![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 858JY
Calculation Name: 3H9W-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3H9W
Chain ID: A
UniProt ID: A1U4R9
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 | 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 | 109 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -927929.073893 |
---|---|
FMO2-HF: Nuclear repulsion | 882601.52558 |
FMO2-HF: Total energy | -45327.548313 |
FMO2-MP2: Total energy | -45459.081722 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024026/ligand_interaction/ligand_F024026.png)
Ligand Interaction
![ligand interaction](./Kdata/F024026/ligand_interaction/ligand_interaction_F024026.png)
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:23:LYS)
Summations of interaction energy for
fragment #1(A:23:LYS)
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. |
-149.279 | -145.035 | 1.533 | -1.456 | -4.318 | -0.01 |
Interaction energy analysis for fragmet #1(A:23:LYS)
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 | 25 | ILE | 0 | 0.016 | 0.007 | 3.235 | 5.453 | 6.889 | 0.050 | -0.370 | -1.115 | 0.000 |
4 | A | 26 | PRO | 0 | -0.009 | 0.017 | 5.960 | 1.186 | 1.186 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 27 | TRP | 0 | 0.017 | -0.003 | 8.828 | 2.354 | 2.354 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 28 | LYS | 1 | 0.893 | 0.944 | 12.382 | 14.848 | 14.848 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 29 | ILE | 0 | -0.031 | -0.008 | 16.008 | 0.344 | 0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 30 | ASN | 0 | -0.021 | -0.009 | 19.091 | 0.539 | 0.539 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 31 | TRP | 0 | 0.060 | 0.016 | 22.678 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 32 | GLN | 0 | -0.009 | 0.005 | 24.206 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 33 | THR | 0 | -0.024 | -0.024 | 25.540 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 34 | MET | 0 | 0.017 | 0.017 | 23.114 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 35 | ALA | 0 | 0.006 | 0.004 | 22.274 | -0.405 | -0.405 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 36 | PHE | 0 | -0.019 | -0.020 | 14.545 | -0.370 | -0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 37 | GLU | -1 | -0.854 | -0.914 | 18.148 | -13.739 | -13.739 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 38 | TYR | 0 | -0.051 | -0.033 | 12.266 | 0.701 | 0.701 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 39 | ILE | 0 | 0.041 | 0.015 | 10.946 | -0.692 | -0.692 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 40 | GLY | 0 | -0.013 | 0.008 | 7.867 | 0.992 | 0.992 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 41 | PRO | 0 | 0.041 | 0.009 | 8.102 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 42 | GLN | 0 | -0.019 | -0.021 | 3.372 | 4.504 | 4.951 | 0.015 | -0.107 | -0.355 | 0.000 |
21 | A | 43 | ILE | 0 | 0.040 | 0.026 | 6.047 | -1.276 | -1.276 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 44 | GLU | -1 | -0.887 | -0.918 | 8.492 | -16.808 | -16.808 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 45 | ALA | 0 | -0.059 | -0.026 | 6.713 | 0.830 | 0.830 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 46 | LEU | 0 | -0.025 | -0.003 | 5.724 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 47 | LEU | 0 | 0.023 | -0.009 | 8.105 | 1.301 | 1.301 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 48 | GLY | 0 | 0.000 | 0.000 | 11.407 | 1.770 | 1.770 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 49 | TRP | 0 | -0.070 | -0.053 | 13.473 | 1.576 | 1.576 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 50 | PRO | 0 | 0.030 | 0.017 | 13.909 | -0.756 | -0.756 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 51 | GLN | 0 | 0.034 | 0.027 | 12.035 | 0.706 | 0.706 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 52 | GLY | 0 | -0.025 | -0.015 | 14.008 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 53 | SER | 0 | -0.064 | -0.064 | 16.657 | 0.664 | 0.664 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 54 | TRP | 0 | 0.037 | 0.026 | 13.417 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 55 | LYS | 1 | 0.892 | 0.952 | 17.192 | 13.449 | 13.449 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 56 | SER | 0 | 0.007 | 0.008 | 20.479 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 57 | VAL | 0 | 0.093 | 0.038 | 19.330 | -0.557 | -0.557 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 58 | GLU | -1 | -0.913 | -0.945 | 20.311 | -12.061 | -12.061 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 59 | ASP | -1 | -0.824 | -0.898 | 18.874 | -14.258 | -14.258 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 60 | TRP | 0 | -0.081 | -0.059 | 14.123 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 61 | ALA | 0 | 0.010 | 0.011 | 17.446 | -0.390 | -0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 62 | THR | 0 | -0.018 | -0.016 | 20.076 | 0.381 | 0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 63 | ARG | 1 | 0.736 | 0.863 | 16.328 | 16.376 | 16.376 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 64 | MET | 0 | -0.004 | 0.005 | 16.071 | -1.132 | -1.132 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 65 | HIS | 0 | 0.007 | 0.001 | 17.783 | 0.771 | 0.771 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 66 | PRO | 0 | 0.024 | 0.005 | 19.621 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 67 | GLU | -1 | -0.815 | -0.894 | 21.788 | -13.300 | -13.300 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 68 | ASP | -1 | -0.773 | -0.874 | 17.151 | -17.337 | -17.337 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 69 | GLN | 0 | -0.051 | -0.032 | 19.984 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 70 | GLU | -1 | -0.971 | -0.985 | 21.795 | -11.432 | -11.432 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 71 | TRP | 0 | -0.099 | -0.042 | 16.352 | 0.371 | 0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 72 | VAL | 0 | 0.008 | 0.008 | 16.518 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 73 | VAL | 0 | 0.041 | 0.019 | 19.513 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 74 | ASN | 0 | -0.002 | -0.008 | 21.645 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 75 | PHE | 0 | -0.023 | -0.003 | 17.236 | 0.459 | 0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 76 | CYS | 0 | 0.026 | 0.005 | 17.004 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 77 | VAL | 0 | 0.019 | 0.042 | 20.161 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 78 | LYS | 1 | 0.963 | 0.986 | 23.549 | 11.601 | 11.601 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 79 | GLN | 0 | -0.027 | -0.019 | 20.506 | 0.509 | 0.509 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 80 | SER | 0 | 0.018 | -0.005 | 20.627 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 81 | GLU | -1 | -0.922 | -0.958 | 22.205 | -11.095 | -11.095 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 82 | CYS | 0 | -0.162 | -0.072 | 25.192 | 0.665 | 0.665 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 83 | GLY | 0 | 0.023 | -0.003 | 23.271 | 0.200 | 0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 84 | VAL | 0 | -0.078 | -0.033 | 20.902 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 85 | ASP | -1 | -0.769 | -0.851 | 16.271 | -17.893 | -17.893 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 86 | HIS | 0 | -0.093 | -0.062 | 16.169 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 87 | GLU | -1 | -0.907 | -0.965 | 11.532 | -27.864 | -27.864 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 88 | ALA | 0 | -0.014 | -0.004 | 12.632 | 1.691 | 1.691 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 89 | ASP | -1 | -0.798 | -0.863 | 10.818 | -28.818 | -28.818 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 90 | TYR | 0 | -0.055 | -0.054 | 12.042 | 1.702 | 1.702 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 91 | ARG | 1 | 0.700 | 0.818 | 12.442 | 14.047 | 14.047 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 92 | ALA | 0 | 0.046 | 0.020 | 12.030 | 1.238 | 1.238 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 93 | LEU | 0 | -0.015 | 0.000 | 14.048 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 94 | HIS | 0 | 0.050 | 0.040 | 12.191 | 0.501 | 0.501 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 95 | ARG | 1 | 0.964 | 0.989 | 15.270 | 15.564 | 15.564 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 96 | ASP | -1 | -0.970 | -0.965 | 16.602 | -15.934 | -15.934 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 97 | GLY | 0 | 0.020 | 0.010 | 18.717 | 0.651 | 0.651 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 98 | HIS | 1 | 0.790 | 0.884 | 12.782 | 19.161 | 19.161 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 99 | TYR | 0 | 0.046 | 0.007 | 15.446 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 100 | VAL | 0 | -0.035 | -0.023 | 8.962 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 101 | TRP | 0 | 0.018 | 0.015 | 10.460 | 0.427 | 0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 102 | ILE | 0 | 0.012 | -0.006 | 7.751 | -3.676 | -3.676 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 103 | ARG | 1 | 0.760 | 0.836 | 6.736 | 34.534 | 34.534 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 104 | ASP | -1 | -0.782 | -0.895 | 7.785 | -29.341 | -29.341 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 105 | VAL | 0 | 0.002 | -0.008 | 8.476 | 1.282 | 1.282 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 106 | VAL | 0 | -0.017 | -0.014 | 10.773 | -0.625 | -0.625 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 107 | HIS | 0 | -0.062 | -0.043 | 13.828 | 0.985 | 0.985 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 108 | VAL | 0 | -0.017 | -0.025 | 15.787 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 109 | VAL | 0 | -0.008 | 0.004 | 18.735 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 110 | ARG | 1 | 0.874 | 0.943 | 21.324 | 12.539 | 12.539 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 111 | ASP | -1 | -0.749 | -0.850 | 25.126 | -10.751 | -10.751 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 112 | ASP | -1 | -0.924 | -0.973 | 27.737 | -10.327 | -10.327 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 113 | SER | 0 | -0.140 | -0.082 | 30.704 | 0.375 | 0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 114 | GLY | 0 | -0.076 | -0.037 | 29.388 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 115 | GLU | -1 | -0.973 | -0.986 | 29.304 | -9.934 | -9.934 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 116 | VAL | 0 | -0.056 | -0.025 | 23.389 | -0.345 | -0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 117 | GLU | -1 | -0.933 | -0.961 | 24.227 | -12.332 | -12.332 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 118 | ALA | 0 | -0.045 | -0.049 | 20.356 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 119 | LEU | 0 | 0.002 | 0.024 | 17.321 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 120 | ILE | 0 | 0.002 | -0.004 | 14.533 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 121 | GLY | 0 | 0.054 | 0.026 | 11.246 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 122 | PHE | 0 | -0.058 | -0.035 | 5.956 | -1.545 | -1.545 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 123 | MET | 0 | 0.004 | 0.028 | 7.214 | 1.126 | 1.126 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 124 | PHE | 0 | -0.049 | -0.045 | 2.137 | -18.054 | -16.747 | 1.446 | -0.745 | -2.007 | -0.010 |
103 | A | 125 | ASP | -1 | -0.797 | -0.867 | 3.381 | -32.439 | -31.780 | 0.022 | -0.133 | -0.547 | 0.000 |
104 | A | 126 | ILE | 0 | -0.033 | -0.019 | 4.067 | -7.838 | -7.443 | 0.000 | -0.101 | -0.294 | 0.000 |
105 | A | 127 | SER | 0 | -0.004 | -0.048 | 6.355 | 5.765 | 5.765 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 128 | LEU | 0 | -0.058 | -0.032 | 6.049 | 2.830 | 2.830 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 129 | GLU | -1 | -0.862 | -0.892 | 7.158 | -32.836 | -32.836 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 130 | HIS | 1 | 0.831 | 0.923 | 10.351 | 25.434 | 25.434 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 131 | HIS | 0 | 0.009 | 0.029 | 10.876 | 2.087 | 2.087 | 0.000 | 0.000 | 0.000 | 0.000 |