![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: MVMMZ
Calculation Name: 5HIZ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5HIZ
Chain ID: A
UniProt ID: P0C6Y4
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 | 99 |
LigandCharge | CYM=-1 |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -709991.527308 |
---|---|
FMO2-HF: Nuclear repulsion | 671829.14212 |
FMO2-HF: Total energy | -38162.385187 |
FMO2-MP2: Total energy | -38275.277746 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024420/ligand_interaction/ligand_F024420.png)
Ligand Interaction
![ligand interaction](./Kdata/F024420/ligand_interaction/ligand_interaction_F024420.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:7:GLY)
Summations of interaction energy for
fragment #1(A:7:GLY)
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. |
0.48 | 1.636 | 0.019 | -0.421 | -0.755 | 0 |
Interaction energy analysis for fragmet #1(A:7:GLY)
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 | 9 | LEU | 0 | 0.010 | 0.006 | 3.772 | 1.266 | 2.219 | -0.004 | -0.348 | -0.601 | 0.000 |
4 | A | 10 | LYS | 1 | 0.989 | 1.004 | 5.640 | -0.484 | -0.484 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 11 | GLN | 0 | 0.029 | 0.008 | 9.357 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 12 | ARG | 1 | 0.854 | 0.909 | 12.196 | -0.208 | -0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | SER | 0 | 0.005 | 0.009 | 15.691 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | ILE | 0 | -0.005 | 0.017 | 18.388 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | LYS | 1 | 0.885 | 0.933 | 20.465 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | ALA | 0 | -0.002 | -0.003 | 21.675 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | GLU | -1 | -0.877 | -0.940 | 23.723 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | GLY | 0 | -0.010 | -0.022 | 25.692 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | ASP | -1 | -0.972 | -0.984 | 28.021 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | GLY | 0 | 0.010 | 0.007 | 31.182 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | ILE | 0 | 0.027 | 0.028 | 28.427 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | VAL | 0 | 0.029 | 0.010 | 27.536 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | GLY | 0 | -0.081 | -0.040 | 25.892 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | GLU | -1 | -0.857 | -0.913 | 22.651 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | GLY | 0 | -0.008 | -0.020 | 20.007 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | LYS | 1 | 0.843 | 0.913 | 15.012 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | ALA | 0 | 0.036 | 0.021 | 14.419 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | LEU | 0 | 0.019 | 0.007 | 9.109 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | TYR | 0 | -0.030 | -0.012 | 9.539 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | ASN | 0 | 0.034 | -0.005 | 4.856 | -1.083 | -1.080 | -0.001 | -0.006 | 0.004 | 0.000 |
25 | A | 31 | ASN | 0 | -0.030 | 0.006 | 8.536 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | GLU | -1 | -0.902 | -0.940 | 7.391 | 2.203 | 2.203 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | GLY | 0 | -0.058 | -0.015 | 11.166 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | GLY | 0 | 0.041 | 0.002 | 11.798 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | ARG | 1 | 0.984 | 0.984 | 14.560 | -0.429 | -0.429 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | THR | 0 | 0.018 | 0.018 | 13.249 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | PHE | 0 | -0.004 | -0.012 | 11.883 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | MET | 0 | 0.005 | 0.017 | 10.703 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | TYR | 0 | -0.033 | -0.028 | 4.649 | 0.077 | 0.130 | -0.001 | -0.001 | -0.051 | 0.000 |
34 | A | 40 | ALA | 0 | 0.001 | -0.014 | 10.168 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | PHE | 0 | 0.013 | 0.007 | 12.373 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | ILE | 0 | 0.036 | 0.033 | 12.995 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | SER | 0 | 0.002 | 0.010 | 16.843 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | ASP | -1 | -0.852 | -0.938 | 20.604 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | LYS | 1 | 0.912 | 0.954 | 23.766 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | PRO | 0 | -0.039 | 0.002 | 24.280 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | ASP | -1 | -0.873 | -0.958 | 25.719 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | LEU | 0 | -0.047 | -0.008 | 22.633 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | ARG | 1 | 0.930 | 0.946 | 23.999 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | VAL | 0 | -0.002 | -0.008 | 22.383 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | VAL | 0 | -0.011 | -0.002 | 18.545 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | LYS | 1 | 0.988 | 1.000 | 21.423 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | TRP | 0 | -0.046 | -0.036 | 14.392 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | GLU | -1 | -0.859 | -0.919 | 20.545 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | PHE | 0 | -0.026 | -0.040 | 16.156 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | ASP | -1 | -0.887 | -0.941 | 17.958 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | GLY | 0 | 0.015 | 0.020 | 21.543 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | GLY | 0 | -0.050 | -0.034 | 21.820 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | CYM | -1 | -0.834 | -0.880 | 22.149 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | ASN | 0 | -0.129 | -0.093 | 20.730 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | THR | 0 | 0.034 | 0.011 | 21.907 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | ILE | 0 | -0.003 | 0.009 | 16.920 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | GLU | -1 | -0.910 | -0.947 | 20.183 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | LEU | 0 | -0.067 | -0.034 | 17.514 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | GLU | -1 | -0.888 | -0.930 | 17.208 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | PRO | 0 | -0.006 | -0.022 | 19.916 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | PRO | 0 | -0.018 | 0.018 | 19.590 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | ARG | 1 | 0.914 | 0.958 | 17.558 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | LYS | 1 | 0.944 | 0.941 | 19.118 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | PHE | 0 | -0.056 | -0.038 | 16.011 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | LEU | 0 | 0.051 | 0.043 | 20.717 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | VAL | 0 | 0.008 | -0.015 | 18.225 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | ASP | -1 | -0.886 | -0.954 | 21.495 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | SER | 0 | -0.040 | 0.010 | 23.380 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 75 | PRO | 0 | 0.032 | 0.006 | 25.167 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | ASN | 0 | -0.077 | -0.058 | 27.983 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | GLY | 0 | 0.005 | 0.028 | 29.990 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | ALA | 0 | 0.051 | 0.025 | 25.976 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | GLN | 0 | 0.005 | 0.022 | 23.865 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | ILE | 0 | -0.044 | -0.028 | 23.764 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 81 | LYS | 1 | 0.952 | 0.985 | 19.004 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 82 | TYR | 0 | 0.010 | -0.004 | 20.459 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 83 | LEU | 0 | 0.016 | -0.003 | 12.985 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 84 | TYR | 0 | -0.004 | 0.001 | 16.327 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 85 | PHE | 0 | 0.011 | 0.013 | 10.841 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 86 | VAL | 0 | 0.046 | 0.021 | 13.598 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 87 | ARG | 1 | 0.994 | 0.991 | 15.401 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 88 | ASN | 0 | -0.035 | -0.012 | 16.421 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 89 | LEU | 0 | 0.022 | 0.037 | 9.431 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 90 | ASN | 0 | 0.060 | 0.014 | 9.659 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 91 | THR | 0 | 0.073 | 0.009 | 10.859 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 92 | LEU | 0 | -0.005 | 0.018 | 6.837 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 93 | ARG | 1 | 1.000 | 1.000 | 5.986 | -0.853 | -0.853 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 94 | ARG | 1 | 0.833 | 0.911 | 7.197 | -0.160 | -0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 95 | GLY | 0 | 0.038 | 0.015 | 8.864 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 96 | ALA | 0 | -0.012 | -0.016 | 3.224 | -0.230 | -0.060 | 0.026 | -0.064 | -0.133 | 0.000 |
91 | A | 97 | VAL | 0 | -0.051 | -0.003 | 5.242 | -0.339 | -0.362 | -0.001 | -0.002 | 0.026 | 0.000 |
92 | A | 98 | LEU | 0 | 0.000 | -0.001 | 7.511 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 99 | GLY | 0 | 0.019 | 0.012 | 7.143 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 100 | TYR | 0 | 0.014 | 0.000 | 5.834 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 101 | ILE | 0 | -0.056 | -0.038 | 7.674 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 102 | GLY | 0 | -0.020 | 0.005 | 11.081 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 103 | ALA | 0 | -0.007 | 0.004 | 9.453 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 104 | THR | 0 | -0.110 | -0.054 | 11.491 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 105 | VAL | 0 | 0.006 | 0.011 | 13.690 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |