Summary of information
PROJECT
Cofactor_(biochemistry)

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Upload 25-01-2012 16:50 (Day-Month-Year, Paris time)



Information about the Author (who submitted the project in R.E.DD.B.)

Firstname Francois-Yves

Lastname Dupradeau

Institute UFR de pharmacie, UPJV

City Amiens

Country FRANCE


General information about the Project

Molecule keywords

Organic cofactor Vitamin Coenzyme Nucleoside Phosphate


Abstract

Introduction
We report on a new force field topology database (FFTopDB; i.e. RESP charges embedded in a set of 89 force field libraries in the Tripos mol2 and mol3 file formats) for more than 200 biochemical cofactors and vitamins involved in numerous biological processes. This FFTopDB is compatible with the Duan et al. force field,[1] and is devoted to condensed phase molecular dynamics simulations and docking studies. The non-exhaustive list of cofactors presented here contains non-phosphorylated and phosphorylated (phosphate and hydrogen-phosphate) derivatives such as:
- X (natural nucleosides and 2'-Deoxynucleosides),
- XYP (Adenosine monophosphate, Adenosine diphosphate, Adenosine triphosphate, ...),
- cyclic-XMP (cyclic AMP, ...),
- NXD+ (Nicotinamide adenine dinucleotide, ...),
- NXDH (the reduced form of NAD+, ...),
- NXDYP (Nicotinamide adenine dinucleotide phosphate, ...),
- NXDYPH (the reduced form of NADP, ...),
- riboflavin,
- FMN (Flavin mononucleotide),
- FMNH2 (the reduced form of Flavin mononucleotide),
- FXD (Flavin adenine dinucleotide, ...),
- FXDH2 (the reduced form of FAD, ...),
- FXDYP (Flavin adenine dinucleotide phosphate, ...),
- FXDYPH2 (the reduced form of FADP, ...),
- acetylated and non-acylated coenzyme XYP (Acetyl Coenzyme A, ...);
with X = 2'-Deoxyadenosine, 2'-Deoxycytidine, 2'-Deoxyguanosine, 2'-Deoxythymidine, Adenosine, Cytidine, Guanosine or Uridine, and Y = any positive integer value.[2]
In this work, the "building block" procedure has been followed: charge derivation and force field library building were performed by using well-defined elementary constituents for the different studied cofactors. Thus, the entire family of cofactors is considered as a single homogeneous biopolymer model in our approach (Figure 1A).[3] Specific charge constraints for fully characterized connecting groups belonging to these building blocks were applied during the charge fitting step allowing the generation of a large number of molecular fragments. The cofactors are then constructed by associating the molecular fragments together by using a dedicated LEaP script. The building block approach presents the following advantages over the whole molecule approach: (i) the cpu time required for geometry optimization and molecular electrostatic potential (MEP) computation is drastically decreased, (ii) the optimized geometry of the conformation(s) of each building block is fully defined and controlled, (iii) conformations not suited for charge derivation, presenting non-bonded interactions only observed in gas phase geometry optimization are discarded, (iv) cofactors and their analogs are simultaneously involved in a single and highly homogenous approach, and finally (v) by generating averaged charge values for connecting groups, additional and highly compatible charge derivation procedures can be performed for an infinity of new cofactor analogs constituting "add-ons" to the present R.E.DD.B. project.

Computational details
The charge derivation procedure and force field library building were automatically carried out by using the R.E.D. IV program allowing a rigorous control of the different parameters, which affect charge values compatible with the non-polarizable RESP charge model.[4] Geometry optimization and MEP computation were carried out by quantum mechanical methods by using the Gaussian 2003 (version E.01) program. The geometries of the 28 building blocks considered in this work were optimized using the HF/6-31G* level of theory.[5] One to four molecular conformations were used for each building block depending on their occurrence in the protein data bank.[6] An energy minimum was considered only if no canonical intra-molecular hydrogen bond [donor (D)-acceptor (A) distance lower than 3.20 Å and the D-H...A angle between 120-180°] was observed in each optimized geometry. Dihedral constraints were used in geometry optimization to prevent intra-molecular hydrogen bond formation when needed.[7] MEP computation employed the B3LYP/cc-pVTZ level of theory, the Polarized Continuum Model - the Integral Equation Formalism mimicking the diethylether environment, and the Connolly surface algorithm defined in the Duan et al. force field.[1] For each building block one or two pairs of molecular orientations based on the rigid-body reorientation algorithm (RBRA) implemented in the R.E.D. program were considered in MEP computation ensuring the reproducibility of the derived charge values.[8] A total of 89 molecular fragments were generated by setting specific intra- and inter-molecular charge constraints between the connecting groups during the charge fitting step (see Figure 1A). Inter-molecular charge equivalencing was used to force the atomic charges between the common elements of the different building blocks to be equivalent leading to a highly consistent set of charge values within the FFTopDB. In this approach, the charges of the C1'/H1' and N1 or N9 connecting atoms between 2'-deoxyribose/ribose and each nucleobase as well as these of the ribose carbons and hydrogens of the nicotinamide nucleoside (oxidized form) were excluded from these constraints to limit the impact on the Relative Root Mean Square (RRMS). [9] RESP charge fitting was carried out by using a standalone version of the RESP program, and following the two RESP stage fitting procedure.[10]


Figure 1
Charge derivation involving multiple orientations, multiple conformations and multiple molecules and FFTopDB building for more than 200 biochemical cofactors have been automatically carried out with the R.E.D. IV program. a) Description of the 28 building blocks involved in RESP charge derivation and FFTopDB building; plain and black arrow: intra-molecular charge constraint within the methyl-hydrogen-phosphate building block (allowing the oligomerization of the PO3(-) group); dashed and gray arrows: inter-molecular charge constraints defined between pairs of building blocks, b) building of the biochemical cofactors using the FFTopDB (89 molecular fragments) generated in this work.

Charge review and FFTopDB validation
The statistics module of the R.E.D. IV program was used to minimize the impact of the intra-molecular charge constraints, inter-molecular charge constraints and inter-molecular charge equivalencing in the charge fitting step for multiple molecules. A RRMS value of 0.026 between the MEP calculated by quantum chemistry and that generated using the derived charge values was obtained for the charge fitting step. A highly similar RRMS value was also obtained in the absence of intra-molecular charge constraints, inter-molecular charge constraints and inter-molecular charge equivalencing. The relative small RRMS values as well as the small difference of RRMS between the charge fitting steps carried out with and without these charge constraints is one of the ways to demonstrate the accuracy of the fitting step performed in this work and the relative weak effect of the constraints used. Finally, rounding off errors of charge values were corrected at the fourth decimal point. RESP charges were validated by molecular dynamics simulations in condensed phase conditions.

This R.E.DD.B. project provides all the computational conditions for charge derivation and force field library building for more than 200 biochemical cofactors. Moreover, this allows any user to rebuild the FFTopDB by applying other choices (different conformations and orientations, different algorithms in MEP computation or ESP charge fitting). A similar FFTopDB compatible with the Cornell et al. force field is also available in the "F-90" R.E.DD.B. project.[11] FFTopDBs for these cofactors with extra-points and/or united carbon atoms are also in preparation.

[1] Duan et al. J. Comput. Chem. 2003, 24, 1999–2012.
[2] Wikipedia, biochemical cofactors.
[3] Cieplak et al. J. Comput. Chem. 1995, 16 1357–1377.
[4] Dupradeau et al. Phys. Chem. Chem. Phys. 2010, 12, 7821–7839.
[5] The names for the 28 building blocks considered in this work are in the order: Dimethyldiphosphate; Methyl-hydrogen-phosphate; Methyl-phosphate; 2'-Deoxyadenosine; 2'-Deoxycytidine; 2'-Deoxyguanosine; 2'-Deoxythymidine; Adenosine; Cytidine; Guanosine; Uridine; 1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide; 3-(aminocarbonyl)-1-D-ribofuranosylpyridinium; (2S,3S,4R)-1-amino-1-deoxypentitol; 7,8,10-trimethylbenzo[g]pteridine-2,4(3H,10H)-dione; 7,8,10-trimethyl-5,10-dihydrobenzo[g]pteridine-2,4(1H,3H)-dione; (2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide; N3-acetyl-N-methyl-b-alaninamide; S-[2-(acetylamino)ethyl]-ethanethioate; N-(2-sulfanylethyl)acetamide; 2'-Deoxy-3',5'-cyclic-adenosine-monophopshate; 2'-Deoxy-3',5'-cyclic-cytidine-monophosphate; 2'-Deoxy-3',5'-cyclic-guanosine-monophosphate; 2'-Deoxy-3',5'-cyclic-thymidine-monophosphate; 3',5'-cyclic-adenosine-monophosphate; 3',5'-cyclic-cytidine-monophosphate; 3',5'-cyclic-guanosine-monophosphate; 3',5'-cyclic-uridine-monophosphate.
[6] Berman et al. Nucl. Acids Res. 2000, 28, 235–242.
[7] The dihedrals, which were constrained during the geometry optimization step are described as it follows: molecule name: total number of constrained dihedral(s); four atom numbers defining the dihedral, the value of the dihedral constraint: Adenosine (conformations C3'endo & C2'endo): 2; 4 3 9 11, 180.0; 9 7 17 18, -70.0; Cytidine (conformations C3'endo & C2'endo): 2; 4 3 9 11, 180.0; 9 7 17 18, -70.0; Guanosine (conformations C3'endo & C2'endo): 2; 4 3 9 11, 180.0; 9 7 17 18, -70.0; Uridine (conformations C3'endo & C2'endo): 2; 4 3 9 11, 180.0; 9 7 17 18, -70.0; 1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide (conformations C3'endo/anti, C2'endo/anti, C2'endo/syn): 2; 4 3 9 11, 180.0; 9 7 17 18, -70.0; 1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide (conformation C3'endo/syn): 3; 2 1 13 11, 180.0; 4 3 9 11, 180.0; 9 7 17 18, -70.0; 3-(aminocarbonyl)-1-D-ribofuranosylpyridinium (conformations C3'endo/anti, C3'endo/syn, C2'endo/anti, C2'endo/syn): 2; 4 3 9 11, 180.0; 9 7 17 18, -70.0; (2S,3S,4R)-1-amino-1-deoxypentitol; 2; 8 7 9 10, 30.0; 16 15 17 18, -170.0; 3',5'-cyclic-adenosine-monophosphate; 1; 10 8 18 19, -70.0; 3',5'-cyclic-cytidine-monophosphate; 1; 10 8 18 19, -70.0; 3',5'-cyclic-guanosine-monophosphate; 1; 10 8 18 19, -70.0; 3',5'-cyclic-uridine-monophosphate; 1; 10 8 18 19, -70.0.
[8] Atoms involved in the RBRA procedure before MEP computation are defined as it follows: molecule number (1-28): total number of molecular orientations; three atom numbers separated by the pipe character: 1: 4; 5 9 13 | 13 9 5 | 6 9 10 | 10 9 6; 2: 2; 1 5 6 | 6 5 1; 3: 2; 1 5 6 | 6 5 1; 4: 4; 5 10 14 | 14 10 5 | 7 12 17 | 17 12 7; 5: 4; 5 10 14 | 14 10 5 | 7 12 17 | 17 12 7; 6: 4; 5 10 14 | 14 10 5 | 7 12 17 | 17 12 7; 7: 4; 5 10 14 | 14 10 5 | 7 12 17 | 17 12 7; 8: 4; 5 9 13 | 13 9 5 | 7 11 16 | 16 11 7; 9: 4; 5 9 13 | 13 9 5 | 7 11 16 | 16 11 7; 10: 4; 5 9 13 | 13 9 5 | 7 11 16 | 16 11 7; 11: 4; 5 9 13 | 13 9 5 | 7 11 16 | 16 11 7; 12: 4; 5 9 13 | 13 9 5 | 7 11 16 | 16 11 7; 13: 4; 5 9 13 | 13 9 5 | 7 11 16 | 16 11 7; 14: 2; 4 7 11 | 11 7 4; 15: 4; 9 10 12 | 12 10 9 | 1 4 8 | 8 4 1; 16: 4; 10 11 14 | 14 11 10 | 1 5 9 | 9 5 1; 17: 2; 3 6 15 | 15 6 3; 18: 2; 9 12 15 | 15 12 9; 19: 2; 9 12 15 | 15 12 9; 20: 2; 9 12 15 | 15 12 9; 21: 4; 6 11 15 | 15 11 6 | 8 13 18 | 18 13 8; 22: 4; 6 11 15 | 15 11 6 | 8 13 18 | 18 13 8; 23: 4; 6 11 15 | 15 11 6 | 8 13 18 | 18 13 8; 24: 4; 6 11 15 | 15 11 6 | 8 13 18 | 18 13 8; 25: 4; 6 10 14 | 14 10 6 | 8 12 17 | 17 12 8; 26: 4; 6 10 14 | 14 10 6 | 8 12 17 | 17 12 8; 27: 4; 6 10 14 | 14 10 6 | 8 12 17 | 17 12 8; 28: 4; 6 10 14 | 14 10 6 | 8 12 17 | 17 12 8.
[9] Inter-molecular charge equivalencing between building blocks applied during the charge fitting stepare are defined as it follows: molecule numbers | atom numbers in the set of molecules: 4 5 6 7 | 1 2 3 4 7 8 9 10 11 12 13 14 15 16 17; 8 9 10 11 12 13 | 1 2 3 4 17 1; 8 9 10 11 12 | 7 8 9 10 11 12 13 14 15 16; 21 22 23 24 | 1 2 3 4 5 8 9 10 11 12 13 14 15 16 17 18; 25 26 27 28 | 1 2 3 4 5 8 9 10 11 12 13 14 15 16 17 18 19; 4 8 21 25 | 18 19 19 20 - 19 20 20 21 - 20 21 21 22 - 21 22 22 23 - 22 23 23 24 - 23 24 24 25 - 24 25 25 26 - 25 26 26 27 - 27 28 28 29 - 28 29 29 30 - 29 30 30 31 - 30 31 31 32 - 31 32 32 33; 5 9 22 26 | 18 19 19 20 - 19 20 20 21 - 20 21 21 22 - 21 22 22 23 - 22 23 23 24 - 23 24 24 25 - 24 25 25 26 - 26 27 27 28 - 27 28 28 29 - 28 29 29 30 - 29 30 30 31; 6 10 23 27 | 18 19 19 20 - 19 20 20 21 - 20 21 21 22 - 21 22 22 23 - 22 23 23 24 - 23 24 24 25 - 24 25 25 26 - 25 26 26 27 - 26 27 27 28 - 28 29 29 30 - 29 30 30 31 - 30 31 31 32 - 31 32 32 33 - 32 33 33 34; 7 24 | 18 19 - 19 20 - 20 21 - 21 22 - 22 23 - 23 24 - 25 26 - 26 27 - 27 28 - 28 29 - 29 30 - 30 31 - 31 32; 11 28 | 19 20 - 20 21 - 21 22 - 22 23 - 23 24 - 24 25 - 26 27 - 27 28 - 28 29 - 29 30.
[10] Bayly et al. J. Phys. Chem. 1993, 97, 10269–10280, and here.
[11] Cornell et al. J. Am. Chem. Soc. 1995, 117, 5179–5197; Hornak et al. Proteins 2006, 65, 712–725.

Is the project published NOT YET

"Whole molecule" or "Molecule fragment" type projectMOLECULE FRAGMENT

Interface R.E.D. used ? YES


Charge derivation procedure

Number of Tripos mol2 file(s) provided by the author(s) 89

Contain charge values & information about molecular topology

No Name Download Wikipedia 3D visualization
1 Fragment-FG1_Dimethyldiphosphate Link Wiki Logo Jmol Logo
2 Fragment-FG2_Methyl-hydrogen-phosphate Link Wiki Logo Jmol Logo
3 Fragment-FG3_Methyl-hydrogen-phosphate Link Wiki Logo Jmol Logo
4 Fragment-FG1_Methyl-phosphate Link Wiki Logo Jmol Logo
5 2'-Deoxyadenosine Link Wiki Logo Jmol Logo
6 Fragment-FG1_2'-Deoxyadenosine Link Wiki Logo Jmol Logo
7 Fragment-FG3_2'-Deoxyadenosine Link Wiki Logo Jmol Logo
8 Fragment-FG4_2'-Deoxyadenosine Link Wiki Logo Jmol Logo
9 2'-Deoxycytidine Link Wiki Logo Jmol Logo
10 Fragment-FG1_2'-Deoxycytidine Link Wiki Logo Jmol Logo
11 Fragment-FG3_2'-Deoxycytidine Link Wiki Logo Jmol Logo
12 Fragment-FG4_2'-Deoxycytidine Link Wiki Logo Jmol Logo
13 2'-Deoxyguanosine Link Wiki Logo Jmol Logo
14 Fragment-FG1_2'-Deoxyguanosine Link Wiki Logo Jmol Logo
15 Fragment-FG3_2'-Deoxyguanosine Link Wiki Logo Jmol Logo
16 Fragment-FG4_2'-Deoxyguanosine Link Wiki Logo Jmol Logo
17 2'-Deoxythymidine Link Wiki Logo Jmol Logo
18 Fragment-FG1_2'-Deoxythymidine Link Wiki Logo Jmol Logo
19 Fragment-FG3_2'-Deoxythymidine Link Wiki Logo Jmol Logo
20 Fragment-FG4_2'-Deoxythymidine Link Wiki Logo Jmol Logo
21 Adenosine Link Wiki Logo Jmol Logo
22 Fragment-FG1_Adenosine Link Wiki Logo Jmol Logo
23 Fragment-FG3_Adenosine Link Wiki Logo Jmol Logo
24 Fragment-FG4_Adenosine Link Wiki Logo Jmol Logo
25 Fragment-FG5_Adenosine Link Wiki Logo Jmol Logo
26 Fragment-FG6_Adenosine Link Wiki Logo Jmol Logo
27 Fragment-FG7_Adenosine Link Wiki Logo Jmol Logo
28 Fragment-FG8_Adenosine Link Wiki Logo Jmol Logo
29 Cytidine Link Wiki Logo Jmol Logo
30 Fragment-FG1_Cytidine Link Wiki Logo Jmol Logo
31 Fragment-FG3_Cytidine Link Wiki Logo Jmol Logo
32 Fragment-FG4_Cytidine Link Wiki Logo Jmol Logo
33 Fragment-FG5_Cytidine Link Wiki Logo Jmol Logo
34 Fragment-FG6_Cytidine Link Wiki Logo Jmol Logo
35 Fragment-FG7_Cytidine Link Wiki Logo Jmol Logo
36 Fragment-FG8_Cytidine Link Wiki Logo Jmol Logo
37 Guanosine Link Wiki Logo Jmol Logo
38 Fragment-FG1_Guanosine Link Wiki Logo Jmol Logo
39 Fragment-FG3_Guanosine Link Wiki Logo Jmol Logo
40 Fragment-FG4_Guanosine Link Wiki Logo Jmol Logo
41 Fragment-FG5_Guanosine Link Wiki Logo Jmol Logo
42 Fragment-FG6_Guanosine Link Wiki Logo Jmol Logo
43 Fragment-FG7_Guanosine Link Wiki Logo Jmol Logo
44 Fragment-FG8_Guanosine Link Wiki Logo Jmol Logo
45 Uridine Link Wiki Logo Jmol Logo
46 Fragment-FG1_Uridine Link Wiki Logo Jmol Logo
47 Fragment-FG3_Uridine Link Wiki Logo Jmol Logo
48 Fragment-FG4_Uridine Link Wiki Logo Jmol Logo
49 Fragment-FG5_Uridine Link Wiki Logo Jmol Logo
50 Fragment-FG6_Uridine Link Wiki Logo Jmol Logo
51 Fragment-FG7_Uridine Link Wiki Logo Jmol Logo
52 Fragment-FG8_Uridine Link Wiki Logo Jmol Logo
53 1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Link Wiki Logo Jmol Logo
54 Fragment-FG1_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Link Wiki Logo Jmol Logo
55 Fragment-FG3_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Link Wiki Logo Jmol Logo
56 Fragment-FG4_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Link Wiki Logo Jmol Logo
57 Fragment-FG5_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Link Wiki Logo Jmol Logo
58 Fragment-FG6_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Link Wiki Logo Jmol Logo
59 Fragment-FG7_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Link Wiki Logo Jmol Logo
60 Fragment-FG8_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Link Wiki Logo Jmol Logo
61 3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Link Wiki Logo Jmol Logo
62 Fragment-FG1_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Link Wiki Logo Jmol Logo
63 Fragment-FG3_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Link Wiki Logo Jmol Logo
64 Fragment-FG4_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Link Wiki Logo Jmol Logo
65 Fragment-FG5_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Link Wiki Logo Jmol Logo
66 Fragment-FG6_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Link Wiki Logo Jmol Logo
67 Fragment-FG7_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Link Wiki Logo Jmol Logo
68 Fragment-FG8_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Link Wiki Logo Jmol Logo
69 Fragment-FG1_(2S,3S,4R)-1-amino-1-deoxypentitol Link Wiki Logo Jmol Logo
70 Fragment-FG3_(2S,3S,4R)-1-amino-1-deoxypentitol Link Wiki Logo Jmol Logo
71 Fragment-FG1_7,8,10-trimethylbenzo[g]pteridine-2,4(3H,10H)-dione Link Wiki Logo Jmol Logo
72 Fragment-FG1_7,8,10-trimethyl-5,10-dihydrobenzo[g]pteridine-2,4(1H,3H)-dione Link Wiki Logo Jmol Logo
73 Fragment-FG1_(2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide Link Wiki Logo Jmol Logo
74 Fragment-FG3_(2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide Link Wiki Logo Jmol Logo
75 Fragment-FG1_N3-acetyl-N-methyl-b-alaninamide Link Wiki Logo Jmol Logo
76 Fragment-FG1_S-[2-(acetylamino)ethyl]-ethanethioate Link Wiki Logo Jmol Logo
77 Fragment-FG1_N-(2-sulfanylethyl)acetamide Link Wiki Logo Jmol Logo
78 2'-Deoxy-3'5'-cyclic-adenosine-monophosphate Link Wiki Logo Jmol Logo
79 2'-Deoxy-3'5'-cyclic-cytidine-monophosphate Link Wiki Logo Jmol Logo
80 2'-Deoxy-3'5'-cyclic-guanosine-monophosphate Link Wiki Logo Jmol Logo
81 2'-Deoxy-3'5'-cyclic-thymidine-monophosphate Link Wiki Logo Jmol Logo
82 3'5'-cyclic-adenosine-monophosphate Link Wiki Logo Jmol Logo
83 Fragment-FG1_3'5'-cyclic-adenosine-monophosphate Link Wiki Logo Jmol Logo
84 3'5'-cyclic-cytidine-monophosphate Link Wiki Logo Jmol Logo
85 Fragment-FG1_3'5'-cyclic-cytidine-monophosphate Link Wiki Logo Jmol Logo
86 3'5'-cyclic-guanosine-monophosphate Link Wiki Logo Jmol Logo
87 Fragment-FG1_3'5'-cyclic-guanosine-monophosphate Link Wiki Logo Jmol Logo
88 3'5'-cyclic-uridine-monophosphate Link Wiki Logo Jmol Logo
89 Fragment-FG1_3'5'-cyclic-uridine-monophosphate Link Wiki Logo Jmol Logo


Number of molecule(s) used in the charge derivation procedure 28

File(s) provided to the PDB format

No Molecule name Conformation No Reorientation procedure Mol. orientation No Download Wikipedia
1 Dimethyldiphosphate 2 Rigid Body Reorient Algo 4 Link Wiki Logo
2 Methyl-hydrogen-phosphate 1 Rigid Body Reorient Algo 2 Link Wiki Logo
3 Methyl-phosphate 1 Rigid Body Reorient Algo 2 Link Wiki Logo
4 2'-Deoxyadenosine 2 Rigid Body Reorient Algo 4 Link Wiki Logo
5 2'-Deoxycytidine 2 Rigid Body Reorient Algo 4 Link Wiki Logo
6 2'-Deoxyguanosine 2 Rigid Body Reorient Algo 4 Link Wiki Logo
7 2'-Deoxythymidine 2 Rigid Body Reorient Algo 4 Link Wiki Logo
8 Adenosine 2 Rigid Body Reorient Algo 4 Link Wiki Logo
9 Cytidine 2 Rigid Body Reorient Algo 4 Link Wiki Logo
10 Guanosine 2 Rigid Body Reorient Algo 4 Link Wiki Logo
11 Uridine 2 Rigid Body Reorient Algo 4 Link Wiki Logo
12 1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide 4 Rigid Body Reorient Algo 4 Link Wiki Logo
13 3-(aminocarbonyl)-1-D-ribofuranosylpyridinium 4 Rigid Body Reorient Algo 4 Link Wiki Logo
14 (2S,3S,4R)-1-amino-1-deoxypentitol 1 Rigid Body Reorient Algo 2 Link Wiki Logo
15 7,8,10-trimethylbenzo[g]pteridine-2,4(3H,10H)-dione 1 Rigid Body Reorient Algo 4 Link Wiki Logo
16 7,8,10-trimethyl-5,10-dihydrobenzo[g]pteridine-2,4(1H,3H)-dione 1 Rigid Body Reorient Algo 4 Link Wiki Logo
17 (2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide 1 Rigid Body Reorient Algo 2 Link Wiki Logo
18 N3-acetyl-N-methyl-b-alaninamide 2 Rigid Body Reorient Algo 2 Link Wiki Logo
19 S-[2-(acetylamino)ethyl]-ethanethioate 2 Rigid Body Reorient Algo 2 Link Wiki Logo
20 N-(2-sulfanylethyl)acetamide 2 Rigid Body Reorient Algo 2 Link Wiki Logo
21 2'-Deoxy-3'5'-cyclic-adenosine-monophosphate 1 Rigid Body Reorient Algo 4 Link Wiki Logo
22 2'-Deoxy-3'5'-cyclic-cytidine-monophosphate 1 Rigid Body Reorient Algo 4 Link Wiki Logo
23 2'-Deoxy-3'5'-cyclic-guanosine-monophosphate 1 Rigid Body Reorient Algo 4 Link Wiki Logo
24 2'-Deoxy-3'5'-cyclic-thymidine-monophosphate 1 Rigid Body Reorient Algo 4 Link Wiki Logo
25 3'5'-cyclic-adenosine-monophosphate 1 Rigid Body Reorient Algo 4 Link Wiki Logo
26 3'5'-cyclic-cytidine-monophosphate 1 Rigid Body Reorient Algo 4 Link Wiki Logo
27 3'5'-cyclic-guanosine-monophosphate 1 Rigid Body Reorient Algo 4 Link Wiki Logo
28 3'5'-cyclic-uridine-monophosphate 1 Rigid Body Reorient Algo 4 Link Wiki Logo



Information regarding Quantum Calculations

Geometry optimization

Program 1 GAUSSIAN 2003

Theory level 1 HF

More information 1 Tight

Basis set 1 6-31G*

Molecular electrostatic potential computation

Program 2 GAUSSIAN 2003

Theory level 2 DFT B3LYP

More information 2 IOp(6/33=2) SCRF(IEFPCM,Solvent=Ether) NoSymm

Basis set 2 cc-pVTZ

Algorithm CONNOLLY SURFACE


Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1 Link

input of stage 2 Link



Files the author of the project wishes to provide...

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...Link
A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...Link
A file to provide new force field parameters compatible with the Tripos mol2 file(s)...Link
A file (choice made by the author) to provide more information about the project...Link
A file (choice made by the author) to provide more information about the project...Link

Download the whole project... Link



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