FMODB ID: LN9G9
Calculation Name: 3CPT-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3CPT
Chain ID: A
UniProt ID: Q9JHS3
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 | 119 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -963372.788036 |
---|---|
FMO2-HF: Nuclear repulsion | 918402.593242 |
FMO2-HF: Total energy | -44970.194795 |
FMO2-MP2: Total energy | -45104.651516 |
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:3:ASP)
Summations of interaction energy for
fragment #1(A:3:ASP)
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. |
-196.556 | -194.184 | 16.677 | -10.613 | -8.437 | 0.115 |
Interaction energy analysis for fragmet #1(A:3:ASP)
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 | 5 | LEU | 0 | 0.070 | 0.030 | 3.550 | -5.266 | -2.958 | 0.004 | -1.021 | -1.291 | 0.005 |
4 | A | 6 | LYS | 1 | 0.893 | 0.939 | 1.681 | -131.324 | -131.745 | 16.672 | -9.381 | -6.870 | 0.109 |
5 | A | 7 | ARG | 1 | 0.979 | 0.984 | 3.795 | -38.331 | -37.846 | 0.001 | -0.211 | -0.276 | 0.001 |
6 | A | 8 | PHE | 0 | 0.006 | 0.004 | 5.679 | -4.709 | -4.709 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | LEU | 0 | 0.044 | 0.012 | 7.669 | -3.064 | -3.064 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | TYR | 0 | -0.013 | 0.001 | 8.010 | -2.501 | -2.501 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | LYS | 1 | 0.893 | 0.935 | 9.681 | -23.478 | -23.478 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | LYS | 1 | 0.879 | 0.921 | 11.702 | -18.923 | -18.923 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | LEU | 0 | -0.047 | 0.013 | 12.291 | -1.461 | -1.461 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | PRO | 0 | -0.010 | -0.014 | 14.712 | -1.019 | -1.019 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | SER | 0 | -0.089 | -0.047 | 17.170 | -0.958 | -0.958 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | VAL | 0 | -0.017 | -0.008 | 19.186 | -0.803 | -0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | GLU | -1 | -0.898 | -0.947 | 20.615 | 12.050 | 12.050 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | GLY | 0 | 0.013 | 0.002 | 22.250 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | LEU | 0 | -0.044 | -0.004 | 16.416 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | HIS | 0 | 0.020 | -0.005 | 17.547 | 0.827 | 0.827 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | ALA | 0 | -0.004 | -0.015 | 14.001 | 1.242 | 1.242 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | ILE | 0 | 0.000 | 0.017 | 11.845 | -1.366 | -1.366 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | VAL | 0 | -0.025 | -0.024 | 11.633 | 2.478 | 2.478 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 24 | VAL | 0 | 0.026 | 0.027 | 10.494 | -1.876 | -1.876 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 25 | SER | 0 | -0.010 | -0.012 | 11.558 | 1.926 | 1.926 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 26 | ASP | -1 | -0.743 | -0.866 | 14.126 | 17.248 | 17.248 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | ARG | 1 | 0.894 | 0.918 | 16.620 | -12.641 | -12.641 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | ASP | -1 | -0.876 | -0.921 | 19.261 | 13.561 | 13.561 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | GLY | 0 | -0.082 | -0.032 | 17.785 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | VAL | 0 | -0.017 | -0.028 | 13.985 | 1.129 | 1.129 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | PRO | 0 | -0.079 | -0.034 | 10.791 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | VAL | 0 | 0.023 | 0.009 | 7.944 | 1.063 | 1.063 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | ILE | 0 | -0.001 | -0.007 | 5.480 | 5.338 | 5.338 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | LYS | 1 | 0.873 | 0.935 | 7.749 | -27.737 | -27.737 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | VAL | 0 | -0.058 | -0.017 | 7.008 | 3.948 | 3.948 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | ALA | 0 | 0.023 | -0.005 | 9.601 | -2.572 | -2.572 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | ASN | 0 | 0.013 | 0.013 | 12.601 | 0.703 | 0.703 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | ASP | -1 | -0.901 | -0.953 | 15.034 | 16.779 | 16.779 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 39 | ASN | 0 | -0.011 | -0.007 | 17.791 | -1.530 | -1.530 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | ALA | 0 | -0.060 | -0.022 | 17.149 | -0.754 | -0.754 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | PRO | 0 | 0.012 | 0.004 | 19.128 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | GLU | -1 | -0.793 | -0.893 | 18.569 | 16.739 | 16.739 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | HIS | 0 | -0.041 | -0.033 | 19.588 | 0.792 | 0.792 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | ALA | 0 | -0.015 | -0.011 | 20.775 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | LEU | 0 | 0.022 | 0.010 | 14.737 | 0.628 | 0.628 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | ARG | 1 | 0.840 | 0.917 | 16.784 | -14.095 | -14.095 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | PRO | 0 | 0.047 | 0.031 | 16.813 | -0.526 | -0.526 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | GLY | 0 | 0.066 | 0.055 | 19.068 | -0.482 | -0.482 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | PHE | 0 | -0.008 | 0.011 | 21.547 | -0.613 | -0.613 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | LEU | 0 | 0.019 | -0.005 | 16.971 | -0.459 | -0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | SER | 0 | 0.041 | 0.002 | 20.959 | -0.564 | -0.564 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | THR | 0 | -0.028 | -0.013 | 22.286 | -0.727 | -0.727 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | PHE | 0 | -0.012 | -0.006 | 22.964 | -0.575 | -0.575 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | ALA | 0 | 0.044 | 0.029 | 22.423 | -0.435 | -0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | LEU | 0 | 0.002 | 0.007 | 24.584 | -0.425 | -0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | ALA | 0 | 0.003 | 0.001 | 27.360 | -0.478 | -0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | THR | 0 | -0.033 | -0.033 | 26.621 | -0.342 | -0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | ASP | -1 | -0.886 | -0.913 | 27.513 | 10.469 | 10.469 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | GLN | 0 | 0.038 | -0.005 | 29.479 | -0.291 | -0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | GLY | 0 | 0.031 | 0.020 | 32.201 | -0.337 | -0.337 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | SER | 0 | -0.040 | -0.038 | 31.958 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | LYS | 1 | 0.808 | 0.909 | 31.001 | -10.143 | -10.143 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | LEU | 0 | -0.037 | -0.020 | 35.633 | -0.265 | -0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | GLY | 0 | 0.011 | 0.017 | 37.282 | -0.259 | -0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | LEU | 0 | -0.065 | -0.011 | 33.705 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | SER | 0 | 0.062 | 0.026 | 33.983 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | LYS | 1 | 0.933 | 0.967 | 26.048 | -11.036 | -11.036 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | ASN | 0 | 0.013 | -0.001 | 27.016 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | LYS | 1 | 0.962 | 0.979 | 25.949 | -9.985 | -9.985 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | SER | 0 | 0.053 | 0.017 | 24.425 | 0.563 | 0.563 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | ILE | 0 | -0.010 | 0.014 | 25.085 | -0.610 | -0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | ILE | 0 | 0.015 | 0.008 | 25.225 | 0.580 | 0.580 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | CYS | 0 | -0.073 | -0.016 | 26.375 | -0.562 | -0.562 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | TYR | 0 | 0.048 | 0.000 | 27.011 | 0.404 | 0.404 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | TYR | 0 | -0.003 | -0.011 | 26.632 | -0.220 | -0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | ASN | 0 | 0.026 | 0.004 | 29.938 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | THR | 0 | 0.013 | 0.005 | 28.090 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | TYR | 0 | 0.001 | 0.012 | 23.810 | 0.381 | 0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | GLN | 0 | 0.007 | 0.013 | 24.067 | -0.538 | -0.538 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | VAL | 0 | -0.021 | -0.010 | 21.167 | 0.709 | 0.709 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | VAL | 0 | 0.007 | 0.011 | 21.491 | -0.675 | -0.675 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 82 | GLN | 0 | -0.028 | -0.029 | 20.111 | 0.375 | 0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | PHE | 0 | 0.002 | -0.009 | 19.447 | -0.955 | -0.955 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | ASN | 0 | -0.019 | -0.018 | 19.996 | 1.017 | 1.017 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | ARG | 1 | 0.783 | 0.867 | 18.004 | -14.712 | -14.712 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | LEU | 0 | 0.030 | 0.051 | 18.717 | 0.488 | 0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | PRO | 0 | 0.018 | -0.012 | 17.211 | -0.393 | -0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | LEU | 0 | 0.007 | 0.019 | 12.963 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | VAL | 0 | -0.010 | -0.002 | 16.305 | -1.215 | -1.215 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | VAL | 0 | 0.001 | 0.012 | 14.487 | 1.246 | 1.246 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | SER | 0 | 0.011 | 0.003 | 15.980 | -1.679 | -1.679 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | PHE | 0 | 0.014 | 0.006 | 16.126 | 1.378 | 1.378 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | ILE | 0 | -0.025 | -0.011 | 16.853 | -0.982 | -0.982 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | ALA | 0 | 0.032 | 0.020 | 18.924 | 0.595 | 0.595 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 95 | SER | 0 | 0.049 | 0.022 | 21.596 | -0.289 | -0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 96 | SER | 0 | -0.037 | -0.026 | 24.830 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 97 | SER | 0 | 0.008 | 0.002 | 27.894 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 98 | ALA | 0 | 0.012 | 0.030 | 24.057 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 99 | ASN | 0 | 0.045 | 0.009 | 26.135 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 100 | THR | 0 | 0.068 | 0.014 | 25.369 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 101 | GLY | 0 | 0.009 | 0.012 | 25.301 | 0.320 | 0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 102 | LEU | 0 | -0.005 | -0.008 | 23.588 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 103 | ILE | 0 | 0.025 | 0.018 | 19.906 | 0.563 | 0.563 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 104 | VAL | 0 | -0.001 | 0.002 | 21.030 | 0.485 | 0.485 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 105 | SER | 0 | -0.043 | -0.015 | 22.632 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 106 | LEU | 0 | 0.056 | 0.022 | 16.132 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 107 | GLU | -1 | -0.820 | -0.883 | 17.768 | 15.512 | 15.512 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 108 | LYS | 1 | 0.889 | 0.940 | 18.383 | -12.503 | -12.503 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 109 | GLU | -1 | -0.883 | -0.925 | 17.878 | 15.844 | 15.844 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 110 | LEU | 0 | -0.010 | -0.013 | 12.846 | 0.556 | 0.556 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 111 | ALA | 0 | 0.004 | 0.014 | 14.598 | 0.894 | 0.894 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 112 | PRO | 0 | 0.002 | 0.000 | 16.019 | 0.343 | 0.343 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 113 | LEU | 0 | 0.056 | 0.036 | 10.591 | 0.471 | 0.471 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 114 | PHE | 0 | -0.035 | -0.033 | 11.441 | 1.105 | 1.105 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 115 | GLU | -1 | -0.824 | -0.882 | 13.228 | 15.476 | 15.476 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 116 | GLU | -1 | -0.895 | -0.954 | 11.772 | 19.544 | 19.544 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 117 | LEU | 0 | -0.033 | -0.012 | 7.764 | 0.741 | 0.741 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 118 | ARG | 1 | 0.737 | 0.818 | 11.017 | -15.000 | -15.000 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 119 | GLN | 0 | -0.089 | -0.041 | 13.690 | -1.017 | -1.017 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 120 | VAL | 0 | -0.033 | 0.005 | 9.748 | 0.965 | 0.965 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 121 | VAL | 0 | -0.046 | -0.018 | 12.942 | -0.668 | -0.668 | 0.000 | 0.000 | 0.000 | 0.000 |