# In this file, comments starting with # are permitted, but only at the begining of a line.
# Order of listing matters: earlier listings take precedence over later ones.
# By convention, all measures that span two residues are from i-1 to i.
#
# 3 May 2007 by Ian W. Davis

# 1. RNA
# 1.1 RNA bond lengths
# 1.1.1 RNA backbone bond lengths

            distance    P--O1P      _P__, _O1P                      ideal 1.485 0.017
            distance    P--O2P      _P__, _O2P                      ideal 1.485 0.017
            distance    P--O5'      _P__, _O5*                      ideal 1.593 0.010
            distance    P--O3'      _P__, i-1 _O3*                  ideal 1.607 0.012
            distance    O5'--C5'    _O5*, _C5*                      ideal 1.440 0.016
            
# 1.1.2 RNA sugar bond lengths

            distance    C5'--C4'    _C5*, _C4*                      ideal 1.510 0.013
            distance    C4'--C3'    _C4*, _C3*                      ideal 1.524 0.011
            distance    C3'--C2'    _C3*, _C2*                      ideal 1.525 0.011
            distance    C2'--C1'    _C2*, _C1*                      ideal 1.528 0.010
            distance    O4'--C1'    _O4*, _C1*                      ideal 1.414 0.012
            distance    O4'--C4'    _O4*, _C4*                      ideal 1.453 0.012
            distance    O3'--C3'    _O3*, _C3*                      ideal 1.423 0.014
            distance    C2'--O2'    _C2*, _O2*                      ideal 1.413 0.013
            
# 1.1.3 RNA base bond lengths

# 1.2 RNA bond angles
# 1.2.1 RNA backbone bond angles

            angle       O1P-P-O2P   _O1P, _P__, _O2P                ideal 119.6 1.5
#### WTF?!  O1P and O2P should be the same, but they aren't: ####
            angle       O5'-P-O1P   _O5*, _P__, _O1P                ideal 108.1 2.9
            angle       O5'-P-O2P   _O5*, _P__, _O2P                ideal 108.3 2.7
            angle       O3'-P-O5'   i-1 _O3*, _P__, _O5*            ideal 104.0 1.9
#### WTF?!  O1P and O2P should be the same, but they aren't: ####
            angle       O2P-P-O3'   _O2P, _P__, i-1 _O3*            ideal 108.3 3.2
            angle       O1P-P-O3'   _O1P, _P__, i-1 _O3*            ideal 107.4 3.2
            angle       O5'-C5'-C4' _O5*, _C5*, _C4*                ideal 110.2 1.4
            angle       P-O5'-C5'   _P__, _O5*, _C5*                ideal 120.9 1.6
            angle       P-O3'-C3'   _P__, i-1 _O3*, i-1 _C3*        ideal 119.7 1.2

# 1.2.2 RNA sugar bond angles

            angle       O4'-C4'-C3' _O4*, _C4*, _C3*                ideal 105.5 1.4
            angle       C5'-C4'-C3' _C5*, _C4*, _C3*                ideal 115.5 1.5
            angle       C5'-C4'-O4' _C5*, _C4*, _O4*                ideal 109.2 1.4
            angle       C1'-O4'-C4' _C1*, _O4*, _C4*                ideal 109.6 0.9
            angle       C4'-C3'-C2' _C4*, _C3*, _C2*                ideal 102.7 1.0
            angle       C3'-C2'-C1' _C3*, _C2*, _C1*                ideal 101.5 0.9
            angle       O4'-C1'-C2' _O4*, _C1*, _C2*                ideal 106.4 1.4

# Residues with an N9 (A, G) will use that; others will use N1:
# Note: Fixed "C4'-C3'-O4' _C4*, _C3*, _O3*" to "C4'-C3'-O3' _C4*, _C3*, _O3*"
# (DAK 10/3/07)
            angle       N19-C1'-C2' _N9_, _C1*, _C2*                ideal 113.4 1.6
            angle       N19-C1'-C2' _N1_, _C1*, _C2*                ideal 113.4 1.6
            angle       O4'-C1'-N19 _O4*, _C1*, _N9_                ideal 108.2 1.0
            angle       O4'-C1'-N19 _O4*, _C1*, _N1_                ideal 108.2 1.0
            
            angle       C1'-C2'-O2' _C1*, _C2*, _O2*                ideal 110.6 3.0
            angle       C3'-C2'-O2' _C3*, _C2*, _O2*                ideal 113.3 2.9
            angle       C4'-C3'-O3' _C4*, _C3*, _O3*                ideal 110.6 2.6
            angle       C2'-C3'-O3' _C2*, _C3*, _O3*                ideal 111.0 2.8

# 1.2.3 RNA base bond angles


