# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 00:53:49 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (1S,2S)-2-nonylcyclopropanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC[C@H]1C[C@@H]1C(O)=O
#
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
 Y39  Y39  '(1S,2S)-2-nonylcyclopropanecarboxylic acid'  ligand  38  15  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y39
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
 Y39  OAB  O  OC    -1  -0.625  -6.5248  -0.4298   0.9449
 Y39  CAM  C  C      0   0.419  -5.6933  -0.0082   0.1129
 Y39  OAC  O  O      0  -0.616  -5.8443   0.9684  -0.6512
 Y39  CAO  C  CH1    0  -0.414  -4.3804  -0.7560   0.0340
 Y39  CAL  C  CH2    0  -0.473  -3.6760  -0.8714  -1.2937
 Y39  CAN  C  CH1    0  -0.218  -3.1090   0.0033  -0.2313
 Y39  CAK  C  CH2    0  -0.421  -1.8292  -0.3877   0.4614
 Y39  CAJ  C  CH2    0  -0.412  -0.5885   0.1244  -0.2623
 Y39  CAI  C  CH2    0  -0.413   0.7124  -0.3399   0.3798
 Y39  CAH  C  CH2    0  -0.412   1.9561   0.2417  -0.2801
 Y39  CAG  C  CH2    0  -0.411   3.2548  -0.2685   0.3312
 Y39  CAF  C  CH2    0  -0.412   4.5010   0.3330  -0.3059
 Y39  CAE  C  CH2    0  -0.406   5.7981  -0.1913   0.2963
 Y39  CAD  C  CH2    0  -0.419   7.0456   0.4168  -0.3324
 Y39  CAA  C  CH3    0  -0.662   8.3365  -0.1154   0.2740
 Y39  H2   H  HCH1   0   0.222  -4.2873  -1.6094   0.6994
 Y39  H3   H  HCH2   0   0.232  -3.1616  -1.8006  -1.5130
 Y39  H4   H  HCH2   0   0.235  -4.1525  -0.4093  -2.1485
 Y39  H5   H  HCH1   0   0.233  -3.2403   1.0709  -0.3826
 Y39  H6   H  HCH2   0   0.215  -1.8296  -0.0076   1.4887
 Y39  H7   H  HCH2   0   0.208  -1.7788  -1.4792   0.5423
 Y39  H8   H  HCH2   0   0.210  -0.6180  -0.2024  -1.3071
 Y39  H9   H  HCH2   0   0.207  -0.6133   1.2194  -0.2876
 Y39  H10  H  HCH2   0   0.206   0.7102  -0.0739   1.4428
 Y39  H11  H  HCH2   0   0.206   0.7610  -1.4340   0.3450
 Y39  H12  H  HCH2   0   0.206   1.9434   0.0100  -1.3509
 Y39  H13  H  HCH2   0   0.206   1.9250   1.3347  -0.2089
 Y39  H14  H  HCH2   0   0.206   3.2591  -0.0557   1.4061
 Y39  H15  H  HCH2   0   0.206   3.2924  -1.3600   0.2415
 Y39  H16  H  HCH2   0   0.206   4.4925   0.1307  -1.3828
 Y39  H17  H  HCH2   0   0.206   4.4685   1.4236  -0.2051
 Y39  H18  H  HCH2   0   0.206   5.8040   0.0043   1.3745
 Y39  H19  H  HCH2   0   0.205   5.8338  -1.2814   0.1893
 Y39  H20  H  HCH2   0   0.210   7.0389   0.2221  -1.4094
 Y39  H21  H  HCH2   0   0.210   7.0110   1.5054  -0.2231
 Y39  H22  H  HCH3   0   0.225   9.2143   0.3344  -0.1914
 Y39  H23  H  HCH3   0   0.216   8.3860   0.0944   1.3443
 Y39  H24  H  HCH3   0   0.215   8.4145  -1.1972   0.1496

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
 Y39  OAC  CAM  deloc   1.249  0.020  1.249
 Y39  CAO  CAL  single  1.507  0.020  1.507
 Y39  CAO  CAM  single  1.513  0.020  1.513
 Y39  CAO  CAN  single  1.504  0.020  1.504
 Y39  CAL  CAN  single  1.488  0.020  1.488
 Y39  CAM  OAB  deloc   1.250  0.020  1.250
 Y39  CAK  CAN  single  1.507  0.020  1.507
 Y39  CAK  CAJ  single  1.525  0.020  1.525
 Y39  CAI  CAJ  single  1.523  0.020  1.523
 Y39  CAI  CAH  single  1.523  0.020  1.523
 Y39  CAG  CAH  single  1.523  0.020  1.523
 Y39  CAG  CAF  single  1.523  0.020  1.523
 Y39  CAF  CAE  single  1.523  0.020  1.523
 Y39  CAD  CAE  single  1.524  0.020  1.524
 Y39  CAD  CAA  single  1.522  0.020  1.522
 Y39  CAO  H2   single  0.970  0.020  1.090
 Y39  CAL  H3   single  0.970  0.020  1.090
 Y39  CAL  H4   single  0.970  0.020  1.090
 Y39  CAN  H5   single  0.970  0.020  1.090
 Y39  CAK  H6   single  0.970  0.020  1.090
 Y39  CAK  H7   single  0.970  0.020  1.090
 Y39  CAJ  H8   single  0.970  0.020  1.090
 Y39  CAJ  H9   single  0.970  0.020  1.090
 Y39  CAI  H10  single  0.970  0.020  1.090
 Y39  CAI  H11  single  0.970  0.020  1.090
 Y39  CAH  H12  single  0.970  0.020  1.090
 Y39  CAH  H13  single  0.970  0.020  1.090
 Y39  CAG  H14  single  0.970  0.020  1.090
 Y39  CAG  H15  single  0.970  0.020  1.090
 Y39  CAF  H16  single  0.970  0.020  1.090
 Y39  CAF  H17  single  0.970  0.020  1.090
 Y39  CAE  H18  single  0.970  0.020  1.090
 Y39  CAE  H19  single  0.970  0.020  1.090
 Y39  CAD  H20  single  0.970  0.020  1.090
 Y39  CAD  H21  single  0.970  0.020  1.090
 Y39  CAA  H22  single  0.970  0.020  1.090
 Y39  CAA  H23  single  0.970  0.020  1.090
 Y39  CAA  H24  single  0.970  0.020  1.090

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
 Y39  CAO  CAM  OAC  117.35  3.000
 Y39  CAO  CAM  OAB  116.45  3.000
 Y39  OAC  CAM  OAB  126.20  3.000
 Y39  H2   CAO  CAN  115.60  3.000
 Y39  H2   CAO  CAL  116.07  3.000
 Y39  CAN  CAO  CAL   59.23  3.000
 Y39  H2   CAO  CAM  115.52  3.000
 Y39  CAN  CAO  CAM  119.54  3.000
 Y39  CAL  CAO  CAM  119.29  3.000
 Y39  H4   CAL  H3   114.52  3.000
 Y39  H4   CAL  CAN  118.72  3.000
 Y39  H3   CAL  CAN  117.85  3.000
 Y39  H4   CAL  CAO  117.21  3.000
 Y39  H3   CAL  CAO  117.73  3.000
 Y39  CAN  CAL  CAO   60.28  3.000
 Y39  H5   CAN  CAK  114.95  3.000
 Y39  H5   CAN  CAL  115.60  3.000
 Y39  CAK  CAN  CAL  119.94  3.000
 Y39  H5   CAN  CAO  114.74  3.000
 Y39  CAK  CAN  CAO  120.38  3.000
 Y39  CAL  CAN  CAO   60.48  3.000
 Y39  H7   CAK  H6   106.05  3.000
 Y39  H7   CAK  CAJ  109.40  3.000
 Y39  H6   CAK  CAJ  109.20  3.000
 Y39  H7   CAK  CAN  109.36  3.000
 Y39  H6   CAK  CAN  109.92  3.000
 Y39  CAJ  CAK  CAN  112.69  3.000
 Y39  H9   CAJ  H8   106.00  3.000
 Y39  H9   CAJ  CAI  109.50  3.000
 Y39  H8   CAJ  CAI  109.53  3.000
 Y39  H9   CAJ  CAK  109.15  3.000
 Y39  H8   CAJ  CAK  109.31  3.000
 Y39  CAI  CAJ  CAK  113.11  3.000
 Y39  H11  CAI  H10  105.86  3.000
 Y39  H11  CAI  CAH  109.35  3.000
 Y39  H10  CAI  CAH  109.22  3.000
 Y39  H11  CAI  CAJ  109.20  3.000
 Y39  H10  CAI  CAJ  109.47  3.000
 Y39  CAH  CAI  CAJ  113.47  3.000
 Y39  H13  CAH  H12  105.91  3.000
 Y39  H13  CAH  CAG  109.41  3.000
 Y39  H12  CAH  CAG  109.34  3.000
 Y39  H13  CAH  CAI  109.24  3.000
 Y39  H12  CAH  CAI  109.46  3.000
 Y39  CAG  CAH  CAI  113.22  3.000
 Y39  H15  CAG  H14  105.88  3.000
 Y39  H15  CAG  CAF  109.33  3.000
 Y39  H14  CAG  CAF  109.28  3.000
 Y39  H15  CAG  CAH  109.27  3.000
 Y39  H14  CAG  CAH  109.39  3.000
 Y39  CAF  CAG  CAH  113.41  3.000
 Y39  H17  CAF  H16  105.90  3.000
 Y39  H17  CAF  CAE  109.36  3.000
 Y39  H16  CAF  CAE  109.36  3.000
 Y39  H17  CAF  CAG  109.29  3.000
 Y39  H16  CAF  CAG  109.38  3.000
 Y39  CAE  CAF  CAG  113.29  3.000
 Y39  H19  CAE  H18  105.87  3.000
 Y39  H19  CAE  CAD  109.28  3.000
 Y39  H18  CAE  CAD  109.29  3.000
 Y39  H19  CAE  CAF  109.36  3.000
 Y39  H18  CAE  CAF  109.39  3.000
 Y39  CAD  CAE  CAF  113.38  3.000
 Y39  H21  CAD  H20  105.96  3.000
 Y39  H21  CAD  CAA  109.56  3.000
 Y39  H20  CAD  CAA  109.57  3.000
 Y39  H21  CAD  CAE  109.26  3.000
 Y39  H20  CAD  CAE  109.27  3.000
 Y39  CAA  CAD  CAE  112.98  3.000
 Y39  H24  CAA  H23  107.39  3.000
 Y39  H24  CAA  H22  107.61  3.000
 Y39  H23  CAA  H22  107.61  3.000
 Y39  H24  CAA  CAD  111.20  3.000
 Y39  H23  CAA  CAD  111.21  3.000
 Y39  H22  CAA  CAD  111.61  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
 Y39  Var_01  CAN  CAL  CAO  CAM   108.90  30.0  1
 Y39  Var_02  CAK  CAN  CAL  CAO   110.15  30.0  1
 Y39  Var_03  CAL  CAO  CAM  OAB   146.83  30.0  2
 Y39  Var_04  CAJ  CAK  CAN  CAO   159.53  30.0  1
 Y39  Var_05  CAI  CAJ  CAK  CAN  -176.34  30.0  3
 Y39  Var_06  CAH  CAI  CAJ  CAK  -176.16  30.0  1
 Y39  Var_07  CAG  CAH  CAI  CAJ  -177.74  30.0  3
 Y39  Var_08  CAF  CAG  CAH  CAI  -178.77  30.0  1
 Y39  Var_09  CAE  CAF  CAG  CAH  -179.32  30.0  3
 Y39  Var_10  CAD  CAE  CAF  CAG  -179.57  30.0  3
 Y39  Var_11  CAA  CAD  CAE  CAF  -179.89  30.0  1
 Y39  Var_12  H22  CAA  CAD  CAE  -179.98  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
 Y39  chir_01  CAO  CAL  CAM  CAN  both
 Y39  chir_02  CAN  CAK  CAL  CAO  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
 Y39  plan-1  OAB  0.020
 Y39  plan-1  CAM  0.020
 Y39  plan-1  OAC  0.020
 Y39  plan-1  CAO  0.020

