# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 20:28:58 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: cyclopentyl hydrogen carbonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)OC1CCCC1
#
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
 12W  12W  'cyclopentyl hydrogen carbonate'  ligand  18  9  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_12W
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
 12W  C25  C  C      0   0.576   1.6798  -0.1140   0.6045
 12W  O26  O  O      0  -0.583   2.0776   0.8494  -0.0567
 12W  O27  O  O2     0  -0.557   0.4245  -0.6304   0.3246
 12W  C28  C  CH1    0   0.074  -0.3961  -0.0098  -0.6435
 12W  C29  C  CH2    0  -0.465  -1.1117   1.2297  -0.0901
 12W  C30  C  CH2    0  -0.439  -2.4601   0.7213   0.4829
 12W  C31  C  CH2    0  -0.418  -2.4361  -0.8022   0.3124
 12W  C32  C  CH2    0  -0.500  -1.5386  -0.9863  -0.9042
 12W  H26  H  HCH1   0   0.249   0.1706   0.2175  -1.5503
 12W  H27  H  HCH2   0   0.259  -0.5039   1.7459   0.6497
 12W  H28  H  HCH2   0   0.169  -1.2860   1.9410  -0.9017
 12W  H29  H  HCH2   0   0.156  -2.6096   1.0196   1.5176
 12W  H30  H  HCH2   0   0.259  -3.2896   1.1407  -0.0890
 12W  H31  H  HCH2   0   0.233  -1.9829  -1.2850   1.1823
 12W  H32  H  HCH2   0   0.262  -3.4313  -1.2287   0.1918
 12W  H33  H  HCH2   0   0.188  -2.0675  -0.6773  -1.8102
 12W  H34  H  HCH2   0   0.216  -1.1928  -2.0108  -1.0577
 12W  OXT  O  OC    -1  -0.679   2.2205  -0.7467   1.5213

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
 12W  C25  O27  deloc   1.386  0.020  1.386
 12W  C25  O26  deloc   1.234  0.020  1.234
 12W  O27  C28  single  1.413  0.020  1.413
 12W  C29  C28  single  1.534  0.020  1.534
 12W  C29  C30  single  1.551  0.020  1.551
 12W  C28  C32  single  1.525  0.020  1.525
 12W  C30  C31  single  1.533  0.020  1.533
 12W  C31  C32  single  1.523  0.020  1.523
 12W  C28  H26  single  0.970  0.020  1.090
 12W  C29  H27  single  0.970  0.020  1.090
 12W  C29  H28  single  0.970  0.020  1.090
 12W  C30  H29  single  0.970  0.020  1.090
 12W  C30  H30  single  0.970  0.020  1.090
 12W  C31  H31  single  0.970  0.020  1.090
 12W  C31  H32  single  0.970  0.020  1.090
 12W  C32  H33  single  0.970  0.020  1.090
 12W  C32  H34  single  0.970  0.020  1.090
 12W  C25  OXT  deloc   1.238  0.020  1.238

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
 12W  OXT  C25  O27  110.77  3.000
 12W  OXT  C25  O26  130.89  3.000
 12W  O27  C25  O26  118.33  3.000
 12W  C28  O27  C25  120.05  3.000
 12W  H26  C28  C32  112.31  3.000
 12W  H26  C28  C29  111.90  3.000
 12W  C32  C28  C29  103.27  3.000
 12W  H26  C28  O27  111.02  3.000
 12W  C32  C28  O27  105.72  3.000
 12W  C29  C28  O27  112.25  3.000
 12W  H28  C29  H27  106.58  3.000
 12W  H28  C29  C30  110.42  3.000
 12W  H27  C29  C30  112.97  3.000
 12W  H28  C29  C28  109.40  3.000
 12W  H27  C29  C28  111.60  3.000
 12W  C30  C29  C28  105.90  3.000
 12W  H30  C30  H29  106.78  3.000
 12W  H30  C30  C31  109.60  3.000
 12W  H29  C30  C31  112.37  3.000
 12W  H30  C30  C29  109.96  3.000
 12W  H29  C30  C29  112.41  3.000
 12W  C31  C30  C29  105.73  3.000
 12W  H32  C31  H31  107.09  3.000
 12W  H32  C31  C32  113.74  3.000
 12W  H31  C31  C32  109.75  3.000
 12W  H32  C31  C30  112.77  3.000
 12W  H31  C31  C30  110.90  3.000
 12W  C32  C31  C30  102.60  3.000
 12W  H34  C32  H33  107.56  3.000
 12W  H34  C32  C31  114.35  3.000
 12W  H33  C32  C31  110.03  3.000
 12W  H34  C32  C28  112.80  3.000
 12W  H33  C32  C28  108.84  3.000
 12W  C31  C32  C28  103.15  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
 12W  CONST_01  C28  O27  C25  O26    0.00   0.0  0
 12W  CONST_02  OXT  C25  O27  C28  180.00   0.0  0
 12W  Var_01    C31  C30  C29  C28    3.21  30.0  1
 12W  Var_02    C30  C31  C32  C28   43.17  30.0  1
 12W  Var_03    C32  C31  C30  C29  -28.30  30.0  1

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
 12W  chir_01  C28  O27  C29  C32  positiv

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
 12W  plan-1  C25  0.020
 12W  plan-1  O26  0.020
 12W  plan-1  O27  0.020
 12W  plan-1  C28  0.020
 12W  plan-1  OXT  0.020

