![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: XV2L1
Calculation Name: 2NLV-A-Xray13
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2NLV
Chain ID: A
UniProt ID: Q3M6F6
Base Structure: X-ray
Registration Date: 2018-03-01
Reference:
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE. |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20181228 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 116 |
LigandCharge | CL-=-1 |
Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
FMO2-HF: Electronic energy | -959297.557826 |
---|---|
FMO2-HF: Nuclear repulsion | 910951.490587 |
FMO2-HF: Total energy | -48346.067238 |
FMO2-MP2: Total energy | -48481.292176 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F000698/ligand_interaction/ligand_F000698.png)
Ligand Interaction
![ligand interaction](./Kdata/F000698/ligand_interaction/ligand_interaction_F000698.png)
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:0:GLY)
Summations of interaction energy for
fragment #1(A:0:GLY)
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. |
-63.347 | -60.664 | 0.993 | -1.291 | -2.384 | -0.009 |
Interaction energy analysis for fragmet #1(A:0:GLY)
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 | 2 | ASP | -1 | -0.842 | -0.916 | 3.801 | -40.485 | -39.267 | -0.004 | -0.466 | -0.748 | -0.002 |
4 | A | 3 | LYS | 1 | 0.880 | 0.947 | 2.452 | 67.564 | 68.702 | 0.998 | -0.727 | -1.409 | -0.007 |
5 | A | 4 | LEU | 0 | 0.028 | 0.026 | 4.122 | 6.881 | 7.208 | -0.001 | -0.098 | -0.227 | 0.000 |
6 | A | 5 | VAL | 0 | 0.057 | 0.019 | 5.683 | 6.190 | 6.190 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | LYS | 1 | 0.961 | 0.987 | 7.686 | 37.528 | 37.528 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | TYR | 0 | -0.056 | -0.078 | 7.192 | 3.059 | 3.059 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | GLN | 0 | -0.026 | -0.023 | 9.670 | 2.547 | 2.547 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | GLU | -1 | -0.944 | -0.968 | 11.711 | -18.511 | -18.511 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | LEU | 0 | -0.049 | -0.015 | 11.996 | 2.002 | 2.002 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | VAL | 0 | 0.008 | 0.012 | 13.349 | 1.579 | 1.579 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | LYS | 1 | 0.957 | 0.982 | 15.031 | 21.840 | 21.840 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | LYS | 1 | 0.961 | 1.001 | 17.410 | 17.111 | 17.111 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | LEU | 0 | -0.031 | 0.004 | 18.519 | 1.073 | 1.073 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | LEU | 0 | 0.019 | 0.001 | 19.091 | 0.812 | 0.812 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | THR | 0 | 0.009 | -0.001 | 21.490 | 0.810 | 0.810 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | ASN | 0 | -0.059 | -0.027 | 23.055 | 0.600 | 0.600 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | TYR | 0 | -0.048 | -0.089 | 22.507 | 0.481 | 0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | ALA | 0 | 0.030 | 0.017 | 25.679 | 0.442 | 0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | SER | 0 | -0.085 | -0.046 | 27.494 | 0.499 | 0.499 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | ASP | -1 | -0.933 | -0.948 | 29.338 | -10.322 | -10.322 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | ASP | -1 | -0.886 | -0.940 | 31.098 | -9.378 | -9.378 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | VAL | 0 | -0.038 | -0.016 | 32.529 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | SER | 0 | -0.136 | -0.072 | 35.179 | 0.361 | 0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | ASP | -1 | -0.824 | -0.930 | 37.067 | -7.532 | -7.532 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | GLN | 0 | -0.067 | -0.044 | 38.647 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | ASP | -1 | -0.944 | -0.947 | 40.024 | -7.486 | -7.486 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | VAL | 0 | -0.123 | -0.082 | 35.227 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | GLU | -1 | -0.858 | -0.915 | 33.291 | -9.479 | -9.479 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | VAL | 0 | -0.025 | -0.020 | 29.135 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | GLN | 0 | -0.009 | -0.008 | 28.123 | -0.390 | -0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | LEU | 0 | -0.005 | -0.014 | 22.980 | -0.425 | -0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | ILE | 0 | -0.018 | 0.004 | 22.464 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | LEU | 0 | -0.018 | -0.025 | 18.774 | -0.975 | -0.975 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | ASP | -1 | -0.785 | -0.870 | 17.878 | -17.205 | -17.205 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | THR | 0 | 0.036 | -0.031 | 14.380 | -0.600 | -0.600 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | GLU | -1 | -0.954 | -0.945 | 13.398 | -20.404 | -20.404 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | ARG | 1 | 0.787 | 0.863 | 13.645 | 15.733 | 15.733 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASN | 0 | -0.002 | 0.029 | 10.270 | -0.652 | -0.652 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | HIS | 1 | 0.858 | 0.910 | 13.869 | 18.020 | 18.020 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | TYR | 0 | -0.020 | -0.017 | 12.655 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | GLN | 0 | 0.033 | -0.002 | 18.654 | 0.453 | 0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | TRP | 0 | 0.033 | 0.029 | 22.221 | -0.230 | -0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | MET | 0 | -0.037 | -0.015 | 25.150 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | ASN | 0 | -0.042 | -0.004 | 28.373 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | VAL | 0 | -0.010 | -0.017 | 31.392 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | GLY | 0 | 0.026 | 0.016 | 34.171 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | TRP | 0 | -0.050 | -0.027 | 37.945 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | GLN | 0 | 0.110 | 0.071 | 39.976 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | GLY | 0 | 0.033 | 0.012 | 43.336 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | LEU | 0 | -0.040 | -0.038 | 45.561 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | ASN | 0 | -0.052 | -0.019 | 42.842 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | ARG | 1 | 0.908 | 0.967 | 36.238 | 8.604 | 8.604 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | ILE | 0 | -0.025 | -0.008 | 35.348 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | TYR | 0 | -0.011 | -0.020 | 30.198 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | ARG | 1 | 0.937 | 0.979 | 31.443 | 9.856 | 9.856 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | CYS | 0 | -0.025 | -0.006 | 25.235 | -0.294 | -0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | VAL | 0 | -0.008 | 0.005 | 27.442 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | ILE | 0 | 0.035 | 0.012 | 21.139 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | HIS | 0 | -0.012 | -0.018 | 18.972 | 0.608 | 0.608 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | PHE | 0 | 0.010 | -0.006 | 15.631 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | ASP | -1 | -0.792 | -0.864 | 14.891 | -17.534 | -17.534 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | ILE | 0 | -0.043 | -0.020 | 8.377 | -1.101 | -1.101 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | LYS | 1 | 0.880 | 0.945 | 10.783 | 19.784 | 19.784 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | ASP | -1 | -0.884 | -0.939 | 8.152 | -28.747 | -28.747 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | GLY | 0 | -0.088 | -0.048 | 5.200 | -3.960 | -3.960 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | LYS | 1 | 0.882 | 0.955 | 6.107 | 25.341 | 25.341 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 68 | ILE | 0 | 0.003 | 0.003 | 9.202 | 1.228 | 1.228 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | TRP | 0 | 0.003 | 0.004 | 11.993 | 1.709 | 1.709 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | LEU | 0 | 0.008 | 0.002 | 15.247 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 71 | GLN | 0 | -0.038 | -0.048 | 18.064 | 0.793 | 0.793 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 72 | GLN | 0 | 0.011 | 0.006 | 20.980 | 0.504 | 0.504 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 73 | ASN | 0 | 0.020 | 0.002 | 23.272 | -0.408 | -0.408 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 74 | LEU | 0 | -0.077 | -0.016 | 25.542 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 75 | THR | 0 | -0.043 | -0.033 | 26.873 | 0.369 | 0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 76 | ASP | -1 | -0.919 | -0.952 | 29.357 | -9.957 | -9.957 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 77 | ARG | 1 | 0.861 | 0.909 | 23.997 | 12.641 | 12.641 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 78 | ASN | 0 | -0.010 | -0.013 | 23.074 | -0.553 | -0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 79 | PRO | 0 | 0.067 | 0.025 | 20.362 | -0.444 | -0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 80 | ALA | 0 | 0.000 | 0.004 | 18.329 | -0.873 | -0.873 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 81 | GLU | -1 | -0.767 | -0.826 | 18.432 | -15.745 | -15.745 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 82 | GLU | -1 | -0.783 | -0.843 | 20.448 | -13.752 | -13.752 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 83 | LEU | 0 | 0.020 | -0.005 | 14.653 | -0.632 | -0.632 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 84 | VAL | 0 | -0.012 | 0.005 | 15.732 | -1.019 | -1.019 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 85 | MET | 0 | -0.080 | -0.019 | 17.031 | -0.310 | -0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 86 | MET | 0 | -0.077 | -0.044 | 16.233 | 0.349 | 0.349 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 87 | GLY | 0 | -0.033 | -0.011 | 13.726 | -1.168 | -1.168 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 88 | VAL | 0 | -0.073 | -0.043 | 10.784 | -2.521 | -2.521 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 89 | PRO | 0 | -0.005 | 0.012 | 9.463 | 1.966 | 1.966 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 90 | ARG | 1 | 0.916 | 0.937 | 12.642 | 15.428 | 15.428 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 91 | GLU | -1 | -0.879 | -0.955 | 11.596 | -23.035 | -23.035 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 92 | ASP | -1 | -0.882 | -0.914 | 7.748 | -38.984 | -38.984 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 93 | ILE | 0 | -0.027 | -0.011 | 10.831 | -0.731 | -0.731 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 94 | VAL | 0 | 0.043 | 0.023 | 13.290 | 0.808 | 0.808 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 95 | LEU | 0 | -0.009 | -0.017 | 15.878 | 0.342 | 0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 96 | GLY | 0 | 0.036 | 0.023 | 18.878 | 0.579 | 0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 97 | LEU | 0 | -0.015 | 0.001 | 20.133 | 0.594 | 0.594 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 98 | GLN | 0 | -0.055 | -0.026 | 22.728 | 1.030 | 1.030 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 99 | ALA | 0 | 0.007 | 0.000 | 23.518 | -0.315 | -0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 100 | PRO | 0 | 0.076 | 0.018 | 22.420 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 101 | TYR | 0 | -0.004 | 0.001 | 23.002 | -0.269 | -0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 102 | LYS | 1 | 0.949 | 0.975 | 25.173 | 11.573 | 11.573 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 103 | ARG | 1 | 0.822 | 0.895 | 18.987 | 15.349 | 15.349 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 104 | GLN | 0 | 0.005 | 0.012 | 20.178 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 105 | TYR | 0 | -0.081 | -0.035 | 21.200 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 106 | THR | 0 | -0.104 | -0.059 | 20.562 | 0.386 | 0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 107 | ASP | -1 | -0.887 | -0.938 | 21.394 | -13.533 | -13.533 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 108 | TYR | 0 | -0.138 | -0.136 | 16.771 | -0.276 | -0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 109 | GLY | 0 | 0.019 | 0.020 | 14.673 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 110 | VAL | 0 | -0.063 | -0.029 | 14.814 | 1.167 | 1.167 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 111 | ALA | -1 | -0.862 | -0.952 | 12.441 | -25.613 | -25.613 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 112 | CL- | -1 | -0.893 | -0.922 | 17.941 | -17.536 | -17.536 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 113 | CL- | -1 | -0.858 | -0.912 | 30.013 | -10.753 | -10.753 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 114 | CL- | -1 | -0.870 | -0.913 | 21.208 | -14.966 | -14.966 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 115 | CL- | -1 | -0.902 | -0.944 | 28.504 | -11.473 | -11.473 | 0.000 | 0.000 | 0.000 | 0.000 |