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Commit 45f0b42c authored by Studer Gabriel's avatar Studer Gabriel
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Ensure that arbitrary compound names can be read by chemdict_tools 

PDB announced they're running out of three letter codes for compounds and
switch to longer names soon. This commit ensures that OpenStructure is ready
for that switch.
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modules/conop/src/compound_lib.cc
+ 11
− 1
View file @ 45f0b42c
......@@ -36,13 +36,23 @@ namespace ost { namespace conop {
namespace {
/*
COMMENT ON CREATE_CMD
CREATE_CMD specifies so called affinities. e.g. VARCHAR(64) where common sense
interprets the number 64 as max length of entries in that column.
However, sqlite 3 totally ignores this an interprets it as TEXT without any
limits. Long story short, don't worry about formulas longer than 64 characters
or longer names etc.
*/
const char* CREATE_CMD[]={
"CREATE TABLE IF NOT EXISTS chemlib_info ( "
" creation_date TIMESTAMP, "
" ost_version_used VARCHAR(64) NOT NULL);",
"CREATE TABLE IF NOT EXISTS chem_compounds ( "
" id INTEGER PRIMARY KEY AUTOINCREMENT, "
" tlc VARCHAR(3) NOT NULL, "
" tlc VARCHAR(5) NOT NULL, "
" olc VARCHAR(1) NOT NULL, "
" dialect VARCHAR(1) NOT NULL, "
" chem_class VARCHAR(1), "
......
modules/conop/tests/CMakeLists.txt
+ 2
− 1
View file @ 45f0b42c
......@@ -9,7 +9,8 @@ set(OST_CONOP_UNIT_TESTS
if (COMPOUND_LIB)
list(APPEND OST_CONOP_UNIT_TESTS test_compound.py
test_cleanup.py)
test_cleanup.py
test_complib.py)
endif()
ost_unittest(MODULE conop
......
modules/conop/tests/test_complib.py 0 → 100644
+ 35
− 0
View file @ 45f0b42c
import unittest, os, sys
import ost
from ost import conop
import subprocess
import tempfile
class TestCompLib(unittest.TestCase):
def test_three_vs_five_letter_code(self):
prefix_path = ost.GetPrefixPath()
chemdict_tool_path = os.path.join(prefix_path, "bin", "chemdict_tool")
if not os.path.exists(chemdict_tool_path):
raise RuntimeError("Expect chemdict_tool:", chemdict_tool_path)
tmp_dir = tempfile.TemporaryDirectory()
compounds_path = os.path.join("testfiles", "test_compounds.cif")
complib_path = os.path.join(tmp_dir.name, "test_complib.dat")
cmd = [chemdict_tool_path, "create", compounds_path, complib_path]
subprocess.run(cmd)
complib = conop.CompoundLib.Load(complib_path)
comp_001 = complib.FindCompound("001")
comp_hello = complib.FindCompound("hello")
self.assertFalse(comp_001 is None)
self.assertFalse(comp_hello is None)
if __name__ == "__main__":
from ost import testutils
if testutils.SetDefaultCompoundLib():
testutils.RunTests()
else:
print('No compound lib available. Ignoring test_complib tests.')
\ No newline at end of file
modules/conop/tests/testfiles/test_compounds.cif 0 → 100644
+ 604
− 0
View file @ 45f0b42c
data_000
#
_chem_comp.id 000
_chem_comp.name "methyl hydrogen carbonate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C2 H4 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-04-27
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 76.051
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 000
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3LIN
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
000 C C C 0 1 N N N 32.880 -0.090 51.314 -0.456 0.028 -0.001 C 000 1
000 O O O 0 1 N N N 32.160 0.180 50.105 -0.376 1.240 0.001 O 000 2
000 OA OA O 0 1 N N N 34.147 -0.940 51.249 0.662 -0.720 0.001 OA 000 3
000 CB CB C 0 1 N N N 33.872 -2.227 50.459 1.929 -0.010 -0.001 CB 000 4
000 OXT OXT O 0 1 N Y N 32.419 0.429 52.564 -1.663 -0.566 -0.000 OXT 000 5
000 HB HB H 0 1 N N N 34.788 -2.834 50.416 1.996 0.613 -0.892 HB 000 6
000 HBA HBA H 0 1 N N N 33.076 -2.800 50.957 1.995 0.618 0.888 HBA 000 7
000 HBB HBB H 0 1 N N N 33.555 -1.969 49.438 2.748 -0.730 0.002 HBB 000 8
000 HXT HXT H 0 1 N Y N 31.625 0.931 52.425 -2.438 0.013 0.002 HXT 000 9
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
000 C OXT SING N N 1
000 O C DOUB N N 2
000 OA C SING N N 3
000 CB OA SING N N 4
000 CB HB SING N N 5
000 CB HBA SING N N 6
000 CB HBB SING N N 7
000 OXT HXT SING N N 8
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
000 SMILES ACDLabs 12.01 "O=C(O)OC"
000 SMILES_CANONICAL CACTVS 3.370 "COC(O)=O"
000 SMILES CACTVS 3.370 "COC(O)=O"
000 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "COC(=O)O"
000 SMILES "OpenEye OEToolkits" 1.7.0 "COC(=O)O"
000 InChI InChI 1.03 "InChI=1S/C2H4O3/c1-5-2(3)4/h1H3,(H,3,4)"
000 InChIKey InChI 1.03 CXHHBNMLPJOKQD-UHFFFAOYSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
000 "SYSTEMATIC NAME" ACDLabs 12.01 "methyl hydrogen carbonate"
000 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "methyl hydrogen carbonate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
000 "Create component" 2010-04-27 RCSB
000 "Modify descriptor" 2011-06-04 RCSB
#
data_001
#
_chem_comp.id 001
_chem_comp.name
;1-[2,2-DIFLUORO-2-(3,4,5-TRIMETHOXY-PHENYL)-ACETYL]-PIPERIDINE-2-CARBOXYLIC ACID
4-PHENYL-1-(3-PYRIDIN-3-YL-PROPYL)-BUTYL ESTER
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C35 H42 F2 N2 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms FKB-001
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-11-06
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 624.715
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 001
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1J4R
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
# #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
001 C01 C01 C 0 1 Y N N 26.108 12.501 25.848 0.484 -0.006 -3.053 C01 001 1
001 C02 C02 C 0 1 Y N N 25.498 13.476 26.660 0.579 1.363 -3.213 C02 001 2
001 C03 C03 C 0 1 Y N N 26.077 13.812 27.910 1.689 1.916 -3.833 C03 001 3
001 C04 C04 C 0 1 Y N N 27.271 13.166 28.347 2.705 1.090 -4.300 C04 001 4
001 C05 C05 C 0 1 Y N N 27.879 12.190 27.538 2.609 -0.286 -4.132 C05 001 5
001 C06 C06 C 0 1 Y N N 27.300 11.861 26.289 1.495 -0.831 -3.510 C06 001 6
001 O03 O03 O 0 1 N N N 25.493 14.769 28.709 1.781 3.264 -3.990 O03 001 7
001 C07 C07 C 0 1 N N N 24.318 15.454 28.253 0.597 3.827 -3.422 C07 001 8
001 O04 O04 O 0 1 N N N 27.862 13.516 29.556 3.796 1.629 -4.910 O04 001 9
001 C08 C08 C 0 1 N N N 27.081 13.366 30.766 3.501 1.688 -6.307 C08 001 10
001 O05 O05 O 0 1 N N N 29.004 11.523 28.001 3.603 -1.098 -4.582 O05 001 11
001 C09 C09 C 0 1 N N N 29.839 10.812 27.079 3.214 -2.438 -4.272 C09 001 12
001 C10 C10 C 0 1 N N N 25.502 12.055 24.548 -0.724 -0.603 -2.378 C10 001 13
001 F10 F10 F 0 1 N N N 24.509 12.877 24.144 -1.837 0.211 -2.610 F10 001 14
001 F11 F11 F 0 1 N N N 24.945 10.855 24.781 -0.964 -1.880 -2.894 F11 001 15
001 C11 C11 C 0 1 N N N 26.460 11.880 23.441 -0.473 -0.700 -0.895 C11 001 16
001 O11 O11 O 0 1 N N N 26.822 10.747 23.163 -0.825 0.199 -0.160 O11 001 17
001 N12 N12 N 0 1 N N N 26.958 12.941 22.761 0.142 -1.785 -0.385 N12 001 18
001 C12 C12 C 0 1 N N N 26.680 14.371 23.122 0.658 -2.838 -1.270 C12 001 19
001 C13 C13 C 0 1 N N N 26.326 15.255 21.885 2.135 -3.077 -0.941 C13 001 20
001 C14 C14 C 0 1 N N N 27.344 15.061 20.741 2.279 -3.385 0.551 C14 001 21
001 C15 C15 C 0 1 N N N 27.564 13.571 20.408 1.790 -2.187 1.369 C15 001 22
001 C16 C16 C 0 1 N N S 27.938 12.754 21.659 0.314 -1.935 1.067 C16 001 23
001 C17 C17 C 0 1 N N N 29.320 13.158 22.147 -0.138 -0.679 1.766 C17 001 24
001 O17 O17 O 0 1 N N N 30.235 13.267 21.354 0.483 0.348 1.624 O17 001 25
001 O18 O18 O 0 1 N N N 29.567 13.406 23.456 -1.230 -0.700 2.546 O18 001 26
001 C18 C18 C 0 1 N N S 30.921 13.770 23.757 -1.665 0.510 3.220 C18 001 27
001 C19 C19 C 0 1 N N N 31.603 12.604 24.468 -0.998 0.597 4.595 C19 001 28
001 C20 C20 C 0 1 N N N 33.010 13.010 24.940 0.522 0.627 4.423 C20 001 29
001 C21 C21 C 0 1 N N N 33.954 11.846 24.721 1.189 0.713 5.797 C21 001 30
001 C22 C22 C 0 1 Y N N 34.617 11.998 23.378 2.687 0.743 5.628 C22 001 31
001 C23 C23 C 0 1 Y N N 35.552 13.034 23.155 3.413 -0.433 5.615 C23 001 32
001 N23 N23 N 0 1 Y N N 36.204 13.109 21.980 4.722 -0.415 5.462 N23 001 33
001 C24 C24 C 0 1 Y N N 35.987 12.205 20.983 5.389 0.714 5.327 C24 001 34
001 C25 C25 C 0 1 Y N N 35.064 11.161 21.140 4.731 1.929 5.335 C25 001 35
001 C26 C26 C 0 1 Y N N 34.371 11.062 22.354 3.354 1.950 5.489 C26 001 36
001 C27 C27 C 0 1 N N N 30.983 15.038 24.632 -3.185 0.480 3.392 C27 001 37
001 C28 C28 C 0 1 N N N 29.607 15.614 24.881 -3.852 0.394 2.018 C28 001 38
001 C29 C29 C 0 1 N N N 29.219 15.326 26.330 -5.372 0.364 2.189 C29 001 39
001 C30 C30 C 0 1 Y N N 28.253 16.389 26.784 -6.028 0.278 0.836 C30 001 40
001 C31 C31 C 0 1 Y N N 27.048 16.577 26.093 -6.299 -0.956 0.276 C31 001 41
001 C32 C32 C 0 1 Y N N 26.148 17.559 26.509 -6.902 -1.034 -0.966 C32 001 42
001 C33 C33 C 0 1 Y N N 26.454 18.360 27.617 -7.234 0.122 -1.647 C33 001 43
001 C34 C34 C 0 1 Y N N 27.662 18.169 28.307 -6.964 1.357 -1.087 C34 001 44
001 C35 C35 C 0 1 Y N N 28.561 17.186 27.889 -6.365 1.435 0.157 C35 001 45
001 H021 1H02 H 0 0 N N N 24.573 13.972 26.319 -0.213 2.004 -2.854 H021 001 46
001 H061 1H06 H 0 0 N N N 27.782 11.099 25.653 1.418 -1.901 -3.383 H061 001 47
001 H071 1H07 H 0 0 N N N 23.845 16.229 28.900 0.626 4.912 -3.524 H071 001 48
001 H072 2H07 H 0 0 N N N 24.535 15.907 27.257 -0.277 3.436 -3.942 H072 001 49
001 H073 3H07 H 0 0 N N N 23.545 14.695 27.986 0.540 3.564 -2.366 H073 001 50
001 H081 1H08 H 0 0 N N N 27.554 13.646 31.735 4.351 2.115 -6.840 H081 001 51
001 H082 2H08 H 0 0 N N N 26.122 13.924 30.653 3.306 0.682 -6.680 H082 001 52
001 H083 3H08 H 0 0 N N N 26.708 12.317 30.832 2.621 2.312 -6.466 H083 001 53
001 H091 1H09 H 0 0 N N N 30.743 10.276 27.451 3.984 -3.128 -4.616 H091 001 54
001 H092 2H09 H 0 0 N N N 29.206 10.088 26.513 3.089 -2.540 -3.195 H092 001 55
001 H093 3H09 H 0 0 N N N 30.150 11.513 26.270 2.272 -2.667 -4.770 H093 001 56
001 H121 1H12 H 0 0 N N N 25.883 14.437 23.899 0.095 -3.757 -1.111 H121 001 57
001 H122 2H12 H 0 0 N N N 27.530 14.809 23.694 0.561 -2.522 -2.308 H122 001 58
001 H131 1H13 H 0 0 N N N 25.282 15.071 21.537 2.505 -3.921 -1.524 H131 001 59
001 H132 2H13 H 0 0 N N N 26.228 16.329 22.166 2.712 -2.185 -1.186 H132 001 60
001 H141 1H14 H 0 0 N N N 27.048 15.638 19.834 1.682 -4.262 0.800 H141 001 61
001 H142 2H14 H 0 0 N N N 28.309 15.571 20.967 3.325 -3.580 0.783 H142 001 62
001 H151 1H15 H 0 0 N N N 26.678 13.136 19.889 1.914 -2.398 2.432 H151 001 63
001 H152 2H15 H 0 0 N N N 28.320 13.443 19.598 2.369 -1.304 1.103 H152 001 64
001 H161 1H16 H 0 0 N N N 27.929 11.677 21.367 -0.280 -2.780 1.414 H161 001 65
001 H181 1H18 H 0 0 N N N 31.451 13.996 22.802 -1.383 1.379 2.625 H181 001 66
001 H191 1H19 H 0 0 N N N 30.982 12.209 25.305 -1.324 1.505 5.100 H191 001 67
001 H192 2H19 H 0 0 N N N 31.626 11.687 23.832 -1.279 -0.272 5.190 H192 001 68
001 H201 1H20 H 0 0 N N N 33.368 13.946 24.452 0.849 -0.282 3.917 H201 001 69
001 H202 2H20 H 0 0 N N N 33.017 13.371 25.994 0.804 1.495 3.827 H202 001 70
001 H211 1H21 H 0 0 N N N 34.692 11.736 25.549 0.863 1.622 6.303 H211 001 71
001 H212 2H21 H 0 0 N N N 33.445 10.860 24.834 0.908 -0.155 6.393 H212 001 72
001 H231 1H23 H 0 0 N N N 35.777 13.801 23.914 2.901 -1.378 5.723 H231 001 73
001 H241 1H24 H 0 0 N N N 36.559 12.318 20.047 6.463 0.689 5.207 H241 001 74
001 H251 1H25 H 0 0 N N N 34.887 10.435 20.328 5.283 2.851 5.224 H251 001 75
001 H261 1H26 H 0 0 N N N 33.636 10.252 22.502 2.813 2.885 5.499 H261 001 76
001 H271 1H27 H 0 0 N N N 31.522 14.845 25.588 -3.466 -0.388 3.988 H271 001 77
001 H272 2H27 H 0 0 N N N 31.669 15.800 24.195 -3.511 1.389 3.898 H272 001 78
001 H281 1H28 H 0 0 N N N 29.543 16.698 24.627 -3.570 1.262 1.422 H281 001 79
001 H282 2H28 H 0 0 N N N 28.848 15.243 24.152 -3.525 -0.515 1.512 H282 001 80
001 H291 1H29 H 0 0 N N N 28.818 14.294 26.469 -5.653 -0.505 2.785 H291 001 81
001 H292 2H29 H 0 0 N N N 30.104 15.237 27.001 -5.698 1.272 2.695 H292 001 82
001 H311 1H31 H 0 0 N N N 26.807 15.949 25.218 -6.040 -1.859 0.808 H311 001 83
001 H321 1H32 H 0 0 N N N 25.199 17.701 25.964 -7.113 -1.998 -1.404 H321 001 84
001 H331 1H33 H 0 0 N N N 25.745 19.139 27.945 -7.704 0.061 -2.618 H331 001 85
001 H341 1H34 H 0 0 N N N 27.906 18.794 29.182 -7.223 2.260 -1.619 H341 001 86
001 H351 1H35 H 0 0 N N N 29.511 17.039 28.429 -6.154 2.399 0.595 H351 001 87
# #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
001 C01 C02 DOUB Y N 1
001 C01 C06 SING Y N 2
001 C01 C10 SING N N 3
001 C02 C03 SING Y N 4
001 C02 H021 SING N N 5
001 C03 C04 DOUB Y N 6
001 C03 O03 SING N N 7
001 C04 C05 SING Y N 8
001 C04 O04 SING N N 9
001 C05 C06 DOUB Y N 10
001 C05 O05 SING N N 11
001 C06 H061 SING N N 12
001 O03 C07 SING N N 13
001 C07 H071 SING N N 14
001 C07 H072 SING N N 15
001 C07 H073 SING N N 16
001 O04 C08 SING N N 17
001 C08 H081 SING N N 18
001 C08 H082 SING N N 19
001 C08 H083 SING N N 20
001 O05 C09 SING N N 21
001 C09 H091 SING N N 22
001 C09 H092 SING N N 23
001 C09 H093 SING N N 24
001 C10 F10 SING N N 25
001 C10 F11 SING N N 26
001 C10 C11 SING N N 27
001 C11 O11 DOUB N N 28
001 C11 N12 SING N N 29
001 N12 C12 SING N N 30
001 N12 C16 SING N N 31
001 C12 C13 SING N N 32
001 C12 H121 SING N N 33
001 C12 H122 SING N N 34
001 C13 C14 SING N N 35
001 C13 H131 SING N N 36
001 C13 H132 SING N N 37
001 C14 C15 SING N N 38
001 C14 H141 SING N N 39
001 C14 H142 SING N N 40
001 C15 C16 SING N N 41
001 C15 H151 SING N N 42
001 C15 H152 SING N N 43
001 C16 C17 SING N N 44
001 C16 H161 SING N N 45
001 C17 O17 DOUB N N 46
001 C17 O18 SING N N 47
001 O18 C18 SING N N 48
001 C18 C19 SING N N 49
001 C18 C27 SING N N 50
001 C18 H181 SING N N 51
001 C19 C20 SING N N 52
001 C19 H191 SING N N 53
001 C19 H192 SING N N 54
001 C20 C21 SING N N 55
001 C20 H201 SING N N 56
001 C20 H202 SING N N 57
001 C21 C22 SING N N 58
001 C21 H211 SING N N 59
001 C21 H212 SING N N 60
001 C22 C23 DOUB Y N 61
001 C22 C26 SING Y N 62
001 C23 N23 SING Y N 63
001 C23 H231 SING N N 64
001 N23 C24 DOUB Y N 65
001 C24 C25 SING Y N 66
001 C24 H241 SING N N 67
001 C25 C26 DOUB Y N 68
001 C25 H251 SING N N 69
001 C26 H261 SING N N 70
001 C27 C28 SING N N 71
001 C27 H271 SING N N 72
001 C27 H272 SING N N 73
001 C28 C29 SING N N 74
001 C28 H281 SING N N 75
001 C28 H282 SING N N 76
001 C29 C30 SING N N 77
001 C29 H291 SING N N 78
001 C29 H292 SING N N 79
001 C30 C31 DOUB Y N 80
001 C30 C35 SING Y N 81
001 C31 C32 SING Y N 82
001 C31 H311 SING N N 83
001 C32 C33 DOUB Y N 84
001 C32 H321 SING N N 85
001 C33 C34 SING Y N 86
001 C33 H331 SING N N 87
001 C34 C35 DOUB Y N 88
001 C34 H341 SING N N 89
001 C35 H351 SING N N 90
# #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
001 SMILES ACDLabs 10.04 "O=C(N3C(C(=O)OC(CCCc1ccccc1)CCCc2cccnc2)CCCC3)C(F)(F)c4cc(OC)c(OC)c(OC)c4"
001 SMILES_CANONICAL CACTVS 3.341 "COc1cc(cc(OC)c1OC)C(F)(F)C(=O)N2CCCC[C@H]2C(=O)O[C@@H](CCCc3ccccc3)CCCc4cccnc4"
001 SMILES CACTVS 3.341 "COc1cc(cc(OC)c1OC)C(F)(F)C(=O)N2CCCC[CH]2C(=O)O[CH](CCCc3ccccc3)CCCc4cccnc4"
001 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "COc1cc(cc(c1OC)OC)C(C(=O)N2CCCC[C@H]2C(=O)O[C@@H](CCCc3ccccc3)CCCc4cccnc4)(F)F"
001 SMILES "OpenEye OEToolkits" 1.5.0 "COc1cc(cc(c1OC)OC)C(C(=O)N2CCCCC2C(=O)OC(CCCc3ccccc3)CCCc4cccnc4)(F)F"
001 InChI InChI 1.03 "InChI=1S/C35H42F2N2O6/c1-42-30-22-27(23-31(43-2)32(30)44-3)35(36,37)34(41)39-21-8-7-19-29(39)33(40)45-28(17-9-14-25-12-5-4-6-13-25)18-10-15-26-16-11-20-38-24-26/h4-6,11-13,16,20,22-24,28-29H,7-10,14-15,17-19,21H2,1-3H3/t28-,29-/m0/s1"
001 InChIKey InChI 1.03 NBYCDVVSYOMFMS-VMPREFPWSA-N
# #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
001 "SYSTEMATIC NAME" ACDLabs 10.04 "(1S)-4-phenyl-1-(3-pyridin-3-ylpropyl)butyl (2S)-1-[difluoro(3,4,5-trimethoxyphenyl)acetyl]piperidine-2-carboxylate"
001 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(4S)-1-phenyl-7-pyridin-3-yl-heptan-4-yl] (2S)-1-[2,2-difluoro-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
001 "Create component" 2001-11-06 RCSB
001 "Modify descriptor" 2011-06-04 RCSB
001 "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 001
_pdbx_chem_comp_synonyms.name FKB-001
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##
data_hello
#
_chem_comp.id hello
_chem_comp.name "N-[(2R)-2-BENZYL-4-(HYDROXYAMINO)-4-OXOBUTANOYL]-L-ISOLEUCYL-L-LEUCINE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H35 N3 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-02-02
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 449.541
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 002
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2FV9
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
002 C1 C1 C 0 1 N N S 46.822 28.736 39.606 -1.036 0.293 0.447 C1 002 1
002 C2 C2 C 0 1 N N S 47.362 28.034 38.343 -1.041 1.804 0.685 C2 002 2
002 C3 C3 C 0 1 N N N 47.592 29.054 37.227 -2.288 2.191 1.482 C3 002 3
002 C4 C4 C 0 1 N N N 48.413 28.490 36.077 -2.201 1.595 2.888 C4 002 4
002 C5 C5 C 0 1 N N N 47.164 31.038 40.170 1.298 -0.400 0.528 C5 002 5
002 C6 C6 C 0 1 N N N 46.616 27.699 40.714 -2.203 -0.081 -0.431 C6 002 6
002 C7 C7 C 0 1 N N S 45.033 26.134 41.646 -4.574 -0.548 -0.745 C7 002 7
002 C8 C8 C 0 1 N N N 44.110 26.453 42.830 -5.705 -1.025 0.168 C8 002 8
002 C9 C9 C 0 1 N N N 49.255 34.145 39.314 3.102 1.743 -0.050 C9 002 9
002 C10 C10 C 0 1 N N N 48.267 33.014 39.174 3.051 0.539 -0.954 C10 002 10
002 C11 C11 C 0 1 N N N 44.371 25.081 40.768 -5.072 0.577 -1.616 C11 002 11
002 C12 C12 C 0 1 N N N 46.362 26.955 37.909 -1.048 2.533 -0.660 C12 002 12
002 N3 N3 N 0 1 N N N 47.721 29.826 39.993 0.214 -0.094 -0.212 N3 002 13
002 O6 O6 O 0 1 N N N 47.572 27.258 41.353 -2.016 -0.388 -1.589 O6 002 14
002 O1 O1 O 0 1 N N N 44.776 23.902 40.843 -4.546 1.663 -1.559 O1 002 15
002 O2 O2 O 0 1 N N N 49.764 36.278 39.767 3.491 4.079 0.300 O2 002 16
002 C13 C13 C 0 1 N N N 44.829 27.070 44.037 -5.227 -2.228 0.984 C13 002 17
002 C20 C20 C 0 1 N N N 46.070 26.260 44.416 -6.295 -2.601 2.015 C20 002 18
002 C21 C21 C 0 1 N N N 43.884 27.145 45.240 -4.984 -3.415 0.050 C21 002 19
002 N1 N1 N 0 1 N N N 48.758 35.374 39.517 3.443 2.947 -0.549 N1 002 20
002 O3 O3 O 0 1 N N N 50.462 33.928 39.241 2.836 1.629 1.128 O3 002 21
002 C22 C22 C 0 1 N N R 48.164 32.160 40.439 2.615 -0.686 -0.148 C22 002 22
002 C23 C23 C 0 1 N N N 47.734 32.989 41.662 3.673 -1.004 0.911 C23 002 23
002 O4 O4 O 0 1 N N N 45.963 31.279 40.109 1.215 -0.446 1.737 O4 002 24
002 N2 N2 N 0 1 N N N 45.328 27.357 40.908 -3.454 -0.074 0.071 N2 002 25
002 O5 O5 O 0 1 N N N 43.450 25.442 40.002 -6.101 0.373 -2.453 O5 002 26
002 C14 C14 C 0 1 Y N N 47.872 32.180 42.937 4.945 -1.443 0.233 C14 002 27
002 C15 C15 C 0 1 Y N N 49.078 32.236 43.691 5.955 -0.528 0.000 C15 002 28
002 C16 C16 C 0 1 Y N N 49.197 31.509 44.911 7.122 -0.931 -0.622 C16 002 29
002 C17 C17 C 0 1 Y N N 48.108 30.717 45.376 7.280 -2.248 -1.010 C17 002 30
002 C18 C18 C 0 1 Y N N 46.912 30.633 44.610 6.270 -3.163 -0.776 C18 002 31
002 C19 C19 C 0 1 Y N N 46.792 31.365 43.390 5.105 -2.761 -0.151 C19 002 32
002 H1 H1 H 0 1 N N N 45.842 29.195 39.406 -1.120 -0.226 1.402 H1 002 33
002 H2 H2 H 0 1 N N N 48.329 27.559 38.563 -0.150 2.086 1.246 H2 002 34
002 H31 1H3 H 0 1 N N N 48.153 29.898 37.656 -3.175 1.805 0.978 H31 002 35
002 H32 2H3 H 0 1 N N N 46.613 29.366 36.835 -2.353 3.277 1.551 H32 002 36
002 H41 1H4 H 0 1 N N N 48.839 27.520 36.372 -3.041 1.949 3.486 H41 002 37
002 H42 2H4 H 0 1 N N N 49.226 29.188 35.830 -2.233 0.507 2.825 H42 002 38
002 H43 3H4 H 0 1 N N N 47.767 28.354 35.197 -1.267 1.905 3.356 H43 002 39
002 H7 H7 H 0 1 N N N 45.990 25.727 42.003 -4.241 -1.373 -1.374 H7 002 40
002 H81 1H8 H 0 1 N N N 43.681 25.498 43.167 -5.992 -0.219 0.843 H81 002 41
002 H82 2H8 H 0 1 N N N 43.351 27.170 42.485 -6.563 -1.315 -0.438 H82 002 42
002 H101 1H10 H 0 0 N N N 48.618 32.363 38.359 4.039 0.361 -1.379 H101 002 43
002 H102 2H10 H 0 0 N N N 47.276 33.442 38.963 2.337 0.718 -1.758 H102 002 44
002 H121 1H12 H 0 0 N N N 45.442 27.047 38.505 -0.961 3.606 -0.493 H121 002 45
002 H122 2H12 H 0 0 N N N 46.804 25.960 38.068 -0.208 2.189 -1.264 H122 002 46
002 H123 3H12 H 0 0 N N N 46.123 27.084 36.843 -1.981 2.321 -1.182 H123 002 47
002 HN3 HN3 H 0 1 N N N 48.702 29.676 40.120 0.261 -0.130 -1.180 HN3 002 48
002 HO2 HO2 H 0 1 N N N 50.212 36.486 38.956 3.753 4.830 -0.249 HO2 002 49
002 H13 H13 H 0 1 N N N 45.144 28.085 43.753 -4.300 -1.974 1.497 H13 002 50
002 H201 1H20 H 0 0 N N N 45.761 25.304 44.864 -5.994 -3.509 2.537 H201 002 51
002 H202 2H20 H 0 0 N N N 46.671 26.828 45.142 -6.406 -1.789 2.733 H202 002 52
002 H203 3H20 H 0 0 N N N 46.671 26.066 43.515 -7.245 -2.770 1.509 H203 002 53
002 H211 1H21 H 0 0 N N N 43.223 26.266 45.242 -4.224 -3.149 -0.685 H211 002 54
002 H212 2H21 H 0 0 N N N 43.277 28.060 45.173 -4.644 -4.272 0.631 H212 002 55
002 H213 3H21 H 0 0 N N N 44.473 27.163 46.169 -5.911 -3.669 -0.463 H213 002 56
002 HN1 HN1 H 0 1 N N N 47.785 35.603 39.490 3.656 3.039 -1.491 HN1 002 57
002 H22 H22 H 0 1 N N N 49.155 31.746 40.677 2.502 -1.540 -0.816 H22 002 58
002 H231 1H23 H 0 0 N N N 46.680 33.278 41.540 3.868 -0.113 1.508 H231 002 59
002 H232 2H23 H 0 0 N N N 48.373 33.882 41.733 3.311 -1.803 1.558 H232 002 60
002 HN2 HN2 H 0 1 N N N 44.589 27.930 40.553 -3.612 0.245 0.974 HN2 002 61
002 HO5 HO5 H 0 1 N N N 43.132 24.692 39.513 -6.421 1.094 -3.012 HO5 002 62
002 H15 H15 H 0 1 N N N 49.906 32.832 43.337 5.832 0.501 0.303 H15 002 63
002 H16 H16 H 0 1 N N N 50.112 31.558 45.483 7.911 -0.216 -0.804 H16 002 64
002 H17 H17 H 0 1 N N N 48.190 30.180 46.310 8.191 -2.563 -1.496 H17 002 65
002 H18 H18 H 0 1 N N N 46.095 30.015 44.951 6.393 -4.192 -1.080 H18 002 66
002 H19 H19 H 0 1 N N N 45.883 31.302 42.810 4.316 -3.476 0.032 H19 002 67
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
002 C1 C2 SING N N 1
002 C1 C6 SING N N 2
002 C1 N3 SING N N 3
002 C1 H1 SING N N 4
002 C2 C3 SING N N 5
002 C2 C12 SING N N 6
002 C2 H2 SING N N 7
002 C3 C4 SING N N 8
002 C3 H31 SING N N 9
002 C3 H32 SING N N 10
002 C4 H41 SING N N 11
002 C4 H42 SING N N 12
002 C4 H43 SING N N 13
002 C5 N3 SING N N 14
002 C5 C22 SING N N 15
002 C5 O4 DOUB N N 16
002 C6 O6 DOUB N N 17
002 C6 N2 SING N N 18
002 C7 C8 SING N N 19
002 C7 C11 SING N N 20
002 C7 N2 SING N N 21
002 C7 H7 SING N N 22
002 C8 C13 SING N N 23
002 C8 H81 SING N N 24
002 C8 H82 SING N N 25
002 C9 C10 SING N N 26
002 C9 N1 SING N N 27
002 C9 O3 DOUB N N 28
002 C10 C22 SING N N 29
002 C10 H101 SING N N 30
002 C10 H102 SING N N 31
002 C11 O1 DOUB N N 32
002 C11 O5 SING N N 33
002 C12 H121 SING N N 34
002 C12 H122 SING N N 35
002 C12 H123 SING N N 36
002 N3 HN3 SING N N 37
002 O2 N1 SING N N 38
002 O2 HO2 SING N N 39
002 C13 C20 SING N N 40
002 C13 C21 SING N N 41
002 C13 H13 SING N N 42
002 C20 H201 SING N N 43
002 C20 H202 SING N N 44
002 C20 H203 SING N N 45
002 C21 H211 SING N N 46
002 C21 H212 SING N N 47
002 C21 H213 SING N N 48
002 N1 HN1 SING N N 49
002 C22 C23 SING N N 50
002 C22 H22 SING N N 51
002 C23 C14 SING N N 52
002 C23 H231 SING N N 53
002 C23 H232 SING N N 54
002 N2 HN2 SING N N 55
002 O5 HO5 SING N N 56
002 C14 C15 DOUB Y N 57
002 C14 C19 SING Y N 58
002 C15 C16 SING Y N 59
002 C15 H15 SING N N 60
002 C16 C17 DOUB Y N 61
002 C16 H16 SING N N 62
002 C17 C18 SING Y N 63
002 C17 H17 SING N N 64
002 C18 C19 DOUB Y N 65
002 C18 H18 SING N N 66
002 C19 H19 SING N N 67
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
002 SMILES ACDLabs 10.04 "O=C(O)C(NC(=O)C(NC(=O)C(Cc1ccccc1)CC(=O)NO)C(C)CC)CC(C)C"
002 SMILES_CANONICAL CACTVS 3.341 "CC[C@H](C)[C@H](NC(=O)[C@@H](CC(=O)NO)Cc1ccccc1)C(=O)N[C@@H](CC(C)C)C(O)=O"
002 SMILES CACTVS 3.341 "CC[CH](C)[CH](NC(=O)[CH](CC(=O)NO)Cc1ccccc1)C(=O)N[CH](CC(C)C)C(O)=O"
002 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC[C@H](C)[C@@H](C(=O)N[C@@H](CC(C)C)C(=O)O)NC(=O)[C@H](Cc1ccccc1)CC(=O)NO"
002 SMILES "OpenEye OEToolkits" 1.5.0 "CCC(C)C(C(=O)NC(CC(C)C)C(=O)O)NC(=O)C(Cc1ccccc1)CC(=O)NO"
002 InChI InChI 1.03
"InChI=1S/C23H35N3O6/c1-5-15(4)20(22(29)24-18(23(30)31)11-14(2)3)25-21(28)17(13-19(27)26-32)12-16-9-7-6-8-10-16/h6-10,14-15,17-18,20,32H,5,11-13H2,1-4H3,(H,24,29)(H,25,28)(H,26,27)(H,30,31)/t15-,17+,18-,20-/m0/s1"
002 InChIKey InChI 1.03 MWZOULASPWUGJJ-NFBUACBFSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
002 "SYSTEMATIC NAME" ACDLabs 10.04 "N-[(2R)-2-benzyl-4-(hydroxyamino)-4-oxobutanoyl]-L-isoleucyl-L-leucine"
002 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-[[(2S,3S)-2-[[(2R)-4-(hydroxyamino)-4-oxo-2-(phenylmethyl)butanoyl]amino]-3-methyl-pentanoyl]amino]-4-methyl-pentanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
002 "Create component" 2006-02-02 RCSB
002 "Modify descriptor" 2011-06-04 RCSB
#
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