![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: ZYQZN
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 | 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 | 90 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -597911.37729 |
---|---|
FMO2-HF: Nuclear repulsion | 561283.235117 |
FMO2-HF: Total energy | -36628.142173 |
FMO2-MP2: Total energy | -36732.759908 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F023356/ligand_interaction/ligand_F023356.png)
Ligand Interaction
![ligand interaction](./Kdata/F023356/ligand_interaction/ligand_interaction_F023356.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. |
-24.644 | -14.621 | 6.34 | -5.175 | -11.189 | -0.019 |
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 | -0.031 | -0.006 | 3.170 | -1.463 | 1.276 | 0.134 | -1.234 | -1.639 | -0.002 |
4 | B | 4 | LEU | 0 | -0.014 | -0.009 | 4.476 | 0.772 | 0.930 | -0.001 | -0.023 | -0.134 | 0.000 |
5 | B | 5 | GLU | -1 | -0.848 | -0.923 | 7.593 | -1.139 | -1.139 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 6 | SER | 0 | -0.016 | -0.029 | 10.964 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 7 | GLU | -1 | -0.893 | -0.943 | 12.395 | -0.495 | -0.495 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 8 | GLN | 0 | 0.084 | 0.046 | 10.623 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 9 | PHE | 0 | 0.030 | 0.020 | 7.098 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 10 | LEU | 0 | 0.020 | 0.006 | 9.853 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 11 | THR | 0 | -0.001 | -0.017 | 13.241 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 12 | GLU | -1 | -0.962 | -0.998 | 8.981 | -0.720 | -0.720 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 13 | LEU | 0 | -0.066 | -0.029 | 10.386 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 14 | THR | 0 | -0.004 | -0.006 | 11.252 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 15 | ARG | 1 | 0.939 | 0.964 | 12.409 | 0.559 | 0.559 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 16 | LEU | 0 | -0.040 | -0.009 | 7.729 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 17 | PHE | 0 | 0.051 | 0.007 | 12.301 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 18 | GLN | 0 | -0.016 | -0.006 | 15.366 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 19 | LYS | 1 | 0.894 | 0.948 | 14.005 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 20 | CYS | 0 | -0.095 | -0.017 | 14.072 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 21 | ARG | 1 | 0.937 | 0.974 | 16.978 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 22 | THR | 0 | 0.010 | 0.004 | 20.484 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 23 | SER | 0 | -0.009 | -0.008 | 20.498 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 24 | GLY | 0 | 0.037 | 0.024 | 16.646 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 25 | SER | 0 | -0.008 | 0.001 | 15.204 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 26 | VAL | 0 | 0.033 | 0.008 | 11.668 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 27 | TYR | 0 | -0.024 | 0.000 | 9.939 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 28 | ILE | 0 | 0.008 | -0.010 | 9.456 | 0.317 | 0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 29 | THR | 0 | -0.072 | -0.030 | 7.459 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 30 | LEU | 0 | 0.047 | 0.015 | 8.334 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 31 | LYS | 1 | 0.953 | 0.982 | 8.124 | -1.147 | -1.147 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 32 | LYS | 1 | 0.969 | 0.997 | 10.246 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 33 | TYR | 0 | -0.078 | -0.062 | 8.139 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 34 | ASP | -1 | -0.789 | -0.890 | 10.956 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 35 | GLY | 0 | 0.007 | 0.003 | 11.007 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 36 | ARG | 1 | 0.874 | 0.939 | 10.369 | -0.246 | -0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 37 | THR | 0 | 0.037 | 0.027 | 9.313 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 38 | LYS | 1 | 0.956 | 0.981 | 10.466 | 0.571 | 0.571 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 39 | PRO | 0 | 0.007 | -0.004 | 12.310 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 40 | ILE | 0 | 0.019 | 0.011 | 13.799 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 41 | PRO | 0 | 0.022 | 0.018 | 16.898 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 42 | LYS | 1 | 0.970 | 0.993 | 19.502 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 50 | GLU | -1 | -0.951 | -0.993 | 15.078 | -0.437 | -0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 51 | PRO | 0 | -0.048 | -0.005 | 16.450 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 52 | ALA | 0 | 0.017 | 0.006 | 15.625 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 53 | ASP | -1 | -0.879 | -0.940 | 15.846 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 54 | ASN | 0 | -0.028 | -0.018 | 17.256 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 55 | LYS | 1 | 0.932 | 0.960 | 11.969 | 0.616 | 0.616 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 56 | CYS | 0 | -0.001 | -0.002 | 11.471 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 57 | LEU | 0 | -0.048 | -0.009 | 3.813 | -0.286 | -0.104 | 0.002 | -0.034 | -0.150 | 0.000 |
51 | B | 58 | LEU | 0 | 0.030 | 0.013 | 7.311 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 59 | ARG | 1 | 0.929 | 0.964 | 2.627 | -5.896 | -4.368 | 0.768 | -0.477 | -1.819 | 0.005 |
53 | B | 60 | ALA | 0 | 0.034 | 0.010 | 5.103 | -1.087 | -1.023 | -0.001 | -0.018 | -0.045 | 0.000 |
54 | B | 61 | THR | 0 | -0.062 | -0.058 | 5.613 | 0.706 | 0.706 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 62 | ASP | -1 | -0.730 | -0.858 | 7.530 | 1.008 | 1.008 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 63 | GLY | 0 | -0.040 | -0.009 | 9.112 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 64 | LYS | 1 | 0.890 | 0.944 | 9.621 | -0.795 | -0.795 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 65 | LYS | 1 | 0.953 | 0.979 | 6.249 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 66 | LYS | 1 | 0.965 | 0.995 | 2.381 | -10.009 | -8.504 | 2.243 | -0.936 | -2.812 | 0.002 |
60 | B | 67 | ILE | 0 | 0.022 | 0.030 | 2.835 | -4.848 | -3.242 | 0.637 | -0.927 | -1.317 | -0.011 |
61 | B | 68 | SER | 0 | -0.027 | -0.037 | 2.541 | -0.580 | 1.610 | 2.555 | -1.504 | -3.241 | -0.013 |
62 | B | 69 | THR | 0 | 0.059 | 0.029 | 4.543 | -1.634 | -1.583 | 0.003 | -0.022 | -0.032 | 0.000 |
63 | B | 70 | VAL | 0 | -0.008 | -0.008 | 6.873 | 0.507 | 0.507 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | B | 71 | VAL | 0 | 0.027 | 0.030 | 9.079 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | B | 72 | SER | 0 | -0.037 | -0.021 | 12.681 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 73 | SER | 0 | 0.087 | 0.014 | 15.758 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 74 | LYS | 1 | 0.929 | 0.970 | 18.558 | 0.461 | 0.461 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 75 | GLU | -1 | -0.860 | -0.929 | 14.153 | -0.668 | -0.668 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | B | 76 | VAL | 0 | -0.006 | 0.005 | 16.668 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | B | 77 | ASN | 0 | 0.026 | 0.008 | 18.217 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | B | 78 | LYS | 1 | 1.005 | 1.015 | 19.235 | 0.352 | 0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | B | 79 | PHE | 0 | 0.009 | 0.000 | 12.346 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | B | 80 | GLN | 0 | 0.022 | -0.013 | 17.712 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | B | 81 | MET | 0 | 0.002 | 0.013 | 19.349 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | B | 82 | ALA | 0 | 0.010 | 0.005 | 18.370 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | B | 83 | TYR | 0 | 0.021 | 0.008 | 13.168 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | B | 84 | SER | 0 | 0.017 | 0.001 | 17.488 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | B | 85 | ASN | 0 | -0.011 | -0.006 | 20.298 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | B | 86 | LEU | 0 | -0.009 | 0.016 | 14.590 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | B | 87 | LEU | 0 | 0.012 | -0.009 | 15.510 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | B | 88 | ARG | 1 | 0.909 | 0.962 | 18.998 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | B | 89 | ALA | 0 | -0.063 | -0.042 | 21.271 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | B | 90 | ASN | 0 | -0.006 | 0.004 | 18.286 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | B | 91 | MET | 0 | -0.070 | -0.012 | 18.494 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | B | 92 | ASP | -1 | -0.911 | -0.942 | 21.333 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | B | 93 | GLY | 0 | 0.021 | 0.005 | 23.929 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | B | 94 | LEU | 0 | 0.027 | 0.010 | 23.809 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | B | 95 | LYS | 1 | 0.943 | 0.964 | 27.828 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | B | 96 | LYS | 1 | 0.960 | 0.960 | 30.744 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | B | 97 | ARG | 1 | 1.014 | 1.038 | 30.319 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |