![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 988Y2
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 | 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 | 97 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -751831.28868 |
---|---|
FMO2-HF: Nuclear repulsion | 711823.501783 |
FMO2-HF: Total energy | -40007.786896 |
FMO2-MP2: Total energy | -40123.916936 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033416/ligand_interaction/ligand_F033416.png)
Ligand Interaction
![ligand interaction](./Kdata/F033416/ligand_interaction/ligand_interaction_F033416.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. |
-8.454 | -18.269 | 27.578 | -9.151 | -8.612 | -0.06 |
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 | 0.018 | 0.023 | 3.837 | -1.698 | -0.301 | -0.018 | -0.659 | -0.720 | 0.001 |
4 | A | 3 | VAL | 0 | 0.033 | 0.011 | 6.067 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | THR | 0 | -0.076 | -0.035 | 8.783 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | LEU | 0 | 0.032 | 0.022 | 12.512 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | VAL | 0 | -0.073 | -0.050 | 15.074 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | GLU | -1 | -0.825 | -0.910 | 18.482 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | ILE | 0 | -0.048 | -0.053 | 21.704 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | ASN | 0 | -0.009 | 0.014 | 24.612 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | VAL | 0 | -0.010 | 0.008 | 28.194 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | HIS | 0 | 0.039 | 0.013 | 30.806 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | GLU | -1 | -0.850 | -0.935 | 34.273 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | ASP | -1 | -0.954 | -0.973 | 35.776 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | LYS | 1 | 0.896 | 0.944 | 34.062 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | VAL | 0 | 0.018 | 0.009 | 30.788 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | ASP | -1 | -0.909 | -0.963 | 31.093 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | GLU | -1 | -0.867 | -0.923 | 32.188 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | PHE | 0 | -0.031 | -0.018 | 23.922 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | ILE | 0 | 0.006 | 0.000 | 27.239 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | GLU | -1 | -0.960 | -0.979 | 27.530 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | VAL | 0 | -0.052 | -0.032 | 27.115 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | PHE | 0 | 0.038 | -0.017 | 20.193 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | ARG | 1 | 0.950 | 0.998 | 23.633 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | GLN | 0 | -0.012 | -0.009 | 24.473 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | ASN | 0 | 0.016 | 0.005 | 20.852 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | HIS | 0 | -0.026 | -0.012 | 18.173 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | LEU | 0 | -0.015 | -0.005 | 19.962 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | GLY | 0 | 0.009 | 0.012 | 21.565 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | SER | 0 | -0.026 | -0.040 | 17.123 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | VAL | 0 | -0.063 | -0.028 | 15.855 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | GLN | 0 | -0.024 | -0.007 | 16.424 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | GLU | -1 | -0.786 | -0.851 | 15.817 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | GLU | -1 | -0.888 | -0.950 | 14.979 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | GLY | 0 | -0.030 | -0.026 | 11.255 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | ASN | 0 | -0.039 | -0.033 | 10.440 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | LEU | 0 | -0.037 | -0.006 | 5.640 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | ARG | 1 | 0.946 | 0.957 | 7.831 | 0.369 | 0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | PHE | 0 | 0.042 | 0.030 | 11.847 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASP | -1 | -0.904 | -0.927 | 14.305 | -0.262 | -0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | VAL | 0 | 0.001 | -0.014 | 16.650 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | LEU | 0 | -0.036 | -0.023 | 16.827 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | GLN | 0 | -0.012 | -0.017 | 21.035 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | ASP | -1 | -0.826 | -0.905 | 24.420 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | PRO | 0 | -0.035 | -0.023 | 24.753 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | GLU | -1 | -0.961 | -0.972 | 27.865 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | VAL | 0 | -0.055 | -0.009 | 29.092 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | ASN | 0 | 0.035 | -0.002 | 29.020 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | SER | 0 | 0.035 | 0.031 | 29.919 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | ARG | 1 | 0.892 | 0.961 | 25.119 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | PHE | 0 | -0.003 | -0.012 | 23.413 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | TYR | 0 | -0.068 | -0.072 | 18.785 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | ILE | 0 | -0.028 | -0.001 | 16.875 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | TYR | 0 | -0.008 | -0.004 | 8.885 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | GLU | -1 | -0.903 | -0.952 | 12.711 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | ALA | 0 | -0.009 | -0.015 | 7.442 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | TYR | 0 | 0.001 | 0.001 | 8.381 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | LYS | 1 | 0.940 | 0.948 | 6.011 | -1.224 | -1.224 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | ASP | -1 | -0.861 | -0.922 | 5.347 | 1.436 | 1.436 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | GLU | -1 | -0.914 | -0.972 | 7.820 | 0.361 | 0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | ASP | -1 | -0.869 | -0.923 | 10.763 | 0.512 | 0.512 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | ALA | 0 | -0.060 | -0.021 | 10.587 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | VAL | 0 | -0.012 | -0.010 | 10.500 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | ALA | 0 | -0.040 | -0.032 | 13.161 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | PHE | 0 | 0.035 | 0.021 | 15.756 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | HIS | 1 | 0.859 | 0.936 | 15.758 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | LYS | 1 | 0.918 | 0.950 | 16.386 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | THR | 0 | -0.111 | -0.057 | 19.966 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 68 | THR | 0 | 0.006 | 0.013 | 20.139 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | PRO | 0 | 0.031 | -0.005 | 22.968 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | HIS | 0 | 0.010 | 0.003 | 19.857 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 71 | TYR | 0 | -0.005 | 0.014 | 20.547 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 72 | LYS | 1 | 0.927 | 0.960 | 23.205 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 73 | THR | 0 | -0.016 | -0.016 | 26.321 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 74 | CYS | 0 | -0.019 | 0.002 | 24.534 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 75 | VAL | 0 | -0.052 | -0.021 | 24.416 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 76 | ALA | 0 | 0.019 | 0.010 | 26.916 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 77 | LYS | 1 | 0.936 | 0.967 | 30.004 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 78 | LEU | 0 | 0.008 | 0.001 | 25.043 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 79 | GLU | -1 | -0.925 | -0.944 | 29.508 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 80 | SER | 0 | -0.036 | -0.015 | 31.760 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 81 | LEU | 0 | -0.067 | -0.044 | 30.001 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 82 | MET | 0 | -0.048 | 0.000 | 25.805 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 83 | THR | 0 | 0.016 | 0.001 | 30.894 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 84 | GLY | 0 | 0.002 | -0.004 | 30.517 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 85 | PRO | 0 | -0.022 | -0.012 | 27.044 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 86 | ARG | 1 | 0.966 | 0.998 | 21.898 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 87 | LYS | 1 | 0.952 | 0.984 | 22.118 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 88 | LYS | 1 | 0.921 | 0.967 | 16.091 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 89 | ARG | 1 | 0.968 | 0.983 | 15.242 | 0.407 | 0.407 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 90 | LEU | 0 | 0.023 | 0.022 | 10.959 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 91 | PHE | 0 | -0.032 | -0.019 | 8.885 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 92 | ASN | 0 | 0.047 | 0.018 | 4.760 | 0.335 | 0.343 | -0.001 | -0.002 | -0.005 | 0.000 |
94 | A | 93 | GLY | 0 | 0.009 | 0.003 | 3.868 | -0.528 | 0.085 | 0.003 | -0.292 | -0.324 | 0.000 |
95 | A | 94 | LEU | 0 | 0.010 | -0.008 | 1.966 | -0.242 | -7.410 | 14.807 | -3.814 | -3.825 | -0.032 |
96 | A | 95 | MET | 0 | -0.016 | -0.019 | 2.992 | -2.410 | -1.013 | 0.321 | -0.620 | -1.098 | -0.007 |
97 | A | 96 | PRO | 0 | 0.039 | 0.043 | 1.763 | -5.723 | -11.785 | 12.466 | -3.764 | -2.640 | -0.022 |