FMODB ID: Z2M9N
Calculation Name: 1K78-I-Xray314
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1K78
Chain ID: I
UniProt ID: P27577
Base Structure: X-ray
Registration Date: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 60 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -317130.757341 |
---|---|
FMO2-HF: Nuclear repulsion | 293858.010977 |
FMO2-HF: Total energy | -23272.746364 |
FMO2-MP2: Total energy | -23340.609483 |
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(I:83:ACE )
Summations of interaction energy for
fragment #1(I:83:ACE )
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. |
2.282 | 3.118 | -0.005 | -0.414 | -0.417 | 0 |
Interaction energy analysis for fragmet #1(I:83:ACE )
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 | I | 85 | GLY | 0 | 0.017 | 0.019 | 3.843 | 1.001 | 1.837 | -0.005 | -0.414 | -0.417 | 0.000 |
4 | I | 86 | SER | 0 | -0.020 | -0.013 | 7.070 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | I | 87 | LYS | 1 | 0.972 | 0.983 | 10.444 | 0.609 | 0.609 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | I | 88 | PRO | 0 | -0.005 | -0.007 | 13.134 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | I | 89 | LYS | 1 | 1.002 | 0.994 | 16.649 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | I | 90 | VAL | 0 | 0.057 | 0.058 | 19.577 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | I | 91 | ALA | 0 | -0.013 | 0.007 | 18.920 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | I | 92 | THR | 0 | -0.005 | -0.009 | 20.200 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | I | 93 | PRO | 0 | 0.071 | 0.011 | 19.920 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | I | 94 | LYS | 1 | 1.020 | 1.018 | 22.392 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | I | 95 | VAL | 0 | 0.022 | 0.016 | 24.540 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | I | 96 | VAL | 0 | -0.022 | -0.031 | 21.108 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | I | 97 | GLU | -1 | -0.923 | -0.952 | 24.548 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | I | 98 | LYS | 1 | 0.928 | 0.976 | 27.145 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | I | 99 | ILE | 0 | -0.026 | -0.001 | 25.549 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | I | 100 | ALA | 0 | -0.001 | -0.002 | 27.485 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | I | 101 | GLU | -1 | -0.928 | -0.970 | 29.399 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | I | 102 | TYR | 0 | -0.091 | -0.118 | 32.273 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | I | 103 | LYS | 1 | 0.913 | 0.961 | 30.436 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | I | 104 | ARG | 1 | 0.948 | 0.975 | 33.376 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | I | 105 | GLN | 0 | 0.028 | 0.045 | 35.273 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | I | 106 | ASN | 0 | 0.033 | 0.014 | 37.441 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | I | 107 | PRO | 0 | 0.035 | 0.009 | 35.382 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | I | 108 | THR | 0 | -0.040 | -0.018 | 36.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | I | 109 | MET | 0 | -0.054 | 0.008 | 35.172 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | I | 110 | PHE | 0 | 0.005 | -0.005 | 35.141 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | I | 111 | ALA | 0 | -0.021 | -0.030 | 30.448 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | I | 112 | TRP | 0 | -0.014 | -0.027 | 32.259 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | I | 113 | GLU | -1 | -0.759 | -0.856 | 34.382 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | I | 114 | ILE | 0 | -0.028 | -0.015 | 30.083 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | I | 115 | ARG | 1 | 0.900 | 0.938 | 30.147 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | I | 116 | ASP | -1 | -0.851 | -0.917 | 32.515 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | I | 117 | ARG | 1 | 0.852 | 0.917 | 35.804 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | I | 118 | LEU | 0 | -0.057 | -0.015 | 28.364 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | I | 119 | LEU | 0 | 0.002 | 0.000 | 32.643 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | I | 120 | ALA | 0 | 0.019 | 0.015 | 34.557 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | I | 121 | GLU | -1 | -0.903 | -0.924 | 35.593 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | I | 122 | ARG | 1 | 0.939 | 0.957 | 35.244 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | I | 123 | VAL | 0 | -0.022 | 0.008 | 29.814 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | I | 124 | CYS | 0 | -0.087 | -0.042 | 28.514 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | I | 125 | ASP | -1 | -0.791 | -0.887 | 29.931 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | I | 126 | ASN | 0 | -0.023 | -0.021 | 30.609 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | I | 127 | ASP | -1 | -0.890 | -0.942 | 29.215 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | I | 128 | THR | 0 | -0.113 | -0.061 | 25.423 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | I | 129 | VAL | 0 | -0.015 | -0.006 | 26.442 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | I | 130 | PRO | 0 | -0.025 | -0.017 | 24.839 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | I | 131 | SER | 0 | 0.040 | 0.006 | 25.225 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | I | 132 | VAL | 0 | 0.117 | 0.037 | 26.792 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | I | 133 | SER | 0 | -0.016 | -0.016 | 24.625 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | I | 134 | SER | 0 | -0.038 | -0.023 | 22.685 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | I | 135 | ILE | 0 | 0.055 | 0.046 | 23.573 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | I | 136 | ASN | 0 | 0.054 | 0.014 | 26.132 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | I | 137 | ARG | 1 | 0.903 | 0.961 | 18.285 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | I | 138 | ILE | 0 | -0.014 | -0.018 | 20.900 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | I | 139 | ILE | 0 | -0.003 | 0.000 | 22.847 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | I | 140 | ARG | 1 | 0.892 | 0.950 | 21.751 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | I | 141 | THR | 0 | -0.092 | -0.027 | 17.843 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | I | 142 | NME | 0 | 0.043 | 0.032 | 21.162 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |