FMODB ID: 8236Y
Calculation Name: 4BWD-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4BWD
Chain ID: B
UniProt ID: Q9UIL1
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 60 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -246417.266436 |
---|---|
FMO2-HF: Nuclear repulsion | 222108.657564 |
FMO2-HF: Total energy | -24308.608872 |
FMO2-MP2: Total energy | -24378.687846 |
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:88:ALA)
Summations of interaction energy for
fragment #1(B:88:ALA)
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. |
-5.193 | -1.297 | 0.482 | -1.761 | -2.618 | 0.007 |
Interaction energy analysis for fragmet #1(B:88:ALA)
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 | 90 | ASN | 0 | -0.036 | -0.032 | 3.112 | -2.323 | 0.400 | 0.119 | -1.325 | -1.518 | 0.006 |
4 | B | 91 | GLN | 0 | -0.030 | -0.010 | 2.726 | -1.911 | -0.916 | 0.364 | -0.395 | -0.963 | 0.001 |
5 | B | 92 | VAL | 0 | 0.057 | 0.026 | 4.534 | -0.645 | -0.467 | -0.001 | -0.041 | -0.137 | 0.000 |
6 | B | 93 | GLU | -1 | -0.908 | -0.943 | 6.446 | 0.637 | 0.637 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 94 | LEU | 0 | -0.024 | -0.014 | 7.971 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 95 | GLU | -1 | -0.938 | -0.958 | 7.471 | -0.385 | -0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 96 | GLU | -1 | -0.950 | -0.978 | 10.338 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 97 | LYS | 1 | 0.951 | 0.975 | 12.397 | -0.423 | -0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 98 | THR | 0 | -0.027 | -0.029 | 12.433 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 99 | ARG | 1 | 0.947 | 0.975 | 11.759 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 100 | LEU | 0 | -0.016 | 0.006 | 16.527 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 101 | ILE | 0 | -0.016 | -0.029 | 16.650 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 102 | ASN | 0 | -0.021 | -0.007 | 18.720 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 103 | GLN | 0 | 0.016 | 0.028 | 20.451 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 104 | VAL | 0 | -0.018 | -0.016 | 22.579 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 105 | MET | 0 | 0.000 | -0.003 | 22.100 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 106 | GLU | -1 | -0.882 | -0.937 | 23.708 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 107 | LEU | 0 | -0.049 | -0.030 | 26.400 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 108 | GLN | 0 | -0.033 | -0.023 | 27.807 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 109 | HIS | 0 | 0.026 | 0.024 | 28.976 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 110 | THR | 0 | -0.008 | -0.004 | 30.183 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 111 | LEU | 0 | -0.045 | -0.025 | 32.451 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 112 | GLU | -1 | -0.910 | -0.936 | 33.636 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 113 | ASP | -1 | -0.907 | -0.955 | 34.941 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 114 | LEU | 0 | -0.102 | -0.053 | 36.656 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 115 | SER | 0 | -0.038 | -0.040 | 37.851 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 116 | ALA | 0 | 0.089 | 0.063 | 39.516 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 117 | ARG | 1 | 0.920 | 0.945 | 39.337 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 118 | VAL | 0 | -0.030 | -0.021 | 42.749 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 119 | ASP | -1 | -0.876 | -0.939 | 43.568 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 120 | ALA | 0 | -0.027 | 0.001 | 45.613 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 121 | VAL | 0 | 0.010 | 0.000 | 47.445 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 122 | LYS | 1 | 0.890 | 0.938 | 47.298 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 123 | GLU | -1 | -0.910 | -0.943 | 49.780 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 124 | GLU | -1 | -0.948 | -0.983 | 51.545 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 125 | ASN | 0 | -0.033 | -0.025 | 52.716 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 126 | LEU | 0 | -0.058 | -0.026 | 53.175 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 127 | LYS | 1 | 0.951 | 0.990 | 55.953 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 128 | LEU | 0 | 0.072 | 0.032 | 56.738 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 129 | LYS | 1 | 0.898 | 0.949 | 56.305 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 130 | SER | 0 | -0.045 | -0.009 | 60.384 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 131 | GLU | -1 | -0.860 | -0.953 | 61.213 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 132 | ASN | 0 | -0.014 | -0.016 | 62.471 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 133 | GLN | 0 | -0.045 | -0.006 | 64.982 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 134 | VAL | 0 | 0.019 | 0.018 | 66.530 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 135 | LEU | 0 | -0.019 | -0.013 | 66.963 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 136 | GLY | 0 | -0.004 | -0.004 | 69.262 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 137 | GLN | 0 | 0.042 | 0.020 | 70.853 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 138 | TYR | 0 | -0.035 | -0.021 | 72.608 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 139 | ILE | 0 | 0.025 | 0.005 | 72.767 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 140 | GLU | -1 | -0.966 | -0.971 | 73.467 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 141 | ASN | 0 | 0.005 | 0.024 | 77.160 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 142 | LEU | 0 | -0.038 | -0.018 | 77.983 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 143 | MET | 0 | -0.034 | -0.026 | 79.178 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 144 | SER | 0 | -0.048 | -0.042 | 80.041 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 145 | ALA | 0 | -0.020 | 0.000 | 82.814 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 146 | SER | 0 | -0.094 | -0.038 | 84.548 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 147 | SER | 0 | -0.003 | 0.007 | 85.444 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |