data_THM
#
_chem_comp.id THM
_chem_comp.name THYMIDINE
_chem_comp.type "DNA OH 5 prime terminus"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C10 H14 N2 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 242.229
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code THM
_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 1KIM
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
THM "O5'" O5* O 0 1 N N N N N N 17.080 94.434 44.011 2.274 -0.724 -3.790 "O5'" THM 1
THM "C5'" C5* C 0 1 N N N N N N 16.780 95.210 45.165 1.208 0.202 -3.574 "C5'" THM 2
THM "C4'" C4* C 0 1 N N R N N N 17.626 96.447 45.302 0.116 -0.463 -2.735 "C4'" THM 3
THM "O4'" O4* O 0 1 N N N N N N 18.982 96.128 45.630 0.600 -0.760 -1.406 "O4'" THM 4
THM "C3'" C3* C 0 1 N N S N N N 17.760 97.332 44.178 -1.055 0.519 -2.484 "C3'" THM 5
THM "O3'" O3* O 0 1 N N N N N N 18.323 98.514 44.657 -1.993 0.481 -3.562 "O3'" THM 6
THM "C2'" C2* C 0 1 N N N N N N 18.903 96.738 43.506 -1.681 -0.046 -1.186 "C2'" THM 7
THM "C1'" C1* C 0 1 N N R N N N 19.875 96.449 44.597 -0.554 -0.889 -0.560 "C1'" THM 8
THM N1 N1 N 0 1 N N N N N N 20.731 95.216 44.411 -0.246 -0.391 0.782 N1 THM 9
THM C2 C2 C 0 1 N N N N N N 22.075 95.429 44.582 0.165 0.879 0.943 C2 THM 10
THM O2 O2 O 0 1 N N N N N N 22.533 96.539 44.822 0.278 1.600 -0.029 O2 THM 11
THM N3 N3 N 0 1 N N N N N N 22.877 94.370 44.420 0.454 1.363 2.165 N3 THM 12
THM C4 C4 C 0 1 N N N N N N 22.432 93.082 44.088 0.329 0.578 3.254 C4 THM 13
THM O4 O4 O 0 1 N N N N N N 23.259 92.155 43.945 0.590 1.015 4.360 O4 THM 14
THM C5 C5 C 0 1 N N N N N N 20.989 92.899 43.924 -0.098 -0.762 3.099 C5 THM 15
THM C5M C5M C 0 1 N N N N N N 20.433 91.458 43.577 -0.241 -1.662 4.299 C5M THM 16
THM C6 C6 C 0 1 N N N N N N 20.205 93.954 44.081 -0.382 -1.222 1.861 C6 THM 17
THM "HO5'" *HO5 H 0 0 N N N N N N 16.545 93.653 43.924 2.939 -0.266 -4.322 "HO5'" THM 18
THM "H5'1" 1H5* H 0 0 N N N N N N 15.696 95.470 45.192 0.792 0.508 -4.534 "H5'1" THM 19
THM "H5'2" 2H5* H 0 0 N N N N N N 16.845 94.585 46.086 1.588 1.077 -3.047 "H5'2" THM 20
THM "H4'" H4* H 0 1 N N N N N N 17.039 96.972 46.091 -0.241 -1.370 -3.222 "H4'" THM 21
THM "H3'" H3* H 0 1 N N N N N N 16.814 97.484 43.606 -0.686 1.532 -2.328 "H3'" THM 22
THM "HO3'" *HO3 H 0 0 N N N N N N 18.411 99.099 43.913 -2.738 1.040 -3.303 "HO3'" THM 23
THM "H2'1" 1H2* H 0 0 N N N N N N 18.649 95.852 42.877 -2.542 -0.673 -1.420 "H2'1" THM 24
THM "H2'2" 2H2* H 0 0 N N N N N N 19.319 97.362 42.681 -1.969 0.764 -0.517 "H2'2" THM 25
THM "H1'" H1* H 0 1 N N N N N N 20.593 97.293 44.715 -0.859 -1.934 -0.506 "H1'" THM 26
THM HN3 HN3 H 0 1 N N N N N N 23.871 94.552 44.555 0.750 2.281 2.263 HN3 THM 27
THM HM51 1HM5 H 0 0 N N N N N N 19.333 91.318 43.452 0.031 -1.112 5.200 HM51 THM 28
THM HM52 2HM5 H 0 0 N N N N N N 20.948 91.085 42.661 -1.275 -1.999 4.378 HM52 THM 29
THM HM53 3HM5 H 0 0 N N N N N N 20.801 90.736 44.343 0.414 -2.525 4.186 HM53 THM 30
THM H6 H6 H 0 1 N N N N N N 19.124 93.783 43.938 -0.713 -2.240 1.723 H6 THM 31
#
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
THM "O5'" "C5'" SING N N 1
THM "O5'" "HO5'" SING N N 2
THM "C5'" "C4'" SING N N 3
THM "C5'" "H5'1" SING N N 4
THM "C5'" "H5'2" SING N N 5
THM "C4'" "O4'" SING N N 6
THM "C4'" "C3'" SING N N 7
THM "C4'" "H4'" SING N N 8
THM "O4'" "C1'" SING N N 9
THM "C3'" "O3'" SING N N 10
THM "C3'" "C2'" SING N N 11
THM "C3'" "H3'" SING N N 12
THM "O3'" "HO3'" SING N N 13
THM "C2'" "C1'" SING N N 14
THM "C2'" "H2'1" SING N N 15
THM "C2'" "H2'2" SING N N 16
THM "C1'" N1 SING N N 17
THM "C1'" "H1'" SING N N 18
THM N1 C2 SING N N 19
THM N1 C6 SING N N 20
THM C2 O2 DOUB N N 21
THM C2 N3 SING N N 22
THM N3 C4 SING N N 23
THM N3 HN3 SING N N 24
THM C4 O4 DOUB N N 25
THM C4 C5 SING N N 26
THM C5 C5M SING N N 27
THM C5 C6 DOUB N N 28
THM C5M HM51 SING N N 29
THM C5M HM52 SING N N 30
THM C5M HM53 SING N N 31
THM C6 H6 SING N N 32
#
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
THM SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CO
THM SMILES_CANONICAL CACTVS 3.341 CC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O
THM SMILES CACTVS 3.341 CC1=CN([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O
THM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
THM SMILES "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O
THM InChI InChI 1.03 InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1
THM InChIKey InChI 1.03 IQFYYKKMVGJFEH-XLPZGREQSA-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
THM "SYSTEMATIC NAME" ACDLabs 10.04 thymidine
THM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
THM 'Create component' 1999-07-08 EBI
THM 'Modify descriptor' 2011-06-04 RCSB
THM 'Modify linking type' 2017-08-21 RCSB
THM 'Modify synonyms' 2020-06-05 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 THM DEOXYTHYMIDINE ? ?
2 THM "2'-DEOXYTHYMIDINE" ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id THM
_pdbe_chem_comp_drugbank_details.drugbank_id DB04485
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Thymidine
_pdbe_chem_comp_drugbank_details.description
'Thymidine is a pyrimidine deoxynucleoside. Thymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used to synchronize the cells in S phase.'
_pdbe_chem_comp_drugbank_details.cas_number 50-89-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
THM DEOXYTHYMIDINE wwPDB ?
THM "2'-DEOXYTHYMIDINE" wwPDB ?
THM "2'-deoxy-5-methyluridine" DrugBank ?
THM "2'-deoxythymidine" DrugBank ?
THM "2'-thymidine" DrugBank ?
THM Deoxyribosylthymine DrugBank ?
THM Deoxythymidine DrugBank ?
THM dThd DrugBank ?
THM Thymidine DrugBank ?
THM "Thymine 2'-deoxyriboside" DrugBank ?
THM 'Thymine deoxyriboside' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id THM
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04485
_pdbe_chem_comp_drugbank_classification.parent "Pyrimidine 2'-deoxyribonucleosides"
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Pyrimidine nucleosides'
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
"This compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2."
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
THM DB04485 'Thymidylate kinase' 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)' P9WKE1 unknown 1
THM DB04485 'Uridine phosphorylase' 'Escherichia coli (strain K12)' P12758 unknown 2
THM DB04485 'Thymidine kinase' EHV-4 P24425 unknown 3
THM DB04485 'Thymidine kinase 2, mitochondrial' Humans O00142 unknown 4
THM DB04485 'Nucleoside-specific channel-forming protein tsx' 'Escherichia coli (strain K12)' P0A927 unknown 5
THM DB04485 'Glucose-1-phosphate thymidylyltransferase' 'Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)' Q9HU22 unknown 6
THM DB04485 'Thymidine kinase, cytosolic' Humans P04183 unknown 7
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
THM "O5'" O 8.722 -4.306 1
THM "C5'" C 7.230 -4.463 2
THM "C4'" C 6.348 -3.250 3
THM "O4'" O 6.812 -1.823 4
THM "C3'" C 4.848 -3.250 5
THM "O3'" O 3.966 -4.463 6
THM "C2'" C 4.385 -1.823 7
THM "C1'" C 5.598 -0.941 8
THM N1 N 5.598 0.559 9
THM C2 C 6.897 1.309 10
THM O2 O 8.196 0.559 11
THM N3 N 6.897 2.809 12
THM C4 C 5.598 3.559 13
THM O4 O 5.598 5.059 14
THM C5 C 4.299 2.809 15
THM C5M C 3.000 3.559 16
THM C6 C 4.299 1.309 17
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
THM "O5'" "C5'" SINGLE NONE 1
THM "C4'" "C5'" SINGLE BEGINDASH 2
THM "C4'" "O4'" SINGLE NONE 3
THM "C4'" "C3'" SINGLE NONE 4
THM "O4'" "C1'" SINGLE NONE 5
THM "C3'" "O3'" SINGLE BEGINWEDGE 6
THM "C3'" "C2'" SINGLE NONE 7
THM "C2'" "C1'" SINGLE NONE 8
THM "C1'" N1 SINGLE BEGINDASH 9
THM N1 C2 SINGLE NONE 10
THM N1 C6 SINGLE NONE 11
THM C2 O2 DOUBLE NONE 12
THM C2 N3 SINGLE NONE 13
THM N3 C4 SINGLE NONE 14
THM C4 O4 DOUBLE NONE 15
THM C4 C5 SINGLE NONE 16
THM C5 C5M SINGLE NONE 17
THM C5 C6 DOUBLE NONE 18
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
THM MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N
THM deoxyribose F1 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
THM pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
THM "C4'" S1 1
THM "O4'" S1 1
THM "C3'" S1 1
THM "C2'" S1 1
THM "C1'" S1 1
THM N1 S1 1
THM C2 S1 1
THM O2 S1 1
THM N3 S1 1
THM C4 S1 1
THM O4 S1 1
THM C5 S1 1
THM C6 S1 1
THM "C1'" F1 1
THM "C2'" F1 1
THM "C3'" F1 1
THM "O3'" F1 1
THM "C4'" F1 1
THM "O4'" F1 1
THM "C5'" F1 1
THM "O5'" F1 1
THM C5 F2 1
THM C4 F2 1
THM N3 F2 1
THM C2 F2 1
THM N1 F2 1
THM C6 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id THM
_pdbe_chem_comp_rdkit_properties.exactmw 242.090
_pdbe_chem_comp_rdkit_properties.amw 242.231
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 116.191
_pdbe_chem_comp_rdkit_properties.tpsa 104.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.231
_pdbe_chem_comp_rdkit_properties.CrippenMR 57.629
_pdbe_chem_comp_rdkit_properties.chi0v 7.936
_pdbe_chem_comp_rdkit_properties.chi1v 4.093
_pdbe_chem_comp_rdkit_properties.chi2v 1.747
_pdbe_chem_comp_rdkit_properties.chi3v 1.747
_pdbe_chem_comp_rdkit_properties.chi4v 1.029
_pdbe_chem_comp_rdkit_properties.chi0n 21.936
_pdbe_chem_comp_rdkit_properties.chi1n 10.856
_pdbe_chem_comp_rdkit_properties.chi2n 1.747
_pdbe_chem_comp_rdkit_properties.chi3n 1.747
_pdbe_chem_comp_rdkit_properties.chi4n 1.029
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.440
_pdbe_chem_comp_rdkit_properties.kappa1 3.532
_pdbe_chem_comp_rdkit_properties.kappa2 4.438
_pdbe_chem_comp_rdkit_properties.kappa3 2.167
_pdbe_chem_comp_rdkit_properties.Phi 0.922
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
THM UniChem ChEMBL CHEMBL52609
THM UniChem DrugBank DB04485
THM UniChem PDBe THM
THM UniChem 'Guide to Pharmacology' 4718
THM UniChem 'KEGG LIGAND' C00214
THM UniChem ChEBI 17748
THM UniChem ZINC ZINC000000025672
THM UniChem fdasrs VC2W18DGKR
THM UniChem HMDB HMDB0000273
THM UniChem 'PubChem TPHARMA' 15196472
THM UniChem Mcule MCULE-7680226016
THM UniChem NMRShiftDB 60020903
THM UniChem ACTor 35902-13-7
THM UniChem ACTor 50-88-4
THM UniChem Recon thymd
THM UniChem Nikkaji J4.548I
THM UniChem BindingDb 1
THM UniChem 'EPA CompTox Dashboard' DTXSID5023661
THM UniChem MetaboLights MTBLC17748
THM UniChem BRENDA 1455
THM UniChem BRENDA 14935
THM UniChem BRENDA 166
THM UniChem BRENDA 173330
THM UniChem BRENDA 3070
THM UniChem BRENDA 63029
THM UniChem Rhea 17748
THM UniChem ChemicalBook CB6134417
THM UniChem ClinicalTrials THYMIDINE
THM UniChem rxnorm THYMIDINE
THM UniChem MedChemExpress HY-N1150
THM UniChem 'Probes And Drugs' PD049699
THM UniChem PubChem 5789
THM UniChem eMolecules 28206777
THM UniChem eMolecules 532057
THM UniChem SureChEMBL SCHEMBL19894
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
THM "O5'" -4.028 1.624 1.026 ETKDGv3 1
THM "C5'" -3.651 0.294 0.796 ETKDGv3 2
THM "C4'" -2.646 0.216 -0.361 ETKDGv3 3
THM "O4'" -1.452 0.872 -0.009 ETKDGv3 4
THM "C3'" -2.291 -1.229 -0.707 ETKDGv3 5
THM "O3'" -3.161 -1.783 -1.665 ETKDGv3 6
THM "C2'" -0.867 -1.132 -1.202 ETKDGv3 7
THM "C1'" -0.422 0.263 -0.757 ETKDGv3 8
THM N1 0.813 0.194 0.041 ETKDGv3 9
THM C2 0.804 -0.287 1.401 ETKDGv3 10
THM O2 -0.269 -0.658 1.950 ETKDGv3 11
THM N3 2.026 -0.347 2.134 ETKDGv3 12
THM C4 3.247 0.032 1.499 ETKDGv3 13
THM O4 4.325 0.002 2.150 ETKDGv3 14
THM C5 3.237 0.454 0.082 ETKDGv3 15
THM C5M 4.518 0.861 -0.592 ETKDGv3 16
THM C6 2.070 0.537 -0.580 ETKDGv3 17
THM "HO5'" -3.299 2.040 1.556 ETKDGv3 18
THM "H5'1" -3.219 -0.154 1.721 ETKDGv3 19
THM "H5'2" -4.560 -0.286 0.530 ETKDGv3 20
THM "H4'" -3.084 0.732 -1.246 ETKDGv3 21
THM "H3'" -2.310 -1.864 0.207 ETKDGv3 22
THM "HO3'" -3.129 -1.215 -2.479 ETKDGv3 23
THM "H2'1" -0.807 -1.215 -2.309 ETKDGv3 24
THM "H2'2" -0.243 -1.938 -0.755 ETKDGv3 25
THM "H1'" -0.253 0.891 -1.662 ETKDGv3 26
THM HN3 2.029 -0.671 3.128 ETKDGv3 27
THM HM51 4.441 0.773 -1.697 ETKDGv3 28
THM HM52 5.353 0.208 -0.260 ETKDGv3 29
THM HM53 4.755 1.913 -0.329 ETKDGv3 30
THM H6 2.072 0.872 -1.611 ETKDGv3 31
#