# This is for adding an -NH2 group to C-terminus of protein/peptide (replaces -OH group)
# Added by who-knows-who, who-knows-when.
# Made to actually work on 11 October 2020, by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org).

NAME Cterm_amidation
TYPES CTERM_AMIDATION
#TYPES CTERM_AMIDATION UPPER_TERMINUS

## general requirements for this patch
BEGIN_SELECTOR
PROPERTY PROTEIN
NOT PROPERTY OLIGOUREA
NOT VARIANT_TYPE N_METHYLATION
NOT VARIANT_TYPE CTERM_AMIDATION
NOT VARIANT_TYPE CUTPOINT_UPPER
NOT PROPERTY PHOSPHONATE
END_SELECTOR

################################

# Apply to UPPER_TERMINUS_VARIANT types:
BEGIN_CASE
BEGIN_SELECTOR
VARIANT_TYPE UPPER_TERMINUS_VARIANT
END_SELECTOR

# If modified, no longer canonical.
DELETE_PROPERTY CANONICAL_AA
DELETE_PROPERTY CANONICAL_NUCLEIC

# Delete the OH at C-term and replace with the following stuff
DELETE_ATOM OXT

# add these atoms and bonds instead
ADD_ATOM  NT   NH2O  NH2  -0.62
ADD_ATOM 1HN    Hpol H    0.3
ADD_ATOM 2HN    Hpol H    0.3
ADD_BOND  C    NT
ADD_BOND  NT  1HN
ADD_BOND  NT  2HN

SET_BACKBONE_HEAVYATOM NT

# set internal coordinates for this functional group
SET_ICOOR	O	180.00000	60.00000	1.2		C  CA N
SET_ICOOR	NT	180.000031	63.799957	1.328686	C  CA O
SET_ICOOR	1HN	180.000000	58.299980	1.000000	NT C  CA
SET_ICOOR	2HN	-179.999878	60.850006	1.000000	NT C  1HN

# change normal atom types appropriately
SET_ATOM_TYPE O ONH2
SET_ATOM_TYPE C CNH2
SET_MM_ATOM_TYPE O O
SET_MM_ATOM_TYPE C CC
SET_ATOMIC_CHARGE C 0.55
SET_ATOMIC_CHARGE O -0.55

SET_POLYMER_CONNECT UPPER NONE

END_CASE # End apply to UPPER_TERMINUS_VARIANT types.

################################

# Apply to all other cases:
BEGIN_CASE

# If modified, no longer canonical.
DELETE_PROPERTY CANONICAL_AA
DELETE_PROPERTY CANONICAL_NUCLEIC

# add these atoms and bonds instead
ADD_ATOM  NT   NH2O  NH2  -0.62
ADD_ATOM 1HN    Hpol H    0.3
ADD_ATOM 2HN    Hpol H    0.3
ADD_BOND  C    NT
ADD_BOND  NT  1HN
ADD_BOND  NT  2HN

SET_BACKBONE_HEAVYATOM NT

# set internal coordinates for this functional group
SET_ICOOR	O	180.00000	60.00000	1.2		C  CA N
SET_ICOOR	NT	180.000031	63.799957	1.328686	C  CA O
SET_ICOOR	1HN	180.000000	58.299980	1.000000	NT C  CA
SET_ICOOR	2HN	-179.999878	60.850006	1.000000	NT C  1HN

# change normal atom types appropriately
SET_ATOM_TYPE O ONH2
SET_ATOM_TYPE C CNH2
SET_MM_ATOM_TYPE O O
SET_MM_ATOM_TYPE C CC
SET_ATOMIC_CHARGE C 0.55
SET_ATOMIC_CHARGE O -0.55

SET_POLYMER_CONNECT UPPER NONE

END_CASE # End apply to all other cases.

################################