![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 228YR
Calculation Name: 2GMQ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2GMQ
Chain ID: A
UniProt ID: Q8KUD5
Base Structure: X-ray
Registration Date: 2023-06-19
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 | 102 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -816169.662632 |
---|---|
FMO2-HF: Nuclear repulsion | 775078.991764 |
FMO2-HF: Total energy | -41090.670868 |
FMO2-MP2: Total energy | -41211.793888 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020718/ligand_interaction/ligand_F020718.png)
Ligand Interaction
![ligand interaction](./Kdata/F020718/ligand_interaction/ligand_interaction_F020718.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:12:GLY)
Summations of interaction energy for
fragment #1(A:12: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. |
-0.549 | 0.82 | -0.011 | -0.783 | -0.575 | 0.004 |
Interaction energy analysis for fragmet #1(A:12: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 | 14 | LYS | 1 | 0.995 | 1.007 | 3.831 | 1.615 | 2.984 | -0.011 | -0.783 | -0.575 | 0.004 |
4 | A | 15 | GLU | -1 | -0.900 | -0.942 | 6.772 | -0.654 | -0.654 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 16 | ILE | 0 | -0.025 | -0.019 | 10.169 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 17 | ALA | 0 | 0.014 | 0.023 | 13.549 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 18 | ILE | 0 | -0.052 | -0.029 | 16.884 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 19 | GLN | 0 | -0.023 | -0.019 | 19.735 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 20 | GLU | -1 | -0.793 | -0.921 | 23.266 | -0.266 | -0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 21 | LYS | 1 | 0.962 | 0.987 | 24.528 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 22 | ASP | -1 | -0.849 | -0.913 | 24.116 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 23 | LEU | 0 | -0.040 | -0.011 | 20.657 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 24 | THR | 0 | -0.080 | -0.035 | 24.595 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 25 | LEU | 0 | 0.040 | 0.018 | 23.611 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 26 | GLN | 0 | 0.017 | 0.015 | 24.783 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 27 | TRP | 0 | 0.052 | 0.035 | 24.772 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 28 | ARG | 1 | 0.954 | 0.956 | 24.359 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 29 | GLY | 0 | 0.047 | 0.022 | 28.602 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 30 | ASN | 0 | -0.013 | 0.007 | 31.160 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 31 | THR | 0 | 0.038 | 0.019 | 31.546 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 32 | GLY | 0 | 0.010 | 0.017 | 29.070 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 33 | LYS | 1 | 0.982 | 0.988 | 19.530 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 34 | LEU | 0 | 0.015 | 0.006 | 20.842 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 35 | VAL | 0 | -0.103 | -0.039 | 21.476 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 36 | LYS | 1 | 0.932 | 0.966 | 20.273 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 37 | VAL | 0 | 0.045 | 0.043 | 19.059 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 38 | ARG | 1 | 0.897 | 0.961 | 20.553 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 39 | LEU | 0 | 0.061 | 0.030 | 19.422 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 40 | LYS | 1 | 0.898 | 0.935 | 23.091 | 0.278 | 0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 41 | ASN | 0 | -0.008 | -0.026 | 26.053 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 42 | THR | 0 | 0.022 | 0.010 | 27.892 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 43 | ARG | 1 | 0.901 | 0.956 | 20.954 | 0.415 | 0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 44 | ALA | 0 | 0.026 | 0.009 | 23.193 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 45 | MET | 0 | -0.006 | -0.008 | 24.049 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 46 | GLU | -1 | -0.913 | -0.953 | 24.082 | -0.340 | -0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 47 | MET | 0 | -0.013 | -0.015 | 19.308 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 48 | TRP | 0 | 0.023 | 0.025 | 21.135 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 49 | TYR | 0 | -0.018 | -0.022 | 23.236 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 50 | ASN | 0 | -0.016 | -0.012 | 21.496 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 51 | LYS | 1 | 0.866 | 0.944 | 18.758 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 52 | GLN | 0 | 0.027 | 0.031 | 17.083 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 53 | ILE | 0 | -0.040 | -0.030 | 14.652 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 54 | THR | 0 | -0.053 | -0.027 | 15.246 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 55 | GLU | -1 | -0.902 | -0.980 | 15.491 | -0.428 | -0.428 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 56 | GLU | -1 | -0.942 | -0.968 | 13.436 | -0.543 | -0.543 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 57 | ASN | 0 | 0.085 | 0.062 | 11.310 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 58 | ILE | 0 | -0.050 | -0.024 | 10.708 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 59 | GLN | 0 | -0.052 | -0.065 | 9.957 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 60 | GLU | -1 | -0.889 | -0.931 | 6.354 | -2.041 | -2.041 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 61 | ILE | 0 | -0.115 | -0.042 | 6.269 | -0.941 | -0.941 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 62 | THR | 0 | 0.038 | 0.009 | 4.894 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 63 | THR | 0 | -0.015 | -0.009 | 8.166 | 0.374 | 0.374 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 64 | LEU | 0 | 0.000 | 0.002 | 10.859 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 65 | ASN | 0 | 0.025 | 0.002 | 14.350 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 66 | ILE | 0 | -0.021 | -0.009 | 16.322 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 67 | ILE | 0 | 0.045 | 0.026 | 19.552 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 68 | LYS | 1 | 0.917 | 0.938 | 22.515 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 69 | ASN | 0 | -0.064 | -0.043 | 26.267 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 70 | GLY | 0 | 0.018 | 0.010 | 27.239 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 71 | LYS | 1 | 0.905 | 0.971 | 25.149 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 72 | SER | 0 | 0.013 | -0.007 | 19.752 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 73 | LEU | 0 | -0.017 | 0.002 | 19.312 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 74 | ALA | 0 | 0.037 | 0.030 | 13.883 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 75 | LEU | 0 | -0.053 | -0.037 | 15.084 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 76 | GLU | -1 | -0.847 | -0.933 | 9.654 | -0.796 | -0.796 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 77 | VAL | 0 | -0.010 | -0.005 | 10.976 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 78 | TYR | 0 | -0.042 | -0.042 | 11.139 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 79 | PRO | 0 | 0.076 | 0.031 | 7.672 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 80 | GLU | -1 | -0.877 | -0.933 | 8.680 | -0.778 | -0.778 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 81 | LYS | 1 | 0.843 | 0.930 | 12.131 | 0.466 | 0.466 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 82 | SER | 0 | -0.039 | -0.005 | 12.249 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 83 | ILE | 0 | 0.029 | 0.033 | 14.926 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 84 | TYR | 0 | 0.066 | 0.028 | 16.957 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 85 | VAL | 0 | -0.044 | -0.017 | 20.730 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 86 | LYS | 1 | 1.037 | 1.006 | 24.212 | 0.162 | 0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 87 | PRO | 0 | -0.055 | -0.020 | 27.776 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 88 | ASN | 0 | -0.015 | -0.004 | 29.163 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 89 | LEU | 0 | 0.012 | -0.007 | 32.381 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 90 | GLY | 0 | 0.060 | 0.023 | 33.583 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 91 | ARG | 1 | 0.912 | 0.976 | 31.073 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 92 | ILE | 0 | 0.040 | 0.025 | 24.581 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 93 | ASN | 0 | 0.017 | 0.003 | 23.969 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 94 | VAL | 0 | -0.022 | -0.015 | 23.113 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 95 | PRO | 0 | 0.058 | 0.040 | 17.886 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 96 | VAL | 0 | -0.080 | -0.034 | 18.791 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 97 | PHE | 0 | 0.077 | 0.036 | 12.962 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 98 | PHE | 0 | -0.012 | -0.023 | 15.926 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 99 | ILE | 0 | -0.011 | -0.012 | 15.642 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 100 | LYS | 1 | 0.871 | 0.946 | 9.244 | 0.792 | 0.792 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 101 | THR | 0 | 0.033 | 0.018 | 14.517 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 102 | PRO | 0 | -0.059 | -0.027 | 16.380 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 103 | ILE | 0 | 0.087 | 0.046 | 20.109 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 104 | ASN | 0 | 0.024 | -0.002 | 22.418 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 105 | ARG | 1 | 0.842 | 0.912 | 26.092 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 106 | GLY | 0 | 0.046 | 0.024 | 28.422 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 107 | VAL | 0 | 0.067 | 0.032 | 25.277 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 108 | PHE | 0 | -0.018 | -0.017 | 22.485 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 109 | GLU | -1 | -0.829 | -0.923 | 26.340 | -0.201 | -0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 110 | GLU | -1 | -0.963 | -0.968 | 29.544 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 111 | ILE | 0 | -0.065 | -0.024 | 23.452 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 112 | PHE | 0 | -0.038 | -0.025 | 22.410 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 113 | GLY | 0 | 0.001 | 0.026 | 28.435 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |