FMODB ID: YZGQ2
Calculation Name: 1HTM-B-Xray372
Preferred Name: Hemagglutinin
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 1HTM
Chain ID: B
ChEMBL ID: CHEMBL1932897
UniProt ID: P03437
Base Structure: X-ray
Registration Date: 2023-09-19
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 | 113 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -762993.862664 |
---|---|
FMO2-HF: Nuclear repulsion | 715356.499568 |
FMO2-HF: Total energy | -47637.363096 |
FMO2-MP2: Total energy | -47774.593356 |
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(B:40:SER)
Summations of interaction energy for
fragment #1(B:40: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. |
-4.405 | -0.915 | 3.003 | -3.171 | -3.322 | 0.004 |
Interaction energy analysis for fragmet #1(B:40: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 | B | 42 | GLN | 0 | 0.074 | 0.044 | 3.703 | -1.701 | 0.351 | 0.011 | -0.946 | -1.117 | 0.004 |
4 | B | 43 | ALA | 0 | 0.058 | 0.022 | 2.121 | -2.794 | -2.460 | 2.985 | -1.707 | -1.612 | -0.001 |
5 | B | 44 | ALA | 0 | -0.032 | -0.009 | 3.492 | -1.010 | 0.001 | 0.008 | -0.512 | -0.507 | 0.001 |
6 | B | 45 | ILE | 0 | 0.018 | -0.006 | 5.245 | 0.089 | 0.182 | -0.001 | -0.006 | -0.086 | 0.000 |
7 | B | 46 | ASP | -1 | -0.870 | -0.924 | 6.780 | 1.607 | 1.607 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 47 | GLN | 0 | -0.037 | -0.030 | 5.909 | -0.430 | -0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 48 | ILE | 0 | -0.075 | -0.019 | 9.138 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 49 | ASN | 0 | 0.017 | -0.009 | 11.012 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 50 | GLY | 0 | 0.039 | 0.039 | 11.876 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 51 | LYS | 1 | 0.867 | 0.913 | 13.053 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 52 | LEU | 0 | 0.000 | -0.012 | 14.955 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 53 | ASN | 0 | 0.046 | 0.025 | 16.106 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 54 | ARG | 1 | 0.941 | 0.982 | 15.473 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 55 | VAL | 0 | -0.062 | -0.029 | 19.286 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 56 | ILE | 0 | 0.012 | 0.039 | 20.878 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 57 | GLU | -1 | -0.816 | -0.927 | 21.263 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 58 | LYS | 1 | 0.924 | 0.960 | 23.728 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 59 | THR | 0 | -0.103 | -0.072 | 25.263 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 60 | ASN | 0 | 0.043 | 0.022 | 25.911 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 61 | GLU | -1 | -0.896 | -0.944 | 28.391 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 62 | LYS | 1 | 0.866 | 0.936 | 29.885 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 63 | PHE | 0 | 0.033 | 0.006 | 29.491 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 64 | HIS | 0 | 0.105 | 0.064 | 33.169 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 65 | GLN | 0 | -0.058 | -0.043 | 33.107 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 66 | ILE | 0 | -0.037 | -0.023 | 34.498 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 67 | GLU | -1 | -0.947 | -0.968 | 36.495 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 68 | LYS | 1 | 0.877 | 0.943 | 36.431 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 69 | GLU | -1 | -0.898 | -0.936 | 40.496 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 70 | PHE | 0 | -0.057 | -0.029 | 40.057 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 71 | SER | 0 | 0.031 | 0.011 | 43.575 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 72 | GLU | -1 | -0.945 | -0.964 | 43.392 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 73 | VAL | 0 | -0.054 | -0.027 | 46.338 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 74 | GLU | -1 | -0.939 | -0.979 | 46.459 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 75 | GLY | 0 | 0.026 | 0.015 | 49.343 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 76 | ARG | 1 | 0.959 | 0.967 | 50.385 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 77 | ILE | 0 | -0.040 | 0.000 | 51.102 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 78 | GLN | 0 | -0.011 | -0.025 | 53.296 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 79 | ASP | -1 | -0.859 | -0.925 | 55.513 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 80 | LEU | 0 | -0.029 | -0.034 | 56.860 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 81 | GLU | -1 | -0.884 | -0.932 | 57.411 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 82 | LYS | 1 | 0.904 | 0.959 | 57.583 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 83 | TYR | 0 | 0.021 | 0.012 | 61.560 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 84 | VAL | 0 | -0.035 | -0.007 | 62.311 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 85 | GLU | -1 | -0.952 | -0.984 | 64.334 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 86 | ASP | -1 | -0.726 | -0.860 | 65.937 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 87 | THR | 0 | -0.007 | -0.001 | 66.510 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 88 | LYS | 1 | 0.896 | 0.947 | 68.637 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 89 | ILE | 0 | -0.027 | -0.027 | 70.554 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 90 | ASP | -1 | -0.815 | -0.892 | 71.631 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 91 | LEU | 0 | -0.032 | -0.028 | 72.112 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 92 | TRP | 0 | -0.051 | -0.031 | 73.654 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 93 | SER | 0 | -0.013 | -0.007 | 76.395 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 94 | TYR | 0 | 0.012 | 0.029 | 78.025 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 95 | ASN | 0 | -0.031 | -0.023 | 79.140 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 96 | ALA | 0 | 0.012 | 0.009 | 81.020 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 97 | GLU | -1 | -0.897 | -0.950 | 80.642 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 98 | LEU | 0 | -0.002 | 0.000 | 83.903 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 99 | LEU | 0 | -0.033 | 0.002 | 85.309 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 100 | VAL | 0 | 0.014 | -0.002 | 86.688 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | B | 101 | ALA | 0 | -0.051 | -0.015 | 88.218 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | B | 102 | LEU | 0 | -0.014 | -0.031 | 89.601 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | B | 103 | GLU | -1 | -0.821 | -0.902 | 91.755 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | B | 104 | ASN | 0 | -0.027 | -0.007 | 91.621 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 105 | GLN | 0 | -0.161 | -0.072 | 94.420 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 106 | HIS | 0 | -0.019 | -0.029 | 96.919 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 107 | THR | 0 | -0.037 | -0.003 | 94.344 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | B | 108 | ILE | 0 | -0.030 | -0.018 | 90.664 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | B | 109 | ASP | -1 | -0.806 | -0.889 | 95.006 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | B | 110 | LEU | 0 | -0.046 | -0.033 | 89.387 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | B | 111 | THR | 0 | -0.088 | -0.061 | 92.038 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | B | 112 | ASP | -1 | -0.833 | -0.895 | 93.935 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | B | 113 | SER | 0 | 0.013 | -0.010 | 92.332 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | B | 114 | GLU | -1 | -1.012 | -1.005 | 89.890 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | B | 115 | MET | 0 | 0.035 | -0.001 | 89.026 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | B | 116 | ASN | 0 | 0.039 | 0.033 | 88.954 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | B | 117 | LYS | 1 | 0.830 | 0.918 | 85.762 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | B | 118 | LEU | 0 | 0.005 | -0.002 | 83.614 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | B | 119 | PHE | 0 | 0.091 | 0.030 | 83.760 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | B | 120 | GLU | -1 | -0.804 | -0.919 | 84.055 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | B | 121 | LYS | 1 | 0.826 | 0.925 | 80.196 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | B | 122 | THR | 0 | -0.047 | -0.036 | 79.316 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | B | 123 | ARG | 1 | 0.939 | 0.986 | 79.662 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | B | 124 | ARG | 1 | 0.814 | 0.886 | 73.507 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | B | 125 | GLN | 0 | 0.016 | 0.007 | 73.850 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | B | 126 | LEU | 0 | -0.019 | 0.004 | 75.042 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | B | 127 | ARG | 1 | 0.866 | 0.945 | 76.384 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | B | 128 | GLU | -1 | -0.908 | -0.936 | 72.696 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | B | 129 | ASN | 0 | -0.073 | -0.038 | 69.678 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | B | 130 | ALA | 0 | 0.002 | -0.004 | 72.503 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | B | 131 | GLU | -1 | -0.946 | -0.965 | 73.424 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | B | 132 | GLU | -1 | -0.881 | -0.944 | 75.895 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | B | 133 | MET | 0 | -0.059 | -0.010 | 79.144 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | B | 134 | GLY | 0 | -0.017 | -0.011 | 81.479 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | B | 135 | ASN | 0 | -0.015 | -0.044 | 85.155 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | B | 136 | GLY | 0 | 0.009 | 0.022 | 85.098 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | B | 137 | CYS | 0 | -0.021 | -0.004 | 83.022 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | B | 138 | PHE | 0 | 0.027 | 0.007 | 78.257 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | B | 139 | LYS | 1 | 0.893 | 0.951 | 75.790 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | B | 140 | ILE | 0 | 0.045 | 0.027 | 72.763 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | B | 141 | TYR | 0 | -0.034 | -0.019 | 69.548 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | B | 142 | HIS | 0 | -0.048 | -0.014 | 67.659 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | B | 143 | LYS | 1 | 0.900 | 0.927 | 63.410 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | B | 144 | CYS | 0 | -0.109 | -0.035 | 58.115 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | B | 145 | ASP | -1 | -0.796 | -0.887 | 61.257 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | B | 146 | ASN | 0 | 0.012 | -0.022 | 62.375 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | B | 147 | ALA | 0 | 0.068 | 0.038 | 58.068 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | B | 149 | ILE | 0 | -0.065 | -0.046 | 59.013 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | B | 150 | GLU | -1 | -0.986 | -1.002 | 58.007 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | B | 151 | SER | 0 | -0.079 | -0.024 | 54.259 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | B | 152 | ILE | 0 | -0.071 | -0.007 | 55.488 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | B | 153 | ARG | 1 | 0.875 | 0.935 | 55.311 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |