FMODB ID: KR143
Calculation Name: 1YN5-A-Xray316
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1YN5
Chain ID: A
UniProt ID: A0A0H3
Base Structure: X-ray
Registration Date: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 103 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -775806.519975 |
---|---|
FMO2-HF: Nuclear repulsion | 735299.248419 |
FMO2-HF: Total energy | -40507.271556 |
FMO2-MP2: Total energy | -40626.700623 |
3D Structure
Ligand structure
Ligand Interaction
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:42:ALA )
Summations of interaction energy for
fragment #1(A:42:ALA )
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. |
-14.775 | -6.85 | 0.833 | -4.081 | -4.677 | -0.018 |
Interaction energy analysis for fragmet #1(A:42:ALA )
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 | 44 | GLU | -1 | -0.878 | -0.930 | 3.766 | -4.026 | -0.635 | -0.030 | -1.763 | -1.598 | -0.001 |
4 | A | 45 | MET | 0 | -0.017 | -0.002 | 5.669 | -1.202 | -1.202 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 46 | GLN | 0 | 0.042 | 0.026 | 8.403 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 47 | ASN | 0 | 0.000 | -0.004 | 10.490 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 48 | VAL | 0 | -0.041 | -0.025 | 12.595 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 49 | PRO | 0 | 0.000 | 0.004 | 15.316 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 50 | TYR | 0 | -0.038 | -0.078 | 18.969 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 51 | THR | 0 | -0.004 | -0.004 | 21.143 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 52 | ILE | 0 | 0.031 | 0.009 | 24.489 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 53 | ALA | 0 | -0.010 | -0.020 | 26.986 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 54 | VAL | 0 | 0.007 | -0.001 | 30.387 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 55 | ASP | -1 | -0.812 | -0.920 | 32.706 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 56 | GLY | 0 | -0.055 | -0.022 | 34.481 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 57 | ILE | 0 | 0.005 | 0.011 | 34.013 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 58 | MET | 0 | 0.023 | 0.006 | 28.383 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 59 | ALA | 0 | -0.014 | -0.009 | 27.961 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 60 | PHE | 0 | 0.027 | 0.036 | 29.976 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 61 | ASN | 0 | -0.048 | -0.033 | 27.939 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 62 | GLN | 0 | 0.005 | -0.020 | 23.193 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 63 | SER | 0 | 0.028 | 0.037 | 21.936 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 64 | TYR | 0 | -0.022 | -0.023 | 17.188 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 65 | LEU | 0 | 0.027 | 0.024 | 13.649 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 66 | ASN | 0 | 0.044 | 0.017 | 11.563 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 67 | LEU | 0 | -0.069 | -0.043 | 9.125 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 68 | PRO | 0 | -0.015 | -0.007 | 4.303 | 0.177 | 0.315 | 0.000 | -0.056 | -0.083 | 0.000 |
28 | A | 69 | LYS | 1 | 0.920 | 0.980 | 3.457 | 0.188 | 0.566 | 0.005 | -0.062 | -0.320 | 0.000 |
29 | A | 70 | ASP | -1 | -0.911 | -0.962 | 2.434 | -8.098 | -6.190 | 0.692 | -1.155 | -1.445 | -0.008 |
30 | A | 71 | SER | 0 | -0.026 | -0.020 | 3.011 | -3.318 | -1.209 | 0.166 | -1.035 | -1.240 | -0.009 |
31 | A | 72 | GLN | 0 | 0.045 | 0.059 | 4.643 | 0.622 | 0.623 | 0.000 | -0.010 | 0.009 | 0.000 |
32 | A | 73 | LEU | 0 | 0.003 | 0.007 | 6.608 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 74 | SER | 0 | 0.086 | 0.063 | 9.830 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 75 | TYR | 0 | 0.008 | -0.015 | 13.468 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 76 | LEU | 0 | -0.027 | 0.010 | 16.377 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 77 | ASP | -1 | -0.862 | -0.930 | 12.708 | -0.431 | -0.431 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 78 | LEU | 0 | -0.063 | -0.026 | 14.299 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 79 | GLY | 0 | 0.023 | -0.002 | 15.790 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 80 | ASN | 0 | -0.008 | -0.004 | 17.641 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 81 | LYS | 1 | 0.971 | 0.982 | 12.204 | 0.578 | 0.578 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 82 | VAL | 0 | -0.003 | 0.009 | 18.351 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 83 | LYS | 1 | 0.842 | 0.900 | 20.903 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 84 | ALA | 0 | -0.012 | 0.001 | 20.602 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 85 | LEU | 0 | 0.021 | 0.019 | 19.599 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 86 | LEU | 0 | -0.025 | -0.006 | 23.255 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 87 | TYR | 0 | -0.041 | -0.008 | 26.152 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 88 | ASP | -1 | -0.904 | -0.960 | 24.191 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 89 | GLU | -1 | -0.864 | -0.906 | 24.270 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 90 | ARG | 1 | 0.790 | 0.895 | 27.954 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 91 | GLY | 0 | 0.020 | 0.036 | 30.125 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 92 | VAL | 0 | -0.070 | -0.032 | 29.518 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 93 | THR | 0 | 0.074 | 0.027 | 29.638 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 94 | PRO | 0 | 0.034 | -0.011 | 28.456 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 95 | GLU | -1 | -0.940 | -0.978 | 30.634 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 96 | LYS | 1 | 0.942 | 0.991 | 33.035 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 97 | ILE | 0 | 0.022 | 0.008 | 27.610 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 98 | ARG | 1 | 0.910 | 0.944 | 31.922 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 99 | ASN | 0 | -0.007 | -0.006 | 34.072 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 100 | ALA | 0 | -0.019 | 0.028 | 33.558 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 101 | LYS | 1 | 0.956 | 1.003 | 35.634 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 102 | SER | 0 | -0.062 | -0.058 | 32.692 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 103 | ALA | 0 | 0.020 | 0.017 | 29.163 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 104 | VAL | 0 | 0.018 | 0.038 | 26.479 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 105 | TYR | 0 | 0.045 | 0.018 | 19.100 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 106 | THR | 0 | -0.006 | -0.005 | 23.370 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 107 | ILE | 0 | -0.006 | 0.002 | 16.939 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 108 | THR | 0 | -0.021 | -0.011 | 19.647 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 109 | TRP | 0 | 0.033 | 0.002 | 14.167 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 110 | LYS | 1 | 0.847 | 0.908 | 12.691 | 0.738 | 0.738 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 111 | ASP | -1 | -0.837 | -0.864 | 17.892 | -0.319 | -0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 112 | GLY | 0 | -0.024 | -0.007 | 20.700 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 113 | SER | 0 | -0.054 | -0.064 | 21.327 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 114 | LYS | 1 | 0.920 | 0.938 | 21.926 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 115 | LYS | 1 | 0.937 | 0.987 | 19.682 | 0.368 | 0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 116 | GLU | -1 | -0.922 | -0.952 | 22.585 | -0.202 | -0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 117 | VAL | 0 | -0.044 | -0.027 | 20.706 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 118 | ASP | -1 | -0.820 | -0.930 | 24.015 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 119 | LEU | 0 | -0.015 | -0.025 | 23.185 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 120 | LYS | 1 | 0.793 | 0.905 | 26.733 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 121 | LYS | 1 | 0.894 | 0.951 | 28.429 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 122 | ASP | -1 | -0.785 | -0.854 | 24.221 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 123 | SER | 0 | -0.031 | -0.048 | 24.779 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 124 | TYR | 0 | -0.028 | -0.007 | 18.889 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 125 | THR | 0 | 0.008 | -0.001 | 18.953 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 126 | ALA | 0 | 0.047 | 0.015 | 17.904 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 127 | ASN | 0 | -0.040 | -0.008 | 16.506 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 128 | LEU | 0 | 0.032 | -0.006 | 11.379 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 129 | PHE | 0 | -0.051 | -0.032 | 11.347 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 130 | ASP | -1 | -0.856 | -0.930 | 8.999 | -1.542 | -1.542 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 131 | SER | 0 | -0.023 | -0.054 | 6.732 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 132 | ASN | 0 | 0.000 | 0.006 | 6.796 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 133 | SER | 0 | 0.020 | 0.000 | 9.773 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 134 | ILE | 0 | -0.001 | 0.014 | 12.184 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 135 | LYS | 1 | 0.902 | 0.963 | 13.975 | 0.281 | 0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 136 | GLN | 0 | -0.063 | -0.050 | 16.824 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 137 | ILE | 0 | -0.028 | -0.003 | 15.872 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 138 | ASP | -1 | -0.817 | -0.860 | 20.056 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 139 | ILE | 0 | -0.006 | -0.015 | 21.560 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 140 | ASN | 0 | -0.052 | -0.029 | 25.142 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 141 | VAL | 0 | 0.038 | 0.018 | 28.784 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 142 | LYS | 1 | 0.907 | 0.957 | 31.224 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 143 | THR | 0 | 0.003 | -0.022 | 34.950 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 144 | LYS | 0 | 0.048 | 0.033 | 37.111 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |