# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 05:57:10 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: cyclopentyl [(1R)-3-oxo-1-phenylpropyl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CC[C@@H](NC(=O)OC1CCCC1)c2ccccc2
#
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
 L62  L62  'cyclopentyl [(1R)-3-oxo-1-phenylpropyl]carbamate'  ligand  38  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L62
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
 L62  O2    O  O     0  -0.518   1.1683  -1.2145   1.0135
 L62  C5    C  C     0   0.759   0.9790  -0.4083   0.1228
 L62  O3    O  O2    0  -0.493   1.9384   0.2763  -0.4969
 L62  C6    C  CH1   0   0.051   3.2979   0.0359  -0.1064
 L62  C7    C  CH2   0  -0.480   4.2368   0.6227  -1.1798
 L62  C8    C  CH2   0  -0.446   5.1678   1.5949  -0.4417
 L62  C9    C  CH2   0  -0.454   5.1384   1.1077   1.0063
 L62  C10   C  CH2   0  -0.476   3.6747   0.7272   1.2065
 L62  N1    N  NH1   0  -0.666  -0.2352  -0.0993  -0.3724
 L62  C4    C  CH1   0  -0.187  -1.4513  -0.6763   0.1627
 L62  C3    C  CH2   0  -0.527  -1.8356  -2.0060  -0.5181
 L62  C2    C  C1    0   0.178  -0.7586  -3.0485  -0.4406
 L62  O1    O  O     0  -0.378  -0.8414  -4.0630   0.2070
 L62  C11   C  CR6   0   0.159  -2.5918   0.3084   0.0538
 L62  C12   C  CR16  0  -0.320  -3.2977   0.6824   1.1917
 L62  C13   C  CR16  0  -0.237  -4.3653   1.5670   1.1043
 L62  C14   C  CR16  0  -0.265  -4.7337   2.0930  -0.1257
 L62  C15   C  CR16  0  -0.238  -4.0310   1.7276  -1.2674
 L62  C16   C  CR16  0  -0.310  -2.9707   0.8372  -1.1784
 L62  H1    H  HNH1  0   0.408  -0.2989   0.5651  -1.1279
 L62  H6    H  HCH1  0   0.245   3.4515  -1.0416  -0.0225
 L62  H71C  H  HCH2  0   0.242   4.8104  -0.1821  -1.6409
 L62  H72C  H  HCH2  0   0.247   3.6765   1.1086  -1.9792
 L62  H101  H  HCH2  0   0.232   3.0749   1.6350   1.3203
 L62  H102  H  HCH2  0   0.245   3.4987   0.0978   2.0783
 L62  H81C  H  HCH2  0   0.236   6.1717   1.6178  -0.8663
 L62  H82C  H  HCH2  0   0.225   4.7725   2.6123  -0.4936
 L62  H91C  H  HCH2  0   0.225   5.7779   0.2278   1.1215
 L62  H92C  H  HCH2  0   0.238   5.4826   1.8560   1.7210
 L62  H4    H  HCH1  0   0.285  -1.2824  -0.8779   1.2216
 L62  H31C  H  HCH2  0   0.266  -2.7467  -2.3868  -0.0550
 L62  H32C  H  HCH2  0   0.268  -2.0389  -1.8177  -1.5769
 L62  HXT   H  H     0   0.191   0.1315  -2.8495  -1.0604
 L62  H12   H  HCR6  0   0.256  -3.0123   0.2790   2.1560
 L62  H16   H  HCR6  0   0.260  -2.4448   0.5550  -2.0841
 L62  H13   H  HCR6  0   0.259  -4.9075   1.8441   1.9991
 L62  H14   H  HCR6  0   0.259  -5.5640   2.7834  -0.1958
 L62  H15   H  HCR6  0   0.260  -4.3113   2.1329  -2.2309

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
 L62  O2   C5    double    1.216  0.020  1.216
 L62  C5   O3    single    1.332  0.020  1.332
 L62  C5   N1    single    1.347  0.020  1.347
 L62  O3   C6    single    1.435  0.020  1.435
 L62  C6   C7    single    1.542  0.020  1.542
 L62  C6   C10   single    1.531  0.020  1.531
 L62  C7   C8    single    1.535  0.020  1.535
 L62  C8   C9    single    1.528  0.020  1.528
 L62  C9   C10   single    1.526  0.020  1.526
 L62  N1   C4    single    1.448  0.020  1.448
 L62  C4   C3    single    1.542  0.020  1.542
 L62  C4   C11   single    1.511  0.020  1.511
 L62  C3   C2    single    1.501  0.020  1.501
 L62  C2   O1    double    1.206  0.020  1.206
 L62  C2   HXT   single    0.930  0.020  1.080
 L62  C11  C12   aromatic  1.390  0.020  1.390
 L62  C11  C16   aromatic  1.393  0.020  1.393
 L62  C12  C13   aromatic  1.389  0.020  1.389
 L62  C13  C14   aromatic  1.388  0.020  1.388
 L62  C14  C15   aromatic  1.390  0.020  1.390
 L62  C15  C16   aromatic  1.387  0.020  1.387
 L62  N1   H1    single    0.860  0.020  1.020
 L62  C6   H6    single    0.970  0.020  1.090
 L62  C7   H71C  single    0.970  0.020  1.090
 L62  C7   H72C  single    0.970  0.020  1.090
 L62  C10  H101  single    0.970  0.020  1.090
 L62  C10  H102  single    0.970  0.020  1.090
 L62  C8   H81C  single    0.970  0.020  1.090
 L62  C8   H82C  single    0.970  0.020  1.090
 L62  C9   H91C  single    0.970  0.020  1.090
 L62  C9   H92C  single    0.970  0.020  1.090
 L62  C4   H4    single    0.970  0.020  1.090
 L62  C3   H31C  single    0.970  0.020  1.090
 L62  C3   H32C  single    0.970  0.020  1.090
 L62  C12  H12   single    0.930  0.020  1.080
 L62  C16  H16   single    0.930  0.020  1.080
 L62  C13  H13   single    0.930  0.020  1.080
 L62  C14  H14   single    0.930  0.020  1.080
 L62  C15  H15   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
 L62  N1    C5   O3    111.12  3.000
 L62  N1    C5   O2    124.16  3.000
 L62  O3    C5   O2    124.71  3.000
 L62  C6    O3   C5    118.03  3.000
 L62  H6    C6   C10   110.19  3.000
 L62  H6    C6   C7    110.09  3.000
 L62  C10   C6   C7    105.98  3.000
 L62  H6    C6   O3    108.64  3.000
 L62  C10   C6   O3    113.01  3.000
 L62  C7    C6   O3    108.89  3.000
 L62  H72C  C7   H71C  106.80  3.000
 L62  H72C  C7   C8    112.45  3.000
 L62  H71C  C7   C8    110.59  3.000
 L62  H72C  C7   C6    111.53  3.000
 L62  H71C  C7   C6    109.49  3.000
 L62  C8    C7   C6    106.00  3.000
 L62  H82C  C8   H81C  107.16  3.000
 L62  H82C  C8   C9    109.57  3.000
 L62  H81C  C8   C9    113.17  3.000
 L62  H82C  C8   C7    110.33  3.000
 L62  H81C  C8   C7    112.61  3.000
 L62  C9    C8   C7    104.01  3.000
 L62  H92C  C9   H91C  107.37  3.000
 L62  H92C  C9   C10   112.82  3.000
 L62  H91C  C9   C10   110.28  3.000
 L62  H92C  C9   C8    113.34  3.000
 L62  H91C  C9   C8    110.18  3.000
 L62  C10   C9   C8    102.85  3.000
 L62  H102  C10  H101  107.92  3.000
 L62  H102  C10  C9    113.83  3.000
 L62  H101  C10  C9    109.44  3.000
 L62  H102  C10  C6    112.68  3.000
 L62  H101  C10  C6    109.21  3.000
 L62  C9    C10  C6    103.66  3.000
 L62  H1    N1   C4    119.10  3.000
 L62  H1    N1   C5    118.92  3.000
 L62  C4    N1   C5    121.97  3.000
 L62  H4    C4   C11   107.89  3.000
 L62  H4    C4   C3    107.92  3.000
 L62  C11   C4   C3    110.00  3.000
 L62  H4    C4   N1    107.59  3.000
 L62  C11   C4   N1    110.33  3.000
 L62  C3    C4   N1    112.93  3.000
 L62  H32C  C3   H31C  108.40  3.000
 L62  H32C  C3   C2    107.62  3.000
 L62  H31C  C3   C2    109.57  3.000
 L62  H32C  C3   C4    108.96  3.000
 L62  H31C  C3   C4    108.77  3.000
 L62  C2    C3   C4    113.40  3.000
 L62  HXT   C2   O1    120.59  3.000
 L62  HXT   C2   C3    115.14  3.000
 L62  O1    C2   C3    124.23  3.000
 L62  C16   C11  C12   118.92  3.000
 L62  C16   C11  C4    121.09  3.000
 L62  C12   C11  C4    119.98  3.000
 L62  H12   C12  C13   119.70  3.000
 L62  H12   C12  C11   119.64  3.000
 L62  C13   C12  C11   120.66  3.000
 L62  H13   C13  C14   120.19  3.000
 L62  H13   C13  C12   119.73  3.000
 L62  C14   C13  C12   120.08  3.000
 L62  H14   C14  C15   120.17  3.000
 L62  H14   C14  C13   120.20  3.000
 L62  C15   C14  C13   119.63  3.000
 L62  H15   C15  C16   119.70  3.000
 L62  H15   C15  C14   120.14  3.000
 L62  C16   C15  C14   120.17  3.000
 L62  H16   C16  C15   118.94  3.000
 L62  H16   C16  C11   120.52  3.000
 L62  C15   C16  C11   120.54  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
 L62  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 L62  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 L62  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 L62  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 L62  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 L62  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 L62  CONST_07  C13  C12  C11  C4    180.00   0.0  0
 L62  CONST_08  C15  C16  C11  C4    180.00   0.0  0
 L62  CONST_09  H13  C13  C12  C11   180.00   0.0  0
 L62  CONST_10  H15  C15  C16  C11   180.00   0.0  0
 L62  CONST_11  H16  C16  C11  C12   180.00   0.0  0
 L62  CONST_12  H14  C14  C13  C12   180.00   0.0  0
 L62  CONST_13  H12  C12  C13  C14   180.00   0.0  0
 L62  Var_01    C9   C8   C7   C6     22.88  30.0  1
 L62  Var_02    C8   C9   C10  C6     40.86  30.0  1
 L62  Var_03    C10  C9   C8   C7    -39.44  30.0  1
 L62  Var_04    N1   C5   O3   C6   -178.50  30.0  2
 L62  Var_05    C4   N1   C5   O2      2.53  30.0  2
 L62  Var_06    O1   C2   C3   C4    111.79  30.0  3

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
 L62  chir_01  C6  O3  C7  C10  negativ
 L62  chir_02  C4  N1  C3  C11  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
 L62  plan-1  C4   0.020
 L62  plan-1  C11  0.020
 L62  plan-1  C12  0.020
 L62  plan-1  C13  0.020
 L62  plan-1  C14  0.020
 L62  plan-1  C15  0.020
 L62  plan-1  C16  0.020
 L62  plan-1  H12  0.020
 L62  plan-1  H16  0.020
 L62  plan-1  H13  0.020
 L62  plan-1  H14  0.020
 L62  plan-1  H15  0.020
 L62  plan-2  O2   0.020
 L62  plan-2  C5   0.020
 L62  plan-2  O3   0.020
 L62  plan-2  N1   0.020
 L62  plan-3  C3   0.020
 L62  plan-3  C2   0.020
 L62  plan-3  O1   0.020
 L62  plan-3  HXT  0.020

