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fix LYS-PLP link #69

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fix LYS-PLP link #69

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33 changes: 11 additions & 22 deletions links_and_mods.cif
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5256,7 +5256,7 @@ _chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
LYS-PLP 1 NZ 2 C4A DOUBLE 1.270 0.0174
LYS-PLP 1 NZ 2 C4A DOUBLE 1.269 0.0164

loop_
_chem_link_angle.link_id
Expand All @@ -5268,9 +5268,9 @@ _chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
LYS-PLP 1 CE 1 NZ 2 C4A 118.382 1.50
LYS-PLP 2 C4 2 C4A 1 NZ 122.438 1.52
LYS-PLP 1 NZ 2 C4A 2 H4A 118.729 1.50
LYS-PLP 1 CE 1 NZ 2 C4A 118.355 1.81
LYS-PLP 2 C4 2 C4A 1 NZ 122.167 2.29
LYS-PLP 1 NZ 2 C4A 2 H4A 118.654 1.50

loop_
_chem_link_tor.link_id
Expand All @@ -5286,7 +5286,9 @@ _chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
LYS-PLP sp2_sp2_1 2 C4 2 C4A 1 NZ 1 CE 180.000 5.00 2
LYS-PLP sp2_sp2_1 2 C4 2 C4A 1 NZ 1 CE 180.000 5.0 2
LYS-PLP sp2_sp2_2 2 C3 2 C4 2 C4A 1 NZ 180.000 5.0 2
LYS-PLP sp2_sp3_2 2 C4A 1 NZ 1 CE 1 CD 120.000 20.0 6

loop_
_chem_link_plane.link_id
Expand Down Expand Up @@ -11442,7 +11444,7 @@ _chem_mod_atom.new_charge
LYSmod4 delete HZ1 . H H 0
LYSmod4 delete HZ2 . H H 0
LYSmod4 delete HZ3 . H H 0
LYSmod4 change NZ . N N 0
LYSmod4 change NZ . N N20 0

loop_
_chem_mod_bond.mod_id
Expand All @@ -11457,7 +11459,7 @@ _chem_mod_bond.new_value_dist_nucleus_esd
LYSmod4 delete NZ HZ1 single . . . .
LYSmod4 delete NZ HZ2 single . . . .
LYSmod4 delete NZ HZ3 single . . . .
LYSmod4 change CE NZ single 1.462 0.0100 1.462 0.0100
LYSmod4 change CD CE single 1.524 0.0136 1.524 0.0136

loop_
_chem_mod_angle.mod_id
Expand All @@ -11483,7 +11485,7 @@ _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
LYSmod4 delete CD CE NZ HZ1 . .
LYSmod4 delete CD CE NZ HZ3 . .

data_mod_PLPmod1
loop_
Expand All @@ -11507,8 +11509,6 @@ _chem_mod_bond.new_value_dist_esd
_chem_mod_bond.new_value_dist_nucleus
_chem_mod_bond.new_value_dist_nucleus_esd
PLPmod1 delete C4A O4A double . . . .
PLPmod1 change C4 C4A single 1.459 0.0148 1.459 0.0148
PLPmod1 change C4A H4A single 0.975 0.010 1.082 0.013

loop_
_chem_mod_angle.mod_id
Expand All @@ -11520,7 +11520,7 @@ _chem_mod_angle.new_value_angle
_chem_mod_angle.new_value_angle_esd
PLPmod1 delete C4 C4A O4A . .
PLPmod1 delete O4A C4A H4A . .
PLPmod1 change C4 C4A H4A 118.833 1.50
PLPmod1 change C4 C4A H4A 119.178 1.50

loop_
_chem_mod_tor.mod_id
Expand All @@ -11543,17 +11543,6 @@ PLPmod1 delete plan-2 C4 0.020
PLPmod1 delete plan-2 C4A 0.020
PLPmod1 delete plan-2 H4A 0.020
PLPmod1 delete plan-2 O4A 0.020
PLPmod1 delete plan-1 C2 0.020
PLPmod1 delete plan-1 C2A 0.020
PLPmod1 delete plan-1 C3 0.020
PLPmod1 delete plan-1 C4 0.020
PLPmod1 delete plan-1 C4A 0.020
PLPmod1 delete plan-1 C5 0.020
PLPmod1 delete plan-1 C5A 0.020
PLPmod1 delete plan-1 C6 0.020
PLPmod1 delete plan-1 H6 0.020
PLPmod1 delete plan-1 N1 0.020
PLPmod1 delete plan-1 O3 0.020

data_mod_TRPmod1
loop_
Expand Down
33 changes: 11 additions & 22 deletions list/mon_lib_list.cif
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41597,7 +41597,7 @@ _chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
LYS-PLP 1 NZ 2 C4A DOUBLE 1.270 0.0174
LYS-PLP 1 NZ 2 C4A DOUBLE 1.269 0.0164

loop_
_chem_link_angle.link_id
Expand All @@ -41609,9 +41609,9 @@ _chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
LYS-PLP 1 CE 1 NZ 2 C4A 118.382 1.50
LYS-PLP 2 C4 2 C4A 1 NZ 122.438 1.52
LYS-PLP 1 NZ 2 C4A 2 H4A 118.729 1.50
LYS-PLP 1 CE 1 NZ 2 C4A 118.355 1.81
LYS-PLP 2 C4 2 C4A 1 NZ 122.167 2.29
LYS-PLP 1 NZ 2 C4A 2 H4A 118.654 1.50

loop_
_chem_link_tor.link_id
Expand All @@ -41627,7 +41627,9 @@ _chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
LYS-PLP sp2_sp2_1 2 C4 2 C4A 1 NZ 1 CE 180.000 5.00 2
LYS-PLP sp2_sp2_1 2 C4 2 C4A 1 NZ 1 CE 180.000 5.0 2
LYS-PLP sp2_sp2_2 2 C3 2 C4 2 C4A 1 NZ 180.000 5.0 2
LYS-PLP sp2_sp3_2 2 C4A 1 NZ 1 CE 1 CD 120.000 20.0 6

loop_
_chem_link_plane.link_id
Expand Down Expand Up @@ -47783,7 +47785,7 @@ _chem_mod_atom.new_charge
LYSmod4 delete HZ1 . H H 0
LYSmod4 delete HZ2 . H H 0
LYSmod4 delete HZ3 . H H 0
LYSmod4 change NZ . N N 0
LYSmod4 change NZ . N N20 0

loop_
_chem_mod_bond.mod_id
Expand All @@ -47798,7 +47800,7 @@ _chem_mod_bond.new_value_dist_nucleus_esd
LYSmod4 delete NZ HZ1 single . . . .
LYSmod4 delete NZ HZ2 single . . . .
LYSmod4 delete NZ HZ3 single . . . .
LYSmod4 change CE NZ single 1.462 0.0100 1.462 0.0100
LYSmod4 change CD CE single 1.524 0.0136 1.524 0.0136

loop_
_chem_mod_angle.mod_id
Expand All @@ -47824,7 +47826,7 @@ _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
LYSmod4 delete CD CE NZ HZ1 . .
LYSmod4 delete CD CE NZ HZ3 . .

data_mod_PLPmod1
loop_
Expand All @@ -47848,8 +47850,6 @@ _chem_mod_bond.new_value_dist_esd
_chem_mod_bond.new_value_dist_nucleus
_chem_mod_bond.new_value_dist_nucleus_esd
PLPmod1 delete C4A O4A double . . . .
PLPmod1 change C4 C4A single 1.459 0.0148 1.459 0.0148
PLPmod1 change C4A H4A single 0.975 0.010 1.082 0.013

loop_
_chem_mod_angle.mod_id
Expand All @@ -47861,7 +47861,7 @@ _chem_mod_angle.new_value_angle
_chem_mod_angle.new_value_angle_esd
PLPmod1 delete C4 C4A O4A . .
PLPmod1 delete O4A C4A H4A . .
PLPmod1 change C4 C4A H4A 118.833 1.50
PLPmod1 change C4 C4A H4A 119.178 1.50

loop_
_chem_mod_tor.mod_id
Expand All @@ -47884,17 +47884,6 @@ PLPmod1 delete plan-2 C4 0.020
PLPmod1 delete plan-2 C4A 0.020
PLPmod1 delete plan-2 H4A 0.020
PLPmod1 delete plan-2 O4A 0.020
PLPmod1 delete plan-1 C2 0.020
PLPmod1 delete plan-1 C2A 0.020
PLPmod1 delete plan-1 C3 0.020
PLPmod1 delete plan-1 C4 0.020
PLPmod1 delete plan-1 C4A 0.020
PLPmod1 delete plan-1 C5 0.020
PLPmod1 delete plan-1 C5A 0.020
PLPmod1 delete plan-1 C6 0.020
PLPmod1 delete plan-1 H6 0.020
PLPmod1 delete plan-1 N1 0.020
PLPmod1 delete plan-1 O3 0.020

data_mod_TRPmod1
loop_
Expand Down
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