Commit 2d31c8e2 authored by jdurrant's avatar jdurrant
Browse files

Merge branch '3.1.3' into 'master'

AutoGrow 3.1.3

See merge request !3
parents 585dbbbf 2f8b132b
INSTALLATION
============
AutoGrow 3 is written in python and so does not need to be compiled. The program
works in conjunction with a number of other required software packages:
MGLTools: http://mgltools.scripps.edu/
Open Babel: http://openbabel.org/wiki/Main_Page
AutoDock Vina: http://vina.scripps.edu/
NumPy: http://www.numpy.org/
SciPy: http://www.scipy.org/
Python, which is preinstalled on many systems, can be downloaded from
http://www.python.org/
AutoGrow 3 program has been specifically tested on Scientific Linux 6.2 with
python 2.6.6, NumPy 1.6.2, SciPy 0.11.0, MGLTools 1.5.4, Open Babel 2.3.1, and
AutoDock Vina 1.1.2, as well as on Mac OS X 10.8.1 with python 2.7.2, NumPy
1.6.1, SciPy 0.12.0dev, MGLTools 1.5.6, Open Babel 2.3.1, and AutoDock Vina
1.1.2.
USAGE
=====
The ./tutorial/ directory contains sample files, including the
./tutorial/run_example_linux_or_macosx file, which has detailed comments that
new users will find helpful. This same file is executable, in case users want to
actually run the example described in the comments.
This diff is collapsed.
# AutoGrow 3.1 includes a subdirectory called tutorial with files that show how to
# use the software.
#
# Step 1: Begin by changing to the tutorial directory:
#
# cd /PATH/TO/AUTOGROW3/tutorial/
#
# Step 2: AutoGrow 3.1 can be run from this directory thusly:
#
# python ../autogrow_3_1_1.py
#
# Step 3: Specify a PDB model of the target protein receptor. In this tutorial, a
# model of TbREL1 (PDB ID: 1XDN), a potential African-sleep-sickness drug target,
# will be used. The center of the TbREL1 active site is roughly located at (39.5,
# 23.7, 15.0). A box 30.0 x 30.0 x 20.0 centered on that point should encompass
# the entire site. These are the AutoGrow 3.1 parameters required:
#
# -filename_of_receptor 1xdn_receptor.pdb -center_x 39.5 -center_y 23.7 -center_z
# 15.0 -size_x 30.0 -size_y 30.0 -size_z 20.0
#
# Step 4: Specify which click-chemisty reactions to use in ligand building. In
# this example, we'll use the azide-alkyne Huisgen cycloaddition. Though it's a
# bit redundant here, we'll also tell AutoGrow 3.1 to avoid click-chemistry
# reactions that merely swap compound moieties (e.g., Br => azide), favoring
# instead joining reactions that actually add new fragments.
#
# -additional_autoclickchem_parameters "-all_reactions +azide_and_alkyne_to_azole"
# -allow_modification_without_frag_addition FALSE
#
# Step 5: Specify the source compounds that will be optimized into predicted
# ligands. The tutorial directory contains a subdirectory called
# starting_compounds with 117 naphthalene PDB files chosen because a number of
# experimentally validated TbREL1 inhibitors contain naphthalene substructures.
# Additionally, these naphthalene models contain azide and/or alkyne groups, so
# they can participate in the azide-alkyne Huisgen cycloaddition. The fragments
# that will be added to these naphthalene building blocks via this cycloaddition
# reaction will be drawn from one of the AutoGrow 3.1 default fragment libraries.
#
# -directory_of_source_compounds ./starting_compounds/ -directory_of_fragments
# ../fragments/MW_250/
#
# Step 6: A number of parameters must also be included to control the behavior of
# the genetic algorithm. Note that the first generation is special in that it can
# have a different number of mutants and crossovers than subsequent generations.
#
# -number_of_mutants_first_generation 10 -number_of_crossovers_first_generation 10
# -number_of_mutants 10 -number_of_crossovers 10
# -top_ones_to_advance_to_next_generation 5 -num_generations 2
# -max_seconds_per_generation 1000000
#
# Step 7: Aside from judging ligand fitness by the docking score, AutoGrow 3.1 can
# be instructed to selectively advance only drug-like compounds to subsequent
# generations. In the current example, we're going to require that ligands satisfy
# Lipinski's Rule of Fives as well as the drug-like criteria described by Ghose et
# al. We're also going to evaluate compound fitness using the AutoDock Vina
# scoring function. The actual docking score will be used, rather than ligand
# efficiency (score / number of heavy atoms).
#
# -use_lipinski_filter TRUE -use_strict_lipinski_filter TRUE -use_ghose_filter
# TRUE -scoring_function VINA -score_by_ligand_efficiency FALSE
#
# Step 8: AutoGrow 3.1 can be instructed to favor compounds that contain certain
# key moieties. In the current example, however, we do not need this
# functionality.
#
# -maintain_core FALSE -minimum_core_atoms_required 0
#
# Step 9: AutoGrow 3.1 requires a number of additional open-source programs. The
# locations of these programs and/or their directories must also be specified.
# Take care to specify the correct paths here. -vina_executable should point to
# the actual vina executable, not a directory. In contrast,
# -openbabel_bin_directory points to a directory that contains the executable
# files babel and obprop, and -mgltools_directory points to a directory that
# contains subdirectories with names like bin and MGLToolsPckgs.
#
# -vina_executable /PATH/TO/VINA/EXECUTABLE/vina -openbabel_bin_directory
# /PATH/TO/OPENBABEL/BIN/DIR/bin/ -mgltools_directory
# /PATH/TO/MGLTOOLS/DIRECTORY/MGLTools-1.5.4/
#
# Step 10: AutoGrow 3.1 runs much faster on multiple processors.
#
# -num_processors 4
#
# Step 11: Finally, the user must specify the directory where the AutoGrow 3.1
# output will be written.
#
# -output_dir ./autogrow_output/
#
# So, putting all this together, we have the following command line:
# python ../autogrow_3_1_1.py -filename_of_receptor 1xdn_receptor.pdb -center_x 39.5 -center_y 23.7 -center_z 15.0 -size_x 30.0 -size_y 30.0 -size_z 20.0 -additional_autoclickchem_parameters "-all_reactions +azide_and_alkyne_to_azole" -allow_modification_without_frag_addition FALSE -directory_of_source_compounds ./starting_compounds/ -directory_of_fragments ../fragments/MW_250/ -number_of_mutants_first_generation 10 -number_of_crossovers_first_generation 10 -number_of_mutants 10 -number_of_crossovers 10 -top_ones_to_advance_to_next_generation 5 -num_generations 2 -max_seconds_per_generation 1000000 -use_lipinski_filter TRUE -use_strict_lipinski_filter TRUE -use_ghose_filter TRUE -scoring_function VINA -score_by_ligand_efficiency FALSE -maintain_core FALSE -minimum_core_atoms_required 0 -vina_executable /PATH/TO/VINA/EXECUTABLE/vina -openbabel_bin_directory /PATH/TO/OPENBABEL/BIN/DIR/bin/ -mgltools_directory /PATH/TO/MGLTOOLS/DIRECTORY/MGLTools-1.5.4/ -num_processors 4 -output_dir ./autogrow_output/
# Some users may find it convenient to break this command into multiple lines
# and to store it in an executable file for subsequent reference.
python ../autogrow_3_1_1.py \
-filename_of_receptor 1xdn_receptor.pdb \
-center_x 39.5 -center_y 23.7 -center_z 15.0 \
-size_x 30.0 -size_y 30.0 -size_z 20.0 \
-additional_autoclickchem_parameters "-all_reactions +azide_and_alkyne_to_azole" \
-allow_modification_without_frag_addition FALSE \
-directory_of_source_compounds ./starting_compounds/ \
-directory_of_fragments ../fragments/MW_250/ \
-number_of_mutants_first_generation 10 -number_of_crossovers_first_generation 10 \
-number_of_mutants 10 -number_of_crossovers 10 \
-top_ones_to_advance_to_next_generation 5 -num_generations 2 \
-max_seconds_per_generation 1000000 \
-use_lipinski_filter TRUE -use_strict_lipinski_filter TRUE -use_ghose_filter TRUE \
-scoring_function VINA -score_by_ligand_efficiency FALSE \
-maintain_core FALSE -minimum_core_atoms_required 0 \
-vina_executable /PATH/TO/VINA/EXECUTABLE/vina \
-openbabel_bin_directory /PATH/TO/OPENBABEL/BIN/DIR/bin/ \
-mgltools_directory /PATH/TO/MGLTOOLS/DIRECTORY/MGLTools-1.5.4/ \
-num_processors 4 \
-output_dir ./autogrow_output/
COMPND acid_anhydrides_MOOSE_ZINC08100874.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 1.440 -0.211 0.060 1.00 0.00 C
HETATM 2 C LIG 1 0.159 0.133 0.107 1.00 0.00 C
HETATM 3 C LIG 1 0.097 1.587 0.115 1.00 0.00 C
HETATM 4 O LIG 1 -0.926 2.268 0.155 1.00 0.00 O
HETATM 5 O LIG 1 1.363 2.065 0.072 1.00 0.00 O
HETATM 6 C LIG 1 2.221 1.018 0.037 1.00 0.00 C
HETATM 7 O LIG 1 3.447 1.095 -0.006 1.00 0.00 O
HETATM 8 H LIG 1 1.861 -1.205 0.041 1.00 0.00 H
HETATM 9 H LIG 1 -0.703 -0.518 0.135 1.00 0.00 H
CONECT 1 8 6 2 2
CONECT 2 1 1 9 3
CONECT 3 2 5 4 4
CONECT 4 3 3
CONECT 5 3 6
CONECT 6 1 5 7 7
CONECT 7 6 6
CONECT 8 1
CONECT 9 2
MASTER 0 0 0 0 0 0 0 0 9 0 9 0
END
COMPND acid_anhydrides_MOOSE_ZINC08100877.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.209 1.612 0.112 1.00 0.00 C
HETATM 2 C LIG 1 0.134 0.100 0.094 1.00 0.00 C
HETATM 3 C LIG 1 -0.932 -0.690 0.112 1.00 0.00 C
HETATM 4 C LIG 1 -0.450 -2.064 0.081 1.00 0.00 C
HETATM 5 O LIG 1 -1.148 -3.076 0.086 1.00 0.00 O
HETATM 6 O LIG 1 0.906 -2.038 0.046 1.00 0.00 O
HETATM 7 C LIG 1 1.318 -0.749 0.052 1.00 0.00 C
HETATM 8 O LIG 1 2.488 -0.370 0.026 1.00 0.00 O
HETATM 9 H LIG 1 0.761 1.955 0.987 1.00 0.00 H
HETATM 10 H LIG 1 -0.790 2.048 0.144 1.00 0.00 H
HETATM 11 H LIG 1 0.715 1.979 -0.781 1.00 0.00 H
HETATM 12 H LIG 1 -1.974 -0.405 0.143 1.00 0.00 H
CONECT 1 10 2 9 11
CONECT 2 1 7 3 3
CONECT 3 2 2 4 12
CONECT 4 3 6 5 5
CONECT 5 4 4
CONECT 6 4 7
CONECT 7 2 6 8 8
CONECT 8 7 7
CONECT 9 1
CONECT 10 1
CONECT 11 1
CONECT 12 3
MASTER 0 0 0 0 0 0 0 0 12 0 12 0
END
COMPND acid_anhydrides_MOOSE_ZINC08100879.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.188 1.420 0.114 1.00 0.00 C
HETATM 2 C LIG 1 0.144 0.078 0.093 1.00 0.00 C
HETATM 3 C LIG 1 -1.070 -0.790 0.119 1.00 0.00 C
HETATM 4 C LIG 1 -0.417 -2.163 0.074 1.00 0.00 C
HETATM 5 O LIG 1 -1.066 -3.207 0.078 1.00 0.00 O
HETATM 6 O LIG 1 0.932 -2.074 0.031 1.00 0.00 O
HETATM 7 C LIG 1 1.322 -0.783 0.040 1.00 0.00 C
HETATM 8 O LIG 1 2.492 -0.405 0.007 1.00 0.00 O
HETATM 9 H LIG 1 1.126 1.956 0.092 1.00 0.00 H
HETATM 10 H LIG 1 -0.721 2.003 0.154 1.00 0.00 H
HETATM 11 H LIG 1 -1.644 -0.651 1.035 1.00 0.00 H
HETATM 12 H LIG 1 -1.703 -0.621 -0.752 1.00 0.00 H
CONECT 1 2 2 9 10
CONECT 2 1 1 7 3
CONECT 3 2 12 4 11
CONECT 4 3 6 5 5
CONECT 5 4 4
CONECT 6 4 7
CONECT 7 2 6 8 8
CONECT 8 7 7
CONECT 9 1
CONECT 10 1
CONECT 11 3
CONECT 12 3
MASTER 0 0 0 0 0 0 0 0 12 0 12 0
END
COMPND acid_anhydrides_MOOSE_ZINC08100881.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.116 0.106 0.130 1.00 0.00 C
HETATM 2 C LIG 1 1.353 -0.580 0.116 1.00 0.00 C
HETATM 3 C LIG 1 2.505 0.222 0.085 1.00 0.00 C
HETATM 4 C LIG 1 2.399 1.593 0.069 1.00 0.00 C
HETATM 5 N LIG 1 1.240 2.282 0.081 1.00 0.00 N
HETATM 6 C LIG 1 0.115 1.526 0.111 1.00 0.00 C
HETATM 7 C LIG 1 3.758 2.134 0.037 1.00 0.00 C
HETATM 8 O LIG 1 4.080 3.321 0.016 1.00 0.00 O
HETATM 9 O LIG 1 4.625 1.070 0.035 1.00 0.00 O
HETATM 10 C LIG 1 3.927 -0.109 0.063 1.00 0.00 C
HETATM 11 O LIG 1 4.418 -1.236 0.069 1.00 0.00 O
HETATM 12 H LIG 1 -0.814 -0.441 0.153 1.00 0.00 H
HETATM 13 H LIG 1 1.407 -1.659 0.129 1.00 0.00 H
HETATM 14 H LIG 1 -0.820 2.066 0.121 1.00 0.00 H
CONECT 1 2 12 6 6
CONECT 2 1 3 3 13
CONECT 3 2 2 10 4
CONECT 4 3 7 5 5
CONECT 5 4 4 6
CONECT 6 1 1 5 14
CONECT 7 4 9 8 8
CONECT 8 7 7
CONECT 9 7 10
CONECT 10 3 9 11 11
CONECT 11 10 10
CONECT 12 1
CONECT 13 2
CONECT 14 6
MASTER 0 0 0 0 0 0 0 0 14 0 14 0
END
COMPND acid_anhydrides_MOOSE_ZINC08100883.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.086 1.195 0.116 1.00 0.00 C
HETATM 2 C LIG 1 1.312 1.908 0.132 1.00 0.00 C
HETATM 3 C LIG 1 1.323 3.322 0.136 1.00 0.00 C
HETATM 4 C LIG 1 0.082 3.983 0.124 1.00 0.00 C
HETATM 5 C LIG 1 -1.108 3.291 0.109 1.00 0.00 C
HETATM 6 C LIG 1 -1.148 1.886 0.104 1.00 0.00 C
HETATM 7 C LIG 1 -2.185 4.279 0.100 1.00 0.00 C
HETATM 8 O LIG 1 -3.393 4.048 0.086 1.00 0.00 O
HETATM 9 O LIG 1 -1.609 5.521 0.110 1.00 0.00 O
HETATM 10 C LIG 1 -0.244 5.407 0.125 1.00 0.00 C
HETATM 11 O LIG 1 0.554 6.342 0.137 1.00 0.00 O
HETATM 12 H LIG 1 0.095 0.115 0.113 1.00 0.00 H
HETATM 13 H LIG 1 2.246 1.366 0.141 1.00 0.00 H
HETATM 14 H LIG 1 2.251 3.874 0.148 1.00 0.00 H
HETATM 15 H LIG 1 -2.087 1.352 0.092 1.00 0.00 H
CONECT 1 2 12 6 6
CONECT 2 1 13 3 3
CONECT 3 2 2 14 4
CONECT 4 3 5 5 10
CONECT 5 4 4 6 7
CONECT 6 1 1 5 15
CONECT 7 5 9 8 8
CONECT 8 7 7
CONECT 9 7 10
CONECT 10 4 9 11 11
CONECT 11 10 10
CONECT 12 1
CONECT 13 2
CONECT 14 3
CONECT 15 6
MASTER 0 0 0 0 0 0 0 0 15 0 15 0
END
COMPND acid_anhydrides_MOOSE_ZINC08100888.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.071 0.133 0.105 1.00 0.00 C
HETATM 2 C LIG 1 1.324 -0.524 0.112 1.00 0.00 C
HETATM 3 N LIG 1 2.518 0.126 0.116 1.00 0.00 N
HETATM 4 C LIG 1 2.520 1.482 0.112 1.00 0.00 C
HETATM 5 C LIG 1 1.314 2.203 0.106 1.00 0.00 C
HETATM 6 C LIG 1 0.112 1.538 0.102 1.00 0.00 C
HETATM 7 C LIG 1 -0.944 2.548 0.095 1.00 0.00 C
HETATM 8 O LIG 1 -2.157 2.343 0.091 1.00 0.00 O
HETATM 9 O LIG 1 -0.338 3.779 0.095 1.00 0.00 O
HETATM 10 C LIG 1 1.026 3.634 0.101 1.00 0.00 C
HETATM 11 O LIG 1 1.847 4.548 0.102 1.00 0.00 O
HETATM 12 H LIG 1 -0.861 -0.413 0.103 1.00 0.00 H
HETATM 13 H LIG 1 1.371 -1.603 0.115 1.00 0.00 H
HETATM 14 H LIG 1 3.478 1.980 0.115 1.00 0.00 H
CONECT 1 2 12 6 6
CONECT 2 1 3 3 13
CONECT 3 2 2 4
CONECT 4 3 14 5 5
CONECT 5 4 4 6 10
CONECT 6 1 1 5 7
CONECT 7 6 9 8 8
CONECT 8 7 7
CONECT 9 7 10
CONECT 10 5 9 11 11
CONECT 11 10 10
CONECT 12 1
CONECT 13 2
CONECT 14 4
MASTER 0 0 0 0 0 0 0 0 14 0 14 0
END
COMPND acid_anhydrides_MOOSE_ZINC08100926.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.035 1.326 0.060 1.00 0.00 C
HETATM 2 C LIG 1 -0.689 1.637 1.375 1.00 0.00 C
HETATM 3 O LIG 1 -0.557 0.853 2.311 1.00 0.00 O
HETATM 4 O LIG 1 -1.435 2.794 1.511 1.00 0.00 O
HETATM 5 C LIG 1 -1.689 3.662 0.465 1.00 0.00 C
HETATM 6 O LIG 1 -2.425 4.636 0.612 1.00 0.00 O
HETATM 7 C LIG 1 -1.018 3.459 -0.898 1.00 0.00 C
HETATM 8 S LIG 1 -0.996 1.726 -1.350 1.00 0.00 S
HETATM 9 H LIG 1 0.286 0.265 0.026 1.00 0.00 H
HETATM 10 H LIG 1 0.969 1.885 0.012 1.00 0.00 H
HETATM 11 H LIG 1 -0.002 3.853 -0.872 1.00 0.00 H
HETATM 12 H LIG 1 -1.565 4.017 -1.659 1.00 0.00 H
CONECT 1 8 10 9 2
CONECT 2 1 4 3 3
CONECT 3 2 2
CONECT 4 2 5
CONECT 5 4 7 6 6
CONECT 6 5 5
CONECT 7 5 12 8 11
CONECT 8 1 7
CONECT 9 1
CONECT 10 1
CONECT 11 7
CONECT 12 7
MASTER 0 0 0 0 0 0 0 0 12 0 12 0
END
COMPND acid_anhydrides_MOOSE_ZINC08100959.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.082 1.654 0.091 1.00 0.00 C
HETATM 2 C LIG 1 1.564 1.965 0.090 1.00 0.00 C
HETATM 3 O LIG 1 2.018 3.107 0.096 1.00 0.00 O
HETATM 4 O LIG 1 2.278 0.818 0.083 1.00 0.00 O
HETATM 5 C LIG 1 1.444 -0.251 0.079 1.00 0.00 C
HETATM 6 O LIG 1 1.804 -1.425 0.072 1.00 0.00 O
HETATM 7 N LIG 1 0.153 0.226 0.084 1.00 0.00 N
HETATM 8 H LIG 1 -0.408 2.030 0.990 1.00 0.00 H
HETATM 9 H LIG 1 -0.411 2.040 -0.801 1.00 0.00 H
HETATM 10 H LIG 1 -0.639 -0.401 0.082 1.00 0.00 H
CONECT 1 9 2 7 8
CONECT 2 1 4 3 3
CONECT 3 2 2
CONECT 4 2 5
CONECT 5 4 6 6 7
CONECT 6 5 5
CONECT 7 1 5 10
CONECT 8 1
CONECT 9 1
CONECT 10 7
MASTER 0 0 0 0 0 0 0 0 10 0 10 0
END
COMPND acid_anhydrides_MOOSE_ZINC08585917.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 1.282 3.526 0.124 1.00 0.00 C
HETATM 2 C LIG 1 1.481 2.016 0.094 1.00 0.00 C
HETATM 3 O LIG 1 2.620 1.544 0.062 1.00 0.00 O
HETATM 4 O LIG 1 0.277 1.361 0.107 1.00 0.00 O
HETATM 5 C LIG 1 0.269 -0.009 0.083 1.00 0.00 C
HETATM 6 O LIG 1 1.224 -0.790 0.050 1.00 0.00 O
HETATM 7 C LIG 1 -1.156 -0.547 0.102 1.00 0.00 C
HETATM 8 H LIG 1 0.708 3.850 -0.744 1.00 0.00 H
HETATM 9 H LIG 1 2.243 4.040 0.114 1.00 0.00 H
HETATM 10 H LIG 1 0.744 3.819 1.026 1.00 0.00 H
HETATM 11 H LIG 1 -1.673 -0.219 1.004 1.00 0.00 H
HETATM 12 H LIG 1 -1.709 -0.188 -0.766 1.00 0.00 H
HETATM 13 H LIG 1 -1.154 -1.637 0.083 1.00 0.00 H
CONECT 1 9 2 8 10
CONECT 2 1 3 3 4
CONECT 3 2 2
CONECT 4 2 5
CONECT 5 4 6 6 7
CONECT 6 5 5
CONECT 7 5 13 11 12
CONECT 8 1
CONECT 9 1
CONECT 10 1
CONECT 11 7
CONECT 12 7
CONECT 13 7
MASTER 0 0 0 0 0 0 0 0 13 0 13 0
END
COMPND acid_anhydrides_MOOSE_ZINC08681668.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.102 1.647 0.106 1.00 0.00 C
HETATM 2 C LIG 1 1.573 2.004 0.134 1.00 0.00 C
HETATM 3 C LIG 1 2.259 0.648 0.114 1.00 0.00 C
HETATM 4 O LIG 1 3.481 0.522 0.129 1.00 0.00 O
HETATM 5 O LIG 1 1.368 -0.357 0.080 1.00 0.00 O
HETATM 6 C LIG 1 0.114 0.129 0.073 1.00 0.00 C
HETATM 7 O LIG 1 -0.914 -0.544 0.044 1.00 0.00 O
HETATM 8 H LIG 1 -0.419 2.006 0.994 1.00 0.00 H
HETATM 9 H LIG 1 -0.394 2.044 -0.780 1.00 0.00 H
HETATM 10 H LIG 1 1.864 2.591 -0.737 1.00 0.00 H
HETATM 11 H LIG 1 1.839 2.553 1.037 1.00 0.00 H
CONECT 1 9 2 6 8
CONECT 2 1 10 3 11
CONECT 3 2 5 4 4
CONECT 4 3 3
CONECT 5 3 6
CONECT 6 1 5 7 7
CONECT 7 6 6
CONECT 8 1
CONECT 9 1
CONECT 10 2
CONECT 11 2
MASTER 0 0 0 0 0 0 0 0 11 0 11 0
END
COMPND acid_anhydrides_MOOSE_ZINC32098832.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.114 1.643 0.269 1.00 0.00 C
HETATM 2 C LIG 1 1.570 2.045 0.153 1.00 0.00 C
HETATM 3 H LIG 1 1.937 2.489 1.079 1.00 0.00 H
HETATM 4 C LIG 1 2.289 0.734 -0.138 1.00 0.00 C
HETATM 5 O LIG 1 3.507 0.612 -0.247 1.00 0.00 O
HETATM 6 O LIG 1 1.399 -0.269 -0.277 1.00 0.00 O
HETATM 7 C LIG 1 0.143 0.167 -0.080 1.00 0.00 C
HETATM 8 O LIG 1 -0.875 -0.517 -0.160 1.00 0.00 O
HETATM 9 N LIG 1 1.815 2.951 -0.984 1.00 0.00 N1+
HETATM 10 H LIG 1 -0.259 1.776 1.285 1.00 0.00 H
HETATM 11 H LIG 1 -0.534 2.191 -0.417 1.00 0.00 H
HETATM 12 H LIG 1 1.331 3.825 -0.836 1.00 0.00 H
HETATM 13 H LIG 1 1.488 2.524 -1.839 1.00 0.00 H
HETATM 14 H LIG 1 2.808 3.126 -1.060 1.00 0.00 H
CONECT 1 11 2 7 10
CONECT 2 1 9 4 3
CONECT 3 2
CONECT 4 2 6 5 5
CONECT 5 4 4
CONECT 6 4 7
CONECT 7 1 6 8 8
CONECT 8 7 7
CONECT 9 2 14 13 12
CONECT 10 1
CONECT 11 1
CONECT 12 9
CONECT 13 9
CONECT 14 9
MASTER 0 0 0 0 0 0 0 0 14 0 14 0
END
COMPND acid_anhydrides_MOOSE_ZINC43411838.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.091 1.675 0.124 1.00 0.00 C
HETATM 2 C LIG 1 0.098 0.138 0.101 1.00 0.00 C
HETATM 3 C LIG 1 0.800 -0.389 -1.147 1.00 0.00 C
HETATM 4 C LIG 1 0.987 -1.913 -1.142 1.00 0.00 C
HETATM 5 O LIG 1 1.028 -2.504 -2.219 1.00 0.00 O
HETATM 6 O LIG 1 1.139 -2.582 0.053 1.00 0.00 O
HETATM 7 C LIG 1 1.016 -1.945 1.270 1.00 0.00 C
HETATM 8 O LIG 1 1.091 -2.564 2.329 1.00 0.00 O
HETATM 9 C LIG 1 0.825 -0.422 1.319 1.00 0.00 C
HETATM 10 O LIG 1 -1.257 -0.277 0.113 1.00 0.00 O
HETATM 11 H LIG 1 1.105 2.075 0.121 1.00 0.00 H
HETATM 12 H LIG 1 -0.410 2.056 1.014 1.00 0.00 H
HETATM 13 H LIG 1 -0.424 2.084 -0.746 1.00 0.00 H
HETATM 14 H LIG 1 0.249 -0.099 -2.042 1.00 0.00 H
HETATM 15 H LIG 1 1.789 0.062 -1.232 1.00 0.00 H
HETATM 16 H LIG 1 1.814 0.030 1.399 1.00 0.00 H
HETATM 17 H LIG 1 0.288 -0.159 2.231 1.00 0.00 H
HETATM 18 H LIG 1 -1.696 0.098 -0.636 1.00 0.00 H
CONECT 1 12 2 11 13
CONECT 2 1 3 10 9
CONECT 3 2 14 15 4
CONECT 4 3 5 5 6
CONECT 5 4 4
CONECT 6 4 7
CONECT 7 6 9 8 8
CONECT 8 7 7
CONECT 9 2 7 16 17
CONECT 10 2 18
CONECT 11 1
CONECT 12 1
CONECT 13 1
CONECT 14 3
CONECT 15 3
CONECT 16 9
CONECT 17 9
CONECT 18 10
MASTER 0 0 0 0 0 0 0 0 18 0 18 0
END
COMPND acid_anhydrides_MOOSE_ZINC45331639.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 -0.019 1.611 0.301 1.00 0.00 C
HETATM 2 C LIG 1 0.201 0.131 -0.051 1.00 0.00 C
HETATM 3 C LIG 1 0.949 -0.088 -1.369 1.00 0.00 C
HETATM 4 O LIG 1 1.323 0.869 -2.054 1.00 0.00 O
HETATM 5 O LIG 1 1.106 -1.427 -1.614 1.00 0.00 O
HETATM 6 C LIG 1 1.756 -1.825 -2.754 1.00 0.00 C
HETATM 7 O LIG 1 2.249 -1.124 -3.643 1.00 0.00 O
HETATM 8 C LIG 1 1.819 -3.353 -2.829 1.00 0.00 C
HETATM 9 C LIG 1 2.534 -3.885 -4.080 1.00 0.00 C
HETATM 10 H LIG 1 0.929 2.140 0.406 1.00 0.00 H
HETATM 11 H LIG 1 -0.554 1.705 1.246 1.00 0.00 H
HETATM 12 H LIG 1 -0.608 2.119 -0.463 1.00 0.00 H
HETATM 13 H LIG 1 -0.762 -0.376 -0.113 1.00 0.00 H
HETATM 14 H LIG 1 0.761 -0.355 0.748 1.00 0.00 H
HETATM 15 H LIG 1 0.801 -3.742 -2.796 1.00 0.00 H
HETATM 16 H LIG 1 2.325 -3.721 -1.935 1.00 0.00 H
HETATM 17 H LIG 1 2.032 -3.563 -4.993 1.00 0.00 H
HETATM 18 H LIG 1 2.549 -4.975 -4.080 1.00 0.00 H
HETATM 19 H LIG 1 3.569 -3.542 -4.124 1.00 0.00 H
CONECT 1 11 2 10 12
CONECT 2 1 3 14 13
CONECT 3 2 4 4 5
CONECT 4 3 3
CONECT 5 3 6
CONECT 6 5 7 7 8
CONECT 7 6 6
CONECT 8 6 9 16 15
CONECT 9 8 18 17 19
CONECT 10 1
CONECT 11 1
CONECT 12 1
CONECT 13 2
CONECT 14 2
CONECT 15 8
CONECT 16 8
CONECT 17 9
CONECT 18 9
CONECT 19 9
MASTER 0 0 0 0 0 0 0 0 19 0 19 0
END
COMPND acid_anhydrides_MOOSE_ZINC49781431.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 0.084 1.550 0.100 1.00 0.00 C
HETATM 2 C LIG 1 1.560 1.967 0.142 1.00 0.00 C
HETATM 3 H LIG 1 1.949 2.203 -0.849 1.00 0.00 H
HETATM 4 C LIG 1 2.276 0.784 0.741 1.00 0.00 C
HETATM 5 H LIG 1 3.039 0.401 0.063 1.00 0.00 H
HETATM 6 C LIG 1 1.171 -0.246 1.009 1.00 0.00 C
HETATM 7 O LIG 1 0.121 0.133 0.134 1.00 0.00 O
HETATM 8 C LIG 1 2.892 1.355 2.012 1.00 0.00 C
HETATM 9 O LIG 1 3.566 0.681 2.787 1.00 0.00 O
HETATM 10 O LIG 1 2.595 2.657 2.163 1.00 0.00 O
HETATM 11 C LIG 1 1.844 3.086 1.135 1.00 0.00 C
HETATM 12 O LIG 1 1.418 4.231 0.990 1.00 0.00 O
HETATM 13 H LIG 1 -0.475 1.912 0.965 1.00 0.00 H
HETATM 14 H LIG 1 -0.419 1.902 -0.801 1.00 0.00 H
HETATM 15 H LIG 1 1.498 -1.266 0.803 1.00 0.00 H
HETATM 16 H LIG 1 0.808 -0.208 2.038 1.00 0.00 H
CONECT 1 14 2 7 13
CONECT 2 1 3 4 11
CONECT 3 2
CONECT 4 2 5 6 8
CONECT 5 4
CONECT 6 4 7 15 16
CONECT 7 1 6
CONECT 8 4 10 9 9
CONECT 9 8 8
CONECT 10 8 11
CONECT 11 2 10 12 12
CONECT 12 11 11
CONECT 13 1
CONECT 14 1
CONECT 15 6
CONECT 16 6
MASTER 0 0 0 0 0 0 0 0 16 0 16 0