FMODB ID: NNK3Q
Calculation Name: 4M78-D-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4M78
Chain ID: D
UniProt ID: P38203
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 75 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -456980.173909 |
---|---|
FMO2-HF: Nuclear repulsion | 427813.511236 |
FMO2-HF: Total energy | -29166.662673 |
FMO2-MP2: Total energy | -29251.82468 |
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(D:10:SER)
Summations of interaction energy for
fragment #1(D:10: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. |
-14.503 | -8.031 | 6.244 | -5.351 | -7.365 | -0.001 |
Interaction energy analysis for fragmet #1(D:10: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 | D | 12 | THR | 0 | -0.030 | -0.017 | 2.727 | -7.607 | -2.978 | 0.367 | -2.317 | -2.679 | 0.016 |
4 | D | 13 | THR | 0 | -0.025 | -0.024 | 1.990 | -3.158 | -2.335 | 5.876 | -2.744 | -3.955 | -0.016 |
5 | D | 14 | GLU | -1 | -0.910 | -0.946 | 3.765 | -4.007 | -2.987 | 0.001 | -0.290 | -0.731 | -0.001 |
6 | D | 15 | PHE | 0 | 0.036 | 0.014 | 5.707 | 0.799 | 0.799 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | D | 16 | LEU | 0 | -0.075 | -0.049 | 7.211 | 0.292 | 0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | D | 17 | SER | 0 | -0.031 | -0.008 | 8.648 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | D | 18 | ASP | -1 | -0.910 | -0.936 | 10.124 | -0.940 | -0.940 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | D | 19 | ILE | 0 | -0.043 | -0.037 | 12.005 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | D | 20 | ILE | 0 | 0.002 | 0.028 | 13.128 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | D | 21 | GLY | 0 | -0.010 | 0.001 | 15.266 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | D | 22 | LYS | 1 | 0.870 | 0.926 | 16.081 | 0.411 | 0.411 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | D | 23 | THR | 0 | -0.023 | -0.013 | 19.129 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | D | 24 | VAL | 0 | -0.008 | -0.016 | 16.762 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | D | 25 | ASN | 0 | 0.020 | 0.045 | 19.686 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | D | 26 | VAL | 0 | 0.023 | 0.003 | 17.853 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | D | 27 | LYS | 1 | 0.852 | 0.961 | 19.363 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | D | 28 | LEU | 0 | -0.006 | 0.005 | 19.751 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | D | 29 | ALA | 0 | 0.018 | -0.001 | 21.539 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | D | 30 | SER | 0 | -0.032 | -0.016 | 22.522 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | D | 31 | GLY | 0 | 0.076 | 0.035 | 24.549 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | D | 32 | LEU | 0 | -0.060 | -0.028 | 25.678 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | D | 33 | LEU | 0 | -0.058 | -0.028 | 22.501 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | D | 34 | TYR | 0 | -0.016 | -0.020 | 22.995 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | D | 35 | SER | 0 | 0.000 | -0.035 | 22.956 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | D | 36 | GLY | 0 | 0.033 | 0.008 | 22.951 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | D | 37 | ARG | 1 | 0.897 | 0.984 | 21.361 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | D | 38 | LEU | 0 | 0.011 | 0.004 | 14.982 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | D | 39 | GLU | -1 | -0.862 | -0.934 | 18.448 | -0.290 | -0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | D | 40 | SER | 0 | -0.021 | -0.028 | 15.776 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | D | 41 | ILE | 0 | -0.004 | -0.005 | 11.179 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | D | 42 | ASP | -1 | -0.807 | -0.889 | 11.431 | -0.519 | -0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | D | 43 | GLY | 0 | 0.045 | 0.013 | 8.893 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | D | 44 | PHE | 0 | -0.108 | -0.057 | 9.737 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | D | 45 | MET | 0 | 0.018 | 0.004 | 10.936 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | D | 46 | ASN | 0 | -0.018 | -0.002 | 13.006 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | D | 47 | VAL | 0 | 0.003 | 0.000 | 15.147 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | D | 48 | ALA | 0 | 0.007 | 0.027 | 17.513 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | D | 49 | LEU | 0 | -0.025 | -0.006 | 19.505 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | D | 50 | SER | 0 | 0.078 | 0.055 | 22.094 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | D | 51 | SER | 0 | -0.082 | -0.051 | 25.206 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | D | 52 | ALA | 0 | 0.025 | 0.025 | 25.609 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | D | 53 | THR | 0 | -0.038 | -0.030 | 27.143 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | D | 54 | GLU | -1 | -0.859 | -0.922 | 27.830 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | D | 55 | HIS | 0 | 0.026 | 0.006 | 28.597 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | D | 56 | TYR | 0 | 0.042 | 0.028 | 28.647 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | D | 57 | GLU | -1 | -0.874 | -0.946 | 26.320 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | D | 58 | SER | 0 | -0.054 | -0.055 | 26.396 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | D | 59 | ASN | 0 | 0.081 | 0.031 | 26.937 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | D | 60 | ASN | 0 | -0.022 | -0.006 | 28.624 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | D | 61 | ASN | 0 | -0.007 | 0.015 | 31.616 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | D | 62 | LYS | 1 | 0.918 | 0.955 | 33.556 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | D | 63 | LEU | 0 | 0.009 | 0.010 | 32.347 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | D | 64 | LEU | 0 | -0.049 | -0.026 | 31.888 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | D | 65 | ASN | 0 | -0.026 | -0.023 | 32.301 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | D | 66 | LYS | 1 | 0.966 | 0.989 | 31.282 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | D | 67 | PHE | 0 | 0.018 | 0.020 | 29.269 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | D | 68 | ASN | 0 | -0.059 | -0.043 | 30.512 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | D | 69 | SER | 0 | -0.038 | -0.017 | 29.865 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | D | 70 | ASP | -1 | -0.841 | -0.937 | 24.389 | -0.185 | -0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | D | 71 | VAL | 0 | -0.069 | -0.022 | 23.968 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | D | 72 | PHE | 0 | -0.003 | -0.004 | 20.096 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | D | 73 | LEU | 0 | 0.012 | -0.014 | 19.939 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | D | 74 | ARG | 1 | 0.936 | 0.962 | 19.282 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | D | 75 | GLY | 0 | 0.107 | 0.043 | 16.211 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | D | 76 | THR | 0 | -0.043 | -0.027 | 16.822 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | D | 77 | GLN | 0 | -0.088 | -0.043 | 18.215 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | D | 78 | VAL | 0 | -0.021 | 0.003 | 15.292 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | D | 79 | MET | 0 | -0.017 | 0.001 | 16.278 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | D | 80 | TYR | 0 | -0.023 | -0.022 | 14.800 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | D | 81 | ILE | 0 | 0.009 | -0.002 | 13.207 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | D | 82 | SER | 0 | 0.008 | 0.010 | 14.651 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | D | 83 | GLU | -1 | -0.915 | -0.940 | 16.330 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | D | 84 | GLN | 0 | -0.046 | -0.017 | 18.388 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |