![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: GN961
Calculation Name: 3NFG-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3NFG
Chain ID: A
UniProt ID: Q6FNZ9
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 94 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -509864.552319 |
---|---|
FMO2-HF: Nuclear repulsion | 472102.650483 |
FMO2-HF: Total energy | -37761.901836 |
FMO2-MP2: Total energy | -37873.455839 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F022867/ligand_interaction/ligand_F022867.png)
Ligand Interaction
![ligand interaction](./Kdata/F022867/ligand_interaction/ligand_interaction_F022867.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:5:ARG)
Summations of interaction energy for
fragment #1(A:5:ARG)
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. |
0.261 | 2.751 | -0.022 | -1.352 | -1.117 | 0.004 |
Interaction energy analysis for fragmet #1(A:5:ARG)
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 | 7 | ILE | 0 | 0.006 | 0.005 | 3.879 | -1.718 | 0.772 | -0.022 | -1.352 | -1.117 | 0.004 |
4 | A | 8 | ALA | 0 | 0.016 | 0.010 | 6.745 | 1.790 | 1.790 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 9 | ILE | 0 | -0.018 | -0.012 | 9.280 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 10 | ASP | -1 | -0.908 | -0.925 | 12.718 | -15.014 | -15.014 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 11 | SER | 0 | -0.040 | -0.037 | 14.997 | 0.976 | 0.976 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 12 | TYR | 0 | -0.089 | -0.080 | 17.172 | -0.983 | -0.983 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 13 | GLN | 0 | 0.009 | 0.006 | 19.536 | 0.616 | 0.616 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 14 | GLU | -1 | -0.882 | -0.907 | 22.326 | -12.336 | -12.336 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 15 | ASP | -1 | -0.907 | -0.954 | 24.778 | -9.354 | -9.354 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 16 | PRO | 0 | -0.119 | -0.076 | 26.996 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 17 | SER | 0 | 0.005 | 0.010 | 25.637 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 18 | VAL | 0 | 0.002 | 0.009 | 23.254 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 19 | VAL | 0 | 0.004 | -0.010 | 26.742 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 20 | VAL | 0 | 0.000 | 0.007 | 22.768 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 21 | SER | 0 | -0.006 | 0.000 | 26.076 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 22 | ASN | 0 | -0.021 | -0.021 | 27.827 | -0.477 | -0.477 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 23 | PHE | 0 | 0.021 | 0.019 | 29.467 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 24 | PHE | 0 | 0.052 | 0.021 | 31.457 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 25 | LYS | 1 | 0.971 | 0.974 | 25.666 | 11.625 | 11.625 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 26 | GLY | 0 | 0.049 | 0.022 | 29.726 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 27 | VAL | 0 | -0.038 | 0.006 | 30.443 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 28 | ARG | 1 | 0.874 | 0.925 | 30.155 | 9.464 | 9.464 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 29 | VAL | 0 | 0.042 | 0.016 | 33.579 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 30 | PRO | 0 | 0.019 | 0.028 | 35.105 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 31 | LYS | 1 | 0.950 | 0.977 | 34.269 | 8.810 | 8.810 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 32 | ASP | -1 | -0.886 | -0.945 | 36.126 | -7.861 | -7.861 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 33 | THR | 0 | -0.061 | -0.038 | 37.322 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 34 | GLU | -1 | -0.930 | -0.954 | 37.478 | -7.569 | -7.569 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 35 | PHE | 0 | -0.033 | -0.025 | 35.564 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 36 | GLN | 0 | -0.012 | -0.007 | 37.238 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 37 | LEU | 0 | -0.005 | 0.005 | 31.517 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 38 | TYR | 0 | 0.022 | 0.009 | 35.567 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 39 | LYS | 1 | 0.976 | 0.988 | 33.106 | 8.723 | 8.723 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 40 | LYS | 1 | 0.969 | 0.986 | 36.327 | 8.069 | 8.069 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 41 | ARG | 1 | 0.922 | 0.949 | 37.712 | 6.866 | 6.866 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 42 | LYS | 1 | 0.847 | 0.898 | 33.428 | 8.788 | 8.788 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 43 | GLN | 0 | -0.013 | -0.002 | 39.335 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 44 | ASP | -1 | -0.808 | -0.872 | 35.139 | -8.630 | -8.630 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 45 | GLN | 0 | 0.031 | 0.008 | 37.123 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 46 | PHE | 0 | -0.004 | -0.017 | 36.287 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 47 | VAL | 0 | 0.015 | 0.006 | 36.035 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 48 | LEU | 0 | -0.041 | -0.010 | 37.043 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 49 | HIS | 1 | 0.839 | 0.875 | 36.688 | 7.771 | 7.771 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 50 | GLY | 0 | -0.009 | -0.004 | 38.485 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 51 | GLU | -1 | -0.812 | -0.887 | 37.545 | -7.665 | -7.665 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 52 | ASN | 0 | -0.008 | 0.000 | 41.247 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 53 | GLU | -1 | -0.811 | -0.901 | 41.056 | -7.129 | -7.129 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 54 | ARG | 1 | 0.900 | 0.952 | 44.242 | 5.892 | 5.892 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 55 | LEU | 0 | -0.056 | -0.016 | 45.989 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 56 | GLU | -1 | -0.825 | -0.919 | 40.073 | -7.461 | -7.461 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 57 | TYR | 0 | -0.027 | -0.021 | 42.358 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 58 | ASP | -1 | -0.805 | -0.882 | 39.550 | -7.672 | -7.672 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 59 | GLY | 0 | 0.004 | -0.005 | 41.363 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 60 | GLU | -1 | -0.823 | -0.887 | 40.853 | -7.277 | -7.277 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 61 | THR | 0 | -0.016 | 0.006 | 40.976 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 62 | ASP | -1 | -0.750 | -0.843 | 42.968 | -6.618 | -6.618 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 63 | GLU | -1 | -0.794 | -0.865 | 41.086 | -7.337 | -7.337 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 64 | LEU | 0 | 0.033 | 0.021 | 43.546 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 65 | THR | 0 | -0.036 | -0.055 | 46.779 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 66 | THR | 0 | -0.068 | -0.044 | 40.747 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 67 | LYS | 1 | 0.759 | 0.856 | 41.918 | 7.188 | 7.188 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 68 | THR | 0 | -0.065 | -0.027 | 44.551 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 69 | ASN | 0 | -0.047 | -0.030 | 47.283 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 70 | GLN | 0 | 0.058 | 0.037 | 45.418 | -0.341 | -0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 71 | TYR | 0 | 0.039 | 0.022 | 46.333 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 72 | MET | 0 | -0.027 | -0.007 | 45.839 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 73 | VAL | 0 | 0.050 | 0.042 | 47.585 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 74 | GLY | 0 | 0.009 | -0.012 | 49.149 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 75 | LEU | 0 | -0.028 | -0.002 | 49.821 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 76 | TYR | 0 | 0.013 | -0.004 | 53.292 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 77 | ASP | -1 | -0.786 | -0.850 | 56.585 | -5.129 | -5.129 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 78 | LYS | 1 | 0.948 | 0.952 | 58.953 | 4.918 | 4.918 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 79 | GLN | 0 | -0.031 | -0.004 | 62.166 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 80 | SER | 0 | -0.070 | -0.073 | 59.014 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 81 | GLY | 0 | 0.010 | 0.014 | 60.678 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 82 | LYS | 1 | 0.925 | 0.970 | 55.446 | 5.369 | 5.369 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 83 | ILE | 0 | 0.001 | -0.013 | 52.953 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 84 | ASN | 0 | -0.037 | 0.008 | 49.309 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 85 | LEU | 0 | -0.001 | -0.018 | 48.586 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 86 | TYR | 0 | 0.030 | 0.008 | 44.345 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 87 | ARG | 1 | 0.858 | 0.909 | 40.283 | 7.396 | 7.396 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 88 | ALA | 0 | -0.002 | 0.001 | 42.784 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 89 | PRO | 0 | 0.005 | 0.014 | 40.646 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 90 | VAL | 0 | -0.014 | -0.013 | 43.429 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 91 | VAL | 0 | 0.003 | -0.001 | 42.144 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 92 | THR | 0 | -0.002 | 0.016 | 45.132 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 93 | SER | 0 | -0.012 | -0.025 | 45.630 | -0.185 | -0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 94 | LYS | 1 | 0.797 | 0.882 | 43.843 | 7.054 | 7.054 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 95 | ILE | 0 | -0.015 | -0.011 | 46.182 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 96 | VAL | 0 | 0.002 | 0.007 | 45.158 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 97 | SER | 0 | -0.016 | -0.007 | 46.604 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 98 | LYS | 1 | 0.772 | 0.880 | 39.560 | 7.195 | 7.195 | 0.000 | 0.000 | 0.000 | 0.000 |