![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: J3V69
Calculation Name: 2ZV3-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2ZV3
Chain ID: A
UniProt ID: Q60363
Base Structure: X-ray
Registration Date: 2023-03-14
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 | 108 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -845200.825927 |
---|---|
FMO2-HF: Nuclear repulsion | 803134.991983 |
FMO2-HF: Total energy | -42065.833944 |
FMO2-MP2: Total energy | -42187.389496 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F019214/ligand_interaction/ligand_F019214.png)
Ligand Interaction
![ligand interaction](./Kdata/F019214/ligand_interaction/ligand_interaction_F019214.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:1:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
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. |
-26.199 | -10.713 | 13.783 | -8.389 | -20.878 | -0.052 |
Interaction energy analysis for fragmet #1(A:1:MET)
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 | 3 | MET | 0 | -0.005 | 0.010 | 3.762 | -3.079 | 1.575 | -0.047 | -2.620 | -1.988 | 0.013 |
4 | A | 4 | VAL | 0 | -0.033 | -0.009 | 6.657 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | VAL | 0 | -0.009 | -0.013 | 9.932 | 0.192 | 0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | VAL | 0 | 0.000 | -0.009 | 13.191 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ILE | 0 | 0.009 | -0.006 | 16.324 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ARG | 1 | 0.817 | 0.885 | 19.617 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ASN | 0 | -0.034 | -0.043 | 23.076 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ASP | -1 | -0.797 | -0.874 | 25.104 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LEU | 0 | -0.019 | -0.008 | 25.789 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLY | 0 | 0.018 | 0.028 | 28.861 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | MET | 0 | -0.051 | -0.017 | 23.204 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLY | 0 | 0.083 | 0.041 | 27.600 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | LYS | 1 | 0.995 | 0.972 | 25.236 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | 0.039 | 0.022 | 24.300 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | LYS | 1 | 0.881 | 0.928 | 24.719 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | MET | 0 | 0.022 | 0.016 | 21.642 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | -0.001 | 0.008 | 19.959 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ALA | 0 | 0.008 | 0.009 | 19.804 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLN | 0 | 0.013 | 0.014 | 20.776 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | GLY | 0 | 0.062 | 0.021 | 17.473 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLY | 0 | -0.015 | 0.006 | 16.130 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | HIS | 0 | 0.010 | -0.006 | 16.655 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | 0.009 | 0.004 | 15.327 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ILE | 0 | 0.006 | -0.014 | 11.418 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ILE | 0 | 0.000 | 0.003 | 11.832 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLU | -1 | -0.854 | -0.941 | 13.183 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ALA | 0 | -0.060 | -0.003 | 9.768 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | PHE | 0 | 0.037 | 0.010 | 8.029 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LEU | 0 | -0.019 | -0.012 | 8.947 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASP | -1 | -0.785 | -0.871 | 10.860 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ALA | 0 | 0.021 | -0.003 | 5.391 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | LYS | 1 | 0.806 | 0.889 | 7.433 | -0.308 | -0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | ARG | 1 | 0.926 | 0.960 | 8.504 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | LYS | 1 | 0.852 | 0.929 | 8.723 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ASN | 0 | 0.005 | -0.010 | 5.565 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | PRO | 0 | 0.051 | 0.022 | 5.635 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ARG | 1 | 0.995 | 0.997 | 7.115 | -1.443 | -1.443 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ALA | 0 | 0.016 | 0.014 | 2.205 | 0.113 | 0.021 | 2.002 | -0.430 | -1.480 | 0.001 |
41 | A | 41 | VAL | 0 | 0.001 | 0.003 | 2.909 | 0.068 | 1.420 | 1.118 | -0.805 | -1.664 | -0.014 |
42 | A | 42 | ASP | -1 | -0.824 | -0.908 | 4.345 | 0.705 | 0.731 | -0.001 | -0.008 | -0.017 | 0.000 |
43 | A | 43 | GLU | -1 | -0.896 | -0.932 | 3.397 | 2.689 | 4.289 | 0.483 | -0.559 | -1.525 | -0.003 |
44 | A | 44 | TRP | 0 | -0.006 | 0.000 | 2.783 | -3.701 | -1.142 | 0.772 | -0.934 | -2.396 | 0.002 |
45 | A | 45 | LEU | 0 | -0.053 | -0.033 | 3.592 | -1.638 | -1.545 | 0.024 | 0.056 | -0.173 | 0.001 |
46 | A | 46 | ARG | 1 | 0.825 | 0.908 | 6.911 | -1.879 | -1.879 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLU | -1 | -0.953 | -0.968 | 2.995 | -5.398 | -3.800 | 0.084 | -0.753 | -0.929 | -0.007 |
48 | A | 48 | GLY | 0 | 0.012 | 0.013 | 6.408 | -0.486 | -0.486 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | GLN | 0 | -0.016 | -0.004 | 5.795 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | LYS | 1 | 0.912 | 0.963 | 4.166 | 5.610 | 5.841 | -0.001 | -0.035 | -0.195 | 0.000 |
51 | A | 51 | LYS | 1 | 0.869 | 0.912 | 6.561 | 1.081 | 1.081 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | VAL | 0 | 0.002 | 0.006 | 8.399 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | VAL | 0 | -0.006 | 0.000 | 11.021 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.025 | 0.021 | 13.578 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LYS | 1 | 0.890 | 0.957 | 16.091 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | VAL | 0 | 0.005 | 0.007 | 19.059 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ASN | 0 | -0.068 | -0.061 | 21.545 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | SER | 0 | 0.057 | 0.033 | 24.772 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | GLU | -1 | -0.781 | -0.880 | 24.761 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | LYS | 1 | 0.898 | 0.926 | 24.687 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | GLU | -1 | -0.833 | -0.916 | 21.558 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | -0.026 | -0.004 | 19.207 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ILE | 0 | 0.017 | -0.004 | 19.809 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ASP | -1 | -0.865 | -0.901 | 20.786 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | ILE | 0 | -0.040 | -0.018 | 15.625 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | TYR | 0 | 0.049 | 0.030 | 15.809 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ASN | 0 | 0.011 | -0.004 | 16.602 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | LYS | 1 | 0.965 | 0.996 | 16.512 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ALA | 0 | 0.036 | 0.018 | 12.361 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ARG | 1 | 0.847 | 0.898 | 13.093 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | SER | 0 | -0.056 | -0.024 | 15.254 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | GLU | -1 | -0.848 | -0.910 | 12.289 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | GLY | 0 | -0.014 | 0.010 | 12.098 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.051 | -0.024 | 7.672 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | PRO | 0 | -0.021 | 0.006 | 6.023 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | CYS | 0 | -0.060 | -0.044 | 9.270 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | SER | 0 | -0.034 | -0.006 | 11.689 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ILE | 0 | 0.038 | 0.004 | 14.890 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | ILE | 0 | -0.020 | 0.006 | 17.630 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ARG | 1 | 0.961 | 0.982 | 20.556 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | ASP | -1 | -0.840 | -0.899 | 24.354 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | ALA | 0 | -0.004 | -0.001 | 26.586 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 90 | GLY | 0 | 0.006 | -0.011 | 30.600 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 91 | THR | 0 | -0.086 | -0.043 | 27.341 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 92 | LEU | 0 | 0.028 | 0.011 | 23.001 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 93 | THR | 0 | -0.010 | -0.036 | 22.810 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 94 | ALA | 0 | 0.009 | -0.006 | 18.177 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 95 | VAL | 0 | 0.001 | 0.009 | 14.607 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 96 | ALA | 0 | -0.008 | 0.015 | 11.484 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 97 | ILE | 0 | 0.000 | -0.002 | 8.610 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 98 | GLY | 0 | 0.025 | 0.041 | 5.670 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 99 | PRO | 0 | -0.040 | -0.047 | 2.460 | -0.617 | 0.111 | 0.479 | -0.239 | -0.967 | 0.001 |
93 | A | 100 | GLU | -1 | -0.798 | -0.916 | 2.089 | 1.142 | 1.339 | 4.435 | -1.760 | -2.872 | -0.007 |
94 | A | 101 | LYS | 1 | 0.960 | 0.983 | 2.267 | -8.734 | -7.568 | 3.025 | 0.192 | -4.383 | -0.018 |
95 | A | 102 | ASP | -1 | -0.745 | -0.881 | 2.535 | -11.003 | -9.800 | 1.409 | -0.469 | -2.142 | -0.021 |
96 | A | 103 | GLU | -1 | -0.809 | -0.915 | 4.175 | 1.294 | 1.465 | 0.001 | -0.025 | -0.147 | 0.000 |
97 | A | 104 | LYS | 1 | 0.854 | 0.922 | 6.051 | -1.208 | -1.208 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 105 | ILE | 0 | -0.030 | -0.013 | 5.295 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 106 | ASP | -1 | -0.836 | -0.902 | 7.979 | -1.251 | -1.251 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 107 | LYS | 1 | 0.795 | 0.899 | 9.946 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 108 | ILE | 0 | -0.074 | -0.035 | 11.442 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 109 | THR | 0 | 0.041 | -0.010 | 11.184 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 110 | GLY | 0 | 0.000 | 0.018 | 12.649 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 111 | HIS | 0 | -0.025 | -0.006 | 13.378 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 112 | LEU | 0 | -0.052 | -0.016 | 15.483 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 113 | LYS | 1 | 0.950 | 0.973 | 16.739 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 114 | LEU | 0 | 0.061 | 0.022 | 14.025 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 115 | LEU | 0 | -0.035 | -0.019 | 17.794 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |