![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: Z641N
Calculation Name: 3ECY-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3ECY
Chain ID: A
UniProt ID: Q9V3I1
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 | OptAll |
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 | 119 |
LigandCharge | CYM=-1 |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -871802.723431 |
---|---|
FMO2-HF: Nuclear repulsion | 826196.530896 |
FMO2-HF: Total energy | -45606.192535 |
FMO2-MP2: Total energy | -45740.077098 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F030011/ligand_interaction/ligand_F030011.png)
Ligand Interaction
![ligand interaction](./Kdata/F030011/ligand_interaction/ligand_interaction_F030011.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:19:THR)
Summations of interaction energy for
fragment #1(A:19:THR)
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. |
-4.598 | -0.563 | 1.377 | -1.998 | -3.415 | -0.001 |
Interaction energy analysis for fragmet #1(A:19:THR)
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 | 21 | VAL | 0 | -0.013 | -0.010 | 2.382 | 0.594 | 2.124 | 0.937 | -0.701 | -1.766 | -0.002 |
4 | A | 22 | LEU | 0 | -0.014 | 0.004 | 4.747 | 0.090 | 0.129 | -0.001 | -0.008 | -0.031 | 0.000 |
5 | A | 23 | ARG | 1 | 0.793 | 0.884 | 2.649 | 1.288 | 2.685 | 0.409 | -0.740 | -1.067 | 0.006 |
6 | A | 24 | PHE | 0 | 0.021 | -0.009 | 9.367 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 25 | ALA | 0 | 0.003 | 0.005 | 13.103 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 26 | LYS | 1 | 0.818 | 0.903 | 15.590 | 0.207 | 0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 27 | LEU | 0 | -0.027 | -0.016 | 19.413 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 28 | THR | 0 | -0.024 | -0.027 | 21.676 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 29 | GLU | -1 | -0.857 | -0.936 | 23.742 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 30 | ASN | 0 | -0.054 | -0.030 | 25.837 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 31 | ALA | 0 | 0.024 | 0.022 | 21.545 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 32 | LEU | 0 | -0.058 | -0.022 | 22.392 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 33 | GLU | -1 | -0.810 | -0.906 | 17.887 | -0.257 | -0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 34 | PRO | 0 | -0.031 | 0.011 | 16.120 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 35 | VAL | 0 | -0.028 | -0.022 | 16.831 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 36 | ARG | 1 | 0.881 | 0.934 | 17.055 | 0.299 | 0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 37 | GLY | 0 | 0.048 | 0.034 | 19.519 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 38 | SER | 0 | -0.015 | -0.024 | 22.443 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 39 | ALA | 0 | 0.043 | 0.014 | 21.901 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 40 | LYS | 1 | 0.940 | 0.958 | 21.624 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 41 | ALA | 0 | -0.012 | 0.020 | 21.118 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 42 | ALA | 0 | 0.055 | 0.024 | 19.496 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 43 | GLY | 0 | 0.055 | 0.034 | 17.133 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 44 | VAL | 0 | -0.083 | -0.041 | 15.521 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 45 | ASP | -1 | -0.819 | -0.912 | 18.358 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 46 | LEU | 0 | -0.008 | 0.002 | 18.198 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 47 | ARG | 1 | 0.895 | 0.919 | 21.818 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 48 | SER | 0 | -0.010 | -0.006 | 24.480 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 49 | ALA | 0 | 0.036 | 0.015 | 25.147 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 50 | TYR | 0 | -0.040 | -0.026 | 26.952 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 51 | ASH | 0 | -0.078 | -0.065 | 30.738 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 52 | VAL | 0 | -0.024 | -0.016 | 31.235 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 53 | VAL | 0 | 0.028 | 0.019 | 34.435 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 54 | VAL | 0 | -0.045 | -0.026 | 34.816 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 55 | PRO | 0 | 0.035 | 0.011 | 37.609 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 56 | ALA | 0 | 0.015 | 0.008 | 41.096 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 57 | ARG | 1 | 0.780 | 0.881 | 42.925 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 58 | GLY | 0 | 0.042 | 0.042 | 40.666 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 59 | LYS | 1 | 0.919 | 0.946 | 35.226 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 60 | ALA | 0 | 0.021 | 0.017 | 34.312 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 61 | ILE | 0 | -0.043 | -0.013 | 27.264 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 62 | VAL | 0 | 0.020 | 0.010 | 28.204 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 63 | LYS | 1 | 0.854 | 0.921 | 23.716 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 64 | THR | 0 | 0.049 | 0.005 | 21.127 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 65 | ASP | -1 | -0.761 | -0.834 | 22.589 | -0.177 | -0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 66 | LEU | 0 | -0.019 | 0.012 | 17.248 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 67 | GLN | 0 | -0.038 | -0.014 | 15.522 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 68 | VAL | 0 | -0.033 | -0.039 | 11.896 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 69 | GLN | 0 | -0.029 | -0.013 | 6.178 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 70 | VAL | 0 | -0.006 | -0.009 | 8.281 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 71 | PRO | 0 | -0.003 | 0.005 | 5.072 | -0.236 | -0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 72 | GLU | -1 | -0.716 | -0.800 | 3.120 | -7.684 | -6.615 | 0.032 | -0.549 | -0.551 | -0.005 |
55 | A | 73 | GLY | 0 | 0.033 | 0.019 | 6.276 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 74 | SER | 0 | -0.138 | -0.096 | 8.769 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 75 | TYR | 0 | 0.049 | 0.017 | 10.865 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 76 | GLY | 0 | 0.021 | 0.004 | 13.302 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 77 | ARG | 1 | 0.783 | 0.859 | 14.985 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 78 | VAL | 0 | -0.002 | 0.000 | 18.714 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 79 | ALA | 0 | 0.024 | 0.007 | 20.906 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 80 | PRO | 0 | 0.062 | 0.019 | 23.473 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 81 | ARG | 1 | 0.889 | 0.956 | 25.168 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 89 | PHE | 0 | 0.033 | 0.016 | 36.666 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 90 | ILE | 0 | -0.055 | -0.032 | 33.991 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 91 | ASP | -1 | -0.878 | -0.927 | 33.192 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 92 | VAL | 0 | -0.034 | -0.034 | 27.781 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 93 | GLY | 0 | 0.061 | 0.043 | 28.876 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 94 | ALA | 0 | -0.022 | -0.019 | 25.256 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 95 | GLY | 0 | -0.001 | -0.007 | 22.927 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 96 | VAL | 0 | -0.052 | -0.026 | 17.664 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 97 | VAL | 0 | -0.028 | 0.008 | 14.771 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 98 | ASP | -1 | -0.777 | -0.910 | 13.412 | -0.508 | -0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 99 | GLU | -1 | -0.826 | -0.912 | 8.977 | -1.101 | -1.101 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 100 | ASP | -1 | -0.869 | -0.915 | 10.762 | -0.382 | -0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 101 | TYR | 0 | -0.078 | -0.036 | 13.650 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 102 | ARG | 1 | 0.848 | 0.905 | 10.700 | 0.518 | 0.518 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 103 | GLY | 0 | 0.027 | 0.027 | 16.487 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 104 | ASN | 0 | 0.003 | -0.025 | 18.675 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 105 | LEU | 0 | 0.035 | 0.023 | 16.160 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 106 | GLY | 0 | -0.010 | -0.007 | 20.442 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 107 | VAL | 0 | -0.018 | 0.011 | 23.620 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 108 | VAL | 0 | -0.037 | -0.019 | 26.447 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 109 | LEU | 0 | 0.003 | 0.014 | 29.988 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 110 | PHE | 0 | 0.006 | -0.027 | 31.812 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 111 | ASN | 0 | -0.001 | -0.001 | 35.913 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 112 | HIS | 0 | -0.032 | -0.015 | 36.926 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 113 | SER | 0 | -0.054 | -0.032 | 41.197 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 114 | ASP | -1 | -0.849 | -0.927 | 43.715 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 115 | VAL | 0 | -0.015 | -0.010 | 44.781 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 116 | ASP | -1 | -0.832 | -0.896 | 42.147 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 117 | PHE | 0 | -0.002 | 0.000 | 34.430 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 118 | GLU | -1 | -0.800 | -0.864 | 37.450 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 119 | VAL | 0 | -0.018 | 0.010 | 30.793 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 120 | LYS | 1 | 0.861 | 0.908 | 33.219 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 121 | HIS | 0 | -0.020 | -0.013 | 27.518 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 122 | GLY | 0 | 0.042 | 0.014 | 27.218 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 123 | ASP | -1 | -0.879 | -0.928 | 27.785 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 124 | ARG | 1 | 0.817 | 0.909 | 25.191 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 125 | ILE | 0 | -0.007 | -0.005 | 25.083 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 126 | ALA | 0 | -0.005 | 0.002 | 23.343 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 127 | GLN | 0 | -0.055 | -0.032 | 21.095 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 128 | PHE | 0 | 0.022 | 0.011 | 12.963 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 129 | ILE | 0 | 0.003 | -0.003 | 16.875 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 130 | CYS | 0 | -0.012 | 0.006 | 11.747 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 131 | GLU | -1 | -0.826 | -0.868 | 13.673 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 132 | ARG | 1 | 0.745 | 0.789 | 6.024 | 1.395 | 1.395 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 133 | ILE | 0 | 0.013 | 0.016 | 13.537 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 134 | PHE | 0 | -0.023 | -0.011 | 14.676 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 135 | TYR | 0 | 0.020 | -0.002 | 15.442 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 136 | PRO | 0 | -0.012 | 0.010 | 19.599 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 137 | GLN | 0 | -0.004 | -0.009 | 21.980 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 138 | LEU | 0 | -0.003 | 0.009 | 25.109 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 139 | VAL | 0 | 0.005 | -0.005 | 27.844 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 140 | MET | 0 | -0.002 | 0.001 | 31.471 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 141 | VAL | 0 | -0.010 | -0.013 | 34.465 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 142 | ASP | -1 | -0.829 | -0.892 | 37.173 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 143 | LYS | 1 | 0.842 | 0.897 | 39.470 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 144 | LEU | 0 | 0.000 | 0.016 | 33.974 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |