![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: MNNMZ
Calculation Name: 3QMQ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3QMQ
Chain ID: A
UniProt ID: P64461
Base Structure: X-ray
Registration Date: 2023-09-21
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 | 97 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -752086.726108 |
---|---|
FMO2-HF: Nuclear repulsion | 712078.134882 |
FMO2-HF: Total energy | -40008.591227 |
FMO2-MP2: Total energy | -40124.704268 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033415/ligand_interaction/ligand_F033415.png)
Ligand Interaction
![ligand interaction](./Kdata/F033415/ligand_interaction/ligand_interaction_F033415.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:0:SER)
Summations of interaction energy for
fragment #1(A:0:SER)
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. |
-14.21 | -13.67 | 13.351 | -6.601 | -7.29 | -0.055 |
Interaction energy analysis for fragmet #1(A:0:SER)
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 | 2 | HIS | 0 | 0.015 | 0.025 | 3.865 | -0.917 | 0.438 | -0.017 | -0.640 | -0.698 | 0.001 |
4 | A | 3 | VAL | 0 | 0.027 | 0.006 | 6.093 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | THR | 0 | -0.045 | -0.024 | 8.875 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | LEU | 0 | 0.011 | 0.017 | 12.613 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | VAL | 0 | -0.066 | -0.046 | 15.162 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | GLU | -1 | -0.763 | -0.853 | 18.569 | -0.253 | -0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | ILE | 0 | -0.035 | -0.042 | 21.791 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | ASN | 0 | -0.035 | -0.021 | 24.681 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | VAL | 0 | 0.000 | 0.010 | 28.265 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | HIS | 0 | 0.053 | 0.024 | 30.858 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | GLU | -1 | -0.825 | -0.898 | 34.306 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | ASP | -1 | -0.964 | -0.981 | 35.812 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | LYS | 1 | 0.827 | 0.894 | 34.035 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | VAL | 0 | 0.016 | 0.006 | 30.788 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | ASP | -1 | -0.883 | -0.948 | 31.081 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | GLU | -1 | -0.847 | -0.904 | 32.156 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | PHE | 0 | -0.015 | -0.004 | 24.015 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | ILE | 0 | 0.011 | 0.006 | 27.242 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | GLU | -1 | -0.845 | -0.889 | 27.483 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | VAL | 0 | -0.053 | -0.037 | 27.153 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | PHE | 0 | 0.036 | -0.018 | 20.303 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | ARG | 1 | 0.839 | 0.912 | 23.581 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | GLN | 0 | -0.007 | -0.003 | 24.499 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | ASN | 0 | 0.001 | -0.007 | 21.213 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | HIS | 0 | -0.028 | -0.012 | 18.550 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | LEU | 0 | -0.015 | -0.003 | 20.035 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | GLY | 0 | 0.015 | 0.015 | 21.615 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | SER | 0 | -0.020 | -0.042 | 17.072 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | VAL | 0 | -0.068 | -0.037 | 15.959 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | GLN | 0 | -0.038 | -0.010 | 16.424 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | GLU | -1 | -0.781 | -0.856 | 15.959 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | GLU | -1 | -0.874 | -0.935 | 15.018 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | GLY | 0 | -0.004 | -0.006 | 11.252 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | ASN | 0 | -0.040 | -0.032 | 10.437 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | LEU | 0 | -0.030 | -0.007 | 5.609 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | ARG | 1 | 0.904 | 0.949 | 8.136 | 0.923 | 0.923 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | PHE | 0 | 0.038 | 0.027 | 11.988 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASP | -1 | -0.864 | -0.921 | 14.221 | -0.565 | -0.565 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | VAL | 0 | 0.008 | -0.003 | 16.696 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | LEU | 0 | -0.038 | -0.023 | 16.750 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | GLN | 0 | -0.006 | -0.017 | 21.025 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | ASP | -1 | -0.807 | -0.895 | 24.429 | -0.266 | -0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | PRO | 0 | -0.021 | -0.020 | 24.908 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | GLU | -1 | -0.960 | -0.973 | 27.882 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | VAL | 0 | -0.050 | -0.008 | 29.257 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | ASN | 0 | 0.048 | 0.013 | 29.058 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | SER | 0 | 0.016 | -0.002 | 29.937 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | ARG | 1 | 0.831 | 0.931 | 25.072 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | PHE | 0 | 0.003 | -0.008 | 23.444 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | TYR | 0 | -0.051 | -0.056 | 18.911 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | ILE | 0 | -0.028 | 0.002 | 16.863 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | TYR | 0 | -0.010 | -0.006 | 9.273 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | GLU | -1 | -0.843 | -0.910 | 12.709 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | ALA | 0 | -0.006 | -0.005 | 7.346 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | TYR | 0 | -0.029 | -0.041 | 8.376 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | LYS | 1 | 0.902 | 0.927 | 6.009 | -1.022 | -1.022 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | ASP | -1 | -0.863 | -0.925 | 5.299 | 1.329 | 1.329 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | GLU | -1 | -0.907 | -0.967 | 7.755 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | ASP | -1 | -0.871 | -0.929 | 10.763 | 0.447 | 0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | ALA | 0 | -0.060 | -0.028 | 10.549 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | VAL | 0 | -0.009 | -0.009 | 10.485 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | ALA | 0 | -0.050 | -0.031 | 13.161 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | PHE | 0 | 0.026 | 0.019 | 15.753 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | HIS | 1 | 0.863 | 0.944 | 15.724 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | LYS | 1 | 0.906 | 0.953 | 15.835 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | THR | 0 | -0.115 | -0.075 | 19.966 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 68 | THR | 0 | 0.012 | 0.026 | 20.150 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | PRO | 0 | 0.046 | 0.001 | 22.968 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | HIS | 0 | 0.012 | 0.007 | 19.896 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 71 | TYR | 0 | -0.002 | 0.013 | 20.214 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 72 | LYS | 1 | 0.905 | 0.949 | 23.205 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 73 | THR | 0 | -0.037 | -0.029 | 26.321 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 74 | CYS | 0 | -0.018 | 0.002 | 24.503 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 75 | VAL | 0 | -0.044 | -0.018 | 24.476 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 76 | ALA | 0 | 0.025 | 0.018 | 26.944 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 77 | LYS | 1 | 0.932 | 0.962 | 30.009 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 78 | LEU | 0 | 0.007 | -0.002 | 25.406 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 79 | GLU | -1 | -0.931 | -0.946 | 29.537 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 80 | SER | 0 | -0.055 | -0.026 | 31.813 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 81 | LEU | 0 | -0.033 | -0.026 | 30.018 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 82 | MET | 0 | -0.043 | -0.004 | 25.853 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 83 | THR | 0 | 0.010 | 0.000 | 30.961 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 84 | GLY | 0 | 0.007 | -0.002 | 30.605 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 85 | PRO | 0 | -0.020 | -0.014 | 27.043 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 86 | ARG | 1 | 0.957 | 0.996 | 22.366 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 87 | LYS | 1 | 0.881 | 0.935 | 22.140 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 88 | LYS | 1 | 0.915 | 0.966 | 15.648 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 89 | ARG | 1 | 0.948 | 0.983 | 15.223 | 0.533 | 0.533 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 90 | LEU | 0 | 0.040 | 0.018 | 10.732 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 91 | PHE | 0 | -0.049 | -0.030 | 9.138 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 92 | ASN | 0 | 0.049 | 0.023 | 4.791 | 0.230 | 0.232 | -0.001 | -0.002 | 0.001 | 0.000 |
94 | A | 93 | GLY | 0 | 0.011 | 0.009 | 3.972 | -0.122 | 0.256 | 0.001 | -0.135 | -0.244 | 0.000 |
95 | A | 94 | LEU | 0 | 0.010 | -0.012 | 2.193 | -4.831 | -5.788 | 6.128 | -2.227 | -2.943 | -0.028 |
96 | A | 95 | MET | 0 | -0.019 | -0.016 | 3.049 | -0.950 | 0.233 | 0.260 | -0.552 | -0.891 | -0.005 |
97 | A | 96 | PRO | 0 | 0.044 | 0.044 | 1.909 | -9.465 | -10.886 | 6.980 | -3.045 | -2.515 | -0.023 |