FMODB ID: R1JG8
Calculation Name: 2D68-A-Xray310
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2D68
Chain ID: A
UniProt ID: O95684
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. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 79 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -471762.910545 |
---|---|
FMO2-HF: Nuclear repulsion | 441901.38961 |
FMO2-HF: Total energy | -29861.520936 |
FMO2-MP2: Total energy | -29951.340335 |
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:57:ACE )
Summations of interaction energy for
fragment #1(A:57: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. |
0.553 | 1.324 | -0.004 | -0.324 | -0.442 | 0 |
Interaction energy analysis for fragmet #1(A:57: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 | A | 59 | ASN | 0 | 0.061 | 0.041 | 3.870 | 1.368 | 2.139 | -0.004 | -0.324 | -0.442 | 0.000 |
4 | A | 60 | GLU | -1 | -0.843 | -0.935 | 6.965 | -0.442 | -0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 61 | SER | 0 | -0.012 | -0.006 | 9.555 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 62 | LEU | 0 | 0.055 | 0.022 | 9.599 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 63 | LYS | 1 | 0.960 | 0.986 | 9.117 | 0.741 | 0.741 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 64 | LYS | 1 | 0.903 | 0.941 | 11.365 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 65 | PHE | 0 | 0.030 | 0.034 | 14.625 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 66 | LEU | 0 | 0.024 | 0.021 | 11.817 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 67 | ASN | 0 | -0.082 | -0.020 | 15.621 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 68 | THR | 0 | -0.050 | -0.032 | 17.257 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 69 | LYS | 1 | 0.980 | 0.984 | 20.415 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 70 | ASP | -1 | -0.850 | -0.938 | 23.003 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 71 | GLY | 0 | 0.018 | 0.005 | 19.146 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 72 | ARG | 1 | 0.824 | 0.909 | 17.968 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 73 | LEU | 0 | 0.005 | 0.005 | 19.679 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 74 | VAL | 0 | 0.012 | 0.010 | 19.708 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 75 | ALA | 0 | 0.009 | -0.003 | 16.602 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 76 | SER | 0 | -0.001 | -0.009 | 18.509 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 77 | LEU | 0 | 0.009 | 0.009 | 20.925 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 78 | VAL | 0 | -0.034 | -0.002 | 18.079 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 79 | ALA | 0 | 0.024 | 0.003 | 18.342 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 80 | GLU | -1 | -0.770 | -0.881 | 20.024 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 81 | PHE | 0 | 0.011 | 0.001 | 22.964 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 82 | LEU | 0 | -0.031 | -0.025 | 18.091 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 83 | GLN | 0 | -0.025 | -0.013 | 21.823 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 84 | PHE | 0 | -0.030 | 0.012 | 24.164 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 85 | PHE | 0 | -0.052 | -0.030 | 26.257 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 86 | ASN | 0 | -0.003 | 0.008 | 25.614 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 87 | LEU | 0 | -0.016 | 0.005 | 22.099 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 88 | ASP | -1 | -0.859 | -0.954 | 20.902 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 89 | PHE | 0 | -0.033 | -0.024 | 19.346 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 90 | THR | 0 | -0.002 | -0.002 | 17.399 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 91 | LEU | 0 | 0.028 | 0.012 | 16.050 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 92 | ALA | 0 | -0.032 | -0.009 | 15.393 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 93 | VAL | 0 | -0.015 | -0.007 | 11.399 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 94 | PHE | 0 | 0.041 | 0.016 | 11.227 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 95 | GLN | 0 | 0.016 | 0.022 | 11.648 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 96 | PRO | 0 | -0.018 | -0.013 | 8.048 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 97 | GLU | -1 | -0.978 | -0.973 | 7.047 | -0.713 | -0.713 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 98 | THR | 0 | -0.076 | -0.047 | 7.402 | -0.257 | -0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 99 | SER | 0 | -0.062 | -0.033 | 6.455 | -0.426 | -0.426 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 100 | THR | 0 | -0.065 | -0.036 | 8.675 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 101 | LEU | 0 | 0.008 | 0.006 | 9.182 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 102 | GLN | 0 | -0.018 | -0.014 | 13.272 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 103 | GLY | 0 | 0.027 | 0.019 | 15.399 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 104 | LEU | 0 | -0.016 | -0.015 | 16.188 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 105 | GLU | -1 | -0.873 | -0.935 | 19.041 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 106 | GLY | 0 | 0.040 | 0.020 | 22.809 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 107 | ARG | 1 | 0.755 | 0.824 | 25.032 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 108 | GLU | -1 | -0.912 | -0.945 | 28.007 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 109 | ASN | 0 | 0.029 | 0.006 | 26.805 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 110 | LEU | 0 | 0.022 | 0.028 | 24.532 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 111 | ALA | 0 | 0.024 | 0.005 | 27.708 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 112 | ARG | 1 | 0.892 | 0.944 | 29.557 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 113 | ASP | -1 | -0.982 | -0.994 | 27.168 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 114 | LEU | 0 | -0.066 | -0.035 | 27.461 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 115 | GLY | 0 | -0.019 | 0.006 | 31.146 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 116 | ILE | 0 | -0.065 | -0.030 | 31.531 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 117 | ILE | 0 | -0.028 | -0.023 | 35.193 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 118 | GLU | -1 | -0.796 | -0.867 | 33.530 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 119 | ALA | 0 | 0.022 | 0.004 | 37.395 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 120 | GLU | -1 | -0.874 | -0.943 | 39.405 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 121 | GLY | 0 | -0.063 | -0.024 | 40.619 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 122 | THR | 0 | -0.021 | -0.025 | 35.504 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 123 | VAL | 0 | -0.011 | -0.008 | 35.032 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 124 | GLY | 0 | -0.027 | -0.007 | 34.911 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 125 | GLY | 0 | -0.027 | -0.014 | 32.981 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 126 | PRO | 0 | 0.006 | 0.029 | 27.924 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 127 | LEU | 0 | 0.059 | 0.006 | 28.045 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 128 | LEU | 0 | -0.003 | -0.010 | 24.780 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 129 | LEU | 0 | -0.037 | -0.014 | 28.668 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 130 | GLU | -1 | -0.853 | -0.932 | 31.906 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 131 | VAL | 0 | -0.028 | -0.020 | 29.574 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 132 | ILE | 0 | -0.013 | -0.010 | 29.814 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 133 | ARG | 1 | 0.887 | 0.942 | 32.976 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 134 | ARG | 1 | 0.834 | 0.918 | 35.799 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 135 | TRP | -1 | -0.959 | -0.941 | 31.868 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |