FMODB ID: 853NY
Calculation Name: 1P8C-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1P8C
Chain ID: A
UniProt ID: Q9X1V5
Base Structure: X-ray
Registration Date: 2023-09-20
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 | OptAll |
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 | 110 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -846963.406631 |
---|---|
FMO2-HF: Nuclear repulsion | 802574.313676 |
FMO2-HF: Total energy | -44389.092955 |
FMO2-MP2: Total energy | -44517.055365 |
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:10:ARG)
Summations of interaction energy for
fragment #1(A:10:ARG)
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. |
-127.024 | -117.66 | 9.463 | -7.7 | -11.127 | -0.071 |
Interaction energy analysis for fragmet #1(A:10:ARG)
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 | 12 | GLU | -1 | -0.768 | -0.858 | 2.957 | -27.793 | -25.634 | 0.078 | -0.895 | -1.343 | 0.002 |
4 | A | 13 | LEU | 0 | 0.023 | 0.009 | 2.354 | 1.154 | 3.155 | 2.004 | -1.364 | -2.640 | 0.000 |
5 | A | 14 | ASN | 0 | 0.004 | -0.002 | 4.185 | 0.798 | 1.162 | 0.000 | -0.144 | -0.220 | 0.000 |
6 | A | 15 | GLU | -1 | -0.794 | -0.878 | 6.173 | -21.888 | -21.888 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 16 | LYS | 1 | 0.794 | 0.875 | 5.931 | 27.815 | 27.815 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 17 | VAL | 0 | -0.007 | -0.005 | 7.768 | 2.029 | 2.029 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 18 | LEU | 0 | -0.001 | 0.002 | 9.823 | 1.937 | 1.937 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 19 | SER | 0 | -0.080 | -0.037 | 11.591 | 1.620 | 1.620 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 20 | ARG | 1 | 0.930 | 0.952 | 12.756 | 16.544 | 16.544 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 21 | GLY | 0 | 0.065 | 0.060 | 14.160 | 0.416 | 0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 22 | THR | 0 | 0.005 | 0.002 | 15.130 | 0.913 | 0.913 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 23 | LEU | 0 | 0.042 | 0.005 | 17.782 | -0.616 | -0.616 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 24 | ASN | 0 | 0.041 | 0.003 | 19.687 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 25 | THR | 0 | 0.024 | 0.028 | 13.436 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 26 | LYS | 1 | 0.900 | 0.945 | 15.223 | 14.519 | 14.519 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 27 | ARG | 1 | 0.950 | 0.983 | 16.353 | 11.709 | 11.709 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 28 | PHE | 0 | 0.025 | 0.019 | 13.641 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 29 | PHE | 0 | 0.040 | 0.003 | 8.675 | -0.478 | -0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 30 | ASN | 0 | -0.056 | -0.031 | 13.564 | -0.421 | -0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 31 | LEU | 0 | -0.003 | -0.005 | 16.282 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 32 | ASP | -1 | -0.857 | -0.905 | 11.859 | -22.527 | -22.527 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 33 | SER | 0 | 0.026 | 0.022 | 13.237 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 34 | ALA | 0 | -0.038 | -0.024 | 14.468 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 35 | VAL | 0 | -0.007 | 0.001 | 16.839 | 0.544 | 0.544 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 36 | TYR | 0 | -0.003 | -0.027 | 13.432 | 0.605 | 0.605 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 37 | ARG | 1 | 0.903 | 0.959 | 16.254 | 16.469 | 16.469 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 38 | PRO | 0 | 0.046 | 0.023 | 19.940 | 0.388 | 0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 39 | GLY | 0 | 0.001 | -0.002 | 23.334 | 0.189 | 0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 40 | LYS | 1 | 0.904 | 0.954 | 26.553 | 9.797 | 9.797 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 41 | LEU | 0 | 0.012 | 0.018 | 24.162 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 42 | ASP | -1 | -0.782 | -0.870 | 22.240 | -13.791 | -13.791 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 43 | VAL | 0 | 0.046 | 0.010 | 18.284 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 44 | LYS | 1 | 0.862 | 0.931 | 17.881 | 13.557 | 13.557 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 45 | THR | 0 | -0.014 | -0.048 | 18.350 | -0.508 | -0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 46 | LYS | 1 | 0.793 | 0.886 | 18.972 | 13.900 | 13.900 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 47 | GLU | -1 | -0.814 | -0.890 | 13.159 | -23.440 | -23.440 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 48 | LEU | 0 | 0.049 | 0.030 | 14.629 | -1.252 | -1.252 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 49 | MET | 0 | -0.041 | -0.017 | 16.735 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 50 | GLY | 0 | 0.020 | 0.010 | 14.697 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 51 | LEU | 0 | 0.006 | 0.019 | 11.007 | -1.380 | -1.380 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 52 | VAL | 0 | 0.009 | 0.018 | 13.568 | -0.413 | -0.413 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 53 | ALA | 0 | 0.001 | 0.000 | 15.932 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 54 | SER | 0 | -0.038 | -0.045 | 10.847 | -0.630 | -0.630 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 55 | THR | 0 | -0.010 | -0.026 | 12.773 | -1.194 | -1.194 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 56 | VAL | 0 | -0.023 | -0.014 | 14.383 | 0.368 | 0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 57 | LEU | 0 | -0.058 | -0.026 | 14.725 | 0.539 | 0.539 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 58 | ARG | 1 | 0.874 | 0.958 | 13.282 | 16.862 | 16.862 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 59 | CYS | 0 | -0.012 | 0.006 | 4.710 | -3.913 | -3.863 | -0.002 | -0.005 | -0.043 | 0.000 |
51 | A | 60 | ASP | -1 | -0.747 | -0.859 | 7.253 | -33.790 | -33.790 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 61 | ASP | -1 | -0.829 | -0.914 | 2.242 | -111.321 | -107.514 | 7.357 | -5.022 | -6.142 | -0.073 |
53 | A | 63 | ILE | 0 | 0.009 | 0.011 | 7.638 | 1.105 | 1.105 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 64 | ARG | 1 | 0.844 | 0.910 | 3.351 | 53.565 | 54.351 | 0.027 | -0.223 | -0.590 | 0.000 |
55 | A | 65 | TYR | 0 | -0.006 | 0.001 | 5.415 | 1.009 | 1.009 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 66 | HIS | 1 | 0.851 | 0.902 | 6.352 | 28.100 | 28.100 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 67 | LEU | 0 | 0.030 | 0.039 | 7.781 | 2.207 | 2.207 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 68 | VAL | 0 | 0.015 | 0.010 | 5.940 | 1.701 | 1.701 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 69 | ARG | 1 | 0.683 | 0.817 | 8.655 | 24.844 | 24.844 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 70 | CYS | 0 | -0.035 | -0.021 | 11.424 | 2.227 | 2.227 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 71 | VAL | 0 | 0.012 | 0.013 | 11.440 | 1.404 | 1.404 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 72 | GLN | 0 | -0.005 | -0.001 | 10.381 | 2.148 | 2.148 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 73 | GLU | -1 | -0.851 | -0.908 | 14.342 | -17.430 | -17.430 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 74 | GLY | 0 | -0.008 | 0.003 | 16.888 | 1.078 | 1.078 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 75 | ALA | 0 | -0.064 | -0.029 | 16.147 | 0.974 | 0.974 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 76 | SER | 0 | -0.015 | -0.031 | 17.215 | -0.882 | -0.882 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 77 | ASP | -1 | -0.757 | -0.889 | 16.388 | -18.504 | -18.504 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 78 | GLU | -1 | -0.855 | -0.915 | 18.258 | -13.965 | -13.965 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 79 | GLU | -1 | -0.791 | -0.867 | 19.723 | -14.232 | -14.232 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 80 | ILE | 0 | -0.012 | -0.016 | 13.782 | -0.372 | -0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 81 | PHE | 0 | -0.013 | -0.008 | 17.166 | -0.551 | -0.551 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 82 | GLU | -1 | -0.916 | -0.947 | 19.156 | -12.030 | -12.030 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 83 | ALA | 0 | -0.051 | -0.020 | 17.709 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 84 | LEU | 0 | -0.016 | -0.023 | 13.569 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 85 | ASP | -1 | -0.868 | -0.939 | 17.758 | -13.835 | -13.835 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 86 | ILE | 0 | -0.042 | -0.015 | 21.369 | 0.485 | 0.485 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 87 | ALA | 0 | -0.008 | -0.015 | 17.827 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 88 | LEU | 0 | -0.035 | -0.018 | 19.759 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 89 | VAL | 0 | -0.047 | -0.025 | 21.052 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 90 | VAL | 0 | -0.048 | -0.019 | 22.603 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 91 | GLY | 0 | -0.013 | -0.003 | 20.661 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 92 | GLY | 0 | 0.035 | 0.024 | 21.736 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 93 | SER | 0 | 0.034 | -0.013 | 21.646 | -0.718 | -0.718 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 94 | ILE | 0 | -0.011 | -0.006 | 19.841 | -0.589 | -0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 95 | VAL | 0 | 0.026 | 0.021 | 16.849 | -0.976 | -0.976 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 96 | ILE | 0 | 0.030 | 0.029 | 16.439 | -1.057 | -1.057 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 97 | PRO | 0 | -0.072 | -0.048 | 15.953 | -0.546 | -0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 98 | HIS | 0 | 0.030 | 0.005 | 11.402 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 99 | LEU | 0 | 0.047 | 0.038 | 12.280 | -1.516 | -1.516 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 100 | ARG | 1 | 0.937 | 0.965 | 14.192 | 16.430 | 16.430 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 101 | ARG | 1 | 0.797 | 0.889 | 9.433 | 25.759 | 25.759 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 102 | ALA | 0 | -0.011 | -0.005 | 9.834 | -1.948 | -1.948 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 103 | VAL | 0 | 0.031 | 0.013 | 10.874 | -0.560 | -0.560 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 104 | GLY | 0 | 0.028 | 0.023 | 12.316 | 0.157 | 0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 105 | PHE | 0 | -0.027 | -0.025 | 4.165 | -3.554 | -3.357 | -0.001 | -0.047 | -0.149 | 0.000 |
96 | A | 106 | LEU | 0 | -0.024 | -0.003 | 9.059 | -0.978 | -0.978 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 107 | GLU | -1 | -0.901 | -0.961 | 11.538 | -17.940 | -17.940 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 108 | GLU | -1 | -0.966 | -0.980 | 7.239 | -35.140 | -35.140 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 109 | LEU | 0 | -0.014 | -0.018 | 6.838 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 110 | ARG | 1 | 0.736 | 0.834 | 10.516 | 19.718 | 19.718 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 111 | GLU | -1 | -0.918 | -0.958 | 13.767 | -15.298 | -15.298 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 112 | MET | 0 | -0.044 | 0.003 | 8.383 | -1.255 | -1.255 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 113 | GLU | -1 | -0.835 | -0.911 | 12.718 | -17.599 | -17.599 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 114 | LYS | 1 | 0.874 | 0.955 | 14.725 | 15.551 | 15.551 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 115 | ASN | 0 | -0.089 | -0.055 | 15.762 | 1.898 | 1.898 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 116 | GLY | 0 | -0.030 | -0.002 | 17.112 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 117 | GLU | -1 | -0.937 | -0.969 | 11.380 | -23.795 | -23.795 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 118 | THR | 0 | -0.053 | -0.036 | 12.240 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 119 | ILE | 0 | 0.047 | 0.030 | 8.173 | -2.324 | -2.324 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 120 | SER | 0 | -0.044 | -0.016 | 7.181 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |