FMODB ID: YZ322
Calculation Name: 1BV4-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1BV4
Chain ID: C
UniProt ID: P08661
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 | OptHSide |
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 | 79 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -531191.349892 |
---|---|
FMO2-HF: Nuclear repulsion | 498678.23686 |
FMO2-HF: Total energy | -32513.113032 |
FMO2-MP2: Total energy | -32604.200269 |
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(C:115:LYS)
Summations of interaction energy for
fragment #1(C:115:LYS)
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. |
-195.408 | -192.983 | 38.194 | -19.254 | -21.365 | -0.21 |
Interaction energy analysis for fragmet #1(C:115:LYS)
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 | C | 117 | PHE | 0 | 0.029 | -0.003 | 2.466 | -3.831 | -0.453 | 2.750 | -2.175 | -3.953 | 0.002 |
4 | C | 118 | MET | 0 | -0.012 | -0.003 | 6.127 | 4.431 | 4.431 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | C | 119 | SER | 0 | 0.035 | 0.031 | 9.554 | -1.389 | -1.389 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 120 | SER | 0 | -0.072 | -0.040 | 12.108 | 0.965 | 0.965 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 121 | VAL | 0 | 0.032 | 0.007 | 15.262 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 122 | ARG | 1 | 0.946 | 0.968 | 18.703 | 14.295 | 14.295 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 123 | ARG | 1 | 0.885 | 0.940 | 18.313 | 13.960 | 13.960 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 124 | MET | 0 | -0.052 | 0.010 | 16.799 | 0.811 | 0.811 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 125 | PRO | 0 | 0.079 | 0.039 | 18.271 | -0.668 | -0.668 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 126 | LEU | 0 | 0.104 | 0.054 | 12.420 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 127 | ASN | 0 | 0.014 | -0.002 | 15.684 | -1.200 | -1.200 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 128 | ARG | 1 | 0.910 | 0.933 | 17.539 | 15.336 | 15.336 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 129 | ALA | 0 | 0.045 | 0.022 | 13.570 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 130 | LYS | 1 | 0.924 | 0.966 | 12.762 | 16.874 | 16.874 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 131 | ALA | 0 | -0.025 | -0.003 | 13.828 | -0.490 | -0.490 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 132 | LEU | 0 | -0.015 | -0.014 | 14.198 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 133 | CYS | 0 | -0.094 | -0.022 | 8.162 | -1.520 | -1.520 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 134 | SER | 0 | 0.051 | 0.031 | 11.281 | -0.596 | -0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 135 | GLU | -1 | -0.980 | -0.974 | 13.059 | -15.856 | -15.856 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 136 | LEU | 0 | -0.077 | -0.039 | 12.028 | 0.813 | 0.813 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 137 | GLN | 0 | -0.052 | -0.029 | 11.058 | -1.149 | -1.149 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 138 | GLY | 0 | 0.034 | 0.023 | 7.637 | -1.716 | -1.716 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 139 | THR | 0 | -0.020 | -0.019 | 5.893 | 3.968 | 3.968 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 140 | VAL | 0 | 0.004 | -0.004 | 7.135 | -2.826 | -2.826 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 141 | ALA | 0 | -0.003 | -0.013 | 4.301 | -3.509 | -3.420 | -0.001 | -0.013 | -0.075 | 0.000 |
28 | C | 142 | THR | 0 | 0.001 | -0.004 | 3.325 | 13.396 | 13.744 | 0.001 | -0.117 | -0.231 | 0.000 |
29 | C | 143 | PRO | 0 | -0.029 | -0.017 | 3.315 | -20.090 | -19.178 | 0.078 | -0.450 | -0.541 | -0.004 |
30 | C | 144 | ARG | 1 | 0.849 | 0.923 | 2.729 | 63.862 | 64.625 | 0.122 | -0.198 | -0.688 | -0.001 |
31 | C | 145 | ASN | 0 | 0.006 | 0.002 | 5.159 | 9.123 | 9.182 | -0.001 | -0.001 | -0.057 | 0.000 |
32 | C | 146 | ALA | 0 | 0.025 | -0.001 | 7.370 | -2.132 | -2.132 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 147 | GLU | -1 | -0.856 | -0.913 | 7.625 | -25.314 | -25.314 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 148 | GLU | -1 | -0.762 | -0.882 | 1.705 | -109.018 | -112.718 | 14.003 | -5.490 | -4.814 | -0.073 |
35 | C | 149 | ASN | 0 | -0.011 | 0.016 | 5.392 | -0.631 | -0.593 | -0.001 | 0.000 | -0.036 | 0.000 |
36 | C | 150 | ARG | 1 | 0.883 | 0.923 | 7.941 | 26.991 | 26.991 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 151 | ALA | 0 | -0.011 | -0.005 | 5.817 | 2.233 | 2.233 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 152 | ILE | 0 | 0.023 | 0.000 | 3.874 | 2.153 | 2.289 | -0.001 | -0.013 | -0.123 | 0.000 |
39 | C | 153 | GLN | 0 | -0.013 | -0.012 | 7.770 | 3.520 | 3.520 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 154 | ASN | 0 | -0.058 | -0.017 | 10.745 | 3.238 | 3.238 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 155 | VAL | 0 | -0.057 | -0.026 | 8.495 | 1.873 | 1.873 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 156 | ALA | 0 | -0.011 | 0.011 | 11.023 | 1.586 | 1.586 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 157 | LYS | 1 | 0.922 | 0.955 | 12.892 | 18.959 | 18.959 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 158 | ASP | -1 | -0.821 | -0.903 | 15.894 | -14.622 | -14.622 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 159 | VAL | 0 | -0.030 | -0.011 | 15.522 | -1.337 | -1.337 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 160 | ALA | 0 | -0.010 | -0.007 | 12.224 | 0.434 | 0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 161 | PHE | 0 | -0.032 | -0.014 | 12.519 | -0.327 | -0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 162 | LEU | 0 | -0.020 | 0.004 | 7.683 | -2.539 | -2.539 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 163 | GLY | 0 | -0.027 | -0.017 | 7.760 | 3.319 | 3.319 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 164 | ILE | 0 | -0.040 | -0.006 | 8.919 | 0.424 | 0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 174 | GLU | -1 | -0.952 | -0.984 | 12.382 | -20.085 | -20.085 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 175 | ASP | -1 | -0.757 | -0.868 | 7.645 | -36.479 | -36.479 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 176 | LEU | 0 | -0.074 | -0.059 | 9.494 | 2.468 | 2.468 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 177 | THR | 0 | -0.110 | -0.051 | 9.128 | 1.213 | 1.213 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 178 | GLY | 0 | 0.018 | 0.034 | 10.688 | -0.187 | -0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | C | 200 | CYS | 0 | -0.004 | -0.017 | 15.504 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | C | 201 | VAL | 0 | 0.026 | 0.009 | 12.510 | 0.607 | 0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | C | 202 | VAL | 0 | -0.012 | -0.001 | 13.224 | -1.210 | -1.210 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | C | 203 | LEU | 0 | -0.030 | -0.001 | 9.586 | 0.599 | 0.599 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | C | 204 | LEU | 0 | 0.026 | -0.001 | 13.256 | 0.829 | 0.829 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | C | 205 | THR | 0 | 0.077 | 0.032 | 15.490 | -0.883 | -0.883 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | C | 206 | ASN | 0 | -0.037 | -0.013 | 17.602 | -0.882 | -0.882 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | C | 207 | GLY | 0 | -0.002 | -0.009 | 14.000 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | C | 208 | LYS | 1 | 0.904 | 0.951 | 13.669 | 16.605 | 16.605 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | C | 209 | TRP | 0 | -0.001 | -0.020 | 9.093 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | C | 210 | ASN | 0 | -0.014 | -0.005 | 15.298 | 0.903 | 0.903 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | C | 211 | ASP | -1 | -0.917 | -0.950 | 16.922 | -17.309 | -17.309 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | C | 212 | VAL | 0 | -0.020 | -0.009 | 17.671 | 0.988 | 0.988 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | C | 213 | PRO | 0 | 0.057 | 0.033 | 19.355 | -0.602 | -0.602 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | C | 215 | SER | 0 | -0.016 | -0.020 | 19.370 | -0.246 | -0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | C | 216 | ASP | -1 | -0.884 | -0.925 | 21.425 | -12.767 | -12.767 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | C | 217 | SER | 0 | -0.058 | -0.049 | 19.970 | -0.777 | -0.777 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | C | 218 | PHE | 0 | 0.041 | 0.010 | 16.544 | 0.499 | 0.499 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | C | 219 | LEU | 0 | -0.003 | 0.013 | 15.213 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | C | 220 | VAL | 0 | 0.021 | 0.006 | 11.631 | -0.755 | -0.755 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | C | 221 | VAL | 0 | 0.069 | 0.031 | 7.289 | 1.149 | 1.149 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | C | 223 | GLU | -1 | -0.775 | -0.896 | 1.858 | -138.019 | -139.948 | 17.377 | -7.784 | -7.663 | -0.108 |
78 | C | 224 | PHE | 0 | 0.022 | 0.010 | 3.667 | 2.106 | 2.594 | 0.005 | -0.133 | -0.359 | 0.000 |
79 | C | 225 | SER | 0 | 0.014 | 0.009 | 2.385 | -4.778 | -2.935 | 3.862 | -2.880 | -2.825 | -0.026 |