![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 8988Y
Calculation Name: 1SV4-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1SV4
Chain ID: A
UniProt ID: Q01842
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 78 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -534425.510227 |
---|---|
FMO2-HF: Nuclear repulsion | 502304.665951 |
FMO2-HF: Total energy | -32120.844276 |
FMO2-MP2: Total energy | -32212.626928 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031801/ligand_interaction/ligand_F031801.png)
Ligand Interaction
![ligand interaction](./Kdata/F031801/ligand_interaction/ligand_interaction_F031801.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:42:GLN)
Summations of interaction energy for
fragment #1(A:42:GLN)
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. |
-9.888 | -4.997 | 0.571 | -2.192 | -3.271 | -0.008 |
Interaction energy analysis for fragmet #1(A:42:GLN)
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 | 44 | PRO | 0 | -0.031 | -0.013 | 3.832 | -1.019 | 0.229 | -0.004 | -0.458 | -0.786 | 0.002 |
4 | A | 45 | PRO | 0 | 0.058 | 0.008 | 5.469 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 46 | SER | 0 | -0.046 | -0.014 | 7.977 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 47 | LEU | 0 | -0.038 | -0.002 | 8.483 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 48 | PRO | 0 | 0.002 | 0.009 | 11.198 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 49 | SER | 0 | 0.069 | 0.027 | 11.942 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 50 | ASP | -1 | -0.827 | -0.906 | 12.983 | 0.322 | 0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 51 | PRO | 0 | 0.071 | 0.015 | 13.239 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 52 | ARG | 1 | 0.883 | 0.938 | 15.555 | -0.249 | -0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 53 | LEU | 0 | -0.071 | -0.040 | 18.033 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 54 | TRP | 0 | -0.046 | 0.002 | 11.012 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 55 | SER | 0 | 0.054 | 0.028 | 17.533 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 56 | ARG | 1 | 0.955 | 0.950 | 18.295 | -0.211 | -0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 57 | GLU | -1 | -0.878 | -0.942 | 17.637 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 58 | ASP | -1 | -0.794 | -0.891 | 14.516 | 0.492 | 0.492 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 59 | VAL | 0 | -0.011 | -0.007 | 13.630 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 60 | LEU | 0 | -0.028 | -0.001 | 14.115 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 61 | VAL | 0 | -0.010 | -0.016 | 9.986 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 62 | PHE | 0 | 0.033 | 0.019 | 8.995 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 63 | LEU | 0 | 0.020 | 0.000 | 9.632 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 64 | ARG | 1 | 0.923 | 0.959 | 10.459 | -0.879 | -0.879 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 65 | PHE | 0 | -0.025 | -0.011 | 2.516 | -0.156 | 1.043 | 0.475 | -0.431 | -1.243 | 0.001 |
25 | A | 66 | CYS | 0 | 0.009 | 0.008 | 6.976 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 67 | VAL | 0 | -0.013 | -0.016 | 8.732 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 68 | ARG | 1 | 0.920 | 0.952 | 4.845 | -3.164 | -3.164 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 69 | GLU | -1 | -0.945 | -0.955 | 3.169 | -5.720 | -3.276 | 0.100 | -1.303 | -1.242 | -0.011 |
29 | A | 70 | PHE | 0 | -0.051 | -0.033 | 6.573 | -0.414 | -0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 71 | ASP | -1 | -0.925 | -0.943 | 9.655 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 72 | LEU | 0 | -0.085 | -0.029 | 11.456 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 73 | PRO | 0 | 0.000 | -0.018 | 14.272 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 74 | LYS | 1 | 0.917 | 0.959 | 16.489 | -0.236 | -0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 75 | LEU | 0 | 0.051 | 0.027 | 14.959 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 76 | ASP | -1 | -0.853 | -0.930 | 18.311 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 77 | PHE | 0 | -0.001 | -0.035 | 14.497 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 78 | ASP | -1 | -0.870 | -0.904 | 19.834 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 79 | LEU | 0 | -0.070 | -0.027 | 22.336 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 80 | PHE | 0 | 0.002 | -0.005 | 18.728 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 81 | GLN | 0 | -0.024 | 0.001 | 20.247 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 82 | MET | 0 | -0.118 | -0.061 | 20.529 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 83 | ASN | 0 | 0.009 | 0.006 | 20.342 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 84 | GLY | 0 | 0.100 | 0.036 | 17.939 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 85 | LYS | 1 | 0.959 | 0.985 | 18.747 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 86 | ARG | 1 | 0.901 | 0.942 | 21.864 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 87 | LEU | 0 | 0.052 | 0.036 | 15.105 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 88 | CYS | 0 | -0.030 | -0.014 | 17.757 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 89 | LEU | 0 | -0.088 | -0.043 | 19.405 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 90 | LEU | 0 | -0.072 | -0.009 | 19.696 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 91 | THR | 0 | 0.006 | -0.024 | 21.556 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 92 | ARG | 1 | 0.978 | 0.982 | 20.749 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 93 | ALA | 0 | 0.003 | -0.010 | 21.807 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 94 | ASP | -1 | -0.803 | -0.851 | 23.267 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 95 | PHE | 0 | -0.001 | -0.010 | 16.431 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 96 | GLY | 0 | -0.018 | -0.009 | 20.755 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 97 | HIS | 0 | -0.072 | -0.062 | 22.687 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 98 | ARG | 1 | 0.856 | 0.923 | 21.492 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 99 | CYS | 0 | -0.029 | 0.004 | 17.116 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 100 | PRO | 0 | 0.019 | 0.007 | 20.652 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 101 | GLY | 0 | -0.025 | 0.001 | 20.564 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 102 | ALA | 0 | 0.052 | 0.005 | 15.597 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 103 | GLY | 0 | 0.027 | 0.018 | 16.183 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 104 | ASP | -1 | -0.883 | -0.959 | 17.109 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 105 | VAL | 0 | 0.029 | 0.028 | 11.649 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 106 | LEU | 0 | -0.008 | 0.003 | 12.445 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 107 | HIS | 0 | -0.003 | -0.003 | 13.403 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 108 | ASN | 0 | -0.003 | -0.009 | 13.460 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 109 | VAL | 0 | 0.057 | 0.019 | 8.053 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 110 | LEU | 0 | -0.007 | -0.005 | 10.969 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 111 | GLN | 0 | 0.000 | -0.006 | 12.869 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 112 | MET | 0 | -0.033 | -0.018 | 9.977 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 113 | LEU | 0 | 0.045 | 0.038 | 7.884 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 114 | ILE | 0 | -0.028 | -0.018 | 11.766 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 115 | ILE | 0 | -0.056 | -0.027 | 15.227 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 116 | GLU | -1 | -0.968 | -0.986 | 9.431 | 1.211 | 1.211 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 117 | SER | 0 | -0.086 | -0.038 | 13.697 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 118 | HIS | 0 | -0.069 | -0.029 | 15.417 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 119 | SER | 0 | -0.034 | -0.007 | 16.412 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |