![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 9GYQ2
Calculation Name: 4UYK-B-Xray323
Preferred Name:
Target Type:
Ligand Name: cytidine-5'-phosphate-2',3'-cyclic phosphate
ligand 3-letter code: CCC
PDB ID: 4UYK
Chain ID: B
UniProt ID: P49458
Base Structure: X-ray
Registration Date: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 93 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -602790.143127 |
---|---|
FMO2-HF: Nuclear repulsion | 565971.836729 |
FMO2-HF: Total energy | -36818.306397 |
FMO2-MP2: Total energy | -36923.581683 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F016590/ligand_interaction/ligand_F016590.png)
Ligand Interaction
![ligand interaction](./Kdata/F016590/ligand_interaction/ligand_interaction_F016590.png)
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:1:MET )
Summations of interaction energy for
fragment #1(B:1:MET )
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. |
-24.62 | -14.605 | 6.746 | -5.311 | -11.451 | -0.02 |
Interaction energy analysis for fragmet #1(B:1:MET )
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 | 3 | LEU | 0 | -0.028 | -0.004 | 3.163 | -1.502 | 1.203 | 0.142 | -1.222 | -1.625 | -0.002 |
4 | B | 4 | LEU | 0 | -0.016 | -0.011 | 4.464 | 0.876 | 1.029 | 0.000 | -0.022 | -0.130 | 0.000 |
5 | B | 5 | GLU | -1 | -0.846 | -0.922 | 7.579 | -1.122 | -1.122 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 6 | SER | 0 | -0.016 | -0.029 | 10.945 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 7 | GLU | -1 | -0.891 | -0.942 | 12.374 | -0.493 | -0.493 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 8 | GLN | 0 | 0.082 | 0.046 | 10.612 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 9 | PHE | 0 | 0.031 | 0.020 | 7.078 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 10 | LEU | 0 | 0.020 | 0.007 | 9.838 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 11 | THR | 0 | -0.002 | -0.018 | 13.225 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 12 | GLU | -1 | -0.961 | -0.999 | 8.937 | -0.714 | -0.714 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 13 | LEU | 0 | -0.073 | -0.033 | 10.336 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 14 | THR | 0 | 0.003 | -0.002 | 11.202 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 15 | ARG | 1 | 0.938 | 0.963 | 12.370 | 0.570 | 0.570 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 16 | LEU | 0 | -0.037 | -0.008 | 7.692 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 17 | PHE | 0 | 0.049 | 0.007 | 12.266 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 18 | GLN | 0 | -0.016 | -0.005 | 15.328 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 19 | LYS | 1 | 0.894 | 0.948 | 13.981 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 20 | CYS | 0 | -0.093 | -0.017 | 14.047 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 21 | ARG | 1 | 0.936 | 0.974 | 16.954 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 22 | THR | 0 | 0.009 | 0.004 | 20.457 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 23 | SER | 0 | -0.010 | -0.008 | 20.480 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 24 | GLY | 0 | 0.040 | 0.025 | 16.632 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 25 | SER | 0 | -0.010 | 0.000 | 15.183 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 26 | VAL | 0 | 0.030 | 0.007 | 11.633 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 27 | TYR | 0 | -0.021 | 0.001 | 9.912 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 28 | ILE | 0 | 0.011 | -0.009 | 9.415 | 0.322 | 0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 29 | THR | 0 | -0.075 | -0.030 | 7.419 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 30 | LEU | 0 | 0.049 | 0.016 | 8.285 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 31 | LYS | 1 | 0.950 | 0.981 | 8.105 | -1.133 | -1.133 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 32 | LYS | 1 | 0.967 | 0.996 | 10.213 | -0.117 | -0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 33 | TYR | 0 | -0.078 | -0.062 | 8.149 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 34 | ASP | -1 | -0.788 | -0.889 | 10.939 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 35 | GLY | 0 | 0.008 | 0.003 | 11.009 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 36 | ARG | 1 | 0.875 | 0.937 | 10.386 | -0.234 | -0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 37 | THR | 0 | 0.041 | 0.029 | 9.327 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 38 | LYS | 1 | 0.953 | 0.979 | 10.494 | 0.585 | 0.585 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 39 | PRO | 0 | 0.012 | -0.001 | 12.323 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 40 | ILE | 0 | 0.026 | 0.015 | 13.812 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 41 | PRO | 0 | 0.032 | 0.021 | 16.903 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 42 | LYS | 1 | 0.887 | 0.932 | 20.010 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 43 | NME | 0 | 0.060 | 0.049 | 23.762 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 49 | ACE | 0 | 0.004 | -0.011 | 22.695 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 50 | GLU | -1 | -0.969 | -0.998 | 15.381 | -0.453 | -0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 51 | PRO | 0 | -0.034 | 0.014 | 16.455 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 52 | ALA | 0 | 0.017 | 0.008 | 15.616 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 53 | ASP | -1 | -0.879 | -0.940 | 15.836 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 54 | ASN | 0 | -0.027 | -0.018 | 17.236 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 55 | LYS | 1 | 0.933 | 0.960 | 11.946 | 0.625 | 0.625 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 56 | CYS | 0 | 0.000 | -0.001 | 11.438 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 57 | LEU | 0 | -0.048 | -0.009 | 3.789 | -0.299 | -0.108 | 0.003 | -0.038 | -0.157 | 0.000 |
53 | B | 58 | LEU | 0 | 0.026 | 0.011 | 7.262 | 0.343 | 0.343 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 59 | ARG | 1 | 0.932 | 0.965 | 2.611 | -5.849 | -4.315 | 0.844 | -0.490 | -1.887 | 0.005 |
55 | B | 60 | ALA | 0 | 0.034 | 0.010 | 5.058 | -1.121 | -1.053 | 0.000 | -0.021 | -0.047 | 0.000 |
56 | B | 61 | THR | 0 | -0.062 | -0.058 | 5.576 | 0.706 | 0.706 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 62 | ASP | -1 | -0.729 | -0.858 | 7.507 | 0.995 | 0.995 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 63 | GLY | 0 | -0.040 | -0.010 | 9.109 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 64 | LYS | 1 | 0.889 | 0.944 | 9.602 | -0.803 | -0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 65 | LYS | 1 | 0.952 | 0.979 | 6.228 | 0.227 | 0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 66 | LYS | 1 | 0.967 | 0.997 | 2.401 | -10.055 | -8.520 | 2.244 | -0.950 | -2.830 | 0.002 |
62 | B | 67 | ILE | 0 | 0.022 | 0.030 | 2.810 | -5.056 | -3.395 | 0.708 | -0.985 | -1.384 | -0.012 |
63 | B | 68 | SER | 0 | -0.030 | -0.038 | 2.535 | -0.445 | 1.672 | 2.801 | -1.563 | -3.355 | -0.013 |
64 | B | 69 | THR | 0 | 0.058 | 0.029 | 4.534 | -1.697 | -1.646 | 0.004 | -0.020 | -0.036 | 0.000 |
65 | B | 70 | VAL | 0 | -0.008 | -0.009 | 6.868 | 0.518 | 0.518 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 71 | VAL | 0 | 0.023 | 0.029 | 9.077 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 72 | SER | 0 | -0.030 | -0.020 | 12.678 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 73 | SER | 0 | 0.084 | 0.013 | 15.756 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | B | 74 | LYS | 1 | 0.930 | 0.972 | 18.558 | 0.464 | 0.464 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | B | 75 | GLU | -1 | -0.859 | -0.929 | 14.152 | -0.674 | -0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | B | 76 | VAL | 0 | -0.009 | 0.003 | 16.625 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | B | 77 | ASN | 0 | 0.028 | 0.010 | 18.212 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | B | 78 | LYS | 1 | 1.005 | 1.016 | 19.230 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | B | 79 | PHE | 0 | 0.009 | -0.001 | 12.337 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | B | 80 | GLN | 0 | 0.022 | -0.013 | 17.706 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | B | 81 | MET | 0 | 0.004 | 0.014 | 19.308 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | B | 82 | ALA | 0 | 0.009 | 0.004 | 18.347 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | B | 83 | TYR | 0 | 0.021 | 0.008 | 13.122 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | B | 84 | SER | 0 | 0.016 | 0.001 | 17.470 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | B | 85 | ASN | 0 | -0.009 | -0.006 | 20.253 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | B | 86 | LEU | 0 | -0.014 | 0.015 | 14.536 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | B | 87 | LEU | 0 | 0.010 | -0.010 | 15.465 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | B | 88 | ARG | 1 | 0.914 | 0.964 | 18.953 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | B | 89 | ALA | 0 | -0.063 | -0.042 | 21.220 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | B | 90 | ASN | 0 | -0.007 | 0.003 | 18.241 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | B | 91 | MET | 0 | -0.071 | -0.013 | 18.447 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | B | 92 | ASP | -1 | -0.909 | -0.940 | 21.290 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | B | 93 | GLY | 0 | 0.020 | 0.005 | 23.890 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | B | 94 | LEU | 0 | 0.029 | 0.010 | 23.768 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | B | 95 | LYS | 1 | 0.948 | 0.966 | 27.789 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | B | 96 | LYS | 1 | 0.958 | 0.955 | 30.701 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | B | 97 | ARG | 1 | 0.930 | 0.981 | 30.491 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | B | 98 | NME | 0 | 0.076 | 0.055 | 36.583 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |