FMODB ID: JLVM9
Calculation Name: 4DS1-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4DS1
Chain ID: A
UniProt ID: Q02647
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 | OptHSide |
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 | 86 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -604653.991736 |
---|---|
FMO2-HF: Nuclear repulsion | 571535.814767 |
FMO2-HF: Total energy | -33118.17697 |
FMO2-MP2: Total energy | -33218.227425 |
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:7:SER)
Summations of interaction energy for
fragment #1(A:7:SER)
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. |
-1.842 | 0.858 | 0.146 | -1.148 | -1.7 | 0 |
Interaction energy analysis for fragmet #1(A:7:SER)
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 | 9 | PRO | 0 | 0.006 | 0.002 | 3.800 | -2.557 | -1.111 | -0.008 | -0.617 | -0.821 | 0.002 |
4 | A | 10 | ILE | 0 | -0.018 | 0.001 | 5.258 | 0.656 | 0.656 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 11 | VAL | 0 | 0.009 | -0.007 | 7.745 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 12 | LYS | 1 | 0.888 | 0.958 | 9.558 | 0.822 | 0.822 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | ALA | 0 | 0.024 | 0.009 | 13.402 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | SER | 0 | -0.023 | -0.020 | 16.289 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | ASP | -1 | -0.845 | -0.913 | 18.435 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | ILE | 0 | -0.049 | -0.013 | 17.640 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | THR | 0 | 0.035 | 0.016 | 21.113 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | ASP | -1 | -0.761 | -0.895 | 18.060 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | LYS | 1 | 0.961 | 0.982 | 17.706 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | LEU | 0 | -0.008 | 0.005 | 18.465 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | LYS | 1 | 0.851 | 0.919 | 14.157 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | GLU | -1 | -0.831 | -0.915 | 12.924 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | ASP | -1 | -0.790 | -0.836 | 13.503 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | ILE | 0 | 0.020 | 0.008 | 13.496 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | LEU | 0 | -0.022 | 0.006 | 9.140 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | THR | 0 | -0.033 | -0.028 | 9.848 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | ILE | 0 | -0.016 | -0.013 | 11.169 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | SER | 0 | -0.019 | -0.031 | 10.139 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | LYS | 1 | 0.927 | 0.956 | 4.410 | -1.338 | -1.253 | -0.001 | -0.008 | -0.076 | 0.000 |
24 | A | 30 | ASP | -1 | -0.794 | -0.863 | 7.928 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | ALA | 0 | -0.008 | -0.007 | 10.723 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | LEU | 0 | -0.039 | -0.036 | 6.020 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | ASP | -1 | -0.926 | -0.939 | 8.325 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | LYS | 1 | 0.750 | 0.856 | 10.500 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | TYR | 0 | -0.045 | -0.022 | 13.277 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | GLN | 0 | 0.048 | 0.021 | 13.261 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | LEU | 0 | -0.036 | -0.009 | 14.836 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | GLU | -1 | -0.807 | -0.910 | 13.152 | -0.596 | -0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | ARG | 1 | 0.873 | 0.909 | 15.203 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | ASP | -1 | -0.818 | -0.886 | 17.733 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | ILE | 0 | 0.029 | 0.026 | 11.085 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | ALA | 0 | 0.008 | -0.004 | 14.867 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | GLY | 0 | -0.016 | -0.013 | 16.641 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | THR | 0 | -0.008 | -0.005 | 15.791 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | VAL | 0 | 0.045 | 0.028 | 13.732 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | LYS | 1 | 0.784 | 0.860 | 17.045 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | LYS | 1 | 0.943 | 0.963 | 20.240 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | GLN | 0 | 0.013 | 0.007 | 16.461 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | LEU | 0 | -0.012 | -0.004 | 17.433 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | ASP | -1 | -0.754 | -0.868 | 21.449 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | VAL | 0 | -0.049 | -0.014 | 24.329 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | LYS | 1 | 0.815 | 0.909 | 19.022 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | TYR | 0 | -0.105 | -0.100 | 19.957 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | GLY | 0 | 0.032 | 0.039 | 25.457 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | ASN | 0 | -0.027 | -0.007 | 26.384 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | THR | 0 | -0.034 | -0.048 | 26.888 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | TRP | 0 | 0.009 | -0.001 | 19.928 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | HIS | 0 | -0.017 | -0.008 | 21.875 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | VAL | 0 | -0.013 | -0.010 | 15.820 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | ILE | 0 | -0.017 | 0.003 | 17.117 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | VAL | 0 | 0.010 | 0.005 | 11.561 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | GLY | 0 | 0.048 | 0.028 | 13.079 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | LYS | 1 | 0.900 | 0.927 | 11.106 | 0.627 | 0.627 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | ASN | 0 | -0.064 | -0.033 | 13.629 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | PHE | 0 | 0.028 | 0.023 | 14.756 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | GLY | 0 | 0.038 | 0.036 | 18.570 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | SER | 0 | -0.035 | -0.037 | 20.878 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | TYR | 0 | 0.028 | 0.021 | 22.539 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | VAL | 0 | -0.012 | 0.006 | 22.314 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | THR | 0 | 0.013 | 0.006 | 25.461 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | HIS | 1 | 0.834 | 0.916 | 23.872 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | GLU | -1 | -0.825 | -0.906 | 26.029 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | LYS | 1 | 1.004 | 1.001 | 25.789 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | GLY | 0 | -0.027 | -0.011 | 24.258 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 75 | HIS | 1 | 0.839 | 0.914 | 22.133 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | PHE | 0 | 0.035 | 0.003 | 19.094 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | VAL | 0 | 0.012 | 0.008 | 14.101 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | TYR | 0 | 0.029 | 0.017 | 14.518 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | PHE | 0 | 0.012 | 0.002 | 8.493 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | TYR | 0 | 0.015 | 0.011 | 6.712 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 81 | ILE | 0 | 0.016 | 0.017 | 3.170 | -0.632 | -0.298 | 0.077 | -0.148 | -0.264 | -0.001 |
76 | A | 82 | GLY | 0 | 0.023 | 0.014 | 3.192 | -0.249 | 0.530 | 0.074 | -0.329 | -0.524 | -0.001 |
77 | A | 83 | PRO | 0 | -0.011 | -0.017 | 4.015 | 0.380 | 0.436 | 0.004 | -0.046 | -0.015 | 0.000 |
78 | A | 84 | LEU | 0 | -0.038 | -0.004 | 6.780 | 0.336 | 0.336 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 85 | ALA | 0 | 0.012 | 0.014 | 8.180 | -0.206 | -0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 86 | PHE | 0 | 0.053 | 0.004 | 7.784 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 87 | LEU | 0 | -0.020 | -0.005 | 12.315 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 88 | VAL | 0 | 0.008 | 0.006 | 14.648 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 89 | PHE | 0 | 0.009 | -0.013 | 17.351 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 90 | LYS | 1 | 0.849 | 0.933 | 20.942 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 91 | THR | 0 | 0.030 | 0.027 | 24.229 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 92 | ALA | 0 | 0.050 | 0.046 | 27.818 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |