FMODB ID: N964Q
Calculation Name: 3R0E-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3R0E
Chain ID: A
UniProt ID: B5LYJ9
Base Structure: X-ray
Registration Date: 2023-06-26
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 | 108 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -781093.0105 |
---|---|
FMO2-HF: Nuclear repulsion | 739379.384424 |
FMO2-HF: Total energy | -41713.626075 |
FMO2-MP2: Total energy | -41835.378926 |
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(A:1:LEU)
Summations of interaction energy for
fragment #1(A:1:LEU)
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. |
-6.652 | -2.927 | 9.059 | -3.9 | -8.886 | -0.02 |
Interaction energy analysis for fragmet #1(A:1:LEU)
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 | THR | 0 | -0.033 | -0.003 | 3.802 | -1.623 | 1.551 | -0.028 | -1.791 | -1.356 | 0.002 |
4 | A | 4 | ASN | 0 | 0.033 | 0.027 | 6.540 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | TYR | 0 | -0.020 | -0.028 | 8.647 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | LEU | 0 | 0.016 | 0.023 | 6.410 | -0.358 | -0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | LEU | 0 | -0.009 | -0.015 | 9.208 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | SER | 0 | 0.035 | 0.021 | 11.592 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | GLY | 0 | -0.020 | -0.007 | 13.604 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLN | 0 | -0.013 | 0.003 | 8.257 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | THR | 0 | -0.023 | -0.023 | 7.416 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | LEU | 0 | -0.039 | -0.007 | 2.564 | -1.613 | -1.114 | 0.279 | -0.228 | -0.550 | -0.001 |
13 | A | 13 | ASP | -1 | -0.846 | -0.935 | 4.404 | 0.709 | 0.822 | -0.001 | -0.006 | -0.107 | 0.000 |
14 | A | 14 | THR | 0 | -0.005 | -0.034 | 5.294 | 1.084 | 1.084 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLU | -1 | -0.858 | -0.925 | 5.685 | 1.794 | 1.794 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | GLY | 0 | -0.023 | 0.009 | 2.522 | 2.516 | 2.389 | 3.930 | -2.134 | -1.669 | 0.002 |
17 | A | 17 | HIS | 0 | -0.046 | -0.043 | 2.184 | -6.939 | -8.269 | 4.524 | 1.239 | -4.433 | -0.014 |
18 | A | 18 | LEU | 0 | -0.047 | -0.017 | 2.988 | -4.286 | -2.890 | 0.355 | -0.980 | -0.771 | -0.009 |
19 | A | 19 | LYS | 1 | 0.888 | 0.938 | 5.723 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ASN | 0 | -0.067 | -0.053 | 7.988 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | GLY | 0 | 0.035 | 0.028 | 11.596 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | ASP | -1 | -0.880 | -0.937 | 12.446 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | PHE | 0 | -0.064 | -0.007 | 12.783 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ASP | -1 | -0.831 | -0.937 | 7.253 | 0.715 | 0.715 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | -0.055 | -0.033 | 8.216 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | VAL | 0 | 0.078 | 0.034 | 6.449 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | MET | 0 | -0.053 | -0.010 | 6.664 | -0.655 | -0.655 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLN | 0 | 0.024 | 0.020 | 8.187 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASP | -1 | -0.831 | -0.928 | 10.270 | 0.722 | 0.722 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ASP | -1 | -0.970 | -0.984 | 11.791 | 0.366 | 0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | CYS | 0 | -0.131 | -0.059 | 12.341 | -0.212 | -0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASN | 0 | 0.023 | 0.045 | 14.389 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | LEU | 0 | 0.009 | 0.013 | 9.335 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | VAL | 0 | 0.010 | -0.005 | 11.455 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LEU | 0 | -0.011 | 0.005 | 11.467 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | TYR | 0 | -0.004 | -0.013 | 10.058 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ASN | 0 | -0.030 | -0.040 | 13.700 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLY | 0 | 0.048 | 0.024 | 16.015 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ASN | 0 | -0.111 | -0.046 | 17.292 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | TRP | 0 | 0.011 | 0.006 | 13.595 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | GLN | 0 | 0.022 | 0.002 | 15.720 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | SER | 0 | 0.007 | 0.006 | 15.400 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | ASN | 0 | -0.055 | -0.015 | 17.057 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | THR | 0 | -0.027 | -0.045 | 15.884 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ALA | 0 | 0.048 | 0.025 | 17.568 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASN | 0 | -0.088 | -0.053 | 18.141 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | ASN | 0 | -0.045 | -0.017 | 18.886 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | GLY | 0 | 0.016 | 0.000 | 17.911 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | ARG | 1 | 0.884 | 0.951 | 15.904 | -0.294 | -0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ASP | -1 | -0.824 | -0.923 | 12.442 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | LYS | 1 | 0.936 | 0.993 | 9.068 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | LEU | 0 | 0.031 | 0.013 | 8.156 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | THR | 0 | -0.057 | -0.017 | 8.918 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | LEU | 0 | 0.023 | 0.005 | 11.510 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | THR | 0 | -0.003 | -0.009 | 13.786 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | ASP | -1 | -0.880 | -0.947 | 17.298 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | TYR | 0 | -0.043 | -0.031 | 19.834 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | GLY | 0 | 0.041 | 0.018 | 17.896 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | GLU | -1 | -0.834 | -0.895 | 18.277 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | LEU | 0 | 0.022 | 0.004 | 11.986 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | VAL | 0 | -0.033 | -0.026 | 14.003 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | ILE | 0 | 0.059 | 0.030 | 12.468 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | LYS | 1 | 0.902 | 0.954 | 13.447 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | ASN | 0 | 0.094 | 0.057 | 13.864 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | GLY | 0 | 0.023 | 0.018 | 15.074 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ASP | -1 | -0.920 | -0.948 | 16.081 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | GLY | 0 | -0.030 | -0.004 | 17.089 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | SER | 0 | -0.085 | -0.061 | 18.131 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | THR | 0 | -0.081 | -0.066 | 18.272 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | VAL | 0 | 0.033 | 0.016 | 16.808 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | TRP | 0 | 0.028 | 0.005 | 15.032 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | LYS | 1 | 0.901 | 0.961 | 17.314 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | SER | 0 | 0.036 | 0.017 | 17.318 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | GLY | 0 | -0.020 | 0.000 | 19.204 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | ALA | 0 | -0.035 | -0.015 | 21.573 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | GLN | 0 | -0.084 | -0.055 | 21.462 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | SER | 0 | 0.004 | 0.014 | 23.325 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | VAL | 0 | 0.027 | 0.004 | 24.940 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | LYS | 1 | 0.964 | 1.001 | 23.722 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 81 | GLY | 0 | -0.044 | -0.022 | 22.446 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 82 | ASN | 0 | -0.035 | -0.006 | 18.377 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 83 | TYR | 0 | 0.008 | -0.018 | 17.082 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 84 | ALA | 0 | -0.009 | -0.005 | 13.932 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 85 | ALA | 0 | -0.014 | 0.007 | 11.405 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 86 | VAL | 0 | 0.009 | -0.001 | 11.534 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 87 | VAL | 0 | 0.037 | 0.026 | 9.705 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | HIS | 0 | -0.012 | -0.012 | 12.788 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | PRO | 0 | 0.003 | -0.004 | 16.004 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | ASP | -1 | -0.911 | -0.957 | 17.014 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | GLY | 0 | -0.020 | -0.011 | 16.160 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 92 | ARG | 1 | 0.923 | 0.966 | 17.211 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | LEU | 0 | 0.020 | 0.012 | 11.604 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | VAL | 0 | -0.055 | -0.029 | 15.077 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | VAL | 0 | 0.014 | 0.009 | 15.142 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | PHE | 0 | -0.026 | -0.013 | 17.068 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | GLY | 0 | -0.002 | -0.002 | 18.600 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | PRO | 0 | 0.016 | 0.014 | 21.256 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | SER | 0 | -0.045 | -0.044 | 20.772 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | VAL | 0 | 0.012 | 0.007 | 22.480 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | PHE | 0 | -0.003 | -0.013 | 24.496 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | LYS | 1 | 0.960 | 0.980 | 20.479 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | ILE | 0 | 0.011 | 0.015 | 23.453 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | ASP | -1 | -0.872 | -0.948 | 22.901 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | PRO | 0 | -0.041 | -0.016 | 21.371 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | TRP | 0 | -0.019 | -0.011 | 18.099 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | VAL | 0 | 0.000 | 0.016 | 24.204 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | ARG | 1 | 0.921 | 0.962 | 27.699 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | GLY | 0 | 0.024 | 0.014 | 31.191 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |