# ------------------------------------------------------------------------------------------------------------------------- # # File: ndb-ntc-extension.dic # Date: 10-MAR-2020 # # Dictionary extension for integrative/hybrid models. # # ------------------------------------------------------------------------------------------------------------------------- # data_ndb-ntc-extension.dic _datablock.id ndb-ntc-extension.dic _datablock.description ; This data block holds the extension dictionary for DNATCO conformer analysis of nucleic acids (https://www.dnatco.org/) for NDB. ; _dictionary.title ndb-ntc-extension.dic _dictionary.datablock_id ndb-ntc-extension.dic _dictionary.version 0.01 # loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 0.01 2020-03-10 ; Changes (bv/cl/bs/jc) + Release as initial version 0.01 ; ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description ## 'inclusive_group' . ; The parent category group containing all of the data categories in the macromolecular dictionary. ; 'ndb_group' 'inclusive_group' ; Categories that describe the DNATCO nucleotide conformers for NDB. ; #################### ## ITEM_TYPE_LIST ## #################### # # # The regular expressions defined here are not compliant # with the POSIX 1003.2 standard as they include the # '\n' and '\t' special characters. These regular expressions # have been tested using version 0.12 of Richard Stallman's # GNU regular expression library in POSIX mode. # # ############################################################################## loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.detail code char '[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words ... ; ucode uchar '[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (case insensitive) ... ; line char '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items ... ; uline uchar '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items (case insensitive)... ; text char '[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; text item types / multi-line text ... ; int numb '[+-]?[0-9]+' ; int item types are the subset of numbers that are the negative or positive integers. ; float numb '-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?' ; float item types are the subset of numbers that are the floating numbers. ; name uchar '_[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+' ; name item types take the form... ; ############################ ## NDB_STRUCT_NTC_OVERALL ## ############################ save_ndb_struct_ntc_overall _category.description ; Data items in the NDB_STRUCT_NTC_OVERALL category defines the overall DNATCO features of the entry. ; _category.id ndb_struct_ntc_overall _category.mandatory_code no loop_ _category_key.name '_ndb_struct_ntc_overall.entry_id' loop_ _category_group.id 'inclusive_group' 'ndb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _ndb_struct_ntc_overall.entry_id _ndb_struct_ntc_overall.confal_score _ndb_struct_ntc_overall.confal_percentile _ndb_struct_ntc_overall.ntc_version _ndb_struct_ntc_overall.cana_version _ndb_struct_ntc_overall.num_steps _ndb_struct_ntc_overall.num_classified _ndb_struct_ntc_overall.num_unclassified _ndb_struct_ntc_overall.num_unclassified_rmsd_close 1bna 59 33 3.1 3.1 22 22 0 0 # ... abbreviated ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ndb_struct_ntc_overall save_ save__ndb_struct_ntc_overall.entry_id _item_description.description ; The entry id. This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_ndb_struct_ntc_overall.entry_id' _item.category_id ndb_struct_ntc_overall _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_overall.entry_id' _item_linked.parent_name '_entry.id' save_ save__ndb_struct_ntc_overall.confal_score _item_description.description ; The confal score. ; _item.name '_ndb_struct_ntc_overall.confal_score' _item.category_id ndb_struct_ntc_overall _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_overall.confal_percentile _item_description.description ; The confal percentile. The percentile will vary as the number of nucleic acid structures increase and is expected to be updated on a yearly basis. ; _item.name '_ndb_struct_ntc_overall.confal_percentile' _item.category_id ndb_struct_ntc_overall _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_overall.NtC_version _item_description.description ; The NtC version used. ; _item.name '_ndb_struct_ntc_overall.NtC_version' _item.category_id ndb_struct_ntc_overall _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_overall.CANA_version _item_description.description ; The CANA version used. ; _item.name '_ndb_struct_ntc_overall.CANA_version' _item.category_id ndb_struct_ntc_overall _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_overall.num_steps _item_description.description ; The number of steps. ; _item.name '_ndb_struct_ntc_overall.num_steps' _item.category_id ndb_struct_ntc_overall _item.mandatory_code no _item_type.code int save_ save__ndb_struct_ntc_overall.num_classified _item_description.description ; The number of steps classified using NtCs. ; _item.name '_ndb_struct_ntc_overall.num_classified' _item.category_id ndb_struct_ntc_overall _item.mandatory_code no _item_type.code int save_ save__ndb_struct_ntc_overall.num_unclassified _item_description.description ; The number of unclassified steps. ; _item.name '_ndb_struct_ntc_overall.num_unclassified' _item.category_id ndb_struct_ntc_overall _item.mandatory_code no _item_type.code int save_ save__ndb_struct_ntc_overall.num_unclassified_rmsd_close _item_description.description ; The number of unclassified steps that have close rmsds to known NtCs in the golden set. ; _item.name '_ndb_struct_ntc_overall.num_unclassified_rmsd_close' _item.category_id ndb_struct_ntc_overall _item.mandatory_code no _item_type.code int save_ ######################### ## NDB_STRUCT_NTC_STEP ## ######################### save_ndb_struct_ntc_step _category.description ; Data items in the NDB_STRUCT_NTC_STEP category defines the dinucleotide steps in the structure. ; _category.id ndb_struct_ntc_step _category.mandatory_code no loop_ _category_key.name '_ndb_struct_ntc_step.id' loop_ _category_group.id 'inclusive_group' 'ndb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _ndb_struct_ntc_step.id _ndb_struct_ntc_step.name _ndb_struct_ntc_step.PDB_model_number _ndb_struct_ntc_step.label_entity_id_1 _ndb_struct_ntc_step.label_asym_id_1 _ndb_struct_ntc_step.label_seq_id_1 _ndb_struct_ntc_step.label_comp_id_1 _ndb_struct_ntc_step.label_alt_id_1 _ndb_struct_ntc_step.label_entity_id_2 _ndb_struct_ntc_step.label_asym_id_2 _ndb_struct_ntc_step.label_seq_id_2 _ndb_struct_ntc_step.label_comp_id_2 _ndb_struct_ntc_step.label_alt_id_2 _ndb_struct_ntc_step.auth_asym_id_1 _ndb_struct_ntc_step.auth_seq_id_1 _ndb_struct_ntc_step.auth_asym_id_2 _ndb_struct_ntc_step.auth_seq_id_2 _ndb_struct_ntc_step.PDB_ins_code_1 _ndb_struct_ntc_step.PDB_ins_code_2 1 '1a9n_Q_C_0_C_1' 1 1 A 1 C . 1 A 2 C . Q 0 Q 1 . . # ... abbreviated ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ndb_struct_ntc_step save_ save__ndb_struct_ntc_step.id _item_description.description ; Unique identifier for the step. ; _item.name '_ndb_struct_ntc_step.id' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code int save_ save__ndb_struct_ntc_step.name _item_description.description ; Step name as referred to in DNATCO. ; _item.name '_ndb_struct_ntc_step.name' _item.category_id ndb_struct_ntc_step _item.mandatory_code no _item_type.code code save_ save__ndb_struct_ntc_step.PDB_model_num _item_description.description ; The PDB model number. ; _item.name '_ndb_struct_ntc_step.PDB_model_num' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ndb_struct_ntc_step.PDB_model_num' _item_linked.parent_name '_atom_site.pdbx_PDB_model_num' save_ save__ndb_struct_ntc_step.label_entity_id_1 _item_description.description ; The entity identifier of the first nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_entity_id_1' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.label_entity_id_1' _item_linked.parent_name '_atom_site.label_entity_id' save_ save__ndb_struct_ntc_step.label_asym_id_1 _item_description.description ; The asym/chain identifier of the first nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_asym_id_1' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.label_asym_id_1' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ndb_struct_ntc_step.label_seq_id_1 _item_description.description ; The residue number identifier of the first nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_seq_id_1' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ndb_struct_ntc_step.label_seq_id_1' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ndb_struct_ntc_step.label_comp_id_1 _item_description.description ; The component/residue name identifier of the first nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_comp_id_1' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code ucode _item_linked.child_name '_ndb_struct_ntc_step.label_comp_id_1' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ndb_struct_ntc_step.label_alt_id_1 _item_description.description ; The alternate conformation identifier of the first nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_alt_id_1' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.label_alt_id_1' _item_linked.parent_name '_atom_site.label_alt_id' save_ save__ndb_struct_ntc_step.label_entity_id_2 _item_description.description ; The entity identifier of the second nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_entity_id_2' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.label_entity_id_2' _item_linked.parent_name '_atom_site.label_entity_id' save_ save__ndb_struct_ntc_step.label_asym_id_2 _item_description.description ; The asym/chain identifier of the second nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_asym_id_2' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.label_asym_id_2' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ndb_struct_ntc_step.label_seq_id_2 _item_description.description ; The residue number identifier of the second nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_seq_id_2' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ndb_struct_ntc_step.label_seq_id_2' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ndb_struct_ntc_step.label_comp_id_2 _item_description.description ; The component/residue name identifier of the second nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_comp_id_2' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code ucode _item_linked.child_name '_ndb_struct_ntc_step.label_comp_id_2' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ndb_struct_ntc_step.label_alt_id_2 _item_description.description ; The alternate conformation identifier of the second nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.label_alt_id_2' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.label_alt_id_2' _item_linked.parent_name '_atom_site.label_alt_id' save_ save__ndb_struct_ntc_step.auth_asym_id_1 _item_description.description ; The author provided asym/chain identifier of the first nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.auth_asym_id_1' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.auth_asym_id_1' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__ndb_struct_ntc_step.auth_seq_id_1 _item_description.description ; The author provided residue number identifier of the first nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.auth_seq_id_1' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.auth_seq_id_1' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__ndb_struct_ntc_step.auth_asym_id_2 _item_description.description ; The author provided asym/chain identifier of the second nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.auth_asym_id_2' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.auth_asym_id_2' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__ndb_struct_ntc_step.auth_seq_id_2 _item_description.description ; The author provided residue number identifier of the second nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.auth_seq_id_2' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.auth_seq_id_2' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__ndb_struct_ntc_step.PDB_ins_code_1 _item_description.description ; The residue insertion code of the first nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.PDB_ins_code_1' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.PDB_ins_code_1' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' save_ save__ndb_struct_ntc_step.PDB_ins_code_2 _item_description.description ; The residue insertion code of the second nucleotide in the step. ; _item.name '_ndb_struct_ntc_step.PDB_ins_code_2' _item.category_id ndb_struct_ntc_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_ntc_step.PDB_ins_code_2' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' save_ ################################# ## NDB_STRUCT_NTC_STEP_SUMMARY ## ################################# save_ndb_struct_ntc_step_summary _category.description ; Data items in the NDB_STRUCT_NTC_STEP_SUMMARY category summarizes the DNATCO features of the dinucleotide steps. ; _category.id ndb_struct_ntc_step_summary _category.mandatory_code no loop_ _category_key.name '_ndb_struct_ntc_step_summary.step_id' loop_ _category_group.id 'inclusive_group' 'ndb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _ndb_struct_ntc_step_summary.step_id _ndb_struct_ntc_step_summary.assigned_CANA _ndb_struct_ntc_step_summary.assigned_NtC _ndb_struct_ntc_step_summary.confal_score _ndb_struct_ntc_step_summary.euclidean_distance_NtC_ideal _ndb_struct_ntc_step_summary.cartesian_rmsd_closest_NtC_representative _ndb_struct_ntc_step_summary.closest_CANA _ndb_struct_ntc_step_summary.closest_NtC _ndb_struct_ntc_step_summary.closest_step_golden 1 B12 BB04 33 ? 0.36 B12 BB04 ? # ... abbreviated ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ndb_struct_ntc_step_summary save_ save__ndb_struct_ntc_step_summary.step_id _item_description.description ; The nucleotide step identifier. ; _item.name '_ndb_struct_ntc_step_summary.step_id' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ndb_struct_ntc_step_summary.step_id' _item_linked.parent_name '_ndb_struct_ntc_step.id' save_ save__ndb_struct_ntc_step_summary.assigned_CANA _item_description.description ; The assigned CANA for the nucleotide step. ; _item.name '_ndb_struct_ntc_step_summary.assigned_CANA' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail 'AAA' 'steps in the A form' 'AAw' 'steps in the A form but some torsions (typically α and ɣ) have values switched from the typical values' 'AAu' 'A forms with bases partially unstacked' 'A-B' 'A to B transition steps (first nucleotide A, second B)' 'B-A' 'B to A transition steps (first nucleotide B, second A)' 'BBB' 'Steps in the B form' 'BBw' 'Steps in the B form but some torsions (typically α and ɣ) have values switched from the typical values' 'B12' 'Steps with torsion values bridging B and BII forms' 'BB2' 'Steps in the BII ("b-two") form' 'miB' 'Steps with B like sugar puckers and stacked bases but untypical torsion values' 'ICL' 'Steps with parallel but distant bases that can be intercalated' 'OPN' 'Steps with unstacked, frequently distant bases and untypical torsion values' 'SYN' 'Steps containing base in the syn orientation' 'ZZZ' 'steps in the Z form' 'NAN' 'Unassigned steps' save_ save__ndb_struct_ntc_step_summary.assigned_NtC _item_description.description ; The assigned NtC for the nucleotide step. ; _item.name '_ndb_struct_ntc_step_summary.assigned_NtC' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail 'AA00' 'the most frequent, canonical A form' 'AA02' 'A-DNA with the B like χ1/χ2' 'AA03' 'A like, similar to AA00, high α2' 'AA04' 'A like, similar to AA00, low α2' 'AA08' 'A form variant' 'AA09' 'A form variant' 'AA01' 'A like, α2/ɣ2 switch (150/180)' 'AA05' 'A like, α2/ɣ2 switch (130/180)' 'AA06' 'A like, α2/ɣ2 switch (130/180)' 'AA10' 'A like, α2/ɣ2 switch (210/140)' 'AA11' 'A like, α2/ɣ2 switch (90/190)' 'AA07' 'A form with distant bases, low ζ1' 'AA12' 'A like backbone, bases can be intercalated' 'AA13' 'A form with distant bases, low ζ1' 'AB01' "A-B: δ1 C3'-endo, δ2 C2'-endo, χ1/χ2 have A-B pattern" 'AB02' "A-B: δ1 O4'-endo, extremely low ε1, χ1/χ2 are B like" 'AB03' 'A-B: similar to AB01 with high α2 and low ζ1, β2, ɣ2' 'AB04' "A-B: δ1 C3'-endo, δ2 C2'-endo, χ1/χ2 have A/B pattern, C'C' high" 'AB05' "A-B: δ1 C3'-endo, δ2 C2'-endo, χ1/χ2 have A/B pattern" 'BA01' "BI-A complex conformer with δ2 from C3' to C4'-exo, χ1/χ2 are B like" 'BA05' "BI-A complex conformer with δ2 from C3' to C4'-exo, χ1/χ2 are B like" 'BA09' 'BI-A: extremely low β2~60, α2/ɣ2 switch (260/170), χ2 A like' 'BA08' 'B-A: low β2' 'BA10' 'B-A complex cluster: α2~90, ɣ2~180, χ2 A like' 'BA13' 'B-A complex cluster: α2~90, ɣ2~180, χ2 A like' 'BA16' 'BII-A: χ2 A like' 'BA17' "BII-A: δ2~O4'-endo, β2~130" 'BB00' 'the most frequent DNA conformer, canonical B form, also called BI' 'BB01' 'less populated variant of BI form' 'BB17' 'less populated variant of BI form, very low ε1, α2, β2' 'BB02' 'BI with α2/ɣ2 typical values switched to 30/300' 'BB03' 'BI with α2/ɣ2 typical values switched to 160/170' 'BB11' 'B form with α2/ɣ2 typical values switched to 120/190 and low both ε1 and ζ1' 'BB16' 'B like, with χ1 A like' 'BB04' 'conformer with torsion transforming BI to BII form' 'BB05' 'BI-BII with α2/ɣ2 typical values switched to 70/220, χ2 A like' 'BB07' 'BII form, typical by ε1/ζ1 switch compared to BI' 'BB08' 'BII form variant with α1/ɣ1 typical values switched to 70/210' 'BB10' 'B form with extremely low values of α2, β2, ɣ2, and low ε1 and ζ1' 'BB12' 'BI like with α2/ɣ2 typical values switched to 260/170, low β2 70, χ2 A like' 'BB13' 'BI like with α2/ɣ2 typical values switched to 220/160, low β2 70, χ2 A like' 'BB14' 'B like with extremely low ε1, high β2' 'BB15' 'BI with high α2 (340) and ɣ2 near 0' 'BB20' 'B like pucker, χ2 A like, unusual combination of ε1, ζ1, α2, ɣ2, χ2' 'IC01' 'A-B backbone, parallel distant bases can be intercalated' 'IC02' 'A-B backbone, parallel distant bases can be intercalated' 'IC03' 'A-B backbone, parallel distant bases can be intercalated, α2/ɣ2 typical values switched to 70/300, χ2 B like' 'IC04' 'A-B backbone, parallel distant bases can be intercalated, α2/ɣ2 typical values switched to 190/180, χ2 B like' 'IC05' 'BII backbone, parallel distant bases can be intercalated' 'IC06' 'B like, parallel distant bases can be intercalated, χ1 A like' 'IC07' 'A like intercalated' 'OP01' 'A pucker and χ torsions, unusual combination of backbone torsions, bases distant, parallel, low rise' 'OP02' 'A pucker and χ torsions, unusual combination of backbone torsions, bases distant, angled' 'OP03' 'A pucker and χ torsions, unusual combination of backbone torsions, base sangled, can be intercalated' 'OP04' 'A pucker and χ torsions, unusual combination of backbone torsions, base sangled, can be intercalated' 'OP05' 'A pucker and χ torsions, unusual combination of backbone torsions, bases distant, perpendicular' 'OP06' 'A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, low rise' 'OP07' 'A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, low rise' 'OP08' 'A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases parallel, low rise' 'OP09' 'A-B pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, angled' 'OP10' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, parallel' 'OP11' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, perpendicular' 'OP12' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, angled' 'OP13' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, perpendicular' 'OP14' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, angled' 'OP15' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases can pair with each other' 'OP16' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, perpendicular' 'OP17' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, angled' 'OP18' 'B pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, angled' 'OP19' 'B pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant' 'OP20' 'B pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant in 4-way junction' 'OP21' 'B pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant in 5'-end dsDNA' 'OP22' 'B pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant angled' 'OP23' 'B like open, parallel bases' 'OP24' 'B like open, low χ2, perpendicular bases' 'OP25' 'B-A open, perpendicular bases' 'OP26' 'B-A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases can pair with each other' 'OP27' 'B-A pucker, A like χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, angled' 'OP28' 'A-B pucker, A like χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant, angled' 'OP29' 'A pucker and χ torsions, unusual combination of backbone torsions, bases distant' 'OP30' 'A pucker and χ torsions, unusual combination of backbone torsions, bases distant, parallel' 'OP31' 'A pucker and χ torsions, unusual combination of ε1, ζ1, α2, β2, bases distant angled' 'OPS1' 'B-A pucker, unusual combination of ε1, ζ1, α2, β2, bases perpendicular, first syn' 'OP1S' 'B pucker, unusual combination of ε1, ζ1, α2, β2, bases angled, second syn' 'AAS1' 'A like with first base in syn orientation' 'AB1S' 'A-B, χ2 syn' 'AB2S' 'A-B, χ2 syn' 'BB1S' 'BI like, unusual β2 and ɣ2, χ2 syn' 'BB2S' 'BI like, α2 50, ɣ2 290, χ2 syn' 'BBS1' 'BI like, χ1 syn' 'ZZ01' 'Z like conformer similar to ZZS2 but both bases anti' 'ZZ02' 'Z like conformer similar to ZZ1S with α2/ɣ2 typical values switched to 230/60 and both bases anti' 'ZZ1S' 'Z form, Y-R step' 'ZZ2S' "Z form, Y-R step, δ2 C2'-endo" 'ZZS1' 'ZI form, R-Y step' 'ZZS2' 'ZII form, R-Y step' 'NANT' 'Unassigned conformations' save_ save__ndb_struct_ntc_step_summary.confal_score _item_description.description ; The confal score. ; _item.name '_ndb_struct_ntc_step_summary.confal_score' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_summary.euclidean_distance_NtC_ideal _item_description.description ; The euclidean distance to ideal NtC values. ; _item.name '_ndb_struct_ntc_step_summary.euclidean_distance_NtC_ideal' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_summary.cartesian_rmsd_closest_NtC_representative _item_description.description ; The carterian rmsd to the best NtC representative in the golden set. Representative is the step with its 12 parameters most similar to ideal NtC values. ; _item.name '_ndb_struct_ntc_step_summary.cartesian_rmsd_closest_NtC_representative' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_summary.closest_NtC _item_description.description ; The closest NtC in the golden set. ; _item.name '_ndb_struct_ntc_step_summary.closest_NtC' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code no _item_type.code code save_ save__ndb_struct_ntc_step_summary.closest_CANA _item_description.description ; The CANA of the closest NtC in the golden set. ; _item.name '_ndb_struct_ntc_step_summary.closest_CANA' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code no _item_type.code code save_ save__ndb_struct_ntc_step_summary.closest_step_golden _item_description.description ; The closest step in the golden set. ; _item.name '_ndb_struct_ntc_step_summary.closest_step_golden' _item.category_id ndb_struct_ntc_step_summary _item.mandatory_code no _item_type.code code save_ #################################### ## NDB_STRUCT_NTC_STEP_PARAMETERS ## #################################### save_ndb_struct_ntc_step_parameters _category.description ; Data items in the NDB_STRUCT_NTC_STEP_PARAMETERS category provides the DNATCO parameters of the dinucleotide steps. ; _category.id ndb_struct_ntc_step_parameters _category.mandatory_code no loop_ _category_key.name '_ndb_struct_ntc_step_parameters.step_id' loop_ _category_group.id 'inclusive_group' 'ndb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _ndb_struct_ntc_step_parameters.step_id _ndb_struct_ntc_step_parameters.tor_delta_1 _ndb_struct_ntc_step_parameters.tor_epsilon_1 _ndb_struct_ntc_step_parameters.tor_zeta_1 _ndb_struct_ntc_step_parameters.tor_alpha_2 _ndb_struct_ntc_step_parameters.tor_beta_2 _ndb_struct_ntc_step_parameters.tor_gamma_2 _ndb_struct_ntc_step_parameters.tor_delta_2 _ndb_struct_ntc_step_parameters.tor_chi_1 _ndb_struct_ntc_step_parameters.tor_chi_2 _ndb_struct_ntc_step_parameters.dist_NN _ndb_struct_ntc_step_parameters.dist_CC _ndb_struct_ntc_step_parameters.tor_NCCN 1 140 201 214 315 153 46 140 263 253 4.6 5.1 29 # ... abbreviated ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ndb_struct_ntc_step_parameters save_ save__ndb_struct_ntc_step_parameters.step_id _item_description.description ; The nucleotide step identifier. ; _item.name '_ndb_struct_ntc_step_parameters.step_id' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ndb_struct_ntc_step_parameters.step_id' _item_linked.parent_name '_ndb_struct_ntc_step.id' save_ save__ndb_struct_ntc_step_parameters.tor_delta_1 _item_description.description ; The delta_1 torsion angle defined by C5'(1)-C4'(1)-C3'(1)-O3'(1) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_delta_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_epsilon_1 _item_description.description ; The epsilon_1 torsion angle defined by C4'(1)-C3'(1)-O3'(1)-P(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_epsilon_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_zeta_1 _item_description.description ; The zeta_1 torsion angle defined by C3'(1)-O3'(1)-P(2)-O5'(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_zeta_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_alpha_2 _item_description.description ; The alpha_2 torsion angle defined by O3'(1)-P(2)-O5'(2)-C5'(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_alpha_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_beta_2 _item_description.description ; The beta_2 torsion angle defined by P(2)-O5'(2)-C5'(2)-C4'(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_beta_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_gamma_2 _item_description.description ; The gamma_2 torsion angle defined by O5'(2)-C5'(2)-C4'(2)-C3'(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_gamma_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_delta_2 _item_description.description ; The delta_2 torsion angle defined by C5'(2)-C4'(2)-C3'(2)-O3'(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_delta_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_chi_1 _item_description.description ; The chi_1 torsion angle defined by O4'(1)-C1'(1)-N1/9(1)-C2/4(1) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_chi_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_chi_2 _item_description.description ; The chi_2 torsion angle defined by O4'(2)-C1'(2)-N1/9(2)-C2/4(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_chi_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.dist_NN _item_description.description ; The NN distance defined by N1/9(1)-N1/9(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.dist_NN' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.dist_CC _item_description.description ; The CC distance defined by C2/4(1)-C2/4(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.dist_CC' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.tor_NCCN _item_description.description ; The NCCN (mu) torsion angle defined by N1/9(1)-C2/4(1)-C2/4(2)-N1/9(2) atoms. ; _item.name '_ndb_struct_ntc_step_parameters.tor_NCCN' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_delta_1 _item_description.description ; The delta_1 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_delta_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_epsilon_1 _item_description.description ; The epsilon_1 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_epsilon_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_zeta_1 _item_description.description ; The zeta_1 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_zeta_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_alpha_2 _item_description.description ; The alpha_2 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_alpha_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_beta_2 _item_description.description ; The beta_2 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_beta_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_gamma_2 _item_description.description ; The gamma_2 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_gamma_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_delta_2 _item_description.description ; The delta_2 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_delta_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_chi_1 _item_description.description ; The chi_1 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_chi_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_chi_2 _item_description.description ; The chi_2 torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_chi_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_dist_NN _item_description.description ; The NN distance difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_dist_NN' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_dist_CC _item_description.description ; The CC distance difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_dist_CC' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.diff_tor_NCCN _item_description.description ; The NCCN torsion angle difference. ; _item.name '_ndb_struct_ntc_step_parameters.diff_tor_NCCN' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_delta_1 _item_description.description ; The delta_1 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_delta_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_epsilon_1 _item_description.description ; The epsilon_1 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_epsilon_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_zeta_1 _item_description.description ; The zeta_1 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_zeta_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_alpha_2 _item_description.description ; The alpha_2 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_alpha_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_beta_2 _item_description.description ; The beta_2 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_beta_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_gamma_2 _item_description.description ; The gamma_2 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_gamma_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_delta_2 _item_description.description ; The delta_2 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_delta_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_chi_1 _item_description.description ; The chi_1 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_chi_1' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_chi_2 _item_description.description ; The chi_2 torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_chi_2' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_dist_NN _item_description.description ; The NN distance confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_dist_NN' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_dist_CC _item_description.description ; The CC distance confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_dist_CC' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.confal_tor_NCCN _item_description.description ; The NCCN torsion angle confal score. ; _item.name '_ndb_struct_ntc_step_parameters.confal_tor_NCCN' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_ntc_step_parameters.details _item_description.description ; Additional details about the step parameters. For unassigned steps close to known NtC, this item contains list of parameters outside cutoff distances. ; _item.name '_ndb_struct_ntc_step_parameters.details' _item.category_id ndb_struct_ntc_step_parameters _item.mandatory_code no _item_type.code text save_ ###################################### ## NDB_STRUCT_SUGAR_STEP_PARAMETERS ## ###################################### save_ndb_struct_sugar_step_parameters _category.description ; Data items in the NDB_STRUCT_SUGAR_STEP_PARAMETERS category provides the sugar parameters for the dinucleotide steps. ; _category.id ndb_struct_sugar_step_parameters _category.mandatory_code no loop_ _category_key.name '_ndb_struct_sugar_step_parameters.step_id' loop_ _category_group.id 'inclusive_group' 'ndb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _ndb_struct_sugar_step_parameters.step_id _ndb_struct_sugar_step_parameters.P_1 _ndb_struct_sugar_step_parameters.tau_1 _ndb_struct_sugar_step_parameters.Pn_1 _ndb_struct_sugar_step_parameters.P_2 _ndb_struct_sugar_step_parameters.tau_2 _ndb_struct_sugar_step_parameters.Pn_2 _ndb_struct_sugar_step_parameters.nu_1_1 _ndb_struct_sugar_step_parameters.nu_1_2 _ndb_struct_sugar_step_parameters.nu_1_3 _ndb_struct_sugar_step_parameters.nu_1_4 _ndb_struct_sugar_step_parameters.nu_1_5 _ndb_struct_sugar_step_parameters.nu_2_1 _ndb_struct_sugar_step_parameters.nu_2_2 _ndb_struct_sugar_step_parameters.nu_2_3 _ndb_struct_sugar_step_parameters.nu_2_4 _ndb_struct_sugar_step_parameters.nu_2_5 1 . . . . . . . . . . . . . . . . # ... abbreviated ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ndb_struct_sugar_step_parameters save_ save__ndb_struct_sugar_step_parameters.step_id _item_description.description ; The nucleotide step identifier. ; _item.name '_ndb_struct_sugar_step_parameters.step_id' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ndb_struct_sugar_step_parameters.step_id' _item_linked.parent_name '_ndb_struct_ntc_step.id' save_ save__ndb_struct_sugar_step_parameters.P_1 _item_description.description ; The P_1 parameter. Pseudorotation phase angle for (deoxy) ribose of residue 1. ; _item.name '_ndb_struct_sugar_step_parameters.P_1' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.tau_1 _item_description.description ; The tau_1 parameter. Maximum degree of pucker for residue 1. ; _item.name '_ndb_struct_sugar_step_parameters.tau_1' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.Pn_1 _item_description.description ; The Pn_1 parameter. First residue pucker name (eg., C2end for C2'-endo or C3exo for C3'-exo puckers). ; _item.name '_ndb_struct_sugar_step_parameters.Pn_1' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.P_2 _item_description.description ; The P_2 parameter. Pseudorotation phase angle for (deoxy) ribose of residue 2. ; _item.name '_ndb_struct_sugar_step_parameters.P_2' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.tau_2 _item_description.description ; The tau_2 parameter. Maximum degree of pucker for residue 2. ; _item.name '_ndb_struct_sugar_step_parameters.tau_2' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.Pn_2 _item_description.description ; The Pn_2 parameter. Second residue pucker name (eg., C2end for C2'-endo or C3exo for C3'-exo puckers). ; _item.name '_ndb_struct_sugar_step_parameters.Pn_2' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_1_1 _item_description.description ; The nu_1_1 parameter. Torsion defined by C4'-O4'-C1'-C2' atoms of residue 1. ; _item.name '_ndb_struct_sugar_step_parameters.nu_1_1' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_1_2 _item_description.description ; The nu_1_2 parameter. Torsion defined by O4'-C1'-C2'-C3' atoms of residue 1. ; _item.name '_ndb_struct_sugar_step_parameters.nu_1_2' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_1_3 _item_description.description ; The nu_1_3 parameter. Torsion defined by C1'-C2'-C3'-C4' atoms of residue 1. ; _item.name '_ndb_struct_sugar_step_parameters.nu_1_3' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_1_4 _item_description.description ; The nu_1_4 parameter. Torsion defined by C2'-C3'-C4'-O4' atoms of residue 1. ; _item.name '_ndb_struct_sugar_step_parameters.nu_1_4' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_1_5 _item_description.description ; The nu_1_5 parameter. Torsion defined by C3'-C4'-O4'-C1' atoms of residue 1. ; _item.name '_ndb_struct_sugar_step_parameters.nu_1_5' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_2_1 _item_description.description ; The nu_2_1 parameter. Torsion defined by C4'-O4'-C1'-C2' atoms of residue 2. ; _item.name '_ndb_struct_sugar_step_parameters.nu_2_1' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_2_2 _item_description.description ; The nu_2_2 parameter. Torsion defined by O4'-C1'-C2'-C3' atoms of residue 2. ; _item.name '_ndb_struct_sugar_step_parameters.nu_2_2' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_2_3 _item_description.description ; The nu_2_3 parameter. Torsion defined by C1'-C2'-C3'-C4' atoms of residue 2. ; _item.name '_ndb_struct_sugar_step_parameters.nu_2_3' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_2_4 _item_description.description ; The nu_2_4 parameter. Torsion defined by C2'-C3'-C4'-O4' atoms of residue 2. ; _item.name '_ndb_struct_sugar_step_parameters.nu_2_4' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.nu_2_5 _item_description.description ; The nu_2_5 parameter. Torsion defined by C3'-C4'-O4'-C1' atoms of residue 2. ; _item.name '_ndb_struct_sugar_step_parameters.nu_2_5' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code yes _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_1_1 _item_description.description ; The nu_1_1 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_1_1' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_1_2 _item_description.description ; The nu_1_2 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_1_2' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_1_3 _item_description.description ; The nu_1_3 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_1_3' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_1_4 _item_description.description ; The nu_1_4 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_1_4' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_1_5 _item_description.description ; The nu_1_5 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_1_5' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_2_1 _item_description.description ; The nu_2_1 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_2_1' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_2_2 _item_description.description ; The nu_2_2 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_2_2' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_2_3 _item_description.description ; The nu_2_3 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_2_3' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_2_4 _item_description.description ; The nu_2_4 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_2_4' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_ save__ndb_struct_sugar_step_parameters.diff_nu_2_5 _item_description.description ; The nu_2_5 parameter difference. ; _item.name '_ndb_struct_sugar_step_parameters.diff_nu_2_5' _item.category_id ndb_struct_sugar_step_parameters _item.mandatory_code no _item_type.code float save_