![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: Z672N
Calculation Name: 4XVV-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4XVV
Chain ID: A
UniProt ID: A6TE95
Base Structure: X-ray
Registration Date: 2023-06-22
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 | OptH |
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 | 76 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -489891.393181 |
---|---|
FMO2-HF: Nuclear repulsion | 458102.109115 |
FMO2-HF: Total energy | -31789.284066 |
FMO2-MP2: Total energy | -31877.110084 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F026416/ligand_interaction/ligand_F026416.png)
Ligand Interaction
![ligand interaction](./Kdata/F026416/ligand_interaction/ligand_interaction_F026416.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. |
-10.918 | -5.274 | 1.093 | -3.364 | -3.371 | -0.019 |
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 | 27 | GLU | -1 | -0.895 | -0.946 | 3.311 | -2.592 | -0.181 | 0.014 | -1.251 | -1.174 | 0.006 |
4 | A | 28 | GLU | -1 | -0.907 | -0.953 | 2.519 | -11.099 | -7.986 | 1.080 | -2.104 | -2.088 | -0.025 |
5 | A | 29 | THR | 0 | -0.106 | -0.041 | 5.240 | 1.333 | 1.453 | -0.001 | -0.009 | -0.109 | 0.000 |
6 | A | 30 | THR | 0 | -0.082 | -0.041 | 7.841 | 0.858 | 0.858 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 31 | PRO | 0 | 0.052 | -0.001 | 9.537 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 32 | GLN | 0 | 0.029 | 0.028 | 9.393 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 33 | ASN | 0 | -0.040 | -0.048 | 7.810 | 0.478 | 0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 34 | MET | 0 | 0.022 | 0.048 | 11.346 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 35 | THR | 0 | -0.008 | -0.008 | 13.672 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 36 | CYS | 0 | -0.039 | -0.028 | 17.060 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 37 | GLN | 0 | -0.046 | -0.025 | 20.420 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 38 | GLU | -1 | -0.834 | -0.920 | 14.910 | -0.785 | -0.785 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 39 | PHE | 0 | -0.009 | -0.020 | 18.880 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 40 | MET | 0 | -0.091 | -0.045 | 19.976 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 41 | ASP | -1 | -0.858 | -0.912 | 21.582 | -0.326 | -0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 42 | MET | 0 | -0.077 | -0.008 | 18.459 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 43 | ASN | 0 | -0.007 | -0.013 | 21.153 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 44 | PRO | 0 | 0.105 | 0.018 | 22.574 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 45 | LYS | 1 | 0.913 | 0.954 | 23.896 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 46 | SER | 0 | 0.005 | 0.012 | 18.785 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 47 | MET | 0 | -0.032 | 0.002 | 20.178 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 48 | THR | 0 | 0.085 | 0.026 | 21.934 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 49 | PRO | 0 | -0.005 | -0.005 | 19.052 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 50 | VAL | 0 | 0.020 | 0.017 | 16.193 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 51 | ALA | 0 | 0.049 | 0.008 | 18.257 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 52 | PHE | 0 | 0.014 | 0.005 | 19.265 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 53 | TRP | 0 | 0.006 | 0.011 | 11.593 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 54 | VAL | 0 | 0.009 | 0.003 | 17.075 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 55 | VAL | 0 | -0.044 | -0.010 | 18.351 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 56 | ASN | 0 | -0.003 | -0.010 | 19.724 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 57 | ARG | 1 | 0.862 | 0.956 | 12.116 | 0.566 | 0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 58 | ASN | 0 | -0.092 | -0.049 | 15.446 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 59 | THR | 0 | -0.042 | -0.024 | 17.423 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 60 | ASP | -1 | -0.847 | -0.927 | 20.923 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 61 | PHE | 0 | -0.017 | -0.030 | 18.642 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 62 | SER | 0 | -0.045 | -0.014 | 23.889 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 63 | GLY | 0 | -0.016 | -0.002 | 26.494 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 64 | GLY | 0 | -0.039 | -0.016 | 28.012 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 65 | ASP | -1 | -0.956 | -0.950 | 26.515 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 66 | TYR | 0 | -0.025 | -0.012 | 23.880 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 67 | VAL | 0 | -0.026 | 0.004 | 24.717 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 68 | ASP | -1 | -0.791 | -0.901 | 25.228 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 69 | TRP | 0 | 0.004 | -0.025 | 20.646 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 70 | HIS | 0 | 0.041 | 0.024 | 26.954 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 71 | GLU | -1 | -0.903 | -0.933 | 28.984 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 72 | VAL | 0 | -0.029 | -0.026 | 23.407 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 73 | GLU | -1 | -0.962 | -0.985 | 26.686 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 74 | THR | 0 | -0.076 | -0.061 | 28.201 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 75 | VAL | 0 | -0.013 | 0.008 | 30.102 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 76 | SER | 0 | -0.013 | -0.017 | 25.135 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 77 | VAL | 0 | 0.017 | 0.021 | 24.470 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 78 | PRO | 0 | 0.008 | 0.001 | 26.440 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 79 | LYS | 1 | 0.860 | 0.956 | 27.741 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 80 | MET | 0 | 0.022 | 0.010 | 19.830 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 81 | LEU | 0 | 0.021 | 0.015 | 25.092 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 82 | GLN | 0 | -0.039 | -0.003 | 26.800 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 83 | GLU | -1 | -0.940 | -0.983 | 25.466 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 85 | HIS | 0 | -0.006 | -0.033 | 24.803 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 86 | LYS | 1 | 0.850 | 0.946 | 28.059 | 0.182 | 0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 87 | ASN | 0 | -0.008 | -0.012 | 23.679 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 88 | PRO | 0 | 0.077 | 0.038 | 23.286 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 89 | ALA | 0 | -0.003 | -0.001 | 20.616 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 90 | ALA | 0 | -0.045 | -0.006 | 19.357 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 91 | LYS | 1 | 0.996 | 0.999 | 13.522 | 0.402 | 0.402 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 92 | LEU | 0 | 0.037 | -0.002 | 15.507 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 93 | GLY | 0 | -0.044 | -0.012 | 14.077 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 94 | ASP | -1 | -0.954 | -0.967 | 14.967 | -0.276 | -0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 95 | LEU | 0 | -0.049 | -0.033 | 18.247 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 96 | SER | 0 | -0.009 | -0.036 | 18.568 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 97 | ALA | 0 | -0.010 | -0.009 | 20.785 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 98 | VAL | 0 | -0.006 | -0.002 | 23.791 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 99 | ILE | 0 | -0.004 | -0.001 | 22.979 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 100 | LYS | 1 | 0.994 | 1.001 | 22.218 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 101 | LYS | 1 | 0.933 | 0.989 | 26.214 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |