Summary of information
PROJECT
Cofactor_(biochemistry)

Wiki_Logo

Upload 15-12-2011 10:00 (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 the first 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 Cornell et al. force field and its successive adaptations,[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 levels of theory used in geometry optimization and MEP computation were chosen to be compatible with the Cornell et al. force field. Hence, 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 Connolly surface algorithm and the HF/6-31G* level of theory, thus taking into account implicit polarization required in condensed phase molecular dynamics simulations when using an additive force field model.[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 0.028 between the MEP calculated by quantum chemistry and that generated using the derived charge values was obtained for the charge fitting step. A RRMS value of 0.026 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 Duan et al. force field is also available in the "F-91" R.E.DD.B. project.[11] FFTopDBs for these cofactors with extra-points and/or united carbon atoms are also in preparation.

[1] Cornell et al. J. Am. Chem. Soc. 1995, 117, 5179–5197; Hornak et al. Proteins 2006, 65, 712–725.
[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] Duan et al. J. Comput. Chem. 2003, 24, 1999–2012.

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 Display 1 3D Display 2
1 Fragment-FG1_Dimethyldiphosphate Wiki_Logo Jmol_Logo JSmol_Logo
2 Fragment-FG2_Methyl-hydrogen-phosphate Wiki_Logo Jmol_Logo JSmol_Logo
3 Fragment-FG3_Methyl-hydrogen-phosphate Wiki_Logo Jmol_Logo JSmol_Logo
4 Fragment-FG1_Methyl-phosphate Wiki_Logo Jmol_Logo JSmol_Logo
5 2'-Deoxyadenosine Wiki_Logo Jmol_Logo JSmol_Logo
6 Fragment-FG1_2'-Deoxyadenosine Wiki_Logo Jmol_Logo JSmol_Logo
7 Fragment-FG3_2'-Deoxyadenosine Wiki_Logo Jmol_Logo JSmol_Logo
8 Fragment-FG4_2'-Deoxyadenosine Wiki_Logo Jmol_Logo JSmol_Logo
9 2'-Deoxycytidine Wiki_Logo Jmol_Logo JSmol_Logo
10 Fragment-FG1_2'-Deoxycytidine Wiki_Logo Jmol_Logo JSmol_Logo
11 Fragment-FG3_2'-Deoxycytidine Wiki_Logo Jmol_Logo JSmol_Logo
12 Fragment-FG4_2'-Deoxycytidine Wiki_Logo Jmol_Logo JSmol_Logo
13 2'-Deoxyguanosine Wiki_Logo Jmol_Logo JSmol_Logo
14 Fragment-FG1_2'-Deoxyguanosine Wiki_Logo Jmol_Logo JSmol_Logo
15 Fragment-FG3_2'-Deoxyguanosine Wiki_Logo Jmol_Logo JSmol_Logo
16 Fragment-FG4_2'-Deoxyguanosine Wiki_Logo Jmol_Logo JSmol_Logo
17 2'-Deoxythymidine Wiki_Logo Jmol_Logo JSmol_Logo
18 Fragment-FG1_2'-Deoxythymidine Wiki_Logo Jmol_Logo JSmol_Logo
19 Fragment-FG3_2'-Deoxythymidine Wiki_Logo Jmol_Logo JSmol_Logo
20 Fragment-FG4_2'-Deoxythymidine Wiki_Logo Jmol_Logo JSmol_Logo
21 Adenosine Wiki_Logo Jmol_Logo JSmol_Logo
22 Fragment-FG1_Adenosine Wiki_Logo Jmol_Logo JSmol_Logo
23 Fragment-FG3_Adenosine Wiki_Logo Jmol_Logo JSmol_Logo
24 Fragment-FG4_Adenosine Wiki_Logo Jmol_Logo JSmol_Logo
25 Fragment-FG5_Adenosine Wiki_Logo Jmol_Logo JSmol_Logo
26 Fragment-FG6_Adenosine Wiki_Logo Jmol_Logo JSmol_Logo
27 Fragment-FG7_Adenosine Wiki_Logo Jmol_Logo JSmol_Logo
28 Fragment-FG8_Adenosine Wiki_Logo Jmol_Logo JSmol_Logo
29 Cytidine Wiki_Logo Jmol_Logo JSmol_Logo
30 Fragment-FG1_Cytidine Wiki_Logo Jmol_Logo JSmol_Logo
31 Fragment-FG3_Cytidine Wiki_Logo Jmol_Logo JSmol_Logo
32 Fragment-FG4_Cytidine Wiki_Logo Jmol_Logo JSmol_Logo
33 Fragment-FG5_Cytidine Wiki_Logo Jmol_Logo JSmol_Logo
34 Fragment-FG6_Cytidine Wiki_Logo Jmol_Logo JSmol_Logo
35 Fragment-FG7_Cytidine Wiki_Logo Jmol_Logo JSmol_Logo
36 Fragment-FG8_Cytidine Wiki_Logo Jmol_Logo JSmol_Logo
37 Guanosine Wiki_Logo Jmol_Logo JSmol_Logo
38 Fragment-FG1_Guanosine Wiki_Logo Jmol_Logo JSmol_Logo
39 Fragment-FG3_Guanosine Wiki_Logo Jmol_Logo JSmol_Logo
40 Fragment-FG4_Guanosine Wiki_Logo Jmol_Logo JSmol_Logo
41 Fragment-FG5_Guanosine Wiki_Logo Jmol_Logo JSmol_Logo
42 Fragment-FG6_Guanosine Wiki_Logo Jmol_Logo JSmol_Logo
43 Fragment-FG7_Guanosine Wiki_Logo Jmol_Logo JSmol_Logo
44 Fragment-FG8_Guanosine Wiki_Logo Jmol_Logo JSmol_Logo
45 Uridine Wiki_Logo Jmol_Logo JSmol_Logo
46 Fragment-FG1_Uridine Wiki_Logo Jmol_Logo JSmol_Logo
47 Fragment-FG3_Uridine Wiki_Logo Jmol_Logo JSmol_Logo
48 Fragment-FG4_Uridine Wiki_Logo Jmol_Logo JSmol_Logo
49 Fragment-FG5_Uridine Wiki_Logo Jmol_Logo JSmol_Logo
50 Fragment-FG6_Uridine Wiki_Logo Jmol_Logo JSmol_Logo
51 Fragment-FG7_Uridine Wiki_Logo Jmol_Logo JSmol_Logo
52 Fragment-FG8_Uridine Wiki_Logo Jmol_Logo JSmol_Logo
53 1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Wiki_Logo Jmol_Logo JSmol_Logo
54 Fragment-FG1_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Wiki_Logo Jmol_Logo JSmol_Logo
55 Fragment-FG3_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Wiki_Logo Jmol_Logo JSmol_Logo
56 Fragment-FG4_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Wiki_Logo Jmol_Logo JSmol_Logo
57 Fragment-FG5_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Wiki_Logo Jmol_Logo JSmol_Logo
58 Fragment-FG6_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Wiki_Logo Jmol_Logo JSmol_Logo
59 Fragment-FG7_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Wiki_Logo Jmol_Logo JSmol_Logo
60 Fragment-FG8_1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide Wiki_Logo Jmol_Logo JSmol_Logo
61 3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Wiki_Logo Jmol_Logo JSmol_Logo
62 Fragment-FG1_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Wiki_Logo Jmol_Logo JSmol_Logo
63 Fragment-FG3_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Wiki_Logo Jmol_Logo JSmol_Logo
64 Fragment-FG4_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Wiki_Logo Jmol_Logo JSmol_Logo
65 Fragment-FG5_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Wiki_Logo Jmol_Logo JSmol_Logo
66 Fragment-FG6_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Wiki_Logo Jmol_Logo JSmol_Logo
67 Fragment-FG7_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Wiki_Logo Jmol_Logo JSmol_Logo
68 Fragment-FG8_3-(aminocarbonyl)-1-D-ribofuranosylpyridinium Wiki_Logo Jmol_Logo JSmol_Logo
69 Fragment-FG1_(2S,3S,4R)-1-amino-1-deoxypentitol Wiki_Logo Jmol_Logo JSmol_Logo
70 Fragment-FG3_(2S,3S,4R)-1-amino-1-deoxypentitol Wiki_Logo Jmol_Logo JSmol_Logo
71 Fragment-FG1_7,8,10-trimethylbenzo[g]pteridine-2,4(3H,10H)-dione Wiki_Logo Jmol_Logo JSmol_Logo
72 Fragment-FG1_7,8,10-trimethyl-5,10-dihydrobenzo[g]pteridine-2,4(1H,3H)-dione Wiki_Logo Jmol_Logo JSmol_Logo
73 Fragment-FG1_(2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide Wiki_Logo Jmol_Logo JSmol_Logo
74 Fragment-FG3_(2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide Wiki_Logo Jmol_Logo JSmol_Logo
75 Fragment-FG1_N3-acetyl-N-methyl-b-alaninamide Wiki_Logo Jmol_Logo JSmol_Logo
76 Fragment-FG1_S-[2-(acetylamino)ethyl]-ethanethioate Wiki_Logo Jmol_Logo JSmol_Logo
77 Fragment-FG1_N-(2-sulfanylethyl)acetamide Wiki_Logo Jmol_Logo JSmol_Logo
78 2'-Deoxy-3'5'-cyclic-adenosine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
79 2'-Deoxy-3'5'-cyclic-cytidine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
80 2'-Deoxy-3'5'-cyclic-guanosine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
81 2'-Deoxy-3'5'-cyclic-thymidine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
82 3'5'-cyclic-adenosine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
83 Fragment-FG1_3'5'-cyclic-adenosine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
84 3'5'-cyclic-cytidine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
85 Fragment-FG1_3'5'-cyclic-cytidine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
86 3'5'-cyclic-guanosine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
87 Fragment-FG1_3'5'-cyclic-guanosine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
88 3'5'-cyclic-uridine-monophosphate Wiki_Logo Jmol_Logo JSmol_Logo
89 Fragment-FG1_3'5'-cyclic-uridine-monophosphate Wiki_Logo Jmol_Logo JSmol_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 Wiki_Logo
2 Methyl-hydrogen-phosphate 1 Rigid Body Reorient Algo 2 Wiki_Logo
3 Methyl-phosphate 1 Rigid Body Reorient Algo 2 Wiki_Logo
4 2'-Deoxyadenosine 2 Rigid Body Reorient Algo 4 Wiki_Logo
5 2'-Deoxycytidine 2 Rigid Body Reorient Algo 4 Wiki_Logo
6 2'-Deoxyguanosine 2 Rigid Body Reorient Algo 4 Wiki_Logo
7 2'-Deoxythymidine 2 Rigid Body Reorient Algo 4 Wiki_Logo
8 Adenosine 2 Rigid Body Reorient Algo 4 Wiki_Logo
9 Cytidine 2 Rigid Body Reorient Algo 4 Wiki_Logo
10 Guanosine 2 Rigid Body Reorient Algo 4 Wiki_Logo
11 Uridine 2 Rigid Body Reorient Algo 4 Wiki_Logo
12 1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide 4 Rigid Body Reorient Algo 4 Wiki_Logo
13 3-(aminocarbonyl)-1-D-ribofuranosylpyridinium 4 Rigid Body Reorient Algo 4 Wiki_Logo
14 (2S,3S,4R)-1-amino-1-deoxypentitol 1 Rigid Body Reorient Algo 2 Wiki_Logo
15 7,8,10-trimethylbenzo[g]pteridine-2,4(3H,10H)-dione 1 Rigid Body Reorient Algo 4 Wiki_Logo
16 7,8,10-trimethyl-5,10-dihydrobenzo[g]pteridine-2,4(1H,3H)-dione 1 Rigid Body Reorient Algo 4 Wiki_Logo
17 (2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide 1 Rigid Body Reorient Algo 2 Wiki_Logo
18 N3-acetyl-N-methyl-b-alaninamide 2 Rigid Body Reorient Algo 2 Wiki_Logo
19 S-[2-(acetylamino)ethyl]-ethanethioate 2 Rigid Body Reorient Algo 2 Wiki_Logo
20 N-(2-sulfanylethyl)acetamide 2 Rigid Body Reorient Algo 2 Wiki_Logo
21 2'-Deoxy-3'5'-cyclic-adenosine-monophosphate 1 Rigid Body Reorient Algo 4 Wiki_Logo
22 2'-Deoxy-3'5'-cyclic-cytidine-monophosphate 1 Rigid Body Reorient Algo 4 Wiki_Logo
23 2'-Deoxy-3'5'-cyclic-guanosine-monophosphate 1 Rigid Body Reorient Algo 4 Wiki_Logo
24 2'-Deoxy-3'5'-cyclic-thymidine-monophosphate 1 Rigid Body Reorient Algo 4 Wiki_Logo
25 3'5'-cyclic-adenosine-monophosphate 1 Rigid Body Reorient Algo 4 Wiki_Logo
26 3'5'-cyclic-cytidine-monophosphate 1 Rigid Body Reorient Algo 4 Wiki_Logo
27 3'5'-cyclic-guanosine-monophosphate 1 Rigid Body Reorient Algo 4 Wiki_Logo
28 3'5'-cyclic-uridine-monophosphate 1 Rigid Body Reorient Algo 4 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 HF

More information 2 IOp(6/33=2) NoSymm

Basis set 2 6-31G*

Algorithm CONNOLLY SURFACE


Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1

input of stage 2



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

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

Download the whole project...



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