#  Bonds defined by QM have a sigma of 0.030
#  Angles defined by QM have a sigma of 3.0
# Number of restraints found:
# Bond lengths
#     lengths/sigmas set by mogul                20
#     bonds to hydrogen set to neutron values    13
#     bonds lengths set by partial QM             0
# Bond Angles
#     angles/sigmas set by mogul                 30
#     non-H angles set by partial QM              0
#     H bond angles set by partial QM            27
# Trigonal planes (atoms bonded to 3 others that are held flat)
#     trigonal atoms from 3 mogul bond angles     4
#     atoms NOT trigonal from 3 mogul angles      0
#     trigonal atoms from partial QM              3
#     atoms not trigonal from partial QM          0
# Torsions and 1-4 planes                                      
#     bonds where mogul states cis/trans          0
#     bonds mogul indicates flat                  0
#     bonds mogul indicates 3-fold staggered      0
#     bonds mogul indicates not flat              0
#     in flat 5/6 membered rings after PQM       11
#     other flat bonds after partial QM           1
#     sp3-sp3 set 3-fold staggered by QM          1
#     All other torsions (unrestrained)           8
# Mogul version used: /public/xtal/ccdc2012/csd/as533be
# BUSTER-KEYWORD TRUSTTORS
# BUSTER-KEYWORD TRUSTCOORD
# Coordinates generated from this CIF by gelly
# GEN: Generated by GRADE trunk from mol2 file /tmp/fileBOnosh.mol2 using mogul+qm
# Compound InChI XGYIMTFOTBMPFP-KQYNXXCUSA-N
# Compound full name 5_-DEOXYADENOSINE
data_comp_list
# 
# 
# 
# 
# 
loop_
_chem_comp.id 
_chem_comp.three_letter_code 
_chem_comp.name 
_chem_comp.group 
_chem_comp.number_atoms_all 
_chem_comp.number_atoms_nh 
_chem_comp.desc_level 
5AD 5AD 5_-DEOXYADENOSINE non-polymer 31 18 . 
data_comp_5AD
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.type_energy 
_chem_comp_atom.partial_charge 
_chem_comp_atom.x 
_chem_comp_atom.y 
_chem_comp_atom.z 
5AD N1     N NRD6 -0.219 -0.693 -0.199 4.006  
5AD C2     C CR16 0.120  -1.586 -0.674 3.132  
5AD N3     N NRD6 -0.216 -1.490 -0.767 1.802  
5AD C4     C CR6  0.167  -0.310 -0.300 1.371  
5AD N9     N NR6  -0.285 0.140  -0.235 0.074  
5AD C8     C CR16 0.100  1.393  0.315  0.143  
5AD N7     N NRD6 -0.231 1.783  0.606  1.361  
5AD C5     C CR6  0.147  0.710  0.221  2.150  
5AD C6     C CR6  0.147  0.490  0.266  3.542  
5AD N6     N NH2  -0.341 1.379  0.739  4.419  
5AD "C1'"  C CH1  0.167  -0.571 -0.661 -1.127 
5AD "C2'"  C CH1  0.128  -1.197 0.489  -1.921 
5AD "C3'"  C CH1  0.111  -0.078 0.817  -2.907 
5AD "C4'"  C CH1  0.087  0.484  -0.567 -3.218 
5AD "C5'"  C CH3  -0.036 1.927  -0.603 -3.661 
5AD "O4'"  O O2   -0.348 0.349  -1.310 -1.988 
5AD "O2'"  O OH1  -0.385 -2.378 0.045  -2.581 
5AD "O3'"  O OH1  -0.387 -0.571 1.404  -4.106 
5AD H2     H HCR  0.105  -2.515 -1.031 3.573  
5AD H8     H HCR  0.103  2.008  0.494  -0.737 
5AD HN61   H HNH2 0.144  1.186  0.757  5.415  
5AD HN62   H HNH2 0.144  2.274  1.095  4.099  
5AD "H1'"  H HCH1 0.087  -1.304 -1.413 -0.837 
5AD "H2'"  H HCH1 0.067  -1.442 1.337  -1.284 
5AD "H3'"  H HCH1 0.065  0.656  1.476  -2.445 
5AD "H4'"  H HCH1 0.062  -0.139 -1.083 -3.946 
5AD "H5'1" H HCH3 0.025  2.259  -1.621 -3.862 
5AD "H5'2" H HCH3 0.025  2.067  -0.036 -4.581 
5AD "H5'3" H HCH3 0.025  2.624  -0.197 -2.930 
5AD "HO2'" H HOH1 0.210  -3.011 0.811  -2.574 
5AD "HO3'" H HOH1 0.210  0.225  1.582  -4.672 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.type 
_chem_comp_bond.value_dist 
_chem_comp_bond.value_dist_esd 
5AD N1    C2     aromatic 1.335 0.010 
5AD N1    C6     aromatic 1.351 0.010 
5AD C2    H2     single   1.089 0.010 
5AD C2    N3     aromatic 1.335 0.010 
5AD N3    C4     aromatic 1.340 0.012 
5AD C4    C5     aromatic 1.386 0.010 
5AD C4    N9     aromatic 1.374 0.008 
5AD N9    "C1'"  single   1.459 0.011 
5AD N9    C8     aromatic 1.370 0.008 
5AD C8    H8     single   1.089 0.010 
5AD C8    N7     aromatic 1.311 0.007 
5AD N7    C5     aromatic 1.387 0.007 
5AD C5    C6     aromatic 1.409 0.010 
5AD C6    N6     single   1.335 0.013 
5AD N6    HN61   single   1.015 0.010 
5AD N6    HN62   single   1.015 0.010 
5AD "C1'" "C2'"  single   1.530 0.014 
5AD "C1'" "H1'"  single   1.089 0.010 
5AD "C1'" "O4'"  single   1.415 0.011 
5AD "C2'" "C3'"  single   1.530 0.013 
5AD "C2'" "H2'"  single   1.089 0.010 
5AD "C2'" "O2'"  single   1.423 0.013 
5AD "C3'" "C4'"  single   1.528 0.013 
5AD "C3'" "H3'"  single   1.089 0.010 
5AD "C3'" "O3'"  single   1.423 0.013 
5AD "C4'" "C5'"  single   1.510 0.010 
5AD "C4'" "H4'"  single   1.089 0.010 
5AD "C4'" "O4'"  single   1.442 0.012 
5AD "C5'" "H5'1" single   1.089 0.010 
5AD "C5'" "H5'2" single   1.089 0.010 
5AD "C5'" "H5'3" single   1.089 0.010 
5AD "O2'" "HO2'" single   0.993 0.010 
5AD "O3'" "HO3'" single   0.993 0.010 
loop_
_chem_comp_angle.comp_id 
_chem_comp_angle.atom_id_1 
_chem_comp_angle.atom_id_2 
_chem_comp_angle.atom_id_3 
_chem_comp_angle.value_angle 
_chem_comp_angle.value_angle_esd 
5AD C2     N1    C6     118.6 0.9 
5AD N1     C2    H2     114.9 3.0 
5AD N1     C2    N3     128.8 0.8 
5AD H2     C2    N3     116.2 3.0 
5AD C2     N3    C4     111.5 1.9 
5AD N3     C4    C5     126.8 0.7 
5AD N3     C4    N9     127.2 1.1 
5AD C5     C4    N9     105.8 0.4 
5AD C4     N9    "C1'"  126.9 1.8 
5AD C4     N9    C8     105.7 0.5 
5AD "C1'"  N9    C8     126.9 1.9 
5AD N9     C8    H8     122.8 3.0 
5AD N9     C8    N7     114.0 0.7 
5AD H8     C8    N7     123.2 3.0 
5AD C8     N7    C5     103.7 0.4 
5AD C4     C5    N7     110.7 0.5 
5AD C4     C5    C6     117.0 0.7 
5AD N7     C5    C6     132.2 0.9 
5AD N1     C6    C5     117.5 0.8 
5AD N1     C6    N6     118.3 1.2 
5AD C5     C6    N6     123.6 1.0 
5AD C6     N6    HN61   121.6 3.0 
5AD C6     N6    HN62   120.3 3.0 
5AD HN61   N6    HN62   118.1 3.0 
5AD N9     "C1'" "C2'"  114.0 1.6 
5AD N9     "C1'" "H1'"  108.0 3.0 
5AD "C2'"  "C1'" "H1'"  112.6 3.0 
5AD N9     "C1'" "O4'"  108.4 1.3 
5AD "C2'"  "C1'" "O4'"  106.5 1.2 
5AD "H1'"  "C1'" "O4'"  106.7 3.0 
5AD "C1'"  "C2'" "C3'"  101.5 1.2 
5AD "C1'"  "C2'" "H2'"  112.2 3.0 
5AD "C3'"  "C2'" "H2'"  112.3 3.0 
5AD "C1'"  "C2'" "O2'"  110.6 2.7 
5AD "C3'"  "C2'" "O2'"  111.9 2.7 
5AD "H2'"  "C2'" "O2'"  109.4 3.0 
5AD "C2'"  "C3'" "C4'"  102.6 1.4 
5AD "C2'"  "C3'" "H3'"  110.6 3.0 
5AD "C4'"  "C3'" "H3'"  112.9 3.0 
5AD "C2'"  "C3'" "O3'"  111.9 2.7 
5AD "C4'"  "C3'" "O3'"  109.3 2.2 
5AD "H3'"  "C3'" "O3'"  110.2 3.0 
5AD "C3'"  "C4'" "C5'"  115.7 0.6 
5AD "C3'"  "C4'" "H4'"  110.8 3.0 
5AD "C5'"  "C4'" "H4'"  109.8 3.0 
5AD "C3'"  "C4'" "O4'"  105.0 1.1 
5AD "C5'"  "C4'" "O4'"  109.1 1.2 
5AD "H4'"  "C4'" "O4'"  105.8 3.0 
5AD "C4'"  "C5'" "H5'1" 111.6 3.0 
5AD "C4'"  "C5'" "H5'2" 111.0 3.0 
5AD "H5'1" "C5'" "H5'2" 107.0 3.0 
5AD "C4'"  "C5'" "H5'3" 113.8 3.0 
5AD "H5'1" "C5'" "H5'3" 106.1 3.0 
5AD "H5'2" "C5'" "H5'3" 106.9 3.0 
5AD "C1'"  "O4'" "C4'"  107.9 2.1 
5AD "C2'"  "O2'" "HO2'" 106.6 3.0 
5AD "C3'"  "O3'" "HO3'" 106.0 3.0 
loop_
_chem_comp_chir.comp_id 
_chem_comp_chir.id 
_chem_comp_chir.atom_id_centre 
_chem_comp_chir.atom_id_1 
_chem_comp_chir.atom_id_2 
_chem_comp_chir.atom_id_3 
_chem_comp_chir.volume_sign 
5AD chir_01 "C1'" "O4'" "C2'"  N9     positive 
5AD chir_02 "C2'" "O2'" "C3'"  "C1'"  positive 
5AD chir_03 "C3'" "O3'" "C4'"  "C2'"  positive 
5AD chir_04 "C4'" "O4'" "C5'"  "C3'"  positive 
5AD chir_05 "C5'" "C4'" "H5'3" "H5'2" both     
loop_
_chem_comp_plane_atom.comp_id 
_chem_comp_plane_atom.plane_id 
_chem_comp_plane_atom.atom_id 
_chem_comp_plane_atom.dist_esd 
5AD csd-C4   C4    0.020 
5AD csd-C4   N3    0.020 
5AD csd-C4   N9    0.020 
5AD csd-C4   C5    0.020 
5AD csd-C5   C5    0.020 
5AD csd-C5   C4    0.020 
5AD csd-C5   N7    0.020 
5AD csd-C5   C6    0.020 
5AD csd-C6   C6    0.020 
5AD csd-C6   N1    0.020 
5AD csd-C6   C5    0.020 
5AD csd-C6   N6    0.020 
5AD csd-N9   N9    0.020 
5AD csd-N9   C4    0.020 
5AD csd-N9   C8    0.020 
5AD csd-N9   "C1'" 0.020 
5AD qm-C2    C2    0.020 
5AD qm-C2    N1    0.020 
5AD qm-C2    N3    0.020 
5AD qm-C2    H2    0.020 
5AD qm-C8    C8    0.020 
5AD qm-C8    N9    0.020 
5AD qm-C8    N7    0.020 
5AD qm-C8    H8    0.020 
5AD qm-N6    N6    0.020 
5AD qm-N6    C6    0.020 
5AD qm-N6    HN61  0.020 
5AD qm-N6    HN62  0.020 
5AD qmf-01   C5    0.020 
5AD qmf-01   C6    0.020 
5AD qmf-01   N6    0.020 
5AD qmf-01   HN61  0.020 
5AD ring5A-1 C4    0.020 
5AD ring5A-1 N9    0.020 
5AD ring5A-1 C8    0.020 
5AD ring5A-1 N7    0.020 
5AD ring5A-2 N9    0.020 
5AD ring5A-2 C8    0.020 
5AD ring5A-2 N7    0.020 
5AD ring5A-2 C5    0.020 
5AD ring5A-3 C8    0.020 
5AD ring5A-3 N7    0.020 
5AD ring5A-3 C5    0.020 
5AD ring5A-3 C4    0.020 
5AD ring5A-4 N7    0.020 
5AD ring5A-4 C5    0.020 
5AD ring5A-4 C4    0.020 
5AD ring5A-4 N9    0.020 
5AD ring5A-5 C5    0.020 
5AD ring5A-5 C4    0.020 
5AD ring5A-5 N9    0.020 
5AD ring5A-5 C8    0.020 
5AD ring6A-1 N1    0.020 
5AD ring6A-1 C2    0.020 
5AD ring6A-1 N3    0.020 
5AD ring6A-1 C4    0.020 
5AD ring6A-2 C2    0.020 
5AD ring6A-2 N3    0.020 
5AD ring6A-2 C4    0.020 
5AD ring6A-2 C5    0.020 
5AD ring6A-3 N3    0.020 
5AD ring6A-3 C4    0.020 
5AD ring6A-3 C5    0.020 
5AD ring6A-3 C6    0.020 
5AD ring6A-4 C4    0.020 
5AD ring6A-4 C5    0.020 
5AD ring6A-4 C6    0.020 
5AD ring6A-4 N1    0.020 
5AD ring6A-5 C5    0.020 
5AD ring6A-5 C6    0.020 
5AD ring6A-5 N1    0.020 
5AD ring6A-5 C2    0.020 
5AD ring6A-6 C6    0.020 
5AD ring6A-6 N1    0.020 
5AD ring6A-6 C2    0.020 
5AD ring6A-6 N3    0.020 
loop_
_chem_comp_tor.comp_id 
_chem_comp_tor.id 
_chem_comp_tor.atom_id_1 
_chem_comp_tor.atom_id_2 
_chem_comp_tor.atom_id_3 
_chem_comp_tor.atom_id_4 
_chem_comp_tor.value_angle 
_chem_comp_tor.value_angle_esd 
_chem_comp_tor.period 
5AD CONST_ring6A-6 C6    N1    C2    N3     0.0   1000000.0 0  
5AD CONST_ring6A-5 C2    N1    C6    C5     0.0   1000000.0 0  
5AD CONST_ring6A-1 N1    C2    N3    C4     0.0   1000000.0 0  
5AD CONST_ring6A-2 C2    N3    C4    C5     0.0   1000000.0 0  
5AD CONST_ring5A-5 C5    C4    N9    C8     0.0   1000000.0 0  
5AD CONST_ring6A-3 N3    C4    C5    C6     0.0   1000000.0 0  
5AD CONST_ring5A-1 C4    N9    C8    N7     0.0   1000000.0 0  
5AD other-001      C4    N9    "C1'" "C2'"  0.0   1000000.0 10 
5AD CONST_ring5A-2 N9    C8    N7    C5     0.0   1000000.0 0  
5AD CONST_ring5A-3 C8    N7    C5    C4     0.0   1000000.0 0  
5AD CONST_ring6A-4 C4    C5    C6    N1     0.0   1000000.0 0  
5AD qmf-01         C5    C6    N6    HN61   180.0 1000000.0 2  
5AD other-002      N9    "C1'" "C2'" "C3'"  0.0   1000000.0 10 
5AD other-003      "C2'" "C1'" "O4'" "C4'"  0.0   1000000.0 10 
5AD other-004      "C1'" "C2'" "C3'" "C4'"  0.0   1000000.0 10 
5AD other-005      "C1'" "C2'" "O2'" "HO2'" 0.0   1000000.0 10 
5AD other-006      "C2'" "C3'" "C4'" "C5'"  0.0   1000000.0 10 
5AD other-007      "C2'" "C3'" "O3'" "HO3'" 0.0   1000000.0 10 
5AD qm-sp3sp3-01   "C3'" "C4'" "C5'" "H5'1" 180.0 15.0      3  
5AD other-008      "C3'" "C4'" "O4'" "C1'"  0.0   1000000.0 10 

# 
# 
