![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R5JL8
Calculation Name: 4UYK-B-Xray372
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: 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 | 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 | 90 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -598664.282156 |
---|---|
FMO2-HF: Nuclear repulsion | 562035.556088 |
FMO2-HF: Total energy | -36628.726069 |
FMO2-MP2: Total energy | -36733.328703 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F023355/ligand_interaction/ligand_F023355.png)
Ligand Interaction
![ligand interaction](./Kdata/F023355/ligand_interaction/ligand_interaction_F023355.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. |
-22.405 | -14.619 | 9.342 | -5.442 | -11.688 | -0.005 |
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 | 0.002 | 3.270 | -1.195 | 1.390 | 0.092 | -1.122 | -1.555 | 0.000 |
4 | B | 4 | LEU | 0 | 0.003 | 0.001 | 4.463 | 0.812 | 0.972 | -0.001 | -0.025 | -0.135 | 0.000 |
5 | B | 5 | GLU | -1 | -0.855 | -0.904 | 7.625 | -1.046 | -1.046 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 6 | SER | 0 | -0.002 | -0.025 | 10.967 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 7 | GLU | -1 | -0.841 | -0.909 | 12.408 | -0.409 | -0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 8 | GLN | 0 | 0.116 | 0.046 | 10.625 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 9 | PHE | 0 | 0.032 | 0.022 | 7.043 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 10 | LEU | 0 | 0.030 | 0.017 | 9.935 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 11 | THR | 0 | 0.001 | 0.004 | 13.324 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 12 | GLU | -1 | -0.831 | -0.899 | 9.144 | -0.681 | -0.681 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 13 | LEU | 0 | -0.059 | -0.032 | 10.073 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 14 | THR | 0 | -0.020 | -0.024 | 11.264 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 15 | ARG | 1 | 0.802 | 0.864 | 11.826 | 0.619 | 0.619 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 16 | LEU | 0 | -0.039 | -0.010 | 7.723 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 17 | PHE | 0 | 0.059 | 0.014 | 12.383 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 18 | GLN | 0 | -0.023 | -0.005 | 15.395 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 19 | LYS | 1 | 0.903 | 0.954 | 13.863 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 20 | CYS | 0 | -0.117 | -0.034 | 14.189 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 21 | ARG | 1 | 0.877 | 0.916 | 17.048 | -0.221 | -0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 22 | THR | 0 | 0.017 | 0.006 | 20.547 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 23 | SER | 0 | 0.005 | -0.001 | 20.579 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 24 | GLY | 0 | 0.023 | 0.018 | 16.702 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 25 | SER | 0 | 0.004 | 0.006 | 15.070 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 26 | VAL | 0 | 0.019 | 0.002 | 11.625 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 27 | TYR | 0 | -0.028 | -0.002 | 10.135 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 28 | ILE | 0 | 0.012 | -0.011 | 9.578 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 29 | THR | 0 | -0.056 | -0.021 | 7.421 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 30 | LEU | 0 | 0.039 | 0.015 | 8.613 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 31 | LYS | 1 | 0.955 | 0.981 | 8.601 | -1.149 | -1.149 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 32 | LYS | 1 | 0.924 | 0.966 | 10.170 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 33 | TYR | 0 | -0.063 | -0.058 | 7.834 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 34 | ASP | -1 | -0.780 | -0.864 | 10.679 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 35 | GLY | 0 | 0.020 | 0.009 | 10.575 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 36 | ARG | 1 | 0.839 | 0.901 | 10.221 | -0.262 | -0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 37 | THR | 0 | 0.042 | 0.031 | 8.827 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 38 | LYS | 1 | 0.957 | 0.985 | 10.129 | 0.593 | 0.593 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 39 | PRO | 0 | 0.010 | -0.005 | 11.994 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 40 | ILE | 0 | 0.013 | 0.009 | 13.513 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 41 | PRO | 0 | 0.016 | 0.015 | 16.629 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 42 | LYS | 1 | 0.978 | 0.995 | 19.180 | -0.150 | -0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 50 | GLU | -1 | -0.952 | -0.993 | 14.577 | -0.475 | -0.475 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 51 | PRO | 0 | -0.047 | -0.014 | 16.026 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 52 | ALA | 0 | 0.017 | 0.014 | 15.149 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 53 | ASP | -1 | -0.874 | -0.940 | 15.469 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 54 | ASN | 0 | 0.019 | 0.005 | 16.831 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 55 | LYS | 1 | 0.924 | 0.969 | 11.695 | 0.552 | 0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 56 | CYS | 0 | -0.057 | -0.020 | 11.293 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 57 | LEU | 0 | -0.012 | -0.008 | 3.790 | -0.312 | -0.110 | 0.003 | -0.038 | -0.167 | 0.000 |
51 | B | 58 | LEU | 0 | 0.030 | 0.018 | 7.303 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 59 | ARG | 1 | 0.927 | 0.955 | 2.389 | -7.491 | -7.418 | 4.553 | -1.242 | -3.384 | 0.013 |
53 | B | 60 | ALA | 0 | 0.032 | 0.017 | 5.289 | -1.155 | -1.103 | -0.001 | -0.020 | -0.031 | 0.000 |
54 | B | 61 | THR | 0 | -0.062 | -0.056 | 5.541 | 0.442 | 0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 62 | ASP | -1 | -0.677 | -0.828 | 7.499 | 0.923 | 0.923 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 63 | GLY | 0 | -0.039 | -0.006 | 9.150 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 64 | LYS | 1 | 0.832 | 0.914 | 9.563 | -0.724 | -0.724 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 65 | LYS | 1 | 0.940 | 0.970 | 6.196 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 66 | LYS | 1 | 0.965 | 0.990 | 2.508 | -7.662 | -6.185 | 1.163 | -0.637 | -2.002 | 0.000 |
60 | B | 67 | ILE | 0 | 0.007 | 0.022 | 3.060 | -4.259 | -2.845 | 0.326 | -0.714 | -1.026 | -0.007 |
61 | B | 68 | SER | 0 | -0.019 | -0.033 | 2.533 | 0.049 | 1.818 | 3.205 | -1.617 | -3.358 | -0.011 |
62 | B | 69 | THR | 0 | -0.011 | -0.024 | 4.634 | -1.681 | -1.627 | 0.002 | -0.027 | -0.030 | 0.000 |
63 | B | 70 | VAL | 0 | 0.011 | -0.001 | 6.744 | 0.533 | 0.533 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | B | 71 | VAL | 0 | 0.005 | 0.015 | 9.062 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | B | 72 | SER | 0 | -0.053 | -0.062 | 12.705 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 73 | SER | 0 | 0.073 | 0.017 | 15.695 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 74 | LYS | 1 | 0.936 | 0.972 | 18.269 | 0.444 | 0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 75 | GLU | -1 | -0.803 | -0.866 | 15.113 | -0.562 | -0.562 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | B | 76 | VAL | 0 | -0.004 | 0.001 | 16.452 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | B | 77 | ASN | 0 | 0.028 | 0.015 | 18.276 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | B | 78 | LYS | 1 | 0.936 | 0.979 | 19.088 | 0.398 | 0.398 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | B | 79 | PHE | 0 | 0.010 | -0.001 | 12.693 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | B | 80 | GLN | 0 | 0.018 | -0.014 | 17.856 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | B | 81 | MET | 0 | 0.013 | 0.029 | 19.434 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | B | 82 | ALA | 0 | 0.013 | 0.004 | 18.443 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | B | 83 | TYR | 0 | 0.025 | 0.010 | 13.167 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | B | 84 | SER | 0 | 0.017 | -0.012 | 17.521 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | B | 85 | ASN | 0 | -0.001 | 0.009 | 20.358 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | B | 86 | LEU | 0 | 0.000 | 0.016 | 14.613 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | B | 87 | LEU | 0 | 0.013 | -0.001 | 15.505 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | B | 88 | ARG | 1 | 0.902 | 0.944 | 19.115 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | B | 89 | ALA | 0 | -0.070 | -0.042 | 21.221 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | B | 90 | ASN | 0 | -0.031 | -0.016 | 18.280 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | B | 91 | MET | 0 | -0.056 | -0.004 | 18.715 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | B | 92 | ASP | -1 | -0.848 | -0.893 | 21.284 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | B | 93 | GLY | 0 | 0.016 | 0.011 | 23.884 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | B | 94 | LEU | 0 | 0.035 | 0.016 | 24.069 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | B | 95 | LYS | 1 | 0.946 | 0.963 | 27.908 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | B | 96 | LYS | 1 | 0.967 | 0.965 | 30.890 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | B | 97 | ARG | 1 | 1.007 | 1.032 | 30.622 | -0.197 | -0.197 | 0.000 | 0.000 | 0.000 | 0.000 |