FMODB ID: 39K5L
Calculation Name: 1OPS-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1OPS
Chain ID: A
UniProt ID: P19608
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 | 64 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -340934.138824 |
---|---|
FMO2-HF: Nuclear repulsion | 316195.860795 |
FMO2-HF: Total energy | -24738.278029 |
FMO2-MP2: Total energy | -24806.27281 |
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:2:SER)
Summations of interaction energy for
fragment #1(A:2: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. |
-3.133 | -0.958 | 0.007 | -0.975 | -1.207 | 0.003 |
Interaction energy analysis for fragmet #1(A:2: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 | 4 | SER | 0 | 0.053 | 0.037 | 3.832 | -2.932 | -1.383 | -0.021 | -0.734 | -0.794 | 0.002 |
4 | A | 5 | VAL | 0 | 0.005 | 0.006 | 6.722 | 0.596 | 0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 6 | VAL | 0 | -0.026 | -0.009 | 9.836 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | ALA | 0 | 0.031 | 0.024 | 12.600 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | THR | 0 | 0.022 | 0.005 | 16.009 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | GLN | 0 | -0.058 | -0.054 | 18.070 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | LEU | 0 | 0.012 | 0.013 | 20.754 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | ILE | 0 | 0.022 | 0.011 | 18.394 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | PRO | 0 | 0.021 | 0.007 | 22.963 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | MET | 0 | 0.018 | 0.046 | 25.133 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | ASN | 0 | -0.044 | -0.033 | 25.208 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | THR | 0 | -0.026 | -0.038 | 23.592 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | ALA | 0 | -0.011 | -0.011 | 22.883 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | LEU | 0 | 0.013 | -0.009 | 16.235 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | THR | 0 | 0.062 | 0.018 | 19.742 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | PRO | 0 | 0.057 | -0.001 | 16.272 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | ALA | 0 | 0.005 | 0.010 | 16.473 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | MET | 0 | -0.040 | 0.016 | 18.282 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | MET | 0 | -0.039 | -0.005 | 12.813 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | GLU | -1 | -0.914 | -0.945 | 12.161 | 0.435 | 0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | GLY | 0 | 0.021 | 0.012 | 7.994 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | LYS | 1 | 0.923 | 0.955 | 7.827 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | VAL | 0 | 0.036 | 0.029 | 3.458 | -1.004 | -0.437 | 0.029 | -0.232 | -0.365 | 0.001 |
26 | A | 27 | THR | 0 | -0.038 | -0.021 | 5.796 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | ASN | 0 | 0.028 | 0.017 | 7.102 | -0.436 | -0.436 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | PRO | 0 | 0.011 | -0.008 | 9.778 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | ILE | 0 | 0.003 | 0.017 | 4.685 | -0.027 | 0.032 | -0.001 | -0.009 | -0.048 | 0.000 |
30 | A | 31 | GLY | 0 | 0.005 | -0.020 | 7.616 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | ILE | 0 | -0.061 | -0.005 | 8.421 | -0.223 | -0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | PRO | 0 | 0.057 | 0.024 | 4.946 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | PHE | 0 | 0.004 | -0.025 | 4.963 | 0.477 | 0.477 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | ALA | 0 | -0.013 | -0.010 | 5.047 | 0.316 | 0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | GLU | -1 | -0.842 | -0.915 | 6.583 | -0.743 | -0.743 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | MET | 0 | 0.007 | 0.012 | 9.205 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | SER | 0 | 0.016 | -0.007 | 11.151 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | GLN | 0 | -0.003 | 0.007 | 13.007 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | LEU | 0 | -0.034 | -0.019 | 12.647 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | VAL | 0 | -0.033 | -0.010 | 15.631 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | GLY | 0 | -0.009 | 0.008 | 17.909 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | LYS | 1 | 0.877 | 0.955 | 17.885 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | GLN | 0 | 0.024 | 0.007 | 20.639 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | VAL | 0 | 0.020 | 0.032 | 19.027 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | ASN | 0 | -0.076 | -0.066 | 21.363 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | THR | 0 | 0.069 | 0.016 | 22.285 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 48 | PRO | 0 | -0.067 | -0.002 | 23.436 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | VAL | 0 | 0.017 | 0.009 | 18.046 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | ALA | 0 | 0.043 | 0.017 | 20.930 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | LYS | 1 | 0.926 | 0.953 | 19.451 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | GLY | 0 | -0.037 | -0.021 | 16.433 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | GLN | 0 | 0.012 | 0.020 | 15.799 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | THR | 0 | 0.006 | -0.009 | 10.507 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | LEU | 0 | 0.004 | -0.013 | 12.755 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | MET | 0 | 0.036 | 0.008 | 12.193 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | PRO | 0 | 0.068 | 0.017 | 12.193 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | ASN | 0 | -0.005 | -0.003 | 14.811 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | MET | 0 | -0.012 | 0.043 | 17.011 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | VAL | 0 | 0.030 | 0.029 | 15.696 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | LYS | 1 | 0.921 | 0.960 | 18.694 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | THR | 0 | -0.009 | -0.028 | 21.035 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | TYR | 0 | -0.057 | -0.049 | 11.030 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | ALA | 0 | 0.014 | 0.008 | 16.375 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | ALA | 0 | -0.025 | 0.006 | 17.996 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |