Skip to content

add TRP-MAN link and modifications #67

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
keitaroyam merged 2 commits into from
Feb 11, 2026
Merged

add TRP-MAN link and modifications #67

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e546bbc
add TRP-MAN link and modifications
louholland Jan 30, 2026
a99c8f1
remove unnecessary torsion angle mods of TRPm1
keitaroyam Feb 7, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
209 changes: 209 additions & 0 deletions links_and_mods.cif
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,7 @@ pept-LYS . DEL-OXT pept LYS LYSmod5 peptide pept-LYS
pept-MDO . DEL-OXT peptide MDO MDOmod2 NON-POLYMER pept-MDO
MS6-pept MS6 MS6mod1 NON-POLYMER . MS6mod2 peptide MS6-pept
pept-MS6 . DEL-OXT peptide MS6 MS6delNH NON-POLYMER pept-MS6
TRP-MAN TRP TRPm1 peptide MAN MANm1 pyranose TRP-MAN

data_mod_list
loop_
Expand Down Expand Up @@ -254,6 +255,8 @@ ASPprot "Protonation of ASP" ASP peptide
GLUprot "Protonation of GLU" GLU peptide
HISprot1 HISTIDINE HIS peptide
HISprot2 HISTIDINE HIS peptide
TRPm1 TRYPTOPHAN TRP peptide
MANm1 'ALPHA-D-MANNOSE' MAN pyranose

data_link_DG9-SER
loop_
Expand Down Expand Up @@ -6001,6 +6004,82 @@ _chem_mod_atom.new_type_energy
_chem_mod_atom.new_partial_charge
CYS-SS delete HG . . . .000

data_link_TRP-MAN
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
TRP-MAN 1 CD1 2 C1 SINGLE 1.506 0.0104

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
TRP-MAN 1 CG 1 CD1 2 C1 127.900 3.00
TRP-MAN 1 NE1 1 CD1 2 C1 123.091 3.00
TRP-MAN 2 C2 2 C1 1 CD1 111.368 3.00
TRP-MAN 2 O5 2 C1 1 CD1 108.025 2.86
TRP-MAN 1 CD1 2 C1 2 H1 107.960 1.50

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
TRP-MAN sp2_sp3_1 1 CG 1 CD1 2 C1 2 C2 150.000 10.0 6
TRP-MAN const_22_1 1 CD2 1 CG 1 CD1 2 C1 180.000 0.0 1
TRP-MAN const_27_1 2 C1 1 CD1 1 NE1 1 CE2 180.000 0.0 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
TRP-MAN 2 C1 2 O5 1 CD1 2 C2 positive

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
TRP-MAN plan-2 1 CE2 0.020
TRP-MAN plan-2 1 CE3 0.020
TRP-MAN plan-2 1 CZ2 0.020
TRP-MAN plan-2 2 C1 0.020
TRP-MAN plan-2 1 CB 0.020
TRP-MAN plan-2 1 CG 0.020
TRP-MAN plan-2 1 CD1 0.020
TRP-MAN plan-2 1 CD2 0.020
TRP-MAN plan-2 1 HE1 0.020
TRP-MAN plan-2 1 NE1 0.020

data_mod_CYSmod1
loop_
_chem_mod_atom.mod_id
Expand Down Expand Up @@ -12451,3 +12530,133 @@ HISprot2 add plan-1 HD2 0.020
HISprot2 add plan-1 HE1 0.020
HISprot2 add plan-1 ND1 0.020
HISprot2 add plan-1 NE2 0.020

data_mod_TRPm1
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_charge
TRPm1 delete HD1 . H H 0
TRPm1 change CD1 . C CR5 0

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
_chem_mod_bond.new_value_dist_nucleus
_chem_mod_bond.new_value_dist_nucleus_esd
TRPm1 delete CD1 HD1 single . . . .
TRPm1 change CG CD2 single 1.433 0.0100 1.433 0.0100
TRPm1 change NE1 HE1 single 0.871 0.0100 1.013 0.0120

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
TRPm1 delete CG CD1 HD1 . .
TRPm1 delete NE1 CD1 HD1 . .
TRPm1 change CB CG CD2 125.104 2.39
TRPm1 change CD1 CG CD2 107.894 1.77

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
TRPm1 delete plan-2 CB 0.020
TRPm1 delete plan-2 CD1 0.020
TRPm1 delete plan-2 CD2 0.020
TRPm1 delete plan-2 CE2 0.020
TRPm1 delete plan-2 CE3 0.020
TRPm1 delete plan-2 CG 0.020
TRPm1 delete plan-2 CZ2 0.020
TRPm1 delete plan-2 HD1 0.020
TRPm1 delete plan-2 HE1 0.020
TRPm1 delete plan-2 NE1 0.020

data_mod_MANm1
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_charge
MANm1 delete O1 . O OH1 0
MANm1 delete HO1 . H H 0

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
_chem_mod_bond.new_value_dist_nucleus
_chem_mod_bond.new_value_dist_nucleus_esd
MANm1 delete C1 O1 single . . . .
MANm1 delete O1 HO1 single . . . .
MANm1 change C1 C2 single 1.530 0.0100 1.530 0.0100

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
MANm1 delete C2 C1 O1 . .
MANm1 delete O1 C1 O5 . .
MANm1 delete O1 C1 H1 . .
MANm1 delete C1 O1 HO1 . .
MANm1 change C2 C1 O5 110.891 3.00
MANm1 change C1 C2 C3 110.082 3.00
MANm1 change C1 C2 O2 108.927 3.00
MANm1 change C1 O5 C5 112.972 2.62

loop_
_chem_mod_tor.mod_id
_chem_mod_tor.function
_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.id
_chem_mod_tor.new_value_angle
_chem_mod_tor.new_value_angle_esd
_chem_mod_tor.new_period
MANm1 delete C2 C1 O1 HO1 . . . 3
MANm1 delete O5 C1 O1 HO1 . . . 3
MANm1 delete H1 C1 O1 HO1 . . . 3
MANm1 change C5 O5 C1 C2 var_ring_1 53.681667 3.0 1
MANm1 change O5 C1 C2 C3 var_ring_2 -48.384090 3.0 1
MANm1 change C1 C2 C3 C4 var_ring_3 50.224220 3.0 1
MANm1 change C2 C3 C4 C5 var_ring_4 -54.215084 3.0 1
MANm1 change C3 C4 C5 O5 var_ring_5 56.747200 3.0 1
MANm1 change C4 C5 O5 C1 var_ring_6 -58.120335 3.0 1

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
MANm1 delete C1 O5 O1 C2 .
Loading