | 34.822 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | VAL | 0 | -0.035 | -0.013 | 36.239 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | GLY | 0 | 0.015 | 0.010 | 39.724 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | GLU | -1 | -0.896 | -0.950 | 41.833 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | LEU | 0 | -0.074 | -0.035 | 42.663 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 39 | ASN | 0 | -0.013 | -0.014 | 45.821 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | ILE | 0 | -0.026 | -0.015 | 49.411 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | SER | 0 | -0.024 | 0.001 | 51.847 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | PRO | 0 | 0.056 | 0.003 | 55.405 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | ASP | -1 | -0.853 | -0.925 | 58.024 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | GLU | -1 | -0.835 | -0.938 | 51.199 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | ILE | 0 | -0.017 | 0.008 | 54.535 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | VAL | 0 | -0.060 | -0.026 | 56.016 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | SER | 0 | -0.031 | -0.019 | 55.683 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | ILE | 0 | 0.000 | 0.005 | 51.289 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | ARG | 1 | 0.803 | 0.892 | 54.760 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | GLU | -1 | -0.984 | -1.000 | 57.459 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | GLN | 0 | 0.040 | 0.025 | 51.991 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | PHE | 0 | -0.046 | -0.017 | 50.760 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | ASN | 0 | -0.060 | -0.018 | 56.763 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | MET | 0 | 0.014 | 0.027 | 55.962 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | SER | 0 | 0.017 | -0.001 | 60.846 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | ARG | 1 | 0.913 | 0.929 | 61.560 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | GLY | 0 | -0.016 | -0.006 | 61.384 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | VAL | 0 | 0.016 | 0.010 | 59.117 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | PHE | 0 | 0.110 | 0.044 | 53.709 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | ALA | 0 | -0.012 | -0.005 | 56.622 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | ARG | 1 | 0.930 | 0.966 | 57.584 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | LEU | 0 | 0.021 | 0.015 | 53.345 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | LEU | 0 | -0.037 | -0.005 | 51.728 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | HIS | 0 | -0.038 | -0.007 | 52.538 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | THR | 0 | 0.005 | 0.005 | 55.477 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | SER | 0 | 0.010 | 0.019 | 57.835 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | SER | 0 | 0.090 | 0.008 | 61.140 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | ARG | 1 | 0.973 | 0.997 | 63.260 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | THR | 0 | 0.001 | 0.016 | 58.611 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | LEU | 0 | 0.054 | 0.044 | 57.433 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | GLU | -1 | -0.930 | -0.976 | 60.070 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | ASN | 0 | -0.096 | -0.085 | 62.203 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | TRP | 0 | 0.046 | 0.022 | 54.949 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | GLU | -1 | -0.760 | -0.881 | 59.456 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | GLN | 0 | -0.055 | -0.033 | 60.951 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | GLY | 0 | 0.041 | 0.034 | 60.672 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | ARG | 1 | 0.800 | 0.914 | 61.755 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | SER | 0 | -0.033 | -0.023 | 59.393 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | VAL | 0 | 0.041 | 0.023 | 53.966 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | PRO | 0 | -0.025 | 0.007 | 52.928 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | ASN | 0 | 0.059 | 0.017 | 50.445 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 82 | GLY | 0 | 0.137 | 0.058 | 47.205 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | GLN | 0 | 0.026 | 0.008 | 44.893 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | ALA | 0 | -0.005 | 0.004 | 47.116 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | VAL | 0 | 0.021 | 0.007 | 47.583 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | THR | 0 | -0.020 | -0.010 | 42.895 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | LEU | 0 | 0.002 | -0.003 | 45.544 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | LEU | 0 | -0.009 | -0.001 | 47.343 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | LYS | 1 | 0.953 | 0.976 | 45.282 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | LEU | 0 | -0.037 | -0.014 | 41.414 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | VAL | 0 | -0.019 | -0.007 | 45.071 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | GLN | 0 | -0.029 | -0.005 | 47.949 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | ARG | 1 | 0.859 | 0.926 | 40.451 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | HIS | 0 | 0.014 | 0.019 | 39.935 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 95 | PRO | 0 | 0.055 | 0.020 | 44.918 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 96 | GLU | -1 | -0.865 | -0.948 | 43.763 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 97 | THR | 0 | -0.003 | 0.016 | 43.467 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 98 | LEU | 0 | 0.008 | 0.009 | 46.168 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 99 | SER | 0 | -0.055 | -0.048 | 48.243 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 100 | HIS | 0 | 0.032 | 0.008 | 42.840 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 101 | ILE | 0 | -0.030 | -0.019 | 47.395 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 102 | ALA | 0 | -0.056 | -0.033 | 49.255 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 103 | GLU | -1 | -1.006 | -0.985 | 49.678 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 104 | LEU | 0 | -0.084 | -0.025 | 45.713 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |