FMODB ID: QVZ9Y
Calculation Name: 1U2H-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1U2H
Chain ID: A
UniProt ID: Q15772
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 96 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -690417.425351 |
---|---|
FMO2-HF: Nuclear repulsion | 651795.971803 |
FMO2-HF: Total energy | -38621.453548 |
FMO2-MP2: Total energy | -38732.037814 |
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:17:LYS)
Summations of interaction energy for
fragment #1(A:17:LYS)
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. |
6.588 | 15.783 | 5.36 | -6.031 | -8.525 | -0.043 |
Interaction energy analysis for fragmet #1(A:17:LYS)
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 | 19 | PRO | 0 | 0.027 | 0.036 | 3.784 | 1.443 | 4.134 | -0.030 | -1.385 | -1.276 | 0.006 |
4 | A | 20 | PRO | 0 | -0.009 | 0.000 | 6.741 | 1.028 | 1.028 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 21 | THR | 0 | -0.066 | -0.037 | 9.469 | 1.142 | 1.142 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 22 | PHE | 0 | 0.033 | 0.007 | 11.815 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 23 | LYS | 1 | 0.870 | 0.936 | 12.233 | 19.890 | 19.890 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 24 | VAL | 0 | 0.008 | 0.014 | 16.038 | 0.653 | 0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 25 | SER | 0 | 0.019 | -0.001 | 18.775 | -0.591 | -0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 26 | LEU | 0 | -0.006 | -0.005 | 20.745 | 0.410 | 0.410 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 27 | MET | 0 | 0.000 | -0.001 | 23.808 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 28 | ASP | -1 | -0.821 | -0.907 | 27.218 | -9.758 | -9.758 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 29 | GLN | 0 | -0.076 | -0.037 | 28.739 | 0.311 | 0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 30 | SER | 0 | 0.057 | 0.024 | 32.915 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 31 | VAL | 0 | 0.025 | 0.043 | 34.927 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 32 | ARG | 1 | 0.867 | 0.922 | 37.810 | 6.785 | 6.785 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 33 | GLU | -1 | -0.792 | -0.902 | 40.259 | -6.988 | -6.988 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 34 | GLY | 0 | -0.015 | 0.001 | 40.941 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 35 | GLN | 0 | -0.029 | -0.010 | 38.052 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 36 | ASP | -1 | -0.799 | -0.889 | 34.167 | -8.101 | -8.101 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 37 | VAL | 0 | -0.038 | -0.020 | 30.710 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 38 | ILE | 0 | -0.018 | -0.011 | 26.588 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 39 | MET | 0 | -0.019 | 0.018 | 25.595 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 40 | SER | 0 | 0.025 | -0.002 | 21.823 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 41 | ILE | 0 | -0.020 | -0.003 | 16.519 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 42 | ARG | 1 | 0.883 | 0.948 | 13.009 | 17.221 | 17.221 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 43 | VAL | 0 | -0.005 | 0.002 | 11.562 | -0.400 | -0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 44 | GLN | 0 | 0.008 | -0.010 | 8.898 | 1.844 | 1.844 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 45 | GLY | 0 | 0.044 | 0.005 | 6.015 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 46 | GLU | -1 | -0.918 | -0.939 | 2.495 | -28.343 | -27.524 | 0.767 | -0.633 | -0.953 | -0.002 |
31 | A | 47 | PRO | 0 | 0.096 | 0.017 | 2.668 | -10.567 | -8.060 | 0.822 | -1.736 | -1.594 | -0.019 |
32 | A | 48 | LYS | 1 | 0.832 | 0.931 | 5.744 | 17.121 | 17.121 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 49 | PRO | 0 | -0.072 | -0.029 | 8.202 | 0.685 | 0.685 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 50 | VAL | 0 | 0.041 | 0.025 | 10.365 | 1.359 | 1.359 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 51 | VAL | 0 | -0.006 | -0.020 | 13.789 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 52 | SER | 0 | -0.029 | -0.009 | 16.348 | 0.786 | 0.786 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 53 | TRP | 0 | 0.069 | 0.019 | 19.819 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 54 | LEU | 0 | -0.042 | -0.023 | 22.507 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 55 | ARG | 1 | 0.935 | 0.977 | 25.708 | 8.764 | 8.764 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 56 | ASN | 0 | -0.013 | -0.017 | 29.176 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 57 | ARG | 1 | 0.814 | 0.876 | 26.614 | 11.084 | 11.084 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 58 | GLN | 0 | 0.021 | 0.029 | 28.016 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 59 | PRO | 0 | 0.010 | -0.003 | 26.024 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 60 | VAL | 0 | 0.015 | 0.012 | 26.303 | 0.416 | 0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 61 | ARG | 1 | 0.918 | 0.969 | 27.347 | 8.494 | 8.494 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 62 | PRO | 0 | -0.003 | -0.001 | 27.435 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 63 | ASP | -1 | -0.848 | -0.937 | 29.940 | -8.393 | -8.393 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 64 | GLN | 0 | 0.062 | 0.018 | 32.455 | -0.322 | -0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 65 | ARG | 1 | 0.779 | 0.875 | 34.358 | 8.058 | 8.058 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 66 | ARG | 1 | 0.914 | 0.957 | 30.010 | 8.859 | 8.859 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 67 | PHE | 0 | -0.005 | 0.004 | 27.240 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 68 | ALA | 0 | -0.002 | 0.001 | 22.562 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 69 | GLU | -1 | -0.758 | -0.850 | 22.697 | -10.774 | -10.774 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 70 | GLU | -1 | -0.845 | -0.926 | 16.255 | -16.133 | -16.133 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 71 | ALA | 0 | -0.022 | -0.008 | 19.172 | 0.422 | 0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 72 | GLU | -1 | -0.883 | -0.940 | 17.257 | -13.437 | -13.437 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 73 | GLY | 0 | 0.015 | -0.010 | 14.574 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 74 | GLY | 0 | 0.034 | 0.010 | 13.814 | -0.514 | -0.514 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 75 | LEU | 0 | -0.064 | -0.025 | 14.527 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 76 | CYS | 0 | -0.011 | 0.008 | 16.478 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 77 | ARG | 1 | 0.875 | 0.918 | 19.317 | 11.781 | 11.781 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 78 | LEU | 0 | -0.011 | 0.009 | 23.027 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 79 | ARG | 1 | 0.840 | 0.897 | 25.649 | 10.091 | 10.091 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 80 | ILE | 0 | -0.012 | -0.006 | 29.035 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 81 | LEU | 0 | -0.014 | -0.004 | 32.382 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 82 | ALA | 0 | -0.004 | -0.009 | 35.495 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 83 | ALA | 0 | -0.023 | 0.003 | 36.518 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 84 | GLU | -1 | -0.853 | -0.937 | 37.872 | -7.147 | -7.147 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 85 | ARG | 1 | 0.873 | 0.906 | 38.729 | 6.580 | 6.580 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 86 | GLY | 0 | -0.018 | -0.003 | 39.053 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 87 | ASP | -1 | -0.756 | -0.850 | 34.422 | -8.476 | -8.476 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 88 | ALA | 0 | -0.015 | 0.016 | 34.013 | -0.324 | -0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 89 | GLY | 0 | -0.009 | -0.012 | 33.299 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 90 | PHE | 0 | -0.001 | 0.000 | 29.345 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 91 | TYR | 0 | -0.004 | -0.029 | 26.380 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 92 | THR | 0 | -0.049 | -0.035 | 21.872 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 93 | CYS | 0 | -0.030 | 0.007 | 19.103 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 94 | LYS | 1 | 0.904 | 0.938 | 17.972 | 13.874 | 13.874 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 95 | ALA | 0 | 0.035 | 0.018 | 12.801 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 96 | VAL | 0 | 0.006 | -0.015 | 12.074 | -0.491 | -0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 97 | ASN | 0 | 0.017 | -0.008 | 5.397 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 98 | GLU | -1 | -0.828 | -0.927 | 6.222 | -27.503 | -27.503 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 99 | TYR | 0 | -0.040 | -0.014 | 2.650 | -12.380 | -9.202 | 3.801 | -2.277 | -4.702 | -0.028 |
84 | A | 100 | GLY | 0 | -0.003 | -0.002 | 6.318 | -0.312 | -0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 101 | ALA | 0 | 0.012 | 0.008 | 9.611 | 0.914 | 0.914 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 102 | ARG | 1 | 0.890 | 0.947 | 12.541 | 20.571 | 20.571 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 103 | GLN | 0 | 0.050 | 0.032 | 14.885 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 104 | CYS | 0 | -0.051 | -0.002 | 18.244 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 105 | GLU | -1 | -0.788 | -0.881 | 20.885 | -11.353 | -11.353 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 106 | ALA | 0 | 0.014 | 0.028 | 24.513 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 107 | ARG | 1 | 0.819 | 0.902 | 27.568 | 8.551 | 8.551 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 108 | LEU | 0 | 0.008 | 0.017 | 31.112 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 109 | GLU | -1 | -0.871 | -0.934 | 32.894 | -7.871 | -7.871 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 110 | VAL | 0 | 0.012 | -0.002 | 36.666 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 111 | ARG | 1 | 0.857 | 0.912 | 39.154 | 7.633 | 7.633 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 112 | GLY | 0 | 0.060 | 0.040 | 42.576 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |