![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: Q13LY
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 | OptAll |
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 | -600386.957941 |
---|---|
FMO2-HF: Nuclear repulsion | 563757.774675 |
FMO2-HF: Total energy | -36629.183266 |
FMO2-MP2: Total energy | -36733.803825 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F023354/ligand_interaction/ligand_F023354.png)
Ligand Interaction
![ligand interaction](./Kdata/F023354/ligand_interaction/ligand_interaction_F023354.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. |
-30.212 | -25.1 | 16.671 | -8.144 | -13.637 | -0.009 |
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 | -0.013 | 0.006 | 3.238 | -1.779 | 0.862 | 0.081 | -1.231 | -1.491 | -0.001 |
4 | B | 4 | LEU | 0 | -0.005 | 0.000 | 4.726 | 0.936 | 1.065 | -0.001 | -0.017 | -0.110 | 0.000 |
5 | B | 5 | GLU | -1 | -0.783 | -0.865 | 7.793 | -1.035 | -1.035 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 6 | SER | 0 | 0.005 | -0.011 | 11.009 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 7 | GLU | -1 | -0.826 | -0.905 | 12.545 | -0.455 | -0.455 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 8 | GLN | 0 | 0.039 | 0.012 | 10.867 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 9 | PHE | 0 | -0.013 | -0.008 | 6.729 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 10 | LEU | 0 | 0.009 | 0.003 | 10.001 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 11 | THR | 0 | 0.006 | 0.009 | 13.425 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 12 | GLU | -1 | -0.796 | -0.877 | 9.439 | -0.831 | -0.831 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 13 | LEU | 0 | -0.018 | -0.010 | 10.109 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 14 | THR | 0 | -0.013 | -0.015 | 11.325 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 15 | ARG | 1 | 0.818 | 0.866 | 12.140 | 0.759 | 0.759 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 16 | LEU | 0 | -0.066 | -0.029 | 7.617 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 17 | PHE | 0 | 0.048 | 0.002 | 12.357 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 18 | GLN | 0 | -0.036 | -0.019 | 15.301 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 19 | LYS | 1 | 0.921 | 0.964 | 13.142 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 20 | CYS | 0 | -0.076 | -0.024 | 14.080 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 21 | ARG | 1 | 0.831 | 0.893 | 17.000 | -0.176 | -0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 22 | THR | 0 | 0.011 | 0.006 | 20.446 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 23 | SER | 0 | 0.014 | 0.004 | 20.377 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 24 | GLY | 0 | 0.012 | 0.005 | 16.446 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 25 | SER | 0 | 0.001 | 0.003 | 14.653 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 26 | VAL | 0 | 0.009 | 0.004 | 12.005 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 27 | TYR | 0 | -0.003 | 0.011 | 9.903 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 28 | ILE | 0 | 0.000 | -0.010 | 9.513 | 0.248 | 0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 29 | THR | 0 | -0.056 | -0.025 | 7.526 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 30 | LEU | 0 | 0.042 | 0.017 | 8.953 | 0.236 | 0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 31 | LYS | 1 | 0.940 | 0.976 | 9.059 | -1.537 | -1.537 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 32 | LYS | 1 | 0.921 | 0.961 | 10.492 | -0.301 | -0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 33 | TYR | 0 | -0.061 | -0.043 | 7.451 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 34 | ASP | -1 | -0.765 | -0.872 | 10.668 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 35 | GLY | 0 | 0.001 | 0.003 | 10.293 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 36 | ARG | 1 | 0.816 | 0.898 | 10.037 | -0.426 | -0.426 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 37 | THR | 0 | -0.006 | -0.005 | 8.546 | -0.177 | -0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 38 | LYS | 1 | 0.887 | 0.947 | 10.111 | 0.552 | 0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 39 | PRO | 0 | 0.006 | -0.006 | 11.711 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 40 | ILE | 0 | 0.008 | 0.012 | 13.113 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 41 | PRO | 0 | 0.041 | 0.029 | 15.906 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 42 | LYS | 1 | 0.937 | 0.967 | 18.539 | -0.193 | -0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 50 | GLU | -1 | -0.784 | -0.898 | 13.307 | -0.569 | -0.569 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 51 | PRO | 0 | -0.047 | -0.013 | 15.128 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 52 | ALA | 0 | 0.021 | 0.003 | 15.000 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 53 | ASP | -1 | -0.866 | -0.938 | 15.096 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 54 | ASN | 0 | 0.016 | 0.000 | 16.640 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 55 | LYS | 1 | 0.915 | 0.961 | 11.711 | 0.482 | 0.482 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 56 | CYS | 0 | -0.059 | -0.028 | 11.294 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 57 | LEU | 0 | -0.002 | 0.000 | 3.805 | -0.371 | -0.182 | 0.002 | -0.031 | -0.159 | 0.000 |
51 | B | 58 | LEU | 0 | 0.013 | 0.012 | 7.502 | 0.400 | 0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 59 | ARG | 1 | 0.918 | 0.940 | 2.432 | -12.692 | -15.730 | 10.499 | -2.595 | -4.866 | 0.023 |
53 | B | 60 | ALA | 0 | 0.031 | 0.019 | 5.146 | -0.902 | -0.902 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 61 | THR | 0 | -0.063 | -0.060 | 5.210 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 62 | ASP | -1 | -0.689 | -0.821 | 7.371 | 0.848 | 0.848 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 63 | GLY | 0 | -0.019 | -0.004 | 9.204 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 64 | LYS | 1 | 0.826 | 0.905 | 9.456 | -0.626 | -0.626 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 65 | LYS | 1 | 0.925 | 0.960 | 5.987 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 66 | LYS | 1 | 0.971 | 0.997 | 2.329 | -6.774 | -5.679 | 1.730 | -0.850 | -1.975 | 0.000 |
60 | B | 67 | ILE | 0 | 0.024 | 0.034 | 2.854 | -5.535 | -3.471 | 0.672 | -1.364 | -1.372 | -0.014 |
61 | B | 68 | SER | 0 | -0.011 | -0.034 | 2.564 | -1.416 | 0.528 | 3.686 | -2.008 | -3.622 | -0.017 |
62 | B | 69 | THR | 0 | -0.001 | -0.014 | 4.391 | -1.591 | -1.503 | 0.002 | -0.048 | -0.042 | 0.000 |
63 | B | 70 | VAL | 0 | 0.006 | -0.003 | 6.433 | 0.700 | 0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | B | 71 | VAL | 0 | -0.008 | 0.009 | 8.873 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | B | 72 | SER | 0 | -0.031 | -0.043 | 12.604 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 73 | SER | 0 | 0.034 | 0.011 | 15.668 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 74 | LYS | 1 | 0.945 | 0.992 | 17.896 | 0.444 | 0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 75 | GLU | -1 | -0.772 | -0.868 | 15.157 | -0.489 | -0.489 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | B | 76 | VAL | 0 | -0.004 | -0.009 | 16.256 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | B | 77 | ASN | 0 | 0.034 | 0.013 | 18.015 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | B | 78 | LYS | 1 | 0.897 | 0.955 | 19.400 | 0.430 | 0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | B | 79 | PHE | 0 | -0.009 | -0.010 | 12.754 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | B | 80 | GLN | 0 | 0.026 | 0.005 | 17.780 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | B | 81 | MET | 0 | 0.036 | 0.033 | 19.730 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | B | 82 | ALA | 0 | 0.024 | 0.016 | 18.600 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | B | 83 | TYR | 0 | 0.025 | 0.003 | 12.981 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | B | 84 | SER | 0 | 0.014 | -0.009 | 17.542 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | B | 85 | ASN | 0 | 0.002 | 0.011 | 20.558 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | B | 86 | LEU | 0 | -0.005 | 0.009 | 14.540 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | B | 87 | LEU | 0 | 0.030 | 0.005 | 15.396 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | B | 88 | ARG | 1 | 0.896 | 0.932 | 18.816 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | B | 89 | ALA | 0 | -0.065 | -0.028 | 21.228 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | B | 90 | ASN | 0 | -0.034 | -0.020 | 18.188 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | B | 91 | MET | 0 | -0.052 | -0.002 | 18.430 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | B | 92 | ASP | -1 | -0.814 | -0.869 | 21.086 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | B | 93 | GLY | 0 | 0.022 | 0.012 | 23.990 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | B | 94 | LEU | 0 | -0.003 | 0.006 | 23.864 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | B | 95 | LYS | 1 | 0.978 | 0.977 | 27.804 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | B | 96 | LYS | 1 | 1.011 | 0.999 | 30.743 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | B | 97 | ARG | 1 | 0.938 | 0.987 | 30.393 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |