FMODB ID: G6YL1
Calculation Name: 3A7M-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3A7M
Chain ID: B
UniProt ID: P0A1N2
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 | 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 | 117 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -787629.191313 |
---|---|
FMO2-HF: Nuclear repulsion | 741281.553036 |
FMO2-HF: Total energy | -46347.638277 |
FMO2-MP2: Total energy | -46483.450865 |
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(B:2:THR)
Summations of interaction energy for
fragment #1(B:2: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. |
-11.782 | -8.927 | 12.717 | -6.531 | -9.04 | 0.036 |
Interaction energy analysis for fragmet #1(B:2: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 | B | 4 | THR | 0 | -0.006 | -0.006 | 2.636 | -3.898 | 1.683 | 1.049 | -3.096 | -3.534 | 0.015 |
4 | B | 5 | VAL | 0 | 0.050 | 0.038 | 1.952 | -3.781 | -7.404 | 11.664 | -3.210 | -4.831 | 0.021 |
5 | B | 6 | GLU | -1 | -0.911 | -0.954 | 3.601 | -4.565 | -3.668 | 0.004 | -0.225 | -0.675 | 0.000 |
6 | B | 7 | PHE | 0 | -0.056 | -0.027 | 5.616 | 0.367 | 0.367 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 8 | ILE | 0 | 0.031 | -0.002 | 7.109 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 9 | ASN | 0 | -0.023 | -0.025 | 7.523 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 10 | ARG | 1 | 0.925 | 0.986 | 8.332 | 0.679 | 0.679 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 11 | TRP | 0 | 0.071 | 0.016 | 11.467 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 12 | GLN | 0 | -0.031 | 0.008 | 10.683 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 13 | ARG | 1 | 0.949 | 0.968 | 13.324 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 14 | ILE | 0 | 0.012 | 0.025 | 15.104 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 15 | ALA | 0 | 0.036 | 0.025 | 17.152 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 16 | LEU | 0 | -0.017 | 0.011 | 16.359 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 17 | LEU | 0 | 0.001 | -0.008 | 19.136 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 18 | SER | 0 | 0.011 | 0.014 | 21.597 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 19 | GLN | 0 | 0.008 | -0.002 | 22.848 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 20 | SER | 0 | -0.090 | -0.037 | 23.654 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 21 | LEU | 0 | 0.042 | -0.004 | 25.282 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 22 | LEU | 0 | -0.005 | 0.008 | 27.523 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 23 | GLU | -1 | -0.897 | -0.956 | 27.805 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 24 | LEU | 0 | -0.116 | -0.037 | 28.212 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 25 | ALA | 0 | 0.008 | 0.018 | 31.687 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 26 | GLN | 0 | -0.070 | -0.036 | 31.548 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 27 | ARG | 1 | 0.845 | 0.931 | 29.946 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 28 | GLY | 0 | 0.036 | 0.018 | 35.651 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 29 | GLU | -1 | -0.917 | -0.961 | 33.862 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 30 | TRP | 0 | 0.096 | 0.019 | 34.284 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 31 | ASP | -1 | -0.928 | -0.959 | 35.372 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 32 | LEU | 0 | -0.007 | 0.001 | 31.204 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 33 | LEU | 0 | 0.005 | 0.004 | 30.056 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 34 | LEU | 0 | 0.011 | -0.006 | 30.845 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 35 | GLN | 0 | -0.074 | -0.034 | 31.084 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 36 | GLN | 0 | -0.024 | -0.025 | 25.673 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 37 | GLU | -1 | -0.891 | -0.935 | 26.413 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 38 | VAL | 0 | 0.068 | 0.032 | 26.892 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 39 | SER | 0 | -0.041 | -0.017 | 23.819 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 40 | TYR | 0 | 0.036 | 0.020 | 21.816 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 41 | LEU | 0 | 0.048 | 0.024 | 22.575 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 42 | GLN | 0 | 0.065 | 0.027 | 23.185 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 43 | SER | 0 | -0.178 | -0.088 | 18.834 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 44 | ILE | 0 | -0.005 | -0.033 | 18.616 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 45 | GLU | -1 | -0.917 | -0.967 | 19.476 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 46 | THR | 0 | 0.005 | 0.018 | 16.146 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 47 | VAL | 0 | -0.107 | -0.070 | 13.507 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 48 | MET | 0 | -0.053 | -0.019 | 15.494 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 49 | GLU | -1 | -0.958 | -0.946 | 18.060 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 50 | LYS | 1 | 0.905 | 0.947 | 11.917 | 0.515 | 0.515 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 51 | GLN | 0 | 0.006 | 0.005 | 11.624 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 52 | THR | 0 | -0.032 | -0.022 | 10.635 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 53 | PRO | 0 | -0.033 | -0.013 | 6.146 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 54 | PRO | 0 | 0.063 | 0.031 | 6.342 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 55 | GLY | 0 | 0.000 | 0.001 | 7.121 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 56 | ILE | 0 | -0.031 | -0.010 | 8.064 | 0.343 | 0.343 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 57 | THR | 0 | 0.047 | 0.025 | 9.203 | -0.271 | -0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 58 | ARG | 1 | 1.018 | 0.991 | 11.575 | -0.352 | -0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 59 | SER | 0 | 0.027 | 0.019 | 11.853 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 60 | ILE | 0 | 0.010 | 0.008 | 6.482 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 61 | GLN | 0 | -0.006 | -0.011 | 10.708 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 62 | ASP | -1 | -0.906 | -0.955 | 13.390 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | B | 63 | MET | 0 | -0.039 | -0.011 | 11.234 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | B | 64 | VAL | 0 | 0.001 | -0.003 | 11.071 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | B | 65 | ALA | 0 | 0.019 | 0.010 | 13.699 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | B | 66 | GLY | 0 | -0.011 | -0.002 | 16.906 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 67 | TYR | 0 | 0.059 | 0.030 | 12.633 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 68 | ILE | 0 | 0.003 | 0.018 | 16.761 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 69 | LYS | 1 | 0.927 | 0.972 | 19.324 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | B | 70 | GLN | 0 | 0.049 | 0.019 | 20.290 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | B | 71 | THR | 0 | -0.025 | -0.035 | 20.045 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | B | 72 | LEU | 0 | -0.036 | -0.034 | 22.599 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | B | 73 | ASP | -1 | -0.901 | -0.947 | 25.045 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | B | 74 | ASN | 0 | -0.054 | -0.038 | 24.024 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | B | 75 | GLU | -1 | -0.935 | -0.970 | 26.559 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | B | 76 | GLN | 0 | -0.024 | -0.009 | 28.301 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | B | 77 | LEU | 0 | -0.038 | -0.015 | 29.854 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | B | 78 | LEU | 0 | 0.024 | 0.017 | 29.368 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | B | 79 | LYS | 1 | 0.982 | 0.989 | 32.210 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | B | 80 | GLY | 0 | -0.006 | 0.006 | 34.315 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | B | 81 | LEU | 0 | 0.023 | -0.003 | 33.910 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | B | 82 | LEU | 0 | -0.019 | -0.011 | 33.484 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | B | 83 | GLN | 0 | -0.052 | -0.017 | 37.479 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | B | 84 | GLN | 0 | 0.030 | 0.015 | 39.889 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | B | 85 | ARG | 1 | 0.864 | 0.943 | 40.268 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | B | 86 | LEU | 0 | -0.032 | -0.014 | 41.377 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | B | 87 | ASP | -1 | -0.877 | -0.948 | 43.090 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | B | 88 | GLU | -1 | -0.900 | -0.959 | 44.320 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | B | 89 | LEU | 0 | 0.006 | -0.001 | 43.722 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | B | 90 | SER | 0 | -0.017 | -0.007 | 46.770 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | B | 91 | SER | 0 | -0.071 | -0.020 | 48.954 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | B | 92 | LEU | 0 | -0.036 | -0.025 | 50.003 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | B | 93 | ILE | 0 | -0.019 | -0.008 | 50.263 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | B | 94 | GLY | 0 | -0.003 | 0.003 | 53.766 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | B | 95 | GLN | 0 | 0.050 | 0.014 | 55.806 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | B | 96 | SER | 0 | -0.017 | 0.004 | 57.360 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | B | 97 | THR | 0 | 0.075 | 0.065 | 58.837 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | B | 98 | ARG | 1 | 0.899 | 0.923 | 60.803 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | B | 99 | GLN | 0 | 0.128 | 0.073 | 60.873 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | B | 100 | LYS | 1 | 1.042 | 1.031 | 63.281 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | B | 101 | SER | 0 | -0.014 | 0.003 | 66.018 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | B | 102 | LEU | 0 | 0.032 | 0.013 | 64.085 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | B | 103 | ASN | 0 | -0.058 | -0.061 | 65.106 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | B | 104 | ASN | 0 | -0.073 | -0.031 | 68.202 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | B | 105 | ALA | 0 | -0.050 | -0.034 | 70.345 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | B | 106 | TYR | 0 | 0.021 | 0.021 | 69.964 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | B | 107 | GLY | 0 | 0.025 | 0.022 | 71.933 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | B | 108 | ARG | 1 | 0.932 | 0.955 | 73.746 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | B | 109 | LEU | 0 | 0.011 | 0.012 | 75.290 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | B | 110 | SER | 0 | -0.038 | -0.048 | 74.115 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | B | 111 | GLY | 0 | -0.025 | 0.012 | 76.758 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | B | 112 | MET | 0 | -0.051 | -0.019 | 79.593 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | B | 113 | LEU | 0 | 0.018 | -0.006 | 82.525 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | B | 114 | LEU | 0 | -0.027 | -0.019 | 85.992 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | B | 115 | VAL | 0 | -0.045 | -0.014 | 83.063 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | B | 116 | PRO | 0 | -0.010 | 0.013 | 86.387 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | B | 117 | ASP | -1 | -0.867 | -0.947 | 86.987 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | B | 118 | ALA | 0 | -0.077 | -0.022 | 87.982 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |