# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:06:41 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: cyclopentanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 YEG  YEG  'cyclopentanol            '  ligand  16  6  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YEG
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
 YEG  C01   C  CH2   0  -0.460   1.4969   0.7701   0.0514
 YEG  C02   C  CH2   0  -0.447   1.5340  -0.7734  -0.0555
 YEG  C03   C  CH2   0  -0.468   0.0635  -1.2311  -0.0757
 YEG  C04   C  CR15  0   0.059  -0.7327  -0.0104   0.3752
 YEG  C05   C  CH2   0  -0.475   0.0464   1.1511  -0.2369
 YEG  O06   O  OH1   0  -0.674  -2.0786  -0.1184  -0.0266
 YEG  H01   H  HCH2  0   0.225   1.7662   1.0818   1.0628
 YEG  H01A  H  HCH2  0   0.234   2.2013   1.2554  -0.6242
 YEG  H02   H  HCH2  0   0.230   2.0527  -1.0983  -0.9580
 YEG  H02A  H  HCH2  0   0.229   2.0752  -1.2070   0.7860
 YEG  H03   H  HCH2  0   0.223  -0.2434  -1.4885  -1.0933
 YEG  H03A  H  HCH2  0   0.235  -0.1177  -2.1066   0.5497
 YEG  H04   H  HCR5  0   0.191  -0.6623   0.0738   1.4707
 YEG  H05   H  HCH2  0   0.233  -0.2335   2.1230   0.1752
 YEG  H05A  H  HCH2  0   0.217  -0.1405   1.1799  -1.3154
 YEG  HO06  H  HOH1  0   0.447  -2.5587   0.6367   0.3257

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
 YEG  C02  C01   single  1.548  0.020  1.548
 YEG  C05  C01   single  1.527  0.020  1.527
 YEG  C01  H01   single  0.970  0.020  1.090
 YEG  C01  H01A  single  0.970  0.020  1.090
 YEG  C03  C02   single  1.540  0.020  1.540
 YEG  C02  H02   single  0.970  0.020  1.090
 YEG  C02  H02A  single  0.970  0.020  1.090
 YEG  C04  C03   single  1.526  0.020  1.526
 YEG  C03  H03   single  0.970  0.020  1.090
 YEG  C03  H03A  single  0.970  0.020  1.090
 YEG  C04  O06   single  1.409  0.020  1.409
 YEG  C04  C05   single  1.527  0.020  1.527
 YEG  C04  H04   single  0.970  0.020  1.090
 YEG  C05  H05   single  0.970  0.020  1.090
 YEG  C05  H05A  single  0.970  0.020  1.090
 YEG  O06  HO06  single  0.850  0.020  0.980

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
 YEG  H01A  C01  H01  106.72  3.000
 YEG  H01A  C01  C05  112.68  3.000
 YEG  H01   C01  C05  109.75  3.000
 YEG  H01A  C01  C02  112.69  3.000
 YEG  H01   C01  C02  110.04  3.000
 YEG  C05   C01  C02  104.98  3.000
 YEG  H02A  C02  H02  106.51  3.000
 YEG  H02A  C02  C03  111.46  3.000
 YEG  H02   C02  C03  110.78  3.000
 YEG  H02A  C02  C01  110.80  3.000
 YEG  H02   C02  C01  111.45  3.000
 YEG  C03   C02  C01  105.93  3.000
 YEG  H03A  C03  H03  107.33  3.000
 YEG  H03A  C03  C04  112.70  3.000
 YEG  H03   C03  C04  108.48  3.000
 YEG  H03A  C03  C02  112.92  3.000
 YEG  H03   C03  C02  110.49  3.000
 YEG  C04   C03  C02  104.87  3.000
 YEG  H04   C04  O06  110.53  3.000
 YEG  H04   C04  C05  107.95  3.000
 YEG  O06   C04  C05  115.56  3.000
 YEG  H04   C04  C03  108.78  3.000
 YEG  C05   C04  C03  102.94  3.000
 YEG  O06   C04  C03  110.67  3.000
 YEG  H05A  C05  H05  107.73  3.000
 YEG  H05A  C05  C04  109.14  3.000
 YEG  H05   C05  C04  113.26  3.000
 YEG  H05A  C05  C01  110.78  3.000
 YEG  H05   C05  C01  113.22  3.000
 YEG  C04   C05  C01  102.66  3.000
 YEG  HO06  O06  C04  108.20  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
 YEG  Var_01  C04  C03  C02  C01  -14.11  30.0  1
 YEG  Var_02  C04  C05  C01  C02   34.63  30.0  1
 YEG  Var_03  C05  C01  C02  C03  -12.73  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
 YEG  chir_01  C04  C03  O06  C05  positiv

