# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 21:50:17 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: benzyl formate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=COCc1ccccc1
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 CBZ  CBZ  'benzyl formate           '  ligand  18  10  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CBZ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CBZ  C     C  C1    0   0.309  -3.0447  -0.0473  -0.0879
 CBZ  O1    O  O     0  -0.419  -3.8494  -0.0534   0.8015
 CBZ  O2    O  O2    0  -0.417  -1.7463   0.0080   0.1538
 CBZ  C1'   C  CH2   0  -0.261  -0.8734   0.0226  -0.9939
 CBZ  C1    C  CR6   0   0.079   0.5361   0.0045  -0.4926
 CBZ  C2    C  CR16  0  -0.285   1.1707  -1.2037  -0.2178
 CBZ  C3    C  CR16  0  -0.242   2.4666  -1.2210   0.2780
 CBZ  C4    C  CR16  0  -0.259   3.1394  -0.0271   0.5063
 CBZ  C5    C  CR16  0  -0.242   2.5132   1.1822   0.2346
 CBZ  C6    C  CR16  0  -0.286   1.2165   1.1961  -0.2611
 CBZ  H     H  H     0   0.203  -3.3153  -0.0875  -1.1542
 CBZ  H1'1  H  HCH2  0   0.263  -1.0758  -0.8496  -1.6192
 CBZ  H1'2  H  HCH2  0   0.263  -1.0652   0.9205  -1.5845
 CBZ  H2    H  HCR6  0   0.257   0.6525  -2.1378  -0.3993
 CBZ  H3    H  HCR6  0   0.260   2.9524  -2.1656   0.4840
 CBZ  H4    H  HCR6  0   0.260   4.1509  -0.0401   0.8912
 CBZ  H5    H  HCR6  0   0.260   3.0342   2.1148   0.4072
 CBZ  H6    H  HCR6  0   0.258   0.7333   2.1419  -0.4753

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
_chem_comp_bond.value_dist_neutron
 CBZ  C    O1    double    1.199  0.020  1.199
 CBZ  C    O2    single    1.322  0.020  1.322
 CBZ  C    H     single    0.930  0.020  1.080
 CBZ  O2   C1'   single    1.442  0.020  1.442
 CBZ  C1'  C1    single    1.496  0.020  1.496
 CBZ  C1'  H1'1  single    0.970  0.020  1.090
 CBZ  C1'  H1'2  single    0.970  0.020  1.090
 CBZ  C1   C2    aromatic  1.392  0.020  1.392
 CBZ  C1   C6    aromatic  1.392  0.020  1.392
 CBZ  C2   C3    aromatic  1.388  0.020  1.388
 CBZ  C2   H2    single    0.930  0.020  1.080
 CBZ  C3   C4    aromatic  1.389  0.020  1.389
 CBZ  C3   H3    single    0.930  0.020  1.080
 CBZ  C4   C5    aromatic  1.389  0.020  1.389
 CBZ  C4   H4    single    0.930  0.020  1.080
 CBZ  C5   C6    aromatic  1.388  0.020  1.388
 CBZ  C5   H5    single    0.930  0.020  1.080
 CBZ  C6   H6    single    0.930  0.020  1.080

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
 CBZ  H     C    O2    114.84  3.000
 CBZ  H     C    O1    123.59  3.000
 CBZ  O2    C    O1    121.57  3.000
 CBZ  C1'   O2   C     116.71  3.000
 CBZ  H1'2  C1'  H1'1  108.33  3.000
 CBZ  H1'2  C1'  C1    110.90  3.000
 CBZ  H1'1  C1'  C1    110.91  3.000
 CBZ  H1'2  C1'  O2    109.42  3.000
 CBZ  H1'1  C1'  O2    109.60  3.000
 CBZ  C1    C1'  O2    107.67  3.000
 CBZ  C6    C1   C2    119.18  3.000
 CBZ  C6    C1   C1'   120.40  3.000
 CBZ  C2    C1   C1'   120.40  3.000
 CBZ  H2    C2   C3    119.72  3.000
 CBZ  H2    C2   C1    119.81  3.000
 CBZ  C3    C2   C1    120.47  3.000
 CBZ  H3    C3   C4    120.10  3.000
 CBZ  H3    C3   C2    119.88  3.000
 CBZ  C4    C3   C2    120.02  3.000
 CBZ  H4    C4   C5    120.10  3.000
 CBZ  H4    C4   C3    120.05  3.000
 CBZ  C5    C4   C3    119.85  3.000
 CBZ  H5    C5   C6    119.87  3.000
 CBZ  H5    C5   C4    120.14  3.000
 CBZ  C6    C5   C4    119.99  3.000
 CBZ  H6    C6   C5    119.73  3.000
 CBZ  H6    C6   C1    119.77  3.000
 CBZ  C5    C6   C1    120.50  3.000

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
 CBZ  CONST_01  C4  C3   C2   C1      0.00   0.0  0
 CBZ  CONST_02  C4  C5   C6   C1      0.00   0.0  0
 CBZ  CONST_03  C5  C6   C1   C2      0.00   0.0  0
 CBZ  CONST_04  C5  C4   C3   C2      0.00   0.0  0
 CBZ  CONST_05  C6  C1   C2   C3      0.00   0.0  0
 CBZ  CONST_06  C6  C5   C4   C3      0.00   0.0  0
 CBZ  CONST_07  C3  C2   C1   C1'   180.00   0.0  0
 CBZ  CONST_08  C5  C6   C1   C1'   180.00   0.0  0
 CBZ  CONST_09  H3  C3   C2   C1    180.00   0.0  0
 CBZ  CONST_10  H5  C5   C6   C1    180.00   0.0  0
 CBZ  CONST_11  H6  C6   C1   C2    180.00   0.0  0
 CBZ  CONST_12  H4  C4   C3   C2    180.00   0.0  0
 CBZ  CONST_13  H2  C2   C3   C4    180.00   0.0  0
 CBZ  Var_01    C2  C1   C1'  O2     86.96  30.0  2
 CBZ  Var_02    C1  C1'  O2   C    -176.70  30.0  3
 CBZ  Var_03    H   C    O2   C1'     0.64  30.0  2

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
 CBZ  plan-1  C1'  0.020
 CBZ  plan-1  C1   0.020
 CBZ  plan-1  C2   0.020
 CBZ  plan-1  C3   0.020
 CBZ  plan-1  C4   0.020
 CBZ  plan-1  C5   0.020
 CBZ  plan-1  C6   0.020
 CBZ  plan-1  H2   0.020
 CBZ  plan-1  H3   0.020
 CBZ  plan-1  H4   0.020
 CBZ  plan-1  H5   0.020
 CBZ  plan-1  H6   0.020
 CBZ  plan-2  C    0.020
 CBZ  plan-2  O1   0.020
 CBZ  plan-2  O2   0.020
 CBZ  plan-2  H    0.020

