# ----------------------------------------------------------------------------- # mon_lib # ======= # The Library of Monomers # # Jean J. Richelle, Alexei Vagin # # Version 2.0 - 18/06/98 # Version 3.0 - 31/05/00 # ----------------------------------------------------------------------------- # # mon_lib defines: # 1. the chemical structure of the monomers (atom's types, # bond's lengths, angles, chirality, planarity), # 2. the tree like structure of each monomer, # 3. the possible links between monomers (peptide bond, # disulfide bridges,...), # 4. the possible modifications of monomers (e.g. termini of # polypeptide chains,...) # # All this information is constant, i.e independent of the # conformation of the molecule. CIFile, describing a macromolecule, # must contain the variable information (coordinates, occupancy, # B-factors) and the list of modifications to and links between # actual monomers. # # The information about the names of chains and monomers, and # the serial numbers of monomers for the links must be present # in the CIFile. # ----------------------------------------------------------------------------- # Monomers # ======== # Definition: A monomer is a set of atoms connected by bonds, or a single # atom. For example, it may be an amino acid, a # polypetide chain, a polypetide chain and a substrate conected # by hydrogen bonds. # It is useful for some programs (dynamics, graphics and # so on) to define a tree like structure of the monomers. # The specification for each atom of the monomer of a 'back atom' # and a 'forward atom' defines the tree like structure of the # monomer. # The 'back atom' of a given atom is its preceding atom in the # tree. # If an atom has some forward branchs, their order is # 1. the first one is the shortest branch; # 2. the last one is the backbone branch or the longest branch. # The 'forward atom' of a given atom is an atom of the last # branch. # The first and the last atom of the tree must be a non-hydrogen # atom # # The following categories describe the monomers: # # _chem_comp. # list of the monomers with their general description (name, type, # number of atoms) # general description of the monomer (name,type,number of atoms) # _chem_comp.id # monomer identifier. # _chem_comp.one_letter_code # one letter code of the monomer # _chem_comp.name # full name of the monomer. # _chem_comp.type # type of the monomer: # "D-peptide" # "L-peptide" # "DNA" # "RNA" # "D-saccharide" # "L-saccharide" # "solvent" # "non-polymer" # _chem_comp.number_atoms_all # number of atoms in the monomer # _chem_comp.number_atoms_nh # number of non-hydrogen atoms in the monomer # # _chem_comp_synonym. # for each monomer, the list of the synomyms of names of # monomers and atoms. # _chem_comp_synonym.comp_id # _chem_comp_synonym.comp_alternative_id # _chem_comp_synonym.mod_id # _chem_comp_synonym.atom_id # _chem_comp_synonym.atom_alternative_id # # _chem_comp_atom. # for each monomer, the list of the atoms and their types. # _chem_comp_atom.comp_id # monomer identifier. # _chem_comp_atom.atom_id # atom name. # _chem_comp_atom.type_symbol # element symbol. # _chem_comp_atom.type_energy # the atom type, it is used in the energetic parameters library # ener_lib. # _chem_comp_atom.charge # charge assigned to atom. # # _chem_comp_tree. # for each monomer the definition of its tree like structure. # # _chem_comp_tree.comp_id # _chem_comp_tree.atom_id # _chem_comp_tree.atom_back # previous atom in the tree like structure of the monomer; # for the first atom the value is '.'. # _chem_comp_tree.back_type # _chem_comp_tree.atom_forward # forward atom in the tree like structure of the monomer; # if the atom hasn't a forward atom the value is '.'; # the value of the last atom of the tree must be 'END'. # _chem_comp_tree.additional_connect_atom_id_1 # _chem_comp_tree.additional_connect_atom_id_2 # _chem_comp_tree.additional_connect_type # # _chem_comp_bond. # for each monomer, the list of bonds and their standard value. # _chem_comp_bond.comp_id # monomer identifier. # _chem_comp_bond.atom_id_1 # _chem_comp_bond.atom_id_2 # the two atoms that form a bond # _chem_comp_bond.type # the chemical type of the bond: "coval", "disulf", "soltbr", # "hydrog", "metal". # _chem_comp_bond.value_dist # standard bond length in angstroms # _chem_comp_bond.value_dist_esd # standard deviation of the bond length # # _chem_comp_angle. # for each monomer, the list of the valence angles and their # standard value. # _chem_comp_angle.chem_id # monomer identifier. # _chem_comp_angle.atom_id_1 # _chem_comp_angle.atom_id_2 # _chem_comp_angle.atom_id_3 # the angles are designated by three atoms, with # the second atom forming the vertex of the angle. # _chem_comp_angle.value_angle # standard value of the angle in degrees # _chem_comp_angle.value_angle_esd # standard deviation of the angle value # # _chem_comp_tor. # for each monomer, the list of torsion angles, their label and # their standard value; an angle my be variable or constant; # the label gives the standard name for variable angles, it is # '.' for constant angles; the order of atoms must follow the # tree like structure. # _chem_comp_tor.comp_id # monomer identifier. # _chem_comp_tor.label # torsion label, it must uniquely identify a torsion angle if # it is variable; if the torsion angles is constant the value # of label must be equal to '.'. # _chem_comp_tor.atom_id_1 # _chem_comp_tor.atom_id_2 # _chem_comp_tor.atom_id_3 # _chem_comp_tor.atom_id_4 # the four atoms that form an torsion # _chem_comp_tor.value_angle # standard value of the angle in degrees; the value of variable # angles is arbitrary and describes some conformation. # _chem_comp_tor.value_angle_esd # standard deviation of the angle value # _chem_comp_tor.period # # _chem_comp_chir. # the chirality of monomer atoms and the type of the chirality. # Chirality: # Let the vector direction atom_1 to atom_2 be v1, # the vector direction atom_1 to atom_3 be v2, # the vector direction atom_1 to atom_4 be v3; # the chiral volume is the volume of the parallelepiped # formed by the three vectors: v1,v2,v3. # # VOLUME = v1 . [ v2 x v3 ] # # The type is the sign of the chiral volume. # _chem_comp_chir.comp_id # monomer identifier. # _chem_comp_chir.atom_id_1 # _chem_comp_chir.atom_id_2 # _chem_comp_chir.atom_id_3 # _chem_comp_chir.atom_id_4 # the atom designated by_chem_comp_chir.atom_id_1 is # the chiral atom; the atoms bonded to the chiral atom are # specified by_chem_comp_chir.atom_id_2, # _lib_mon_chiral_atom_id_3 and_chem_comp_chir.atom_id_4 # _chem_comp_chir.volume_sign # the value of type must be equal 'positiv' or 'negativ'. # # _chem_comp_plane. # the list of the atoms lying in the same plan and # their standard deviation from the plan # _chem_comp_plane.comp_id # monomer identifier. # _chem_comp_plane.id # the label must uniquely identify a plan in a monomer # _chem_comp_plane.atom_id # an atom of the plan # _chem_comp_plane.esd # standard deviation of the atom distance to the plan # # ----------------------------------------------------------------------------- # Links # ===== # Categories to describe the type of links between two atoms of # different monomers. # They describe only the type of the link, the atom # names and the monomer flags. # The information about the names of the chains and monomers, and # the serial numbers of the monomers is given in the CIFile. # # The monomer flag designates the first or the second monomer in # the category _entity_link_ having its value given in the # CIFile. # # _entity_link_id # _entity_link_entity_id_1 # _entity_link_mon_id_1 # _entity_link_set_num_1 # _entity_link_entity_id_2 # _entity_link_mon_id_2 # _entity_link_set_num_2 # SS Ach CYS 20 Cch CYS 40 # # The link "TRANS" is the default for polypeptide chain, # "pd", the default for DNA, "pr", the default for RNA. # # _chem_link. # _chem_link.link_id # _chem_link.one_letter_code # _chem_link.name # _chem_link.comp_id_1 # _chem_link.type_comp_1 # _chem_link.mod_id_1 # _chem_link.comp_id_2 # _chem_link.type_comp_2 # _chem_link.mod_id_2 # # _chem_link_tree. # _chem_link_tree.link_id # _chem_link_tree.atom_comp_id # _chem_link_tree.atom_id # _chem_link_tree.atom_back_comp_id # _chem_link_tree.atom_back # _chem_link_tree.back_type # _chem_link_tree.atom_forward_comp_id # _chem_link_tree.atom_forward # _chem_link_tree.additional_connect_atom_1_comp_id # _chem_link_tree.additional_connect_atom_id_1 # _chem_link_tree.additional_connect_atom_2_comp_id # _chem_link_tree.additional_connect_atom_id_2 # _chem_link_tree.additional_connect_type # # _chem_link_bond. # _chem_link_bond.link_id # _chem_link_bond.atom_1_comp_id # _chem_link_bond.atom_id_1 # _chem_link_bond.atom_2_comp_id # _chem_link_bond.atom_id_2 # _chem_link_bond.type # _chem_link_bond.value_dist # _chem_link_bond.value_dist_esd # # _chem_link_angle. # _chem_link_angle.link_id # _chem_link_angle.atom_1_comp_id # _chem_link_angle.atom_id_1 # _chem_link_angle.atom_2_comp_id # _chem_link_angle.atom_id_2 # _chem_link_angle.atom_3_comp_id # _chem_link_angle.atom_id_3 # _chem_link_angle.value_angle # _chem_link_angle.value_angle_esd # # _chem_link_tor. # _chem_link_tor.link_id # _chem_link_tor.label # _chem_link_tor.atom_1_comp_id # _chem_link_tor.atom_id_1 # _chem_link_tor.atom_2_comp_id # _chem_link_tor.atom_id_2 # _chem_link_tor.atom_3_comp_id # _chem_link_tor.atom_id_3 # _chem_link_tor.atom_4_comp_id # _chem_link_tor.atom_id_4 # _chem_link_tor.value_angle # _chem_link_tor.value_angle_esd # _chem_link_tor.period # # _chem_link_chir. # _chem_link_chir.link_id # _chem_link_chir.atom_1_comp_id # _chem_link_chir.atom_id_1 # _chem_link_chir.atom_2_comp_id # _chem_link_chir.atom_id_2 # _chem_link_chir.atom_3_comp_id # _chem_link_chir.atom_id_3 # _chem_link_chir.atom_4_comp_id # _chem_link_chir.atom_id_4 # _chem_link_chir.volume_sign # # _chem_link_plane. # _chem_link_plane.link_id # _chem_link_plane.id # _chem_link_plane.atom_comp_id # _chem_link_plane.atom_id # _chem_link_plane.esd # # ----------------------------------------------------------------------------- # Modifications # ============= # Categories to describe the possible modifications of monomers: # the 'function' (add, delete, change), and the atoms, bonds, # angles, # chirality, planarity that will be modified. # The information about the names and serial numbers of monomers # is described in the CIFile. # For example: # _entity_mod_id # _entity_mod_entity_id # _entity_mod_mon_id # _entity_mod_set_num # COO Cchain CYS 30 # # The modifications "NH3" and "COO" are the default for # the polypeptide chain termini. # The modifications "d5*END" and "d3*END" are the default for # DNA termini. # The modifications "r5*END" and "r3*END" are default for # RNA termini. # # _chem_mod. # _chem_mod.mod_id # identifier of the modification # _chem_mod.one_letter_code # _chem_mod.name # _chem_mod.sub_mod_id # _chem_mod.sub_mod_order # # _chem_mod_atom. # _chem_mod_atom.mod_id # identifier of the modification # _chem_mod_atom.function # the function describing the type of modification: # "add", "delete", "change" # _chem_mod_atom.atom_id # atom that will be modified. # _chem_mod_atom.new_atom_id # new atom that will be added. # _chem_mod_atom.new_type_energy # _chem_mod_atom.new_type_symbol # _chem_mod_atom.new_charge # # _chem_mod_tree. # _chem_mod_tree.mod_id # _chem_mod_tree.function # _chem_mod_tree.atom_id # _chem_mod_tree.atom_back # _chem_mod_tree.back_type # _chem_mod_tree.atom_forward # _chem_mod_tree.additional_connect_atom_id_1 # _chem_mod_tree.additional_connect_atom_id_2 # _chem_mod_tree.additional_connect_type # # _chem_mod_bond. # _chem_mod_bond.mod_id # _chem_mod_bond.function # _chem_mod_bond.atom_id_1 # _chem_mod_bond.atom_id_2 # _chem_mod_bond.new_type # _chem_mod_bond.new_value_dist # _chem_mod_bond.new_value_dist_esd # # _chem_mod_angle. # _chem_mod_angle.mod_id # _chem_mod_angle.function # _chem_mod_angle.atom_id_1 # _chem_mod_angle.atom_id_2 # _chem_mod_angle.atom_id_3 # _chem_mod_angle.new_value_angle # _chem_mod_angle.new_value_angle_esd # # _chem_mod_tor. # _chem_mod_tor.mod_id # _chem_mod_tor.function # _chem_mod_tor.label # _chem_mod_tor.atom_id_1 # _chem_mod_tor.atom_id_2 # _chem_mod_tor.atom_id_3 # _chem_mod_tor.atom_id_4 # _chem_mod_tor.new_value_angle # _chem_mod_tor.new_value_angle_esd # _chem_mod_tor.new_period # # _chem_mod_chir. # _chem_mod_chir.mod_id # _chem_mod_chir.function # _chem_mod_chir.atom_id_1 # _chem_mod_chir.atom_id_2 # _chem_mod_chir.atom_id_3 # _chem_mod_chir.atom_id_4 # _chem_mod_chir.new_volume_sign # # _chem_mod_plane. # _chem_mod_plane.mod_id # _chem_mod_plane.function # _chem_mod_plane.id # _chem_mod_plane.atom_id # _chem_mod_plane.new_esd # # ----------------------------------------------------------------------------- # # The values for the amino acid bond lengths # and angles have been taken from Engh and Huber paper # Acta Cryst. A47 (1991). # The values for the purine and pyrimidine bond lengths # and angles have been taken from O. Kennard & R. Taylor (1982), # J. Am. Soc. Chem. vol. 104, pp. 3209-3212. # The values for the sugar-phosphate backbone bond lengths # and bond angles have been taken from the W. Saenger's "Principles # of Nucleic Acid Structure", (1983), Springer-Verlag, pp. 70,86. # # ----------------------------------------------------------------------------- global_ _lib_name mon_lib _lib_version 3.1 _lib_update 16/07/00 _lib_history ; 13-Jul-94 Draft version 7-Dec-94 Version 1.O 29-Dec-94 Modification of introduction; use new category names: lib_mon_list, lib_mod_list, lib_link_list; use new items: _lib_mon_list_mon_id, _lib_mon_atom_atom_id, _lib_mod_atom_atom_id, _lib_mod_atom_new_atom_id, _lib_link_atom_atom_id. 30-Dec-94 Version 1.0.1 18-Jan-95 Correction of '_' into '-' for some data items 18-Jan-95 Version 1.0.2 19-Jan-95 Correct remaining _lib_mon_atom_id, _lib_link_atom_id; correct CB-SG bond of CYS. 19-Jan-95 When _lib_mod_function is 'add', _lib_mod_atom_new_atom_id get the added atoms, and _lib_mod_atom_atom_id is '.'; When _lib_mod_function is 'change', and that atom_id value is not changed, gives to _lib_mod_atom_new_atom_id the same value as _lib_mod_atom_atom_id. 23-Jan-95 Correction: use '.' instead of '-' where its meaning is 'Not Applicable'. Use 'CONST' as a value for '_lib_mon_tors_label' when the torsion is constant. Correct _lib_mon_atom_* change d5*END into r5*END in data_mod_r5*END and d3*END into r3*END in data_mod_r3*END. When _lib_mod_atom_back|forward is the same as in original monomer, explicit the values. 25-Jan-95 Version 1.0.3 30-Jan-95 Correct Fe _lib_mon_atom_type_symbol for _mon_id FE and HEM Suppress 'default-' in _lib_mod_list_detail data value. Introduce _lib_mod_list_sub_mod_id|sub_mod_order. 03-Feb-95 Correct dates in _lib_history between 19-Jan-95 and 23-Jan-95 Introduce the data for _lib_mod_mon_list. Introduce the data for _lib_mod_list_code1 and _lib_link_list_code1. 09-Mar-95 Add hetero monomers; only _lib_mon_atom and _lib_mon_bond info is provided; further verification must be done. 18-Jun-98 Version 2.0.0 06-Nov-98 Version 2.1.0 31-May-00 Version 3.0.0 16-Jul-00 Version 3.1.0 ; # ------------------------------------------------ # # --- LIST OF SYNONYMS --- # data_synonym_list loop_ _chem_comp_synonym.comp_id _chem_comp_synonym.comp_alternative_id _chem_comp_synonym.mod_id TRP TRY . ALA-D DAL . VAL-D DVA . PHE-D DPN . PRO DPR . TRP-D DTR . THR DTH . LEU-D DLE . Ad A . Cd C . Gd G . Td T . Ur U . Ad +A . Cd +C . Gd +G . Td +T . Ur +U . XYL XLS . SO4 SUL . SO4 SO1 . SO4 SO2 . PO4 PHO . P SPS . P IPS . ZN ZN1 . ZN ZN2 . 3GP GMP . HOH WAT . HOH H2O . HOH OH2 . HOH DOD . BEZ BOX . ATA AMT . GTT GSH . PLM PAM . loop_ _chem_comp_synonym_atom.comp_id _chem_comp_synonym_atom.comp_alternative_id _chem_comp_synonym_atom.atom_id _chem_comp_synonym_atom.atom_alternative_id 5GP . P PA 5GP . O1P O1A 5GP . O2P O2A 5GP . O3P O3A 2AM . P PA 2AM . O1P O1A 2AM . O2P O2A 2AM . O3P O3A 3GP . P PA 3GP . O1P O1A 3GP . O2P O2A 3GP . O3P O3A HOH . O OW HYP . CD CD2 HYP . OD OD1 CH3 . C C1 CH3 . C C1A CH3 . H1 H11 CH3 . H2 H12 CH3 . H3 H13 CH3 . H1 HC1 CH3 . H2 HC2 CH3 . H3 HC3 CH3 . H1 H1A1 CH3 . H2 H1A2 CH3 . H3 H1A3 NCO . N1 NH1 NCO . N2 NH2 NCO . N3 NH3 NCO . N4 NH4 NCO . N5 NH5 NCO . N6 NH6 2GP . O2P O4P 2GP . C5* C5R 2GP . O5* O5R 2GP . C4* C4R 2GP . O4* O4R 2GP . C1* C1R 2GP . C2* C2R 2GP . O2* O2R 2GP . C3* C3R 2GP . O3* O3R AMP . P PA AMP . O1P O1A AMP . O2P O2A AMP . O3P O3A MO5 . O1 OA MO5 . O2 OB MO5 . O3 OC MO5 . O4 OD MO5 . O5 OE MO4 . O1 OB MO4 . O2 OC MO4 . O3 OD MO4 . O4 OF MO6 . O1 OA MO6 . O2 OB MO6 . O3 OC MO6 . O4 OD MO6 . O5 OE MO6 . O6 OF FOL . O4 OH4 TML . CM1 CH1 TML . CM2 CH2 TML . CM3 CH3 BEN . C C7 BOC . O1 OT1 BOC . C CT1 BOC . O2 OT2 BOC . CT CT2 BOC . C1 CT3 BOC . C2 CT4 BOC . C3 CT5 M2G . C2A CM2 M2G . C2B CM1 2MG . C2A CM2 OMC . C2A CM2 OMG . C2A CM2 OMU . C2A CM2 5MC . C5A CM5 5MU . C5A CM5 1MA . C1 CM1 7MG . C7 CM7 OME . C1 CM OME . O1 O FBP . O1P O11 FBP . O2P O12 FBP . O3P O13 FBP . P2 P6 FBP . O4P O61 FBP . O5P O62 FBP . O6P O63 CB3 . O4 OA4 MAE . O1 O1A MAE . O2 O1B MAE . O3 O4A MAE . O4 O4B MPD . CM C6 MPD . O2 O7 MPD . O4 O8 NBN . C C1 NBN . C1 C3 NBN . C2 C4 NBN . N N2 NBN . C3 C5 NBN . C4 C6 PMP . N4A N4 PMP . O4P OP4 PMP . O1P OP1 PMP . O2P OP2 PMP . O3P OP3 BEZ BOX C C1, BEZ BOX O1 O1, BEZ BOX O2 O2, CBZ . O1 O CBZ . O2 OA CBZ . C1, CB CBZ . C1 CG CBZ . C2 CD1 CBZ . C6 CD2 CBZ . C5 CE1 CBZ . C3 CE2 CBZ . C4 CZ OAA . O4 O6 OAA . O3 O7 OAA . C4 C6 PLM . C10 CA PLM . C11 CB PLM . C12 CC PLM . C13 CD PLM . C14 CE PLM . C15 CF PLM . C16 CG SPH . N2 N SPH . C2 CA SPH . C1 C SPH . O1 O TFA . C C1 TFA . CT C2 TOS . O1S O1 TOS . O2S O2 MPR . C C1 MPR . CA C2 MPR . HA1 H21 MPR . HA2 H22 MPR . CB C3 MPR . HB1 H31 MPR . HB2 H32 MPR . SG S3 ADD . N N3 ADD . C C1 ACB . N N2 ILG . H HN1 ILG-D . H HN1 ALA . H HN1 HEM . NA N_A HEM . NB N_B HEM . NC N_C HEM . ND N_D HEC . NA N_A HEC . NB N_B HEC . NC N_C HEC . ND N_D HMD . NA N_A HMD . NB N_B HMD . NC N_C HMD . ND N_D # # --- LIST OF LINKS --- # data_link_list loop_ _chem_link.id _chem_link.name _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 SS SS-bridge CYS . . CYS . . MPR-CYS SS-bridge MPR . . CYS . . CYS-MPR SS-bridge CYS . . MPR . . TRANS default-peptide-link . . peptide . . peptide PTRANS default-peptide-link_pro . . peptide PRO . . CIS cis-peptide-link . . peptide . . peptide PCIS cis-peptide-link_pro . . peptide PRO . . gap gap-link . . . . . . p default-DNA/RNA-link . . DNA/RNA . . DNA/RNA FOR_C-N bond_FOR-C_=_N-peptide FOR . . . . peptide FOR_C-C bond_FOR-C_=_C-peptide . . peptide FOR . . FOR-LYZ bond_FOR-C_=_NZ-LYZ LYZ . . FOR . . ACE_C-N bond_ACE-C_=_N_peptide ACE . . . . peptide AHT-ALA bond_AHT-N2_=_CB-ALA AHT . . ALA . . DFO-NME bond_DFO-C_=_N-NME DFO . . NME . . DFO_C-N bond_DFO-C_=_N-peptide DFO . . . . peptide DFO_N-C bond_DFO-N_=_C-peptide . . peptide DFO . . STA-NME bond_DFO-C_=_N-NME DFO . . NME . . STA_C-N bond_DFO-C_=_N-peptide DFO . . . . peptide STA_N-C bond_DFO-N_=_C-peptide . . peptide DFO . . STA_DFO bond_STA-C_=_N-DFO STA . . DFO . . DFO_STA bond_DFO-C_=_N-STA DFO . . STA . . STA_STA bond_STA-C_=_N-STA STA . . STA . . DFO_DFO bond_DFO-C_=_N-DFO DFO . . DFO . . IVA_C-N bond_IVA-C_=_N-peptide IVA . . . . peptide BOC_C-N bond_BOC-C_=_N-peptide BOC . . . . peptide NME_N-C bond_NME-N_=_C-peptide . . peptide NME . . LINK_C-N bond_C_=_N . . polymer . . polymer LINK_CNp bond_C_=_N-peptide . . polymer . . peptide LINK_CpN bond_C-peptide_=_N . . peptide . . polymer BETA1-2 glycosidic_bond_beta1-2 . DEL-HO2 pyranose . DEL-O1 pyranose BETA1-3 glycosidic_bond_beta1-3 . DEL-HO3 pyranose . DEL-O1 pyranose BETA2-3 glycosidic_bond_beta1-3 . DEL-O2 pyranose SIA . . BETA1-4 glycosidic_bond_beta1-4 . DEL-HO4 pyranose . DEL-O1 pyranose BETA1-6 glycosidic_bond_beta1-6 . DEL-HO6 pyranose . DEL-O1 pyranose ALPHA1-2 glycosidic_bond_alpha1-2 . DEL-HO2 pyranose . DEL-O1 pyranose ALPHA1-3 glycosidic_bond_alpha1-3 . DEL-HO3 pyranose . DEL-O1 pyranose ALPHA2-3 glycosidic_bond_alpha1-3 . DEL-O2 pyranose SIA . . ALPHA1-4 glycosidic_bond_alpha1-4 . DEL-HO4 pyranose . DEL-O1 pyranose ALPHA1-6 glycosidic_bond_alpha1-6 . DEL-HO6 pyranose . DEL-O1 pyranose MAN-SER bond_MAN-C1_=_SER-OG MAN DEL-O1 . SER . . NAG-SER bond_NAG-C1_=_SER-OG NAG DEL-O1 . SER . . NAG-THR bond_NAG-C1_=_THR-OG1 NAG DEL-O1 . THR . . MAN-THR bond_MAN-C1_=_THR-OG1 MAN DEL-O1 . THR . . NAG-ASN bond_NAG-C1_=_ASN-ND2 NAG DEL-O1 . ASN . . MAN-ASN bond_MAN-C1_=_ASN-ND2 MAN DEL-O1 . ASN . . XYS-THR bond_XYS-C1_=_THR-OG1 XYS XYS-O1 . THR . . XYS-SER bond_XYS-C1_=_SER-OG XYS XYS-O1 . SER . . XYS-ASN bond_XYS-C1_=_ASN-ND2 XYS XYS-O1 . ASN . . ZN-CYS bond_ZN_=_CYS-SG ZN . . CYS . . FE-CYS bond_FE_=_CYS-SG FE . . CYS . . SFN-TYR bond_SFN-S_=_TYR-OH SFN . . TYR . . CH2-N2 bond_CH2-CH2_=_Ar-N2 CH2 . . . . DNA/RNA DM1-CH2 bond_DM1-N3*_=_CH2-CH2 DM1 . . CH2 . . CH3-N1 bond_CH3-C_=_Ar-N1 CH3 . . . . DNA/RNA CH3-O2* bond_CH3-C_=-O2* CH3 . . . . DNA/RNA MG-O1P bond_MG_=-O1P MG . . . . DNA/RNA MG-O2P bond_MG_=-O2P MG . . . . DNA/RNA BR-C5 bond_BR_=-C5 BR . . . . DNA/RNA ILG_CD-N bond_ILG-CD_=N-polymer ILG . . . . polymer ILG_CD-p bond_ILG-CD_=N-peptide ILG . . . . peptide symmetry dummy_link . . . . . . # # --- LIST OF MODIFICATIONS --- # data_mod_list loop_ _chem_mod.id _chem_mod.name _chem_mod.comp_id _chem_mod.group_id NH3 NH3-terminus . peptide COO COO-terminus . peptide CM-COO CM-COO-terminus . polymer 5*END DNA/RNA-5*-terminus . DNA/RNA 3*END DNA/RNA-3*-terminus . DNA/RNA p5*END DNA/RNA-p5*-terminus . DNA/RNA p3*END DNA/RNA-p3*-terminus . DNA/RNA FOR-N N-terminus_of_formyl . . FOR-C C-terminus_of_formyl . . G-N2 delete_N2_from_guanosine . DNA/RNA DEL-O1 delete_O1_from_saccharide . pyranose DEL-O2 delete_O2_from_saccharide . . DEL-HO2 delete_HO2_from_saccharide . pyranose DEL-HO3 delete_HO3_from_saccharide . pyranose DEL-HO4 delete_HO4_from_saccharide . pyranose DEL-HO6 delete_HO6_from_saccharide . pyranose DEL-OXT delete_OXT_from_peptide . . SUG-b-L change_sugar_to_beta_L . pyranose SUG-a-D change_sugar_to_alpha_D . pyranose SUG-b-D change_sugar_to_beta_D . pyranose SUG-a-L change_sugar_to_alpha_L . pyranose O1MET O1_metyl_of_sugar . pyranose S2O4 O4_sulfonyl_of_GAL GAL-b-D . PEPT-D change_peptide_to_D . peptide 1MA N1-metyl_of_adenosine . DNA/RNA 1MG N1-metyl_of_guanosine . DNA/RNA 2MG N2-metyl_of_guanosine . DNA/RNA M2G N2-dimetyl_of_guanosine . DNA/RNA O2*MET O2*_metyl . DNA/RNA C5MET C5_metyl . DNA/RNA N7MET N7_metyl . DNA/RNA RNA-O2* delete_O2*_from_RNA . DNA/RNA XYS-O1 delete_O1_from_XYS . . B2C replace_B_to_C . peptide B2C_D replace_B_to_C_for_D-peptide . peptide RENAME change_monomer"s_name . . TERMINUS chain_terminus_without_modification . . # # # --- DESCRIPTION OF MODIFICATIONS --- # data_mod_NH3 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge NH3 change N N . NT3 -0.200 NH3 add . H1 H HNT3 0.100 NH3 add . H2 H HNT3 0.100 NH3 change H H3 . HNT3 0.100 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type NH3 change N n/a CA START NH3 add H1 N . . NH3 add H2 N . . NH3 change H3 N . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd NH3 add N H1 coval 0.960 0.020 NH3 add N H2 coval 0.960 0.020 NH3 change N H3 coval 0.960 0.020 NH3 change N CA coval 1.491 0.021 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd NH3 add H2 N H3 109.470 3.000 NH3 change H3 N CA 109.470 3.000 NH3 add H2 N CA 109.470 3.000 NH3 add H1 N H2 109.470 3.000 NH3 add H1 N H3 109.470 3.000 NH3 add H1 N CA 109.470 3.000 # data_mod_COO # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge COO change C C . C 0.340 COO change O O . OC -0.350 COO add . OXT O OC -0.350 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type COO add OXT C . END COO change C . OXT . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd COO change C O coval 1.231 0.020 COO add C OXT coval 1.231 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd COO change CA C O 121.000 3.000 COO add CA C OXT 121.000 3.000 loop_ _chem_mod_tor.mod_id _chem_mod_tor.function _chem_mod_tor.id _chem_mod_tor.atom_id_1 _chem_mod_tor.atom_id_2 _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd _chem_mod_tor.new_period COO add psi N CA C OXT 160.00 30.0 2 loop_ _chem_mod_plane_atom.mod_id _chem_mod_plane_atom.function _chem_mod_plane_atom.plane_id _chem_mod_plane_atom.atom_id _chem_mod_plane_atom.new_dist_esd COO add oxt C 0.020 COO add oxt CA 0.020 COO add oxt O 0.020 COO add oxt OXT 0.020 # data_mod_CM-COO # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge CM-COO change C C . C 0.340 CM-COO change O O . OC -0.350 CM-COO add . OXT O OC -0.350 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type CM-COO add OXT C . END CM-COO change C . OXT . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd CM-COO change C O coval 1.231 0.020 CM-COO add C OXT coval 1.231 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd CM-COO change CM C O 121.000 3.000 CM-COO add CM C OXT 121.000 3.000 loop_ _chem_mod_tor.mod_id _chem_mod_tor.function _chem_mod_tor.id _chem_mod_tor.atom_id_1 _chem_mod_tor.atom_id_2 _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd _chem_mod_tor.new_period CM-COO add psi CH CM C OXT 160.00 30.0 2 # data_mod_5*END # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge 5*END delete P . . . 0.000 5*END delete O1P . . . 0.000 5*END delete O2P . . . 0.000 5*END change O5* O5* . OH1 -0.212 5*END add . HO5* H HOH1 0.142 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type 5*END delete P . . . 5*END delete O1P . . . 5*END delete O2P . . . 5*END change O5* n/a C5* START 5*END add HO5* O5* . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd 5*END add O5 HO5* coval 0.980 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd 5*END add C5* O5* HO5* 120.000 3.000 # data_mod_3*END # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge 3*END change O3* O3* . OH1 -0.257 3*END add . HO3* H HOH1 0.156 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type 3*END change O3* C3* . END 3*END add HO3* O3* . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd 3*END add O3* HO3* coval 0.980 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd 3*END add C3* O3* HO3* 120.000 3.000 loop_ _chem_mod_tor.mod_id _chem_mod_tor.function _chem_mod_tor.id _chem_mod_tor.atom_id_1 _chem_mod_tor.atom_id_2 _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd _chem_mod_tor.new_period 3*END add hh C4* C3* O3* HO3* 0.00 30.0 3 # data_mod_FOR-N # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge FOR-N add . H H HC1 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type FOR-N add H C . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd FOR-N add C H coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd FOR-N add H C O 121.000 3.000 # data_mod_FOR-C # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge FOR-C change O O . OC -0.350 FOR-C add . OXT O OC -0.350 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type FOR-C add OXT C . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd FOR-C change C O coval 1.231 0.020 FOR-C add C OXT coval 1.231 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd FOR-C add O C OXT 120.000 3.000 # data_mod_G-N2 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge G-N2 delete N2 . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type G-N2 delete N2 . . . # data_mod_DEL-O1 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge DEL-O1 delete O1 . . . 0.000 DEL-O1 delete HO1 . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type DEL-O1 delete O1 . . . DEL-O1 delete HO1 . . . # data_mod_DEL-O2 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge DEL-O2 delete O2 . . . 0.000 DEL-O2 delete HO2 . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type DEL-O2 delete O2 . . . DEL-O2 delete HO2 . . . # data_mod_DEL-HO2 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge DEL-HO2 delete HO2 . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type DEL-HO2 change O2 . . END # data_mod_DEL-HO3 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge DEL-HO3 delete HO3 . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type DEL-HO3 change O3 . . END # data_mod_DEL-HO4 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge DEL-HO4 delete HO4 . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type DEL-HO4 change O4 . . END # data_mod_DEL-HO6 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge DEL-HO6 delete HO6 . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type DEL-HO6 change O6 . . END # data_mod_1MA # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge 1MA change N1 . . NR6 0.000 1MA add . C1 C CH3 0.000 1MA add . H11 H HCH 0.000 1MA add . H12 H HGH 0.000 1MA add . H13 H HCH 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type 1MA add C1 N1 H13 . 1MA add H11 C1 . . 1MA add H12 C1 . . 1MA add H13 C1 . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd 1MA add C1 N1 coval 1.465 0.020 1MA add C1 H11 coval 0.960 0.020 1MA add C1 H12 coval 0.960 0.020 1MA add C1 H13 coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd 1MA add N1 C1 H11 109.470 3.000 1MA add N1 C1 H12 109.470 3.000 1MA add N1 C1 H13 109.470 3.000 1MA add H12 C1 H11 109.470 3.000 1MA add H13 C1 H11 109.470 3.000 1MA add H13 C1 H12 109.470 3.000 # data_mod_1MG # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge 1MG change N1 . . NR6 0.000 1MG add . C1A C CH3 0.000 1MG add . H1A1 H HCH 0.000 1MG add . H1A2 H HGH 0.000 1MG add . H1A3 H HCH 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type 1MG add C1A N1 H1A3 . 1MG add H1A1 C1A . . 1MG add H1A2 C1A . . 1MG add H1A3 C1A . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd 1MG add C1A N1 coval 1.465 0.020 1MG add C1A H1A1 coval 0.960 0.020 1MG add C1A H1A2 coval 0.960 0.020 1MG add C1A H1A3 coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd 1MG add N1 C1A H1A1 109.470 3.000 1MG add N1 C1A H1A2 109.470 3.000 1MG add N1 C1A H1A3 109.470 3.000 1MG add H1A2 C1A H1A1 109.470 3.000 1MG add H1A3 C1A H1A1 109.470 3.000 1MG add H1A3 C1A H1A2 109.470 3.000 # data_mod_2MG # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge 2MG change N2 . . NH1 0.000 2MG add . C2A C CH3 0.000 2MG add . H2A1 H HCH 0.000 2MG add . H2A2 H HGH 0.000 2MG add . H2A3 H HCH 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type 2MG change N2 C2 C2A . 2MG add C2A N2 H2A3 . 2MG add H2A1 C2A . . 2MG add H2A2 C2A . . 2MG add H2A3 C2A . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd 2MG add C2A N2 coval 1.465 0.020 2MG add C2A H2A1 coval 0.960 0.020 2MG add C2A H2A2 coval 0.960 0.020 2MG add C2A H2A3 coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd 2MG add C2 N2 C2A 115.000 3.000 2MG add N2 C2A H2A1 109.470 3.000 2MG add N2 C2A H2A2 109.470 3.000 2MG add N2 C2A H2A3 109.470 3.000 2MG add H2A2 C2A H2A1 109.470 3.000 2MG add H2A3 C2A H2A1 109.470 3.000 2MG add H2A3 C2A H2A2 109.470 3.000 # data_mod_M2G # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge M2G change N2 . . NH1 0.000 M2G add . C2A C CH3 0.000 M2G add . H2A1 H HCH 0.000 M2G add . H2A2 H HGH 0.000 M2G add . H2A3 H HCH 0.000 M2G add . C2B C CH3 0.000 M2G add . H2B1 H HCH 0.000 M2G add . H2B2 H HGH 0.000 M2G add . H2B3 H HCH 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type M2G change N2 C2 C2A . M2G add C2A N2 H2A3 . M2G add H2A1 C2A . . M2G add H2A2 C2A . . M2G add H2A3 C2A . . M2G add C2B N2 H2B3 . M2G add H2B1 C2B . . M2G add H2B2 C2B . . M2G add H2B3 C2B . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd M2G add C2A N2 coval 1.465 0.020 M2G add C2A H2A1 coval 0.960 0.020 M2G add C2A H2A2 coval 0.960 0.020 M2G add C2A H2A3 coval 0.960 0.020 M2G add C2B N2 coval 1.465 0.020 M2G add C2B H2B1 coval 0.960 0.020 M2G add C2B H2B2 coval 0.960 0.020 M2G add C2B H2B3 coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd M2G add C2 N2 C2A 118.000 3.000 M2G add C2 N2 C2B 118.000 3.000 M2G add C2A N2 C2B 124.000 3.000 M2G add N2 C2A H2A1 109.470 3.000 M2G add N2 C2A H2A2 109.470 3.000 M2G add N2 C2A H2A3 109.470 3.000 M2G add H2A2 C2A H2A1 109.470 3.000 M2G add H2A3 C2A H2A1 109.470 3.000 M2G add H2A3 C2A H2A2 109.470 3.000 M2G add N2 C2B H2B1 109.470 3.000 M2G add N2 C2B H2B2 109.470 3.000 M2G add N2 C2B H2B3 109.470 3.000 M2G add H2B2 C2B H2B1 109.470 3.000 M2G add H2B3 C2B H2B1 109.470 3.000 M2G add H2B3 C2B H2B2 109.470 3.000 # data_mod_O2*MET # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge O2*MET change O2* . . OC2 0.000 O2*MET delete HO2* . . . 0.000 O2*MET add . C2A C CH3 0.000 O2*MET add . H2A1 H HCH 0.000 O2*MET add . H2A2 H HGH 0.000 O2*MET add . H2A3 H HCH 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type O2*MET change O2* C2* C2A . O2*MET add C2A O2* H2A3 . O2*MET add H2A1 C2A . . O2*MET add H2A2 C2A . . O2*MET add H2A3 C2A . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd O2*MET add O2* C2A coval 1.420 0.020 O2*MET add C2A H2A1 coval 0.960 0.020 O2*MET add C2A H2A2 coval 0.960 0.020 O2*MET add C2A H2A3 coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd O2*MET add C2* O2* C2A 120.000 3.000 O2*MET add O2* C2A H2A1 109.470 3.000 O2*MET add O2* C2A H2A2 109.470 3.000 O2*MET add O2* C2A H2A3 109.470 3.000 O2*MET add H2A2 C2A H2A1 109.470 3.000 O2*MET add H2A3 C2A H2A1 109.470 3.000 O2*MET add H2A3 C2A H2A2 109.470 3.000 # data_mod_O1MET # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge O1MET change O1 . . O2 0.000 O1MET delete HO1 . . . 0.000 O1MET add . CM C CH3 0.000 O1MET add . HM1 H HCH 0.000 O1MET add . HM2 H HGH 0.000 O1MET add . HM3 H HCH 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type O1MET change O1 C1 CM . O1MET delete HO1 . . . O1MET add CM O1 HM3 . O1MET add HM1 CM . . O1MET add HM2 CM . . O1MET add HM3 CM . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd O1MET add O1 CM coval 1.420 0.020 O1MET add CM HM1 coval 0.960 0.020 O1MET add CM HM2 coval 0.960 0.020 O1MET add CM HM3 coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd O1MET add C1 O1 CM 120.000 3.000 O1MET add O1 CM HM1 109.470 3.000 O1MET add O1 CM HM2 109.470 3.000 O1MET add O1 CM HM3 109.470 3.000 O1MET add HM2 CM HM1 109.470 3.000 O1MET add HM3 CM HM1 109.470 3.000 O1MET add HM3 CM HM2 109.470 3.000 # data_mod_S2O4 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge S2O4 change O4 . . O2 0.000 S2O4 delete HO4 . . . 0.000 S2O4 add . S S S 0.000 S2O4 add . O1S O O 0.000 S2O4 add . O2S O O 0.000 S2O4 add . O3S O O 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type S2O4 change O4 C4 S . S2O4 delete HO4 . . . S2O4 add S O4 O3S . S2O4 add O1S S . . S2O4 add O2S S . . S2O4 add O3S S . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd S2O4 add O4 S coval 1.590 0.020 S2O4 add S O1S coval 1.440 0.020 S2O4 add S O2S coval 1.440 0.020 S2O4 add S O3S coval 1.440 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd S2O4 add C4 O4 S 120.000 3.000 S2O4 add O4 S O1S 109.470 3.000 S2O4 add O4 S O2S 109.470 3.000 S2O4 add O4 S O3S 109.470 3.000 S2O4 add O2S S O1S 109.470 3.000 S2O4 add O3S S O1S 109.470 3.000 S2O4 add O3S S O2S 109.470 3.000 # data_mod_C5MET # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge C5MET change C5 . . CR6 0.000 C5MET add . C5A C CH3 0.000 C5MET add . H5A1 H HCH 0.000 C5MET add . H5A2 H HGH 0.000 C5MET add . H5A3 H HCH 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type C5MET add C5A C5 H5A3 . C5MET add H5A1 C5A . . C5MET add H5A2 C5A . . C5MET add H5A3 C5A . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd C5MET add C5A C5 coval 1.500 0.020 C5MET add C5A H5A1 coval 0.960 0.020 C5MET add C5A H5A2 coval 0.960 0.020 C5MET add C5A H5A3 coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd C5MET add C4 C5 C5A 122.000 3.000 C5MET add C6 C5 C5A 118.000 3.000 C5MET add C5 C5A H5A2 109.470 3.000 C5MET add C5 C5A H5A3 109.470 3.000 C5MET add H5A2 C5A H5A1 109.470 3.000 C5MET add H5A3 C5A H5A1 109.470 3.000 C5MET add H5A3 C5A H5A2 109.470 3.000 # data_mod_N7MET # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge N7MET change N7 . . NR5 0.000 N7MET add . C7 C CH3 0.000 N7MET add . H71 H HCH 0.000 N7MET add . H72 H HGH 0.000 N7MET add . H73 H HCH 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type N7MET add C7 N7 H73 . N7MET add H71 C7 . . N7MET add H72 C7 . . N7MET add H73 C7 . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd N7MET add C7 N7 coval 1.465 0.020 N7MET add C7 H71 coval 0.960 0.020 N7MET add C7 H72 coval 0.960 0.020 N7MET add C7 H73 coval 0.960 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd N7MET add C5 N7 C7 126.000 3.000 N7MET add C8 N7 C7 126.000 3.000 N7MET add N7 C7 H71 109.470 3.000 N7MET add N7 C7 H72 109.470 3.000 N7MET add N7 C7 H73 109.470 3.000 N7MET add H72 C7 H71 109.470 3.000 N7MET add H73 C7 H71 109.470 3.000 N7MET add H73 C7 H72 109.470 3.000 # data_mod_p5*END # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge p5*END add . O3T O OP -0.340 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type p5*END change P O3T O5* . p5*END add O3T n/a P START loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd p5*END add O3T P coval 1.600 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd p5*END add O3T P O1P 109.470 3.000 p5*END add O3T P O2P 109.470 3.000 p5*END add O3T P O5* 109.470 3.000 # data_mod_p3*END # # data_mod_RNA-O2* # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge RNA-O2* delete O2* . . . 0.000 RNA-O2* delete HO2* . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type RNA-O2* delete O2* . . . RNA-O2* delete HO2* . . . # # data_mod_DEL-OXT # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge DEL-OXT delete OXT . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type DEL-OXT delete OXT . . . # # data_mod_XYS-O1 # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge XYS-O1 delete O1 . . . 0.000 XYS-O1 delete HO1 . . . 0.000 loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type XYS-O1 delete O1 . . . XYS-O1 delete HO1 . . . # data_mod_B2C # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge B2C change C B B B . B2C change O O1 O O . B2C add . O2 O O . loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type B2C change B CA . END B2C change CA N B . B2C change O1 B . . B2C add O2 B . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd B2C change B CA coval 1.560 0.020 B2C change B O1 coval 1.480 0.020 B2C add B O2 coval 1.480 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd B2C add O1 B O2 112.000 3.000 B2C change CA B O1 126.000 3.000 B2C add CA B O2 126.000 3.000 loop_ _chem_mod_tor.mod_id _chem_mod_tor.function _chem_mod_tor.id _chem_mod_tor.atom_id_1 _chem_mod_tor.atom_id_2 _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd _chem_mod_tor.new_period B2C add hhb N CA B O2 0.00 30.0 3 loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign B2C change CA N CB B negativ # data_mod_B2C_D # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge B2C_D change C B B B . B2C_D change O O1 O O . B2C_D add . O2 O O . loop_ _chem_mod_tree.mod_id _chem_mod_tree.function _chem_mod_tree.atom_id _chem_mod_tree.atom_back _chem_mod_tree.atom_forward _chem_mod_tree.connect_type B2C_D change B CA . END B2C_D change CA N B . B2C_D change O1 B . . B2C_D add O2 B . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd B2C_D change B CA coval 1.560 0.020 B2C_D change B O1 coval 1.480 0.020 B2C_D add B O2 coval 1.480 0.020 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd B2C_D add O1 B O2 112.000 3.000 B2C_D change CA B O1 126.000 3.000 B2C_D add CA B O2 126.000 3.000 loop_ _chem_mod_tor.mod_id _chem_mod_tor.function _chem_mod_tor.id _chem_mod_tor.atom_id_1 _chem_mod_tor.atom_id_2 _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd _chem_mod_tor.new_period B2C_D add hhb N CA B O2 0.00 30.0 3 loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign B2C_D change CA N CB B positiv # data_mod_RENAME # data_mod_TERMINUS # # data_mod_SUG-b-L # loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign SUG-b-L change C5 C4 O5 C6 negativ SUG-b-L change C1 O1 O5 C2 positiv # # data_mod_SUG-a-D # loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign SUG-a-D change C5 C4 O5 C6 positiv SUG-a-D change C1 O1 O5 C2 negativ # data_mod_SUG-b-D # loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign SUG-b-D change C5 C4 O5 C6 positiv SUG-b-D change C1 O1 O5 C2 positiv # # data_mod_SUG-a-L # loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign SUG-a-L change C5 C4 O5 C6 negativ SUG-a-L change C1 O1 O5 C2 negativ # data_mod_PEPT-D # loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign PEPT-D change CA N CB C positiv # # # ------------------------------------------------------ # # --- DESCRIPTION OF LINKS --- # data_link_SS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd SS 1 SG 2 SG disulf 2.031 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd SS 1 CB 1 SG 2 SG 110.000 3.000 SS 1 SG 2 SG 2 CB 110.000 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period SS ss 1 CB 1 SG 2 SG 2 CB 90.00 10.0 2 # data_link_MPR-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd MPR-CYS 1 SG 2 SG disulf 2.031 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd MPR-CYS 1 CB 1 SG 2 SG 110.000 3.000 MPR-CYS 1 SG 2 SG 2 CB 110.000 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period MPR-CYS ss 1 CB 1 SG 2 SG 2 CB 90.00 10.0 2 # data_link_CYS-MPR # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd CYS-MPR 1 SG 2 SG disulf 2.031 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd CYS-MPR 1 CB 1 SG 2 SG 110.000 3.000 CYS-MPR 1 SG 2 SG 2 CB 110.000 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period CYS-MPR ss 1 CB 1 SG 2 SG 2 CB 90.00 10.0 2 # data_link_TRANS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd TRANS 1 C 2 N coval 1.329 0.014 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd TRANS 1 O 1 C 2 N 123.000 1.600 TRANS 1 CA 1 C 2 N 116.200 2.000 TRANS 1 C 2 N 2 H 124.300 3.000 TRANS 1 C 2 N 2 CA 121.700 1.800 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period TRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2 TRANS omega 1 CA 1 C 2 N 2 CA 180.00 10.0 1 #TRANS peph 1 CA 1 C 2 N 2 H 0.00 10.0 0 TRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3 loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd TRANS plane1 1 CA 0.02 TRANS plane1 1 C 0.02 TRANS plane1 1 O 0.02 TRANS plane1 2 N 0.02 TRANS plane2 1 C 0.02 TRANS plane2 2 N 0.02 TRANS plane2 2 CA 0.02 TRANS plane2 2 H 0.02 # data_link_PTRANS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd PTRANS 1 C 2 N coval 1.329 0.014 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd PTRANS 1 O 1 C 2 N 123.000 1.600 PTRANS 1 CA 1 C 2 N 116.200 2.000 PTRANS 1 C 2 N 2 CD 124.300 3.000 PTRANS 1 C 2 N 2 CA 121.700 1.800 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period PTRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2 PTRANS omega 1 CA 1 C 2 N 2 CA 180.00 10.0 1 #PTRANS peph 1 CA 1 C 2 N 2 CD 0.00 10.0 0 PTRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3 loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd PTRANS plane1 1 CA 0.02 PTRANS plane1 1 C 0.02 PTRANS plane1 1 O 0.02 PTRANS plane1 2 N 0.02 PTRANS plane2 1 C 0.05 PTRANS plane2 2 N 0.05 PTRANS plane2 2 CA 0.05 PTRANS plane2 2 CD 0.05 # data_link_gap # # data_link_PCIS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd PCIS 1 C 2 N coval 1.329 0.014 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd PCIS 1 O 1 C 2 N 123.000 1.600 PCIS 1 CA 1 C 2 N 116.200 2.000 PCIS 1 C 2 N 2 CD 124.300 3.000 PCIS 1 C 2 N 2 CA 121.700 1.800 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period PCIS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2 PCIS omega 1 CA 1 C 2 N 2 CA 0.00 10.0 0 #PCIS peph 1 CA 1 C 2 N 2 CD 180.00 10.0 0 PCIS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3 loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd PCIS plane1 1 CA 0.02 PCIS plane1 1 C 0.02 PCIS plane1 1 O 0.02 PCIS plane1 2 N 0.02 PCIS plane2 1 C 0.05 PCIS plane2 2 N 0.05 PCIS plane2 2 CA 0.05 PCIS plane2 2 CD 0.05 # data_link_CIS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd CIS 1 C 2 N coval 1.329 0.014 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd CIS 1 O 1 C 2 N 123.000 1.600 CIS 1 CA 1 C 2 N 116.200 2.000 CIS 1 C 2 N 2 H 124.300 3.000 CIS 1 C 2 N 2 CA 121.700 1.800 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period CIS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2 CIS omega 1 CA 1 C 2 N 2 CA 0.00 10.0 0 #CIS peph 1 CA 1 C 2 N 2 H 180.00 10.0 0 CIS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3 loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd CIS plane1 1 CA 0.02 CIS plane1 1 C 0.02 CIS plane1 1 O 0.02 CIS plane1 2 N 0.02 CIS plane2 1 C 0.02 CIS plane2 2 N 0.02 CIS plane2 2 CA 0.02 CIS plane2 2 H 0.02 # data_link_p # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd p 1 O3* 2 P coval 1.600 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd p 1 O3* 2 P 2 O5* 103.000 3.000 p 1 O3* 2 P 2 O1P 108.000 3.000 p 1 O3* 2 P 2 O2P 108.000 3.000 p 1 C3* 1 O3* 2 P 120.000 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period p epsil 1 C4* 1 C3* 1 O3* 2 P 190.00 30.0 3 p zeta 1 C3* 1 O3* 2 P 2 O5* 260.00 30.0 3 p alpha 1 O3* 2 P 2 O5* 2 C5* 300.00 20.0 3 # data_link_LINK_CNp # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd LINK_CNp 1 C 2 N coval 1.329 0.020 # data_link_LINK_CpN # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd LINK_CpN 1 C 2 N coval 1.329 0.020 # data_link_LINK_C-N # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd LINK_C-N 1 C 2 N coval 1.329 0.020 # data_link_FOR_C-N # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd FOR_C-N 1 C 2 N coval 1.329 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd FOR_C-N 1 C 2 N 2 CA 121.700 3.000 FOR_C-N 1 O 1 C 2 N 123.000 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period FOR_C-N var1 1 O 1 C 2 N 2 CA 0.00 30.0 2 # data_link_FOR_C-C # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd FOR_C-C 1 C 2 C coval 1.521 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd FOR_C-C 1 C 2 C 2 O 124.100 3.000 FOR_C-C 1 O 1 C 2 C 129.100 3.000 # data_link_FOR-LYZ # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd FOR-LYZ 1 NZ 2 C coval 1.329 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd FOR-LYZ 2 C 1 NE 1 CE 111.000 3.000 FOR-LYZ 2 O 2 C 1 NZ 120.000 3.000 FOR-LYZ 2 OXT 2 C 1 NZ 120.000 3.000 FOR-LYZ 2 O 2 C 2 OXT 120.000 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period FOR-LYZ var1 1 CD 1 CE 1 NZ 2 C 180.00 30.0 2 FOR-LYZ var2 1 CE 1 NZ 2 C 2 OXT 180.00 30.0 2 # data_link_ACE_C-N # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ACE_C-N 1 C 2 N coval 1.329 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd ACE_C-N 1 C 2 N 2 CA 121.700 3.000 ACE_C-N 1 O 1 C 2 N 123.000 3.000 ACE_C-N 1 CH3 1 C 2 N 116.200 3.000 ACE_C-N 1 C 2 N 2 H 124.300 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period ACE_C-N omega 1 CH3 1 C 2 N 2 CA 180.00 10.0 2 ACE_C-N phi 1 C 2 N 2 CA 2 C 60.00 20.0 3 # data_link_AHT-ALA # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd AHT-ALA 1 N2 2 CB coval 1.521 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd AHT-ALA 1 N2 2 CB 2 CA 109.900 3.000 AHT-ALA 1 C2 1 N2 2 CB 119.300 3.000 # data_link_DFO-NME # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd DFO-NME 1 C 2 N coval 1.308 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd DFO-NME 1 C 2 N 2 CH3 123.400 3.000 DFO-NME 1 O 1 C 2 N 126.200 3.000 # data_link_DFO_C-N # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd DFO_C-N 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd DFO_C-N 1 O 1 C 2 N 129.100 3.000 DFO_C-N 1 C 2 N 2 CA 119.300 3.000 # data_link_DFO_N-C # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd DFO_N-C 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd DFO_N-C 1 O 1 C 2 N 129.100 3.000 DFO_N-C 1 C 2 N 2 CA 119.300 3.000 # data_link_STA-NME # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd STA-NME 1 C 2 N coval 1.308 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd STA-NME 1 C 2 N 2 CH3 123.400 3.000 STA-NME 1 O 1 C 2 N 126.200 3.000 # data_link_STA_C-N # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd STA_C-N 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd STA_C-N 1 O 1 C 2 N 129.100 3.000 STA_C-N 1 C 2 N 2 CA 119.300 3.000 # data_link_STA_N-C # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd STA_N-C 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd STA_N-C 1 O 1 C 2 N 129.100 3.000 STA_N-C 1 C 2 N 2 CA 119.300 3.000 # data_link_STA_DFO # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd STA_DFO 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd STA_DFO 1 O 1 C 2 N 129.100 3.000 STA_DFO 1 C 2 N 2 CA 119.300 3.000 # data_link_DFO_DFO # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd DFO_DFO 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd DFO_DFO 1 O 1 C 2 N 129.100 3.000 DFO_DFO 1 C 2 N 2 CA 119.300 3.000 # data_link_STA_STA # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd STA_STA 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd STA_STA 1 O 1 C 2 N 129.100 3.000 STA_STA 1 C 2 N 2 CA 119.300 3.000 # data_link_DFO_STA # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd DFO_STA 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd DFO_STA 1 O 1 C 2 N 129.100 3.000 DFO_STA 1 C 2 N 2 CA 119.300 3.000 # data_link_IVA_C-N # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd IVA_C-N 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd IVA_C-N 1 O 1 C 2 N 129.100 3.000 IVA_C-N 1 C 2 N 2 CA 119.300 3.000 # data_link_BOC_C-N # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd BOC_C-N 1 C 2 N coval 1.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd BOC_C-N 1 O1 1 C 2 N 129.100 3.000 BOC_C-N 1 C 2 N 2 CA 119.300 3.000 # data_link_NME_N-C # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd NME_N-C 1 C 2 N coval 1.308 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd NME_N-C 1 O 1 C 2 N 126.200 3.000 NME_N-C 1 C 2 N 2 CH3 123.400 3.000 # data_link_BETA1-2 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd BETA1-2 1 O2 2 C1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd BETA1-2 1 C2 1 O2 2 C1 108.700 3.000 BETA1-2 1 O2 2 C1 2 O5 112.300 3.000 BETA1-2 1 O2 2 C1 2 C2 109.470 3.000 BETA1-2 1 O2 2 C1 2 H1 109.470 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period BETA1-2 BETA_1 1 O2 2 C1 2 C2 2 C3 0.00 20.0 1 BETA1-2 BETA_2 1 C2 1 O2 2 C1 2 C2 0.00 20.0 1 BETA1-2 BETA_3 1 C1 1 C2 1 O2 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign BETA1-2 2 C1 1 O2 2 O5 2 C2 positiv # beta # data_link_BETA1-3 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd BETA1-3 1 O3 2 C1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd BETA1-3 1 C3 1 O3 2 C1 108.700 3.000 BETA1-3 1 O3 2 C1 2 O5 112.300 3.000 BETA1-3 1 O3 2 C1 2 C2 109.470 3.000 BETA1-3 1 O3 2 C1 2 H1 109.470 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period BETA1-3 BETA_1 1 O3 2 C1 2 C2 2 C3 0.00 20.0 1 BETA1-3 BETA_2 1 C3 1 O3 2 C1 2 C2 0.00 20.0 1 BETA1-3 BETA_3 1 C2 1 C3 1 O3 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign BETA1-3 2 C1 1 O3 2 O5 2 C2 positiv # beta # data_link_BETA2-3 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd BETA2-3 1 C2 2 O3 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd BETA2-3 1 C2 2 O3 2 C1 108.700 3.000 BETA2-3 1 C1 1 C2 2 O3 112.300 3.000 # data_link_BETA1-4 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd BETA1-4 1 O4 2 C1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd BETA1-4 1 C4 1 O4 2 C1 108.700 3.000 BETA1-4 1 O4 2 C1 2 O5 112.300 3.000 BETA1-4 1 O4 2 C1 2 C2 109.470 3.000 BETA1-4 1 O4 2 C1 2 H1 109.470 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period BETA1-4 BETA_1 1 O4 2 C1 2 C2 2 C3 0.00 20.0 1 BETA1-4 BETA_2 1 C4 1 O4 2 C1 2 C2 0.00 20.0 1 BETA1-4 BETA_3 1 C3 1 C4 1 O4 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign BETA1-4 2 C1 1 O4 2 O5 2 C2 positiv # beta # data_link_BETA1-6 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd BETA1-6 1 O6 2 C1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd BETA1-6 1 C6 1 O6 2 C1 108.700 3.000 BETA1-6 1 O6 2 C1 2 O5 112.300 3.000 BETA1-6 1 O6 2 C1 2 C2 109.470 3.000 BETA1-6 1 O6 2 C1 2 H1 109.470 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period BETA1-6 BETA_1 1 O6 2 C1 2 C2 2 C3 0.00 20.0 1 BETA1-6 BETA_2 1 C6 1 O6 2 C1 2 C2 0.00 20.0 1 BETA1-6 BETA_3 1 C5 1 C6 1 O6 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign BETA1-6 2 C1 1 O6 2 O5 2 C2 positiv # beta # data_link_ALPHA1-2 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ALPHA1-2 1 O2 2 C1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd ALPHA1-2 1 C2 1 O2 2 C1 108.700 3.000 ALPHA1-2 1 O2 2 C1 2 O5 112.300 3.000 ALPHA1-2 1 O2 2 C1 2 C2 109.470 3.000 ALPHA1-2 1 O2 2 C1 2 H1 109.470 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period ALPHA1-2 ALPHA_1 1 O2 2 C1 2 C2 2 C3 0.00 20.0 1 ALPHA1-2 ALPHA_2 1 C2 1 O2 2 C1 2 C2 0.00 20.0 1 ALPHA1-2 ALPHA_3 1 C1 1 C2 1 O2 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign ALPHA1-2 2 C1 1 O2 2 O5 2 C2 negativ # alpha # data_link_ALPHA1-3 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ALPHA1-3 1 O3 2 C1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd ALPHA1-3 1 C3 1 O3 2 C1 108.700 3.000 ALPHA1-3 1 O3 2 C1 2 O5 112.300 3.000 ALPHA1-3 1 O3 2 C1 2 C2 109.470 3.000 ALPHA1-3 1 O3 2 C1 2 H1 109.470 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period ALPHA1-3 ALPHA_1 1 O3 2 C1 2 C2 2 C3 0.00 20.0 1 ALPHA1-3 ALPHA_2 1 C3 1 O3 2 C1 2 C2 0.00 20.0 1 ALPHA1-3 ALPHA_3 1 C2 1 C3 1 O3 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign ALPHA1-3 2 C1 1 O3 2 O5 2 C2 negativ # alpha # data_link_ALPHA2-3 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ALPHA2-3 1 C2 2 O3 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd ALPHA2-3 1 C2 2 O3 2 C1 108.700 3.000 ALPHA2-3 1 C1 1 C2 2 O3 112.300 3.000 # data_link_ALPHA1-4 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ALPHA1-4 1 O4 2 C1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd ALPHA1-4 1 C4 1 O4 2 C1 108.700 3.000 ALPHA1-4 1 O4 2 C1 2 O5 112.300 3.000 ALPHA1-4 1 O4 2 C1 2 C2 109.470 3.000 ALPHA1-4 1 O4 2 C1 2 H1 109.470 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period ALPHA1-4 ALPHA_1 1 O4 2 C1 2 C2 2 C3 0.00 20.0 1 ALPHA1-4 ALPHA_2 1 C4 1 O4 2 C1 2 C2 0.00 20.0 1 ALPHA1-4 ALPHA_3 1 C3 1 C4 1 O4 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign ALPHA1-4 2 C1 1 O4 2 O5 2 C2 negativ # alpha # data_link_ALPHA1-6 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ALPHA1-6 1 O6 2 C1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd ALPHA1-6 1 C6 1 O6 2 C1 108.700 3.000 ALPHA1-6 1 O6 2 C1 2 O5 112.300 3.000 ALPHA1-6 1 O6 2 C1 2 C2 109.470 3.000 ALPHA1-6 1 O6 2 C1 2 H1 109.470 3.000 loop_ _chem_link_tor.link_id _chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period ALPHA1-6 ALPHA_1 1 O6 2 C1 2 C2 2 C3 0.00 20.0 1 ALPHA1-6 ALPHA_2 1 C6 1 O6 2 C1 2 C2 0.00 20.0 1 ALPHA1-6 ALPHA_3 1 C5 1 C6 1 O6 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign ALPHA1-6 2 C1 1 O6 2 O5 2 C2 negativ # alpha # data_link_MAN-SER # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd MAN-SER 1 C1 2 OG coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd MAN-SER 1 C1 2 OG 2 CB 108.700 3.000 MAN-SER 1 O5 1 C1 2 OG 112.300 3.000 # data_link_NAG-SER # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd NAG-SER 1 C1 2 OG coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd NAG-SER 1 C1 2 OG 2 CB 108.700 3.000 NAG-SER 1 O5 1 C1 2 OG 112.300 3.000 # data_link_NAG-THR # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd NAG-THR 1 C1 2 OG1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd NAG-THR 1 C1 2 OG1 2 CB 108.700 3.000 NAG-THR 1 O5 1 C1 2 OG1 112.300 3.000 # data_link_MAN-THR # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd MAN-THR 1 C1 2 OG1 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd MAN-THR 1 C1 2 OG1 2 CB 108.700 3.000 MAN-THR 1 O5 1 C1 2 OG1 112.300 3.000 # data_link_NAG-ASN # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd NAG-ASN 1 C1 2 ND2 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd NAG-ASN 1 C1 2 ND2 2 CG 108.700 3.000 NAG-ASN 1 O5 1 C1 2 ND2 112.300 3.000 # data_link_MAN-ASN # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd MAN-ASN 1 C1 2 ND2 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd MAN-ASN 1 C1 2 ND2 2 CG 108.700 3.000 MAN-ASN 1 O5 1 C1 2 ND2 112.300 3.000 # data_link_XYS-THR # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd XYS-THR 1 C1 2 OG1 coval 1.413 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd XYS-THR 1 C1 2 OG1 2 CB 118.700 3.000 XYS-THR 1 O5 1 C1 2 OG1 116.100 3.000 # data_link_XYS-SER # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd XYS-SER 1 C1 2 OG coval 1.413 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd XYS-SER 1 C1 2 OG 2 CB 118.700 3.000 XYS-SER 1 O5 1 C1 2 OG 116.100 3.000 # data_link_XYS-ASN # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd XYS-ASN 1 C1 2 ND2 coval 1.439 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd XYS-ASN 1 C1 2 ND2 2 CG 118.700 3.000 XYS-ASN 1 O5 1 C1 2 ND2 116.100 3.000 # data_link_ZN-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ZN-CYS 1 ZN 2 SG coval 2.340 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000 # data_link_FE-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd FE-CYS 1 FE 2 SG coval 2.260 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd FE-CYS 1 FE 2 SG 2 CB 109.470 3.000 # data_link_SFN-TYR # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd SFN-TYR 1 S 2 OH coval 1.669 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd SFN-TYR 1 S 2 OH 2 CZ 120.000 3.000 SFN-TYR 1 O3 1 S 2 OH 98.000 3.000 # data_link_CH2-N2 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd CH2-N2 1 CH2 2 N2 coval 1.465 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd CH2-N2 1 CH2 2 N2 2 C2 111.100 3.000 # # data_link_CH3-N1 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd CH3-N1 1 C 2 N1 coval 1.465 0.020 # data_link_CH3-O2* # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd CH3-O2* 1 C 2 O2* coval 1.410 0.020 # data_link_MG-O1P # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd MG-O1P 1 MG 2 O1P coval 2.180 0.020 # data_link_BR-C5 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd BR-C5 1 BR 2 C5 coval 1.820 0.020 # data_link_MG-O2P # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd MG-O2P 1 MG 2 O2P coval 2.180 0.020 # data_link_DM1-CH2 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd DM1-CH2 1 N3* 2 CH2 coval 1.529 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd DM1-CH2 1 C3* 1 N3* 2 CH2 117.400 3.000 # data_link_ILG_CD-N # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ILG_CD-N 1 CD 2 N . 1.330 0.020 # data_link_ILG_CD-p # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ILG_CD-p 1 CD 2 N . 1.330 0.020 # data_link_symmetry # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd symmetry . . . . . . . # ------------------------------------------------------