Following is a list of standard links and modifications, distributed with REFMAC
# # --- 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 . .