FMODB ID: 8585Y
Calculation Name: 3LYX-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3LYX
Chain ID: A
UniProt ID: Q486I1
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 | 118 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -953013.212434 |
---|---|
FMO2-HF: Nuclear repulsion | 905974.412738 |
FMO2-HF: Total energy | -47038.799696 |
FMO2-MP2: Total energy | -47174.987593 |
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:4:ASP)
Summations of interaction energy for
fragment #1(A:4:ASP)
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. |
-87.515 | -81.674 | 1.924 | -3.092 | -4.673 | 0.022 |
Interaction energy analysis for fragmet #1(A:4:ASP)
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 | 6 | LEU | 0 | -0.007 | -0.007 | 3.057 | -10.917 | -8.263 | 0.079 | -1.203 | -1.530 | 0.008 |
4 | A | 7 | LYS | 1 | 0.981 | 0.991 | 2.742 | -49.902 | -48.061 | 1.825 | -1.335 | -2.331 | 0.012 |
5 | A | 8 | GLN | 0 | 0.040 | 0.002 | 3.692 | -17.481 | -16.135 | 0.020 | -0.554 | -0.812 | 0.002 |
6 | A | 9 | ARG | 1 | 0.910 | 0.957 | 5.884 | -36.200 | -36.200 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 10 | ALA | 0 | 0.039 | 0.019 | 7.568 | -3.131 | -3.131 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 11 | LYS | 1 | 0.937 | 0.983 | 8.161 | -28.718 | -28.718 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 12 | ALA | 0 | 0.000 | -0.004 | 9.932 | -2.026 | -2.026 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 13 | PHE | 0 | 0.062 | 0.039 | 12.561 | -1.504 | -1.504 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 14 | ASP | -1 | -0.841 | -0.925 | 14.572 | 15.906 | 15.906 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 15 | TYR | 0 | -0.109 | -0.070 | 12.978 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 16 | VAL | 0 | -0.061 | -0.016 | 16.263 | -0.617 | -0.617 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 17 | PHE | 0 | -0.006 | -0.007 | 18.707 | -0.433 | -0.433 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 18 | ASP | -1 | -0.832 | -0.914 | 21.069 | 13.157 | 13.157 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 19 | ALA | 0 | -0.001 | 0.008 | 21.501 | 0.542 | 0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 20 | ILE | 0 | -0.060 | -0.032 | 17.883 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 21 | VAL | 0 | 0.014 | 0.003 | 21.003 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 22 | VAL | 0 | -0.003 | 0.007 | 17.553 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 23 | THR | 0 | -0.011 | -0.005 | 20.975 | -0.474 | -0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 24 | ASP | -1 | -0.779 | -0.895 | 22.598 | 11.434 | 11.434 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 25 | LEU | 0 | -0.006 | -0.006 | 24.246 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 26 | GLN | 0 | -0.080 | -0.027 | 26.940 | -0.195 | -0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 27 | GLY | 0 | 0.017 | 0.021 | 27.858 | -0.316 | -0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 28 | PHE | 0 | -0.043 | -0.033 | 27.489 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 29 | ILE | 0 | -0.020 | -0.006 | 23.856 | 0.506 | 0.506 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 30 | ILE | 0 | -0.020 | -0.020 | 19.594 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 31 | ASP | -1 | -0.887 | -0.978 | 16.079 | 17.371 | 17.371 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 32 | TRP | 0 | -0.038 | -0.026 | 19.452 | -0.479 | -0.479 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 33 | ASN | 0 | 0.010 | 0.029 | 18.288 | -0.317 | -0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 34 | LYS | 1 | 0.974 | 0.965 | 18.737 | -16.045 | -16.045 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 35 | GLY | 0 | 0.024 | 0.030 | 20.938 | -0.597 | -0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 36 | SER | 0 | 0.015 | -0.028 | 22.695 | -0.771 | -0.771 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 37 | GLU | -1 | -0.954 | -0.963 | 24.121 | 11.706 | 11.706 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 38 | THR | 0 | -0.084 | -0.034 | 25.172 | -0.526 | -0.526 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 39 | LEU | 0 | -0.038 | -0.012 | 27.073 | -0.423 | -0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 40 | TYR | 0 | 0.030 | -0.009 | 26.587 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 41 | GLY | 0 | -0.015 | 0.002 | 29.391 | -0.402 | -0.402 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 42 | TYR | 0 | -0.015 | -0.012 | 28.453 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 43 | SER | 0 | 0.072 | 0.041 | 26.444 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 44 | LYS | 1 | 0.990 | 0.989 | 18.546 | -15.097 | -15.097 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 45 | GLU | -1 | -0.954 | -0.998 | 23.141 | 12.421 | 12.421 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 46 | GLN | 0 | -0.039 | -0.008 | 25.903 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 47 | ALA | 0 | 0.028 | 0.019 | 25.556 | -0.273 | -0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 48 | ILE | 0 | -0.025 | 0.002 | 21.514 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 49 | GLY | 0 | -0.026 | -0.009 | 25.370 | -0.302 | -0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 50 | GLN | 0 | -0.039 | -0.011 | 27.728 | -0.631 | -0.631 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 51 | PRO | 0 | 0.010 | 0.020 | 28.921 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 52 | VAL | 0 | 0.112 | 0.031 | 27.600 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 53 | ASN | 0 | -0.001 | 0.000 | 29.743 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 54 | MET | 0 | -0.066 | -0.015 | 30.186 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 55 | LEU | 0 | -0.043 | -0.028 | 28.112 | -0.106 | -0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 56 | HIS | 0 | 0.028 | 0.020 | 32.076 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 57 | VAL | 0 | 0.021 | 0.028 | 35.593 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 58 | PRO | 0 | 0.008 | -0.023 | 39.185 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 59 | GLY | 0 | -0.033 | -0.017 | 40.651 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 60 | ASP | -1 | -0.787 | -0.891 | 38.608 | 7.695 | 7.695 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 61 | THR | 0 | -0.015 | -0.012 | 36.355 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 62 | GLU | -1 | -0.935 | -0.950 | 37.499 | 7.276 | 7.276 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 63 | HIS | 0 | 0.052 | 0.002 | 39.076 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 64 | ILE | 0 | 0.020 | 0.025 | 33.807 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 65 | THR | 0 | -0.023 | -0.026 | 33.631 | 0.317 | 0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 66 | SER | 0 | -0.024 | -0.009 | 34.364 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 67 | GLU | -1 | -0.881 | -0.931 | 35.428 | 8.626 | 8.626 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 68 | VAL | 0 | -0.015 | -0.019 | 29.682 | 0.221 | 0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 69 | ILE | 0 | 0.004 | -0.006 | 31.098 | 0.261 | 0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 70 | SER | 0 | -0.006 | 0.014 | 32.148 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 71 | ALA | 0 | 0.050 | 0.022 | 31.176 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 72 | VAL | 0 | -0.049 | -0.026 | 26.522 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 73 | GLU | -1 | -0.943 | -0.980 | 28.257 | 9.605 | 9.605 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 74 | ASN | 0 | -0.109 | -0.048 | 30.554 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 75 | GLN | 0 | -0.056 | -0.037 | 30.734 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 76 | GLY | 0 | -0.013 | 0.016 | 26.773 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 77 | LYS | 1 | 0.885 | 0.922 | 24.700 | -11.500 | -11.500 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 78 | TRP | 0 | -0.015 | 0.005 | 27.173 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 79 | THR | 0 | -0.068 | -0.056 | 28.134 | 0.483 | 0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 80 | GLY | 0 | 0.051 | 0.034 | 30.451 | -0.318 | -0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 81 | GLU | -1 | -0.949 | -0.957 | 32.492 | 8.966 | 8.966 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 82 | ILE | 0 | 0.005 | 0.004 | 31.870 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 83 | ARG | 1 | 0.824 | 0.900 | 35.275 | -7.463 | -7.463 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 84 | MET | 0 | -0.048 | -0.013 | 31.989 | 0.248 | 0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 85 | LEU | 0 | -0.010 | -0.008 | 34.760 | -0.301 | -0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 86 | HIS | 0 | -0.012 | 0.005 | 32.443 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 87 | LYS | 1 | 0.907 | 0.962 | 32.473 | -9.454 | -9.454 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 88 | ASP | -1 | -0.907 | -0.948 | 34.747 | 8.145 | 8.145 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 89 | GLY | 0 | 0.037 | 0.025 | 37.809 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 90 | HIS | 1 | 0.762 | 0.874 | 35.861 | -8.660 | -8.660 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 91 | ILE | 0 | 0.027 | 0.001 | 38.205 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 92 | GLY | 0 | -0.027 | -0.011 | 36.586 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 93 | TRP | 0 | -0.012 | -0.002 | 36.208 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 94 | ILE | 0 | 0.002 | -0.009 | 29.889 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 95 | GLU | -1 | -0.865 | -0.913 | 29.744 | 10.394 | 10.394 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 96 | SER | 0 | -0.050 | -0.046 | 28.179 | 0.399 | 0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 97 | MET | 0 | 0.013 | -0.002 | 24.042 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 98 | CYS | 0 | -0.040 | -0.004 | 24.869 | 0.389 | 0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 99 | VAL | 0 | -0.001 | -0.009 | 20.698 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 100 | PRO | 0 | 0.033 | 0.033 | 22.179 | 0.276 | 0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 101 | ILE | 0 | -0.017 | -0.008 | 17.170 | 0.725 | 0.725 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 102 | TYR | 0 | -0.015 | -0.028 | 18.827 | -0.523 | -0.523 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 103 | GLY | 0 | 0.017 | 0.015 | 18.222 | 0.727 | 0.727 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 104 | GLU | -1 | -0.948 | -0.988 | 18.794 | 13.858 | 13.858 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 105 | ASN | 0 | -0.069 | -0.049 | 21.150 | -0.381 | -0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 106 | TYR | 0 | -0.012 | -0.015 | 21.331 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 107 | GLN | 0 | 0.033 | 0.046 | 23.198 | -0.432 | -0.432 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 108 | MET | 0 | 0.015 | 0.012 | 22.720 | 0.569 | 0.569 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 109 | VAL | 0 | 0.000 | 0.000 | 20.649 | -0.362 | -0.362 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 110 | GLY | 0 | 0.036 | 0.009 | 22.212 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 111 | ALA | 0 | -0.028 | 0.003 | 22.352 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 112 | LEU | 0 | -0.003 | 0.001 | 17.441 | 0.347 | 0.347 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 113 | GLY | 0 | 0.041 | 0.022 | 21.107 | -0.389 | -0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 114 | ILE | 0 | -0.048 | -0.024 | 20.699 | 0.529 | 0.529 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 115 | ASN | 0 | -0.011 | 0.001 | 23.370 | -0.908 | -0.908 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 116 | ARG | 1 | 0.843 | 0.914 | 24.657 | -11.835 | -11.835 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 117 | ASP | -1 | -0.769 | -0.857 | 28.142 | 9.106 | 9.106 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 118 | ILE | 0 | -0.061 | -0.035 | 31.414 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 119 | THR | 0 | -0.002 | -0.017 | 34.334 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 120 | LYS | 1 | 0.886 | 0.951 | 36.728 | -8.175 | -8.175 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 121 | ARG | 1 | 0.940 | 0.980 | 31.796 | -9.853 | -9.853 | 0.000 | 0.000 | 0.000 | 0.000 |