FMODB ID: 4NMMN
Calculation Name: 2XG8-F-Xray316
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2XG8
Chain ID: F
UniProt ID: P0A3F4
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 | 82 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -503876.550695 |
---|---|
FMO2-HF: Nuclear repulsion | 470891.251686 |
FMO2-HF: Total energy | -32985.299009 |
FMO2-MP2: Total energy | -33082.662397 |
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(F:2:ACE )
Summations of interaction energy for
fragment #1(F:2: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. |
-0.504 | 0.465 | -0.005 | -0.394 | -0.57 | -0.001 |
Interaction energy analysis for fragmet #1(F:2: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 | F | 4 | GLU | -1 | -0.883 | -0.886 | 3.840 | 0.180 | 1.149 | -0.005 | -0.394 | -0.570 | -0.001 |
4 | F | 5 | ASN | 0 | 0.023 | 0.008 | 6.618 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | F | 6 | TYR | 0 | -0.064 | -0.069 | 9.316 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | F | 7 | LEU | 0 | 0.008 | -0.002 | 13.212 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | F | 8 | ASN | 0 | 0.010 | -0.001 | 16.749 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | F | 9 | HIS | 0 | -0.010 | -0.003 | 20.223 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | F | 10 | PRO | 0 | -0.003 | -0.012 | 22.489 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | F | 11 | THR | 0 | -0.029 | 0.002 | 25.906 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | F | 12 | PHE | 0 | -0.027 | -0.029 | 22.908 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | F | 13 | GLY | 0 | 0.047 | 0.042 | 22.243 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | F | 14 | LEU | 0 | 0.005 | 0.014 | 15.523 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | F | 15 | LEU | 0 | -0.039 | -0.023 | 16.222 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | F | 16 | TYR | 0 | 0.011 | -0.007 | 10.827 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | F | 17 | GLN | 0 | 0.010 | 0.003 | 8.573 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | F | 18 | ILE | 0 | -0.074 | -0.025 | 9.137 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | F | 19 | CYS | 0 | -0.038 | -0.030 | 8.862 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | F | 20 | SER | 0 | 0.049 | 0.016 | 9.924 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | F | 21 | PHE | 0 | -0.050 | -0.042 | 11.693 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | F | 22 | GLY | 0 | 0.007 | 0.016 | 14.920 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | F | 23 | ASP | -1 | -0.943 | -0.973 | 14.100 | -0.127 | -0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | F | 24 | SER | 0 | -0.003 | -0.009 | 16.315 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | F | 25 | LYS | 1 | 0.937 | 0.992 | 17.384 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | F | 26 | GLU | -1 | -0.895 | -0.945 | 11.664 | -0.448 | -0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | F | 27 | LEU | 0 | -0.037 | -0.007 | 13.455 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | F | 28 | PHE | 0 | 0.028 | 0.006 | 12.611 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | F | 29 | ALA | 0 | -0.007 | -0.006 | 14.850 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | F | 30 | THR | 0 | -0.014 | -0.020 | 16.408 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | F | 31 | LEU | 0 | 0.019 | 0.003 | 14.353 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | F | 32 | TYR | 0 | 0.029 | 0.021 | 17.564 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | F | 33 | ALA | 0 | 0.032 | 0.032 | 21.184 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | F | 34 | GLN | 0 | -0.019 | -0.005 | 20.405 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | F | 35 | ARG | 1 | 0.912 | 0.941 | 16.848 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | F | 36 | LEU | 0 | -0.069 | -0.003 | 21.025 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | F | 37 | PHE | 0 | 0.004 | -0.006 | 16.532 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | F | 38 | PHE | 0 | 0.012 | -0.008 | 18.376 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | F | 39 | LEU | 0 | 0.007 | 0.006 | 17.829 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | F | 40 | VAL | 0 | 0.000 | 0.002 | 17.031 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | F | 41 | ALA | 0 | 0.035 | 0.001 | 18.218 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | F | 42 | PHE | 0 | -0.031 | -0.015 | 16.706 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | F | 43 | ASP | -1 | -0.757 | -0.844 | 22.040 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | F | 44 | ALA | 0 | -0.084 | -0.024 | 24.950 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | F | 45 | ARG | 1 | 0.971 | 0.983 | 25.699 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | F | 46 | GLY | 0 | 0.030 | -0.003 | 26.668 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | F | 47 | THR | 0 | -0.034 | -0.016 | 20.797 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | F | 48 | ARG | 1 | 0.927 | 0.948 | 23.059 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | F | 49 | PHE | 0 | 0.024 | -0.005 | 21.632 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | F | 50 | GLU | -1 | -0.918 | -0.954 | 22.485 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | F | 51 | PRO | 0 | -0.008 | 0.011 | 22.619 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | F | 52 | ILE | 0 | 0.020 | 0.009 | 19.522 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | F | 53 | GLY | 0 | 0.038 | 0.015 | 22.835 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | F | 54 | ARG | 1 | 1.003 | 0.982 | 20.746 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | F | 55 | ASN | 0 | 0.006 | -0.001 | 21.395 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | F | 56 | GLU | -1 | -0.831 | -0.895 | 22.357 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | F | 57 | ALA | 0 | 0.031 | 0.007 | 18.090 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | F | 58 | ARG | 1 | 0.872 | 0.924 | 17.969 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | F | 59 | MET | 0 | 0.028 | 0.020 | 18.631 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | F | 60 | LEU | 0 | -0.004 | -0.004 | 17.869 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | F | 61 | VAL | 0 | 0.009 | -0.001 | 12.788 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | F | 62 | ASP | -1 | -0.840 | -0.912 | 14.832 | 0.162 | 0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | F | 63 | ASN | 0 | -0.058 | -0.039 | 17.012 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | F | 64 | ARG | 1 | 0.954 | 0.998 | 11.013 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | F | 65 | LEU | 0 | 0.015 | -0.029 | 11.663 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | F | 66 | ARG | 1 | 0.862 | 0.931 | 13.961 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | F | 67 | GLN | 0 | 0.027 | 0.015 | 15.055 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | F | 68 | LEU | 0 | -0.054 | 0.013 | 9.181 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | F | 69 | ARG | 1 | 0.917 | 0.947 | 12.228 | -0.298 | -0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | F | 70 | ARG | 1 | 0.935 | 0.976 | 13.571 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | F | 71 | NME | 0 | 0.006 | 0.013 | 15.474 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | F | 78 | ACE | 0 | 0.034 | 0.009 | 19.855 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | F | 79 | GLN | 0 | -0.011 | -0.024 | 20.706 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | F | 80 | LEU | 0 | 0.068 | 0.037 | 21.830 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | F | 81 | GLN | 0 | 0.026 | 0.016 | 23.184 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | F | 82 | GLN | 0 | 0.000 | 0.002 | 24.937 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | F | 83 | VAL | 0 | 0.064 | 0.018 | 26.943 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | F | 84 | PHE | 0 | -0.019 | -0.016 | 27.032 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | F | 85 | LYS | 1 | 0.893 | 0.951 | 28.180 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | F | 86 | GLN | 0 | 0.012 | 0.019 | 30.872 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | F | 87 | THR | 0 | -0.061 | -0.032 | 31.946 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | F | 88 | PHE | 0 | -0.079 | -0.047 | 30.486 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | F | 89 | LEU | -1 | -0.928 | -0.933 | 31.606 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |