FMODB ID: VQ8M1
Calculation Name: 2R5X-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2R5X
Chain ID: A
UniProt ID: Q5L106
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 121 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -1039308.582743 |
---|---|
FMO2-HF: Nuclear repulsion | 989999.910454 |
FMO2-HF: Total energy | -49308.672289 |
FMO2-MP2: Total energy | -49453.32847 |
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:0:SER)
Summations of interaction energy for
fragment #1(A:0:SER)
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. |
-14.906 | -8.202 | 0.716 | -3.372 | -4.048 | -0.018 |
Interaction energy analysis for fragmet #1(A:0:SER)
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 | 2 | LYS | 1 | 0.968 | 0.976 | 3.791 | -1.417 | -0.365 | -0.011 | -0.434 | -0.607 | 0.003 |
4 | A | 3 | PHE | 0 | -0.049 | -0.031 | 6.147 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | GLU | -1 | -0.854 | -0.936 | 9.686 | 0.500 | 0.500 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | ASN | 0 | -0.058 | -0.038 | 12.206 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | THR | 0 | 0.057 | 0.032 | 13.541 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | GLY | 0 | 0.022 | 0.004 | 16.342 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | LEU | 0 | 0.005 | 0.004 | 14.495 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | GLU | -1 | -0.867 | -0.919 | 13.298 | 0.398 | 0.398 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | ASN | 0 | -0.034 | -0.024 | 17.037 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | GLN | 0 | -0.023 | 0.005 | 20.058 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | THR | 0 | -0.004 | 0.002 | 21.210 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | VAL | 0 | 0.010 | 0.007 | 21.659 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | GLU | -1 | -0.877 | -0.937 | 24.089 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | LEU | 0 | 0.013 | -0.001 | 21.652 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | SER | 0 | -0.004 | 0.000 | 24.005 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | ARG | 1 | 0.989 | 0.998 | 26.300 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | LEU | 0 | -0.013 | -0.001 | 18.436 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | ASP | -1 | -0.787 | -0.920 | 21.634 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | ASP | -1 | -0.903 | -0.937 | 22.764 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | ILE | 0 | -0.067 | -0.034 | 20.771 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | MET | 0 | -0.059 | -0.037 | 17.116 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | GLU | -1 | -0.926 | -0.952 | 19.678 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | ARG | 1 | 0.897 | 0.950 | 21.966 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | LEU | 0 | -0.073 | -0.025 | 19.254 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | GLY | 0 | -0.021 | -0.010 | 18.631 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | PHE | 0 | -0.065 | -0.034 | 12.668 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | VAL | 0 | 0.014 | 0.009 | 16.291 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | ARG | 1 | 0.889 | 0.944 | 16.080 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | ALA | 0 | -0.031 | -0.019 | 13.246 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | ALA | 0 | -0.021 | -0.033 | 12.887 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | GLN | 0 | -0.004 | -0.011 | 14.996 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | TRP | 0 | 0.026 | 0.024 | 13.610 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | ASP | -1 | -0.910 | -0.956 | 15.678 | 0.337 | 0.337 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | TYR | 0 | 0.043 | 0.022 | 18.409 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | GLU | -1 | -0.968 | -0.973 | 18.593 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | ARG | 1 | 0.840 | 0.903 | 10.837 | -0.610 | -0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | VAL | 0 | 0.016 | 0.027 | 17.201 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | THR | 0 | 0.017 | -0.008 | 11.586 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | TYR | 0 | -0.033 | -0.011 | 13.342 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | ASP | -1 | -0.786 | -0.863 | 10.625 | 0.590 | 0.590 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | ARG | 1 | 0.922 | 0.975 | 12.009 | -0.354 | -0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | LYS | 1 | 0.930 | 0.961 | 12.014 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | TYR | 0 | 0.022 | 0.008 | 11.847 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | VAL | 0 | -0.034 | -0.013 | 13.218 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | VAL | 0 | -0.016 | -0.009 | 13.600 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | LYS | 1 | 0.980 | 0.983 | 16.491 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | GLU | -1 | -0.906 | -0.959 | 13.132 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | GLY | 0 | 0.050 | 0.038 | 13.164 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | THR | 0 | -0.079 | -0.032 | 11.178 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | TYR | 0 | 0.067 | 0.043 | 7.650 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | TYR | 0 | -0.044 | -0.024 | 6.470 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | LEU | 0 | -0.008 | 0.010 | 7.252 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | ARG | 1 | 0.844 | 0.880 | 7.254 | -0.756 | -0.756 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | VAL | 0 | 0.020 | 0.007 | 9.144 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | GLN | 0 | 0.011 | -0.007 | 10.997 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | GLY | 0 | 0.028 | 0.014 | 13.038 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | TYR | 0 | 0.018 | 0.022 | 16.253 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | ALA | 0 | 0.028 | 0.009 | 18.521 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | ILE | 0 | -0.067 | -0.024 | 22.297 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | GLU | -1 | -0.894 | -0.949 | 23.823 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | GLY | 0 | -0.018 | 0.006 | 26.477 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | ASN | 0 | 0.010 | -0.018 | 25.455 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | VAL | 0 | 0.036 | 0.014 | 20.533 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | ASP | -1 | -0.948 | -0.961 | 23.611 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | SER | 0 | -0.077 | -0.024 | 26.469 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | ARG | 1 | 0.962 | 0.978 | 27.197 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 68 | TYR | 0 | -0.038 | -0.016 | 28.323 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | ALA | 0 | 0.050 | 0.021 | 25.048 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | LEU | 0 | -0.010 | 0.006 | 25.224 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 71 | ILE | 0 | 0.001 | -0.005 | 19.183 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 72 | LYS | 1 | 0.912 | 0.965 | 16.352 | -0.363 | -0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 73 | LEU | 0 | -0.006 | -0.012 | 15.741 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 74 | LEU | 0 | -0.031 | -0.027 | 11.761 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 75 | THR | 0 | -0.033 | -0.031 | 8.802 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 76 | PRO | 0 | -0.028 | 0.003 | 9.025 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 77 | ILE | 0 | 0.003 | 0.000 | 3.624 | -0.221 | 0.000 | 0.002 | -0.037 | -0.186 | 0.000 |
79 | A | 78 | MET | 0 | -0.032 | -0.025 | 4.354 | -0.751 | -0.632 | -0.001 | -0.018 | -0.100 | 0.000 |
80 | A | 79 | GLY | 0 | 0.006 | 0.022 | 3.145 | 2.559 | 3.434 | 0.224 | -0.496 | -0.603 | -0.002 |
81 | A | 80 | LYS | 1 | 0.900 | 0.932 | 4.166 | 0.151 | 0.221 | -0.001 | -0.003 | -0.066 | 0.000 |
82 | A | 81 | HIS | 0 | -0.006 | 0.000 | 6.311 | -0.451 | -0.451 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 82 | TYR | 0 | -0.039 | -0.001 | 8.384 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 83 | TYR | 0 | -0.092 | -0.053 | 11.940 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 84 | PRO | 0 | -0.001 | -0.011 | 15.549 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 85 | HIS | 0 | -0.070 | -0.075 | 15.697 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 86 | GLY | 0 | 0.126 | 0.063 | 12.758 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 87 | VAL | 0 | -0.053 | -0.048 | 13.748 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 88 | GLU | -1 | -0.827 | -0.866 | 7.813 | -1.416 | -1.416 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 89 | TYR | 0 | -0.017 | -0.005 | 12.394 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 90 | GLY | 0 | -0.021 | -0.019 | 9.780 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 91 | ASP | -1 | -0.968 | -0.988 | 9.020 | -1.041 | -1.041 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 92 | ASP | -1 | -0.909 | -0.949 | 6.897 | -2.290 | -2.290 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 93 | GLU | -1 | -0.941 | -0.967 | 2.813 | -9.534 | -5.922 | 0.339 | -2.058 | -1.893 | -0.022 |
95 | A | 94 | HIS | 0 | -0.010 | 0.001 | 6.707 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 95 | PHE | 0 | 0.023 | -0.012 | 3.204 | -1.109 | -0.354 | 0.164 | -0.326 | -0.593 | 0.003 |
97 | A | 96 | PRO | 0 | -0.012 | 0.006 | 9.117 | -0.127 | -0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 97 | SER | 0 | 0.072 | 0.018 | 12.152 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 98 | SER | 0 | 0.010 | 0.002 | 14.165 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 99 | LEU | 0 | 0.051 | 0.016 | 10.645 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 100 | VAL | 0 | 0.035 | 0.016 | 9.503 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 101 | SER | 0 | -0.005 | -0.001 | 11.832 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 102 | GLN | 0 | -0.032 | -0.017 | 14.861 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 103 | CYS | 0 | -0.019 | -0.002 | 10.825 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 104 | GLN | 0 | 0.027 | 0.006 | 12.839 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 105 | ASN | 0 | -0.016 | -0.005 | 14.559 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 106 | VAL | 0 | -0.013 | 0.002 | 14.969 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 107 | LEU | 0 | 0.002 | -0.002 | 11.091 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 108 | ALA | 0 | 0.014 | 0.019 | 15.753 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 109 | GLN | 0 | -0.021 | -0.017 | 19.085 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 110 | VAL | 0 | 0.024 | 0.014 | 16.208 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 111 | LYS | 1 | 0.825 | 0.902 | 19.120 | -0.229 | -0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 112 | SER | 0 | -0.028 | -0.017 | 20.607 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 113 | GLU | -1 | -0.831 | -0.924 | 22.865 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 114 | LEU | 0 | -0.020 | -0.015 | 19.666 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 115 | GLU | -1 | -0.919 | -0.977 | 24.044 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 116 | LYS | 1 | 0.830 | 0.927 | 26.387 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 117 | ILE | 0 | 0.009 | 0.014 | 25.886 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 118 | LYS | 1 | 0.894 | 0.964 | 25.785 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 119 | GLU | -1 | -0.952 | -0.975 | 28.920 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 120 | GLU | -1 | -1.035 | -1.003 | 31.310 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |