FMODB ID: Z6M3N
Calculation Name: 1JB2-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1JB2
Chain ID: A
UniProt ID: P61972
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 | 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 | 123 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1077548.790958 |
---|---|
FMO2-HF: Nuclear repulsion | 1027556.508007 |
FMO2-HF: Total energy | -49992.282952 |
FMO2-MP2: Total energy | -50136.415812 |
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:4:LYS)
Summations of interaction energy for
fragment #1(A:4: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. |
-204.385 | -199.692 | 21.735 | -13.348 | -13.079 | -0.13 |
Interaction energy analysis for fragmet #1(A:4: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 | 6 | ILE | 0 | 0.066 | 0.018 | 3.127 | -6.954 | -4.441 | 0.108 | -1.288 | -1.333 | 0.002 |
4 | A | 7 | TRP | 0 | 0.069 | 0.022 | 5.789 | 0.406 | 0.406 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 8 | GLU | -1 | -0.818 | -0.902 | 1.664 | -129.594 | -130.056 | 20.558 | -10.954 | -9.142 | -0.126 |
6 | A | 9 | GLN | 0 | -0.084 | -0.048 | 2.578 | -3.263 | -1.277 | 1.070 | -0.937 | -2.119 | -0.005 |
7 | A | 10 | ILE | 0 | 0.022 | 0.020 | 4.453 | 1.750 | 1.861 | 0.000 | -0.019 | -0.091 | 0.000 |
8 | A | 11 | GLY | 0 | 0.065 | 0.039 | 7.294 | 2.292 | 2.292 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 12 | SER | 0 | -0.048 | -0.027 | 3.702 | 0.484 | 0.871 | 0.001 | -0.148 | -0.240 | -0.001 |
10 | A | 13 | SER | 0 | -0.049 | -0.041 | 5.630 | 5.109 | 5.109 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 14 | PHE | 0 | 0.002 | 0.004 | 8.221 | 3.104 | 3.104 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 15 | ILE | 0 | 0.025 | 0.015 | 8.240 | 2.290 | 2.290 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 16 | ASN | 0 | -0.028 | -0.017 | 8.442 | 3.087 | 3.087 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 17 | HIS | 0 | 0.002 | 0.001 | 10.223 | 1.712 | 1.712 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 18 | TYR | 0 | 0.012 | 0.011 | 13.181 | 1.837 | 1.837 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 19 | TYR | 0 | 0.006 | -0.046 | 12.057 | 0.988 | 0.988 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 20 | GLN | 0 | -0.018 | 0.018 | 13.328 | 2.227 | 2.227 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 21 | LEU | 0 | 0.041 | 0.014 | 16.272 | 1.155 | 1.155 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 22 | PHE | 0 | -0.040 | -0.023 | 18.175 | 1.093 | 1.093 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 23 | ASP | -1 | -0.782 | -0.867 | 17.820 | -16.305 | -16.305 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 24 | ASN | 0 | -0.112 | -0.057 | 18.804 | 1.056 | 1.056 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 25 | ASP | -1 | -0.823 | -0.888 | 21.899 | -11.538 | -11.538 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 26 | ARG | 1 | 0.933 | 0.969 | 22.798 | 11.427 | 11.427 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 27 | THR | 0 | -0.095 | -0.046 | 23.812 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 28 | GLN | 0 | -0.056 | -0.050 | 22.937 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 29 | LEU | 0 | 0.003 | 0.008 | 19.394 | -0.448 | -0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 30 | GLY | 0 | 0.010 | 0.002 | 21.832 | -0.307 | -0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 31 | ALA | 0 | -0.048 | -0.026 | 22.052 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 32 | ILE | 0 | 0.004 | 0.014 | 17.338 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 33 | TYR | 0 | -0.042 | -0.027 | 19.810 | -0.369 | -0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 34 | ILE | 0 | 0.025 | 0.009 | 22.493 | 0.470 | 0.470 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 35 | ASP | -1 | -0.870 | -0.953 | 25.275 | -10.751 | -10.751 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 36 | ALA | 0 | -0.027 | -0.022 | 26.606 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 37 | SER | 0 | -0.011 | -0.022 | 22.310 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 38 | CYS | 0 | -0.112 | -0.046 | 23.794 | 0.793 | 0.793 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 39 | LEU | 0 | 0.026 | 0.019 | 22.136 | -0.648 | -0.648 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 40 | THR | 0 | -0.051 | -0.020 | 23.420 | 0.771 | 0.771 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 41 | TRP | 0 | -0.008 | -0.022 | 21.550 | -0.655 | -0.655 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 42 | GLU | -1 | -0.859 | -0.946 | 24.488 | -11.498 | -11.498 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 43 | GLY | 0 | -0.072 | -0.041 | 26.050 | 0.435 | 0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 44 | GLN | 0 | 0.000 | 0.013 | 27.922 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 45 | GLN | 0 | -0.032 | -0.016 | 28.134 | -0.371 | -0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 46 | PHE | 0 | 0.028 | 0.000 | 27.778 | 0.426 | 0.426 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 47 | GLN | 0 | 0.021 | 0.003 | 27.705 | -0.425 | -0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 48 | GLY | 0 | 0.059 | 0.033 | 28.283 | 0.434 | 0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 49 | LYS | 1 | 0.871 | 0.933 | 25.385 | 12.272 | 12.272 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 50 | ALA | 0 | -0.002 | -0.004 | 28.111 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 51 | ALA | 0 | 0.061 | 0.035 | 30.686 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 52 | ILE | 0 | -0.032 | -0.001 | 24.200 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 53 | VAL | 0 | 0.018 | -0.009 | 26.790 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 54 | GLU | -1 | -0.952 | -0.953 | 28.195 | -9.155 | -9.155 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 55 | LYS | 1 | 0.912 | 0.981 | 27.509 | 11.203 | 11.203 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 56 | LEU | 0 | -0.006 | -0.004 | 23.221 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 57 | SER | 0 | -0.049 | -0.042 | 26.918 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 58 | SER | 0 | -0.097 | -0.047 | 29.741 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 59 | LEU | 0 | -0.059 | -0.021 | 25.190 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 60 | PRO | 0 | 0.038 | 0.005 | 29.346 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 61 | PHE | 0 | -0.002 | 0.019 | 24.259 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 62 | GLN | 0 | -0.051 | -0.041 | 29.180 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 63 | LYS | 1 | 0.859 | 0.932 | 25.787 | 10.788 | 10.788 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 64 | ILE | 0 | -0.053 | -0.019 | 21.522 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 65 | GLN | 0 | -0.016 | 0.008 | 18.728 | -0.494 | -0.494 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 66 | HIS | 1 | 0.803 | 0.871 | 15.727 | 17.278 | 17.278 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 67 | SER | 0 | -0.014 | -0.008 | 14.115 | -0.165 | -0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 68 | ILE | 0 | -0.037 | -0.018 | 8.820 | 0.516 | 0.516 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 69 | THR | 0 | -0.029 | -0.030 | 10.694 | -0.771 | -0.771 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 70 | ALA | 0 | -0.007 | -0.002 | 8.200 | -1.400 | -1.400 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 71 | GLN | 0 | 0.025 | 0.016 | 4.900 | -4.958 | -4.887 | -0.001 | -0.001 | -0.069 | 0.000 |
69 | A | 72 | ASP | -1 | -0.885 | -0.912 | 6.396 | -38.927 | -38.927 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 73 | HIS | 0 | 0.005 | -0.012 | 4.482 | 6.471 | 6.558 | -0.001 | -0.001 | -0.085 | 0.000 |
71 | A | 74 | GLN | 0 | -0.033 | -0.010 | 7.956 | 0.503 | 0.503 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 75 | PRO | 0 | 0.018 | 0.023 | 9.619 | 0.571 | 0.571 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 76 | THR | 0 | 0.012 | -0.005 | 11.691 | 0.754 | 0.754 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 77 | PRO | 0 | 0.034 | -0.002 | 15.528 | -0.106 | -0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 78 | ASP | -1 | -0.967 | -0.971 | 18.322 | -14.107 | -14.107 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 79 | SER | 0 | -0.056 | -0.032 | 15.213 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 80 | CYS | 0 | -0.069 | -0.017 | 15.105 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 81 | ILE | 0 | -0.004 | -0.009 | 9.202 | -0.972 | -0.972 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 82 | ILE | 0 | -0.015 | 0.006 | 12.500 | 1.241 | 1.241 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 83 | SER | 0 | -0.030 | -0.046 | 9.222 | -1.492 | -1.492 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 84 | GLU | -1 | -0.872 | -0.917 | 9.869 | -19.549 | -19.549 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 85 | VAL | 0 | -0.030 | -0.014 | 9.745 | -3.668 | -3.668 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 86 | VAL | 0 | 0.034 | 0.021 | 11.391 | 2.585 | 2.585 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 87 | GLY | 0 | 0.048 | 0.020 | 12.210 | -2.061 | -2.061 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 88 | GLN | 0 | -0.060 | -0.025 | 14.593 | 1.942 | 1.942 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 89 | LEU | 0 | 0.006 | 0.000 | 17.456 | -0.772 | -0.772 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 90 | LYS | 1 | 0.855 | 0.923 | 20.139 | 12.098 | 12.098 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 91 | ALA | 0 | 0.039 | 0.019 | 23.371 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 92 | ASP | -1 | -0.768 | -0.890 | 26.012 | -10.258 | -10.258 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 93 | GLU | -1 | -0.874 | -0.948 | 28.618 | -10.564 | -10.564 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 94 | ASP | -1 | -0.921 | -0.933 | 27.956 | -10.437 | -10.437 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 95 | PRO | 0 | -0.043 | -0.027 | 27.840 | -0.276 | -0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 96 | ILE | 0 | -0.012 | -0.012 | 21.591 | -0.208 | -0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 97 | MET | 0 | -0.004 | 0.007 | 22.652 | 0.424 | 0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 98 | GLY | 0 | 0.058 | 0.032 | 19.489 | -0.756 | -0.756 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 99 | PHE | 0 | -0.064 | -0.023 | 14.596 | 0.800 | 0.800 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 100 | HIS | 0 | -0.042 | -0.037 | 15.401 | -0.418 | -0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 101 | GLN | 0 | 0.000 | -0.020 | 15.325 | 0.761 | 0.761 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 102 | MET | 0 | -0.017 | 0.008 | 14.338 | -1.370 | -1.370 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 103 | PHE | 0 | 0.034 | -0.004 | 13.280 | 0.966 | 0.966 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 104 | LEU | 0 | -0.031 | 0.005 | 14.382 | -1.126 | -1.126 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 105 | LEU | 0 | 0.003 | -0.008 | 11.526 | 0.888 | 0.888 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 106 | LYS | 1 | 0.990 | 0.981 | 15.594 | 14.364 | 14.364 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 107 | ASN | 0 | -0.039 | -0.018 | 15.813 | 0.829 | 0.829 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 108 | ILE | 0 | -0.001 | -0.022 | 17.596 | 0.785 | 0.785 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 109 | ASN | 0 | -0.070 | -0.042 | 21.353 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 110 | ASP | -1 | -0.884 | -0.927 | 18.422 | -15.484 | -15.484 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 111 | ALA | 0 | 0.047 | 0.045 | 18.147 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 112 | TRP | 0 | -0.037 | -0.020 | 12.838 | -0.127 | -0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 113 | VAL | 0 | 0.006 | 0.013 | 16.357 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 114 | CYS | 0 | -0.042 | -0.009 | 16.959 | -0.592 | -0.592 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 115 | THR | 0 | 0.000 | 0.001 | 18.341 | 0.807 | 0.807 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 116 | ASN | 0 | -0.004 | 0.003 | 19.499 | 0.674 | 0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 117 | ASP | -1 | -0.696 | -0.813 | 18.520 | -17.717 | -17.717 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 118 | MET | 0 | -0.042 | -0.025 | 18.764 | 1.062 | 1.062 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 119 | PHE | 0 | 0.046 | 0.038 | 18.942 | -0.930 | -0.930 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 120 | ARG | 1 | 0.952 | 0.968 | 20.360 | 13.732 | 13.732 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 121 | LEU | 0 | 0.055 | 0.043 | 20.896 | -0.677 | -0.677 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 122 | ALA | 0 | -0.053 | -0.041 | 20.297 | 0.189 | 0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 123 | LEU | 0 | -0.007 | -0.010 | 22.353 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 124 | HIS | 0 | -0.034 | -0.010 | 22.410 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 125 | ASN | 0 | -0.011 | -0.006 | 17.072 | -0.932 | -0.932 | 0.000 | 0.000 | 0.000 | 0.000 |
123 | A | 126 | PHE | 0 | 0.052 | 0.027 | 13.865 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |