![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: M3L9Z
Calculation Name: 3D33-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3D33
Chain ID: A
UniProt ID: A6KX32
Base Structure: X-ray
Registration Date: 2023-03-14
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 | 94 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -666591.396435 |
---|---|
FMO2-HF: Nuclear repulsion | 629601.000213 |
FMO2-HF: Total energy | -36990.396222 |
FMO2-MP2: Total energy | -37097.852939 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F019310/ligand_interaction/ligand_F019310.png)
Ligand Interaction
![ligand interaction](./Kdata/F019310/ligand_interaction/ligand_interaction_F019310.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:34:PRO)
Summations of interaction energy for
fragment #1(A:34:PRO)
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. |
-5.329 | -2.701 | 0.124 | -1.456 | -1.296 | -0.002 |
Interaction energy analysis for fragmet #1(A:34:PRO)
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 | 36 | LYS | 1 | 0.887 | 0.937 | 3.041 | -1.910 | 0.718 | 0.124 | -1.456 | -1.296 | -0.002 |
4 | A | 37 | ASP | -1 | -0.877 | -0.945 | 5.745 | -0.540 | -0.540 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 38 | VAL | 0 | -0.106 | -0.056 | 7.792 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 39 | GLU | -1 | -0.884 | -0.929 | 11.459 | -0.547 | -0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 40 | LEU | 0 | -0.077 | -0.041 | 13.379 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 41 | ASP | -1 | -0.875 | -0.923 | 16.690 | -0.371 | -0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 42 | GLY | 0 | -0.019 | -0.028 | 20.012 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 43 | ARG | 1 | 0.747 | 0.843 | 23.314 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 44 | TRP | 0 | 0.055 | 0.005 | 23.012 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 45 | ASP | -1 | -0.828 | -0.871 | 24.960 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 46 | ASP | -1 | -0.913 | -0.943 | 27.407 | -0.106 | -0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 54 | ASN | 0 | -0.034 | -0.035 | 15.983 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 55 | CYS | 0 | 0.017 | 0.030 | 17.864 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 56 | PRO | 0 | 0.037 | 0.023 | 17.679 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 57 | ILE | 0 | -0.004 | 0.005 | 17.087 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 58 | THR | 0 | 0.009 | 0.008 | 11.815 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 59 | VAL | 0 | 0.038 | 0.000 | 12.276 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 60 | PHE | 0 | -0.010 | 0.006 | 7.157 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 61 | THR | 0 | -0.001 | -0.006 | 8.345 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 62 | ASP | -1 | -0.932 | -0.967 | 6.237 | -1.716 | -1.716 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 63 | GLY | 0 | 0.020 | 0.010 | 7.468 | 0.485 | 0.485 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 64 | TYR | 0 | -0.073 | -0.058 | 9.475 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 65 | LEU | 0 | -0.013 | 0.000 | 11.783 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 66 | LEU | 0 | 0.018 | 0.016 | 11.333 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 67 | THR | 0 | -0.009 | -0.017 | 11.381 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 68 | LEU | 0 | 0.022 | 0.016 | 12.712 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 69 | LYS | 1 | 0.903 | 0.946 | 11.737 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 70 | ASN | 0 | 0.086 | 0.039 | 15.877 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 71 | ALA | 0 | -0.047 | -0.031 | 17.530 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 72 | SER | 0 | -0.069 | -0.048 | 19.296 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 73 | PRO | 0 | -0.027 | -0.010 | 22.276 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 74 | ASP | -1 | -0.801 | -0.857 | 24.634 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 75 | ARG | 1 | 0.761 | 0.852 | 26.674 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 76 | ASP | -1 | -0.857 | -0.916 | 27.381 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 77 | MET | 0 | -0.049 | -0.033 | 21.275 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 78 | THR | 0 | -0.030 | -0.018 | 25.986 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 79 | ILE | 0 | -0.047 | -0.010 | 19.782 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 80 | ARG | 1 | 0.863 | 0.911 | 23.222 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 81 | ILE | 0 | -0.010 | 0.000 | 19.086 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 82 | THR | 0 | -0.030 | -0.022 | 22.657 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 83 | ASP | -1 | -0.776 | -0.883 | 23.412 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 84 | MET | 0 | 0.007 | -0.003 | 22.165 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 85 | ALA | 0 | -0.042 | 0.007 | 25.208 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 86 | LYS | 1 | 0.822 | 0.882 | 27.575 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 87 | GLY | 0 | 0.010 | 0.023 | 28.345 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 88 | GLY | 0 | -0.035 | -0.016 | 28.838 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 89 | VAL | 0 | -0.010 | -0.006 | 26.864 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 90 | VAL | 0 | -0.043 | -0.021 | 22.862 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 91 | TYR | 0 | -0.017 | -0.019 | 22.655 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 92 | GLU | -1 | -0.844 | -0.911 | 25.168 | -0.184 | -0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 93 | ASN | 0 | -0.053 | -0.026 | 23.802 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 94 | ASP | -1 | -0.820 | -0.876 | 26.272 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 95 | ILE | 0 | -0.047 | -0.032 | 22.968 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 96 | PRO | 0 | 0.011 | 0.002 | 27.053 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 97 | GLU | -1 | -0.879 | -0.929 | 27.437 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 98 | VAL | 0 | -0.039 | -0.020 | 26.680 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 99 | GLN | 0 | -0.068 | -0.043 | 25.408 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 100 | SER | 0 | -0.029 | -0.030 | 23.308 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 101 | ALA | 0 | 0.031 | 0.018 | 20.623 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 102 | TYR | 0 | -0.056 | -0.044 | 14.262 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 103 | ILE | 0 | 0.022 | 0.030 | 17.561 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 104 | THR | 0 | -0.020 | 0.000 | 14.546 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 105 | ILE | 0 | -0.017 | -0.008 | 16.150 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 106 | SER | 0 | -0.010 | 0.003 | 16.216 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 107 | ILE | 0 | 0.043 | 0.019 | 13.373 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 108 | ALA | 0 | 0.008 | 0.002 | 16.906 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 109 | ASN | 0 | -0.044 | -0.029 | 17.777 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 110 | PHE | 0 | 0.037 | 0.029 | 19.264 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 111 | PRO | 0 | 0.005 | -0.002 | 20.447 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 112 | ALA | 0 | -0.009 | 0.009 | 19.193 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 113 | GLU | -1 | -0.846 | -0.911 | 19.212 | -0.288 | -0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 114 | GLU | -1 | -0.952 | -0.987 | 18.424 | -0.559 | -0.559 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 115 | TYR | 0 | -0.055 | -0.054 | 18.694 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 116 | LYS | 1 | 0.888 | 0.935 | 19.077 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 117 | LEU | 0 | -0.041 | -0.026 | 16.074 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 118 | GLU | -1 | -0.815 | -0.900 | 19.839 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 119 | ILE | 0 | -0.008 | -0.010 | 18.091 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 120 | THR | 0 | 0.012 | -0.001 | 22.405 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 121 | GLY | 0 | 0.002 | 0.002 | 25.880 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 122 | THR | 0 | -0.044 | 0.013 | 27.673 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 123 | PRO | 0 | -0.012 | -0.033 | 31.343 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 124 | SER | 0 | -0.026 | -0.027 | 30.721 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 125 | GLY | 0 | 0.045 | 0.029 | 26.651 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 126 | HIS | 0 | -0.072 | -0.047 | 25.203 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 127 | LEU | 0 | 0.020 | 0.024 | 19.289 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 128 | THR | 0 | 0.000 | -0.016 | 20.718 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 129 | GLY | 0 | 0.084 | 0.050 | 16.699 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 130 | TYR | 0 | -0.012 | -0.006 | 16.249 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 131 | PHE | 0 | -0.026 | -0.015 | 13.637 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 132 | THR | 0 | 0.061 | 0.028 | 14.327 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 133 | LYS | 1 | 0.741 | 0.896 | 13.938 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 134 | GLU | -1 | -0.873 | -0.935 | 13.542 | -0.383 | -0.383 | 0.000 | 0.000 | 0.000 | 0.000 |