## fullatom protein oop_pre patch, used for oligooxopiperazine (OOPs) 
## By Kevin Drew, May 2011, kdrew@nyu.edu

NAME oop_pre 
TYPES OOP_PRE

## general requirements for this patch

BEGIN_SELECTOR
PROPERTY PROTEIN

# variants and residues which do not have primary backbone amines
NOT VARIANT_TYPE N_ACETYLATION 
NOT VARIANT_TYPE ACTYLATED_NTERMINUS 
NOT VARIANT_TYPE OOP_PRE
NOT VARIANT_TYPE OOP_POST
NOT AA PRO 
NOT NAME3 DPR 
NOT NAME3 HPR 
NOT NAME3 B19 
NOT NAME3 C89 
NOT NAME3 B59 

# variants which cannot be the first residue of an OOP 
# because they are the last residue of a chain
NOT VARIANT_TYPE UPPER_TERMINUS
NOT VARIANT_TYPE CUTPOINT_UPPER 

END_SELECTOR

BEGIN_CASE ### n-terminal ##########################################

BEGIN_SELECTOR
VARIANT_TYPE LOWER_TERMINUS
END_SELECTOR

ADD_ATOM	CYP	CH2	CT2	-0.18	
ADD_ATOM	VZP	VIRT	VIRT	0.00	
ADD_ATOM	1HYP	Hapo	HA  0.09	
ADD_ATOM	2HYP	Hapo	HA  0.09	

ADD_BOND	CYP	N		
ADD_BOND	CYP	VZP
ADD_BOND	CYP	1HYP	
ADD_BOND	CYP	2HYP	

SET_ICOOR CYP    41.5503	66.516	1.45	N	CA	C  
SET_ICOOR 1HYP   57.5499	69.981	0.97	CYP	N	CA
SET_ICOOR 2HYP  119.1912	70.066 	0.99	CYP	N	1HYP 
SET_ICOOR VZP  -120.7064	70.554	1.50	CYP	N	1HYP 

DELETE_ATOM 3H
DELETE_ATOM 2H
DELETE_ATOM 1H

ADD_ATOM  H   HNbb H    0.31
ADD_BOND  N   H

SET_ICOOR H -84.35 66.6 1.02 N CA C

SET_BACKBONE_HEAVYATOM CYP
SET_BACKBONE_HEAVYATOM VZP
ADD_CONNECT CYP ICOOR  41.5503   66.5161   1.4592  N  CA  C  


END_CASE

BEGIN_CASE ### THE GENERAL CASE ##########################################

ADD_ATOM  CYP  CH2    CT2    -0.18 
ADD_ATOM VZP  VIRT 	 VIRT  	0.00 
ADD_ATOM 1HYP  Hapo   HA     0.09 
ADD_ATOM 2HYP  Hapo   HA     0.09 
ADD_BOND  N   CYP    
ADD_BOND  CYP  VZP
ADD_BOND  CYP  1HYP 
ADD_BOND  CYP  2HYP 

SET_ICOOR CYP   178.0 66.5161   1.4592  N  CA  LOWER  
SET_ICOOR 1HYP  57.55  69.9817  0.9764  CYP   N  CA
SET_ICOOR 2HYP  119.1912	70.066 0.9903  CYP   N  1HYP 
SET_ICOOR VZP  -120.7064	70.5547		1.50	CYP N 1HYP

DELETE_ATOM H

SET_BACKBONE_HEAVYATOM CYP
SET_BACKBONE_HEAVYATOM VZP
ADD_CONNECT CYP ICOOR  180.0  60.0   1.467  CYP	N  CA  

END_CASE