![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: N1Y3Q
Calculation Name: 3NFG-H-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3NFG
Chain ID: H
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 | 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 | 120 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -843880.19157 |
---|---|
FMO2-HF: Nuclear repulsion | 797279.290783 |
FMO2-HF: Total energy | -46600.900787 |
FMO2-MP2: Total energy | -46737.857953 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F022025/ligand_interaction/ligand_F022025.png)
Ligand Interaction
![ligand interaction](./Kdata/F022025/ligand_interaction/ligand_interaction_F022025.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(H:24:GLY)
Summations of interaction energy for
fragment #1(H:24:GLY)
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. |
0.036 | 0.996 | -0.005 | -0.366 | -0.59 | 0.001 |
Interaction energy analysis for fragmet #1(H:24:GLY)
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 | H | 26 | GLN | 0 | 0.017 | 0.003 | 3.844 | -0.298 | 0.662 | -0.005 | -0.366 | -0.590 | 0.001 |
4 | H | 27 | PRO | 0 | -0.038 | -0.004 | 6.579 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | H | 28 | PRO | 0 | 0.015 | 0.014 | 10.127 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | H | 29 | SER | 0 | 0.005 | -0.003 | 13.276 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | H | 30 | ASP | -1 | -0.900 | -0.948 | 14.751 | -0.358 | -0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | H | 31 | TYR | 0 | -0.024 | -0.001 | 14.213 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | H | 32 | LYS | 1 | 0.963 | 0.975 | 14.034 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | H | 33 | GLN | 0 | -0.044 | -0.028 | 11.307 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | H | 34 | CYS | 0 | 0.003 | 0.006 | 14.258 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | H | 35 | LYS | 1 | 0.999 | 0.982 | 12.902 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | H | 36 | HIS | 0 | -0.053 | -0.023 | 17.556 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | H | 37 | LEU | 0 | 0.013 | 0.019 | 17.881 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | H | 38 | LYS | 1 | 0.914 | 0.953 | 21.880 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | H | 39 | SER | 0 | 0.006 | 0.001 | 24.980 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | H | 40 | PHE | 0 | 0.062 | 0.026 | 26.449 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | H | 41 | PRO | 0 | 0.035 | 0.027 | 28.212 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | H | 42 | VAL | 0 | 0.009 | -0.010 | 26.190 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | H | 43 | SER | 0 | -0.052 | -0.043 | 29.258 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | H | 44 | GLU | -1 | -0.899 | -0.952 | 32.553 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | H | 45 | LEU | 0 | -0.018 | 0.003 | 28.792 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | H | 46 | LYS | 1 | 0.819 | 0.913 | 28.828 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | H | 47 | GLY | 0 | 0.033 | 0.011 | 34.402 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | H | 48 | ASP | -1 | -0.920 | -0.949 | 38.095 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | H | 49 | ASN | 0 | -0.026 | -0.020 | 40.420 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | H | 50 | LYS | 1 | 0.887 | 0.958 | 36.912 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | H | 51 | GLU | -1 | -0.720 | -0.837 | 37.817 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | H | 52 | LEU | 0 | -0.112 | -0.042 | 29.847 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | H | 53 | TRP | 0 | 0.005 | -0.027 | 34.398 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | H | 54 | LEU | 0 | -0.024 | -0.007 | 29.591 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | H | 55 | MET | 0 | -0.012 | 0.003 | 33.023 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | H | 56 | LYS | 1 | 0.951 | 0.994 | 32.743 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | H | 57 | VAL | 0 | 0.034 | 0.005 | 34.335 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | H | 58 | PRO | 0 | -0.023 | -0.004 | 35.244 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | H | 59 | ALA | 0 | 0.017 | -0.003 | 33.679 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | H | 60 | ASN | 0 | -0.090 | -0.054 | 35.360 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | H | 61 | ILE | 0 | -0.009 | 0.009 | 38.316 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | H | 62 | ASP | -1 | -0.818 | -0.889 | 37.725 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | H | 63 | ILE | 0 | 0.022 | -0.013 | 36.030 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | H | 64 | SER | 0 | -0.071 | -0.046 | 37.063 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | H | 65 | GLN | 0 | -0.051 | -0.025 | 38.826 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | H | 66 | LEU | 0 | -0.042 | -0.004 | 40.753 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | H | 67 | LYS | 1 | 0.921 | 0.956 | 42.424 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | H | 68 | SER | 0 | -0.014 | -0.014 | 44.731 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | H | 69 | LEU | 0 | 0.042 | 0.023 | 39.537 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | H | 70 | PRO | 0 | -0.020 | -0.002 | 44.261 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | H | 71 | LEU | 0 | -0.010 | -0.013 | 41.007 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | H | 72 | ASP | -1 | -0.871 | -0.937 | 45.721 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | H | 73 | THR | 0 | -0.028 | -0.033 | 44.665 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | H | 74 | ASP | -1 | -0.907 | -0.939 | 45.500 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | H | 75 | ALA | 0 | -0.033 | -0.001 | 48.046 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | H | 76 | THR | 0 | -0.034 | -0.016 | 44.489 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | H | 77 | VAL | 0 | 0.007 | -0.008 | 44.893 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | H | 78 | SER | 0 | 0.014 | 0.009 | 46.909 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | H | 79 | THR | 0 | -0.052 | -0.033 | 47.892 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | H | 80 | VAL | 0 | 0.020 | 0.014 | 44.292 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | H | 81 | GLU | -1 | -0.951 | -0.979 | 47.580 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | H | 82 | LEU | 0 | -0.007 | 0.013 | 42.435 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | H | 83 | GLY | 0 | -0.012 | -0.010 | 46.553 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | H | 84 | SER | 0 | -0.040 | -0.023 | 47.219 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | H | 85 | LYS | 1 | 0.989 | 0.989 | 45.660 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | H | 86 | ASN | 0 | 0.042 | 0.017 | 47.949 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | H | 87 | PHE | 0 | -0.031 | -0.010 | 43.244 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | H | 88 | ASN | 0 | 0.010 | 0.000 | 44.947 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | H | 89 | VAL | 0 | 0.015 | 0.003 | 42.322 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | H | 90 | LEU | 0 | 0.021 | 0.013 | 40.189 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | H | 91 | GLN | 0 | 0.007 | 0.012 | 40.433 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | H | 92 | ASN | 0 | 0.019 | -0.012 | 37.025 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | H | 93 | THR | 0 | 0.050 | 0.026 | 36.629 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | H | 94 | SER | 0 | -0.014 | 0.020 | 39.216 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | H | 95 | THR | 0 | -0.023 | -0.016 | 41.226 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | H | 96 | GLN | 0 | 0.000 | -0.016 | 41.653 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | H | 97 | GLU | -1 | -0.978 | -0.978 | 39.221 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | H | 98 | GLY | 0 | -0.006 | -0.009 | 36.512 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | H | 99 | SER | 0 | 0.013 | 0.016 | 36.992 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | H | 100 | ASP | -1 | -0.875 | -0.916 | 32.739 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | H | 101 | ASN | 0 | -0.026 | -0.029 | 31.610 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | H | 102 | THR | 0 | -0.061 | -0.043 | 29.547 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | H | 103 | ASN | 0 | 0.000 | 0.005 | 26.562 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | H | 104 | LEU | 0 | -0.060 | -0.023 | 25.197 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | H | 105 | SER | 0 | 0.042 | 0.019 | 22.525 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | H | 106 | LEU | 0 | 0.019 | 0.018 | 23.411 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | H | 107 | LEU | 0 | -0.023 | -0.017 | 17.552 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | H | 108 | ILE | 0 | 0.021 | 0.008 | 21.277 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | H | 109 | PRO | 0 | 0.028 | 0.011 | 19.714 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | H | 110 | SER | 0 | -0.059 | -0.021 | 18.315 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | H | 111 | GLU | -1 | -0.873 | -0.970 | 20.347 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | H | 112 | LYS | 1 | 0.878 | 0.948 | 18.868 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | H | 113 | LYS | 1 | 0.998 | 1.003 | 14.315 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | H | 114 | LYS | 1 | 1.000 | 1.007 | 17.611 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | H | 115 | GLU | -1 | -0.908 | -0.956 | 12.298 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | H | 116 | THR | 0 | -0.038 | -0.014 | 12.367 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | H | 117 | LEU | 0 | 0.027 | 0.000 | 14.965 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | H | 118 | LYS | 1 | 0.917 | 0.961 | 15.957 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | H | 119 | VAL | 0 | 0.065 | 0.036 | 18.502 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | H | 120 | ALA | 0 | -0.009 | 0.008 | 21.285 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | H | 121 | THR | 0 | 0.018 | 0.015 | 23.328 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | H | 122 | SER | 0 | -0.034 | -0.032 | 25.950 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | H | 123 | LYS | 1 | 0.934 | 0.948 | 28.300 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | H | 124 | ASP | -1 | -0.854 | -0.909 | 29.652 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | H | 125 | ASN | 0 | -0.045 | -0.026 | 24.618 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | H | 126 | LYS | 1 | 0.965 | 0.988 | 27.306 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | H | 127 | SER | 0 | -0.002 | -0.014 | 25.425 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | H | 128 | VAL | 0 | -0.028 | -0.016 | 27.517 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | H | 129 | TYR | 0 | 0.024 | 0.028 | 28.362 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | H | 130 | PHE | 0 | -0.031 | -0.025 | 28.134 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | H | 131 | ASP | -1 | -0.830 | -0.902 | 32.778 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | H | 132 | ARG | 1 | 0.812 | 0.903 | 36.305 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | H | 133 | VAL | 0 | -0.022 | -0.021 | 33.793 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | H | 134 | PHE | 0 | 0.015 | -0.002 | 36.181 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | H | 135 | THR | 0 | -0.039 | -0.028 | 36.289 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | H | 136 | ILE | 0 | -0.018 | 0.004 | 38.321 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | H | 137 | SER | 0 | 0.024 | -0.005 | 39.259 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | H | 138 | GLU | -1 | -0.882 | -0.939 | 41.397 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | H | 139 | THR | 0 | 0.018 | 0.013 | 43.801 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | H | 140 | ALA | 0 | 0.015 | 0.002 | 46.876 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | H | 141 | ARG | 1 | 0.904 | 0.959 | 45.263 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | H | 142 | ILE | 0 | 0.002 | 0.008 | 47.819 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | H | 143 | PRO | 0 | -0.003 | 0.006 | 45.753 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |