FMODB ID: LJQ69
Calculation Name: 1B79-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1B79
Chain ID: A
UniProt ID: P0ACB0
Base Structure: X-ray
Registration Date: 2023-03-13
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 | 102 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -775685.27202 |
---|---|
FMO2-HF: Nuclear repulsion | 736096.020751 |
FMO2-HF: Total energy | -39589.251269 |
FMO2-MP2: Total energy | -39705.5955 |
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:26:PRO)
Summations of interaction energy for
fragment #1(A:26:PRO)
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. |
-4.025 | -1.132 | 0.581 | -1.235 | -2.237 | -0.001 |
Interaction energy analysis for fragmet #1(A:26:PRO)
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 | 28 | HIS | 1 | 0.880 | 0.963 | 3.754 | -1.571 | 0.053 | -0.008 | -0.862 | -0.753 | 0.002 |
4 | A | 29 | SER | 0 | -0.070 | -0.039 | 6.352 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 30 | ILE | 0 | 0.081 | 0.029 | 8.694 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 31 | GLU | -1 | -0.823 | -0.917 | 8.703 | -0.324 | -0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 32 | ALA | 0 | 0.019 | 0.031 | 6.014 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 33 | GLU | -1 | -0.722 | -0.853 | 7.983 | -0.252 | -0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 34 | GLN | 0 | -0.050 | -0.041 | 11.352 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 35 | SER | 0 | -0.018 | -0.034 | 9.841 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 36 | VAL | 0 | -0.040 | 0.000 | 10.288 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 37 | LEU | 0 | 0.008 | 0.000 | 12.784 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 38 | GLY | 0 | 0.055 | 0.021 | 15.523 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 39 | GLY | 0 | -0.001 | -0.011 | 15.092 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 40 | LEU | 0 | -0.014 | -0.009 | 16.090 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 41 | MET | 0 | -0.073 | -0.020 | 18.277 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 42 | LEU | 0 | -0.091 | -0.051 | 18.215 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 43 | ASP | -1 | -0.902 | -0.963 | 18.755 | -0.184 | -0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 44 | ASN | 0 | 0.006 | -0.015 | 20.076 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 45 | GLU | -1 | -0.863 | -0.911 | 21.898 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 46 | ARG | 1 | 0.795 | 0.911 | 14.422 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 47 | TRP | 0 | -0.004 | -0.006 | 17.627 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 48 | ASP | -1 | -0.832 | -0.919 | 19.033 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 49 | ASP | -1 | -0.848 | -0.918 | 15.501 | -0.267 | -0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 50 | VAL | 0 | -0.037 | -0.028 | 13.923 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 51 | ALA | 0 | 0.003 | 0.002 | 15.514 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 52 | GLU | -1 | -0.993 | -0.989 | 17.469 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 53 | ARG | 1 | 0.729 | 0.876 | 11.209 | 0.355 | 0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 54 | VAL | 0 | -0.082 | -0.037 | 12.664 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 55 | VAL | 0 | 0.017 | 0.006 | 14.522 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 56 | ALA | 0 | 0.058 | 0.021 | 16.872 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 57 | ASP | -1 | -0.914 | -0.975 | 18.053 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 58 | ASP | -1 | -0.818 | -0.869 | 13.529 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 59 | PHE | 0 | -0.077 | -0.032 | 13.701 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 60 | TYR | 0 | -0.020 | -0.027 | 10.862 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 61 | THR | 0 | -0.011 | -0.001 | 15.386 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 62 | ARG | 1 | 1.003 | 0.985 | 18.030 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 63 | PRO | 0 | 0.040 | 0.022 | 20.172 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 64 | HIS | 0 | 0.009 | 0.001 | 14.470 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 65 | ARG | 1 | 0.818 | 0.923 | 18.392 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 66 | HIS | 0 | -0.061 | -0.035 | 19.896 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 67 | ILE | 0 | 0.031 | 0.009 | 19.608 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 68 | PHE | 0 | 0.040 | 0.021 | 16.415 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 69 | THR | 0 | -0.020 | -0.028 | 20.273 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 70 | GLU | -1 | -0.799 | -0.867 | 23.466 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 71 | MET | 0 | -0.019 | -0.010 | 18.375 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 72 | ALA | 0 | 0.044 | 0.027 | 22.763 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 73 | ARG | 1 | 0.846 | 0.922 | 24.277 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 74 | LEU | 0 | -0.048 | -0.025 | 26.382 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 75 | GLN | 0 | 0.080 | 0.040 | 24.123 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 76 | GLU | -1 | -0.933 | -0.957 | 25.295 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 77 | SER | 0 | -0.155 | -0.083 | 28.738 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 78 | GLY | 0 | -0.041 | -0.022 | 30.600 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 79 | SER | 0 | -0.083 | -0.027 | 30.225 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 80 | PRO | 0 | 0.026 | 0.012 | 27.702 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 81 | ILE | 0 | 0.008 | -0.003 | 21.491 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 82 | ASP | -1 | -0.831 | -0.883 | 23.572 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 83 | LEU | 0 | -0.013 | -0.020 | 24.022 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 84 | ILE | 0 | -0.040 | -0.022 | 25.475 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 85 | THR | 0 | 0.001 | -0.020 | 28.497 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 86 | LEU | 0 | 0.018 | 0.009 | 22.889 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 87 | ALA | 0 | -0.026 | -0.026 | 27.249 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 88 | GLU | -1 | -0.856 | -0.893 | 28.511 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 89 | SER | 0 | -0.043 | -0.054 | 29.276 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 90 | LEU | 0 | 0.017 | 0.000 | 25.310 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 91 | GLU | -1 | -0.973 | -0.985 | 30.031 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 92 | ARG | 1 | 0.810 | 0.890 | 32.898 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 93 | GLN | 0 | -0.103 | -0.058 | 30.513 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 94 | GLY | 0 | -0.040 | -0.018 | 33.908 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 95 | GLN | 0 | 0.026 | 0.024 | 28.970 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 96 | LEU | 0 | 0.024 | 0.034 | 27.801 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 97 | ASP | -1 | -0.885 | -0.944 | 28.086 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 98 | SER | 0 | -0.079 | -0.049 | 27.785 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 99 | VAL | 0 | -0.011 | 0.001 | 22.999 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 100 | GLY | 0 | 0.011 | 0.002 | 23.200 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 101 | GLY | 0 | -0.006 | -0.005 | 25.118 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 102 | PHE | 0 | 0.039 | 0.003 | 26.029 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 103 | ALA | 0 | -0.024 | -0.013 | 26.089 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 104 | TYR | 0 | -0.001 | -0.002 | 17.125 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 105 | LEU | 0 | 0.062 | 0.038 | 21.385 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 106 | ALA | 0 | -0.040 | -0.031 | 22.174 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 107 | GLU | -1 | -0.934 | -0.979 | 18.555 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 108 | LEU | 0 | -0.008 | 0.006 | 16.339 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 109 | SER | 0 | -0.002 | -0.006 | 17.887 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 110 | LYS | 1 | 0.870 | 0.936 | 20.238 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 111 | ASN | 0 | -0.019 | -0.006 | 15.899 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 112 | THR | 0 | -0.027 | 0.018 | 13.763 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 113 | PRO | 0 | -0.005 | 0.011 | 13.115 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 114 | SER | 0 | 0.053 | 0.009 | 14.733 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 115 | ALA | 0 | -0.065 | -0.021 | 14.733 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 116 | ALA | 0 | 0.029 | 0.011 | 10.595 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 117 | ASN | 0 | -0.011 | -0.011 | 8.290 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 118 | ILE | 0 | 0.076 | 0.030 | 8.962 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 119 | SER | 0 | 0.051 | 0.025 | 10.689 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 120 | ALA | 0 | -0.004 | 0.008 | 5.560 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 121 | TYR | 0 | -0.028 | -0.023 | 5.425 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 122 | ALA | 0 | 0.010 | 0.009 | 7.478 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 123 | ASP | -1 | -0.828 | -0.932 | 7.198 | -0.422 | -0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 124 | ILE | 0 | -0.085 | -0.039 | 2.599 | -1.411 | -0.142 | 0.589 | -0.373 | -1.484 | -0.003 |
100 | A | 125 | VAL | 0 | -0.073 | -0.044 | 5.584 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 126 | ARG | 1 | 0.891 | 0.954 | 9.048 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 127 | GLU | -1 | -1.037 | -1.011 | 6.287 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |