# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 13:36:52 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  39  15  .  2022-09-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  OH1   0  -0.599  -6.4897  -0.4117   0.9813
 Y39  CAM  C  C     0   0.566  -5.6458   0.0664   0.0718
 Y39  OAC  O  O     0  -0.462  -5.8924   1.0366  -0.6073
 Y39  CAO  C  CH1   0  -0.420  -4.3971  -0.7156   0.0037
 Y39  CAL  C  CH2   0  -0.459  -3.6945  -0.8058  -1.3308
 Y39  CAN  C  CH1   0  -0.215  -3.1103   0.0342  -0.2600
 Y39  CAK  C  CH2   0  -0.425  -1.8488  -0.3919   0.4444
 Y39  CAJ  C  CH2   0  -0.416  -0.6005   0.1252  -0.2620
 Y39  CAI  C  CH2   0  -0.415   0.6934  -0.3547   0.3824
 Y39  CAH  C  CH2   0  -0.412   1.9392   0.2244  -0.2757
 Y39  CAG  C  CH2   0  -0.412   3.2386  -0.2888   0.3316
 Y39  CAF  C  CH2   0  -0.412   4.4807   0.3190  -0.3075
 Y39  CAE  C  CH2   0  -0.406   5.7833  -0.2029   0.2846
 Y39  CAD  C  CH2   0  -0.419   7.0237   0.4127  -0.3510
 Y39  CAA  C  CH3   0  -0.662   8.3213  -0.1151   0.2446
 Y39  H1   H  HOH1  0   0.479  -7.2920   0.1310   1.0008
 Y39  H2   H  HCH1  0   0.281  -4.3393  -1.5767   0.6587
 Y39  H3   H  HCH2  0   0.263  -3.2198  -1.7530  -1.5562
 Y39  H4   H  HCH2  0   0.263  -4.1691  -0.3254  -2.1762
 Y39  H5   H  HCH1  0   0.262  -3.2268   1.1068  -0.3829
 Y39  H6   H  HCH2  0   0.229  -1.8619  -0.0298   1.4769
 Y39  H7   H  HCH2  0   0.219  -1.8141  -1.4848   0.5012
 Y39  H8   H  HCH2  0   0.216  -0.6228  -0.1846  -1.3120
 Y39  H9   H  HCH2  0   0.212  -0.6199   1.2203  -0.2690
 Y39  H10  H  HCH2  0   0.209   0.6909  -0.0934   1.4465
 Y39  H11  H  HCH2  0   0.209   0.7343  -1.4488   0.3408
 Y39  H12  H  HCH2  0   0.207   1.9251  -0.0048  -1.3471
 Y39  H13  H  HCH2  0   0.207   1.9108   1.3173  -0.2020
 Y39  H14  H  HCH2  0   0.207   3.2451  -0.0810   1.4071
 Y39  H15  H  HCH2  0   0.206   3.2776  -1.3797   0.2362
 Y39  H16  H  HCH2  0   0.206   4.4673   0.1217  -1.3853
 Y39  H17  H  HCH2  0   0.206   4.4450   1.4090  -0.2016
 Y39  H18  H  HCH2  0   0.206   5.7960  -0.0109   1.3634
 Y39  H19  H  HCH2  0   0.205   5.8225  -1.2925   0.1736
 Y39  H20  H  HCH2  0   0.210   7.0102   0.2207  -1.4284
 Y39  H21  H  HCH2  0   0.210   6.9846   1.5007  -0.2385
 Y39  H22  H  HCH3  0   0.225   9.1934   0.3401  -0.2261
 Y39  H23  H  HCH3  0   0.216   8.3777   0.0923   1.3149
 Y39  H24  H  HCH3  0   0.216   8.4035  -1.1961   0.1167

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  double  1.210  0.020  1.210
 Y39  CAO  CAL  single  1.511  0.020  1.511
 Y39  CAO  CAM  single  1.475  0.020  1.475
 Y39  CAO  CAN  single  1.512  0.020  1.512
 Y39  CAL  CAN  single  1.481  0.020  1.481
 Y39  CAM  OAB  single  1.330  0.020  1.330
 Y39  CAK  CAN  single  1.506  0.020  1.506
 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  OAB  H1   single  0.850  0.020  0.980
 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  H1   OAB  CAM  109.75  3.000
 Y39  CAO  CAM  OAC  124.88  3.000
 Y39  CAO  CAM  OAB  112.23  3.000
 Y39  OAC  CAM  OAB  122.89  3.000
 Y39  H2   CAO  CAN  117.01  3.000
 Y39  H2   CAO  CAL  117.50  3.000
 Y39  CAN  CAO  CAL   58.67  3.000
 Y39  H2   CAO  CAM  116.01  3.000
 Y39  CAN  CAO  CAM  117.74  3.000
 Y39  CAL  CAO  CAM  117.78  3.000
 Y39  H4   CAL  H3   114.70  3.000
 Y39  H4   CAL  CAN  119.09  3.000
 Y39  H3   CAL  CAN  118.27  3.000
 Y39  H4   CAL  CAO  117.36  3.000
 Y39  H3   CAL  CAO  116.09  3.000
 Y39  CAN  CAL  CAO   60.72  3.000
 Y39  H5   CAN  CAK  114.97  3.000
 Y39  H5   CAN  CAL  115.85  3.000
 Y39  CAK  CAN  CAL  120.53  3.000
 Y39  H5   CAN  CAO  114.72  3.000
 Y39  CAK  CAN  CAO  119.39  3.000
 Y39  CAL  CAN  CAO   60.61  3.000
 Y39  H7   CAK  H6   106.36  3.000
 Y39  H7   CAK  CAJ  109.66  3.000
 Y39  H6   CAK  CAJ  109.56  3.000
 Y39  H7   CAK  CAN  109.46  3.000
 Y39  H6   CAK  CAN  109.74  3.000
 Y39  CAJ  CAK  CAN  111.90  3.000
 Y39  H9   CAJ  H8   106.05  3.000
 Y39  H9   CAJ  CAI  109.44  3.000
 Y39  H8   CAJ  CAI  109.51  3.000
 Y39  H9   CAJ  CAK  109.12  3.000
 Y39  H8   CAJ  CAK  109.37  3.000
 Y39  CAI  CAJ  CAK  113.12  3.000
 Y39  H11  CAI  H10  105.97  3.000
 Y39  H11  CAI  CAH  109.44  3.000
 Y39  H10  CAI  CAH  109.32  3.000
 Y39  H11  CAI  CAJ  109.28  3.000
 Y39  H10  CAI  CAJ  109.50  3.000
 Y39  CAH  CAI  CAJ  113.09  3.000
 Y39  H13  CAH  H12  105.91  3.000
 Y39  H13  CAH  CAG  109.35  3.000
 Y39  H12  CAH  CAG  109.29  3.000
 Y39  H13  CAH  CAI  109.20  3.000
 Y39  H12  CAH  CAI  109.41  3.000
 Y39  CAG  CAH  CAI  113.40  3.000
 Y39  H15  CAG  H14  105.91  3.000
 Y39  H15  CAG  CAF  109.37  3.000
 Y39  H14  CAG  CAF  109.35  3.000
 Y39  H15  CAG  CAH  109.33  3.000
 Y39  H14  CAG  CAH  109.43  3.000
 Y39  CAF  CAG  CAH  113.19  3.000
 Y39  H17  CAF  H16  105.89  3.000
 Y39  H17  CAF  CAE  109.34  3.000
 Y39  H16  CAF  CAE  109.34  3.000
 Y39  H17  CAF  CAG  109.25  3.000
 Y39  H16  CAF  CAG  109.32  3.000
 Y39  CAE  CAF  CAG  113.42  3.000
 Y39  H19  CAE  H18  105.88  3.000
 Y39  H19  CAE  CAD  109.29  3.000
 Y39  H18  CAE  CAD  109.29  3.000
 Y39  H19  CAE  CAF  109.39  3.000
 Y39  H18  CAE  CAF  109.43  3.000
 Y39  CAD  CAE  CAF  113.30  3.000
 Y39  H21  CAD  H20  105.96  3.000
 Y39  H21  CAD  CAA  109.57  3.000
 Y39  H20  CAD  CAA  109.56  3.000
 Y39  H21  CAD  CAE  109.25  3.000
 Y39  H20  CAD  CAE  109.25  3.000
 Y39  CAA  CAD  CAE  113.00  3.000
 Y39  H24  CAA  H23  107.40  3.000
 Y39  H24  CAA  H22  107.62  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  111.60  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  CONST_01  H1   OAB  CAM  CAO   180.00   0.0  0
 Y39  Var_01    CAN  CAL  CAO  CAM   107.17  30.0  1
 Y39  Var_02    CAK  CAN  CAL  CAO   108.77  30.0  1
 Y39  Var_03    CAL  CAO  CAM  OAB   148.94  30.0  1
 Y39  Var_04    CAJ  CAK  CAN  CAO   160.57  30.0  1
 Y39  Var_05    CAI  CAJ  CAK  CAN  -176.77  30.0  3
 Y39  Var_06    CAH  CAI  CAJ  CAK  -176.78  30.0  1
 Y39  Var_07    CAG  CAH  CAI  CAJ  -177.97  30.0  3
 Y39  Var_08    CAF  CAG  CAH  CAI  -178.60  30.0  1
 Y39  Var_09    CAE  CAF  CAG  CAH  -179.32  30.0  3
 Y39  Var_10    CAD  CAE  CAF  CAG  -179.67  30.0  3
 Y39  Var_11    CAA  CAD  CAE  CAF  -179.92  30.0  1
 Y39  Var_12    H22  CAA  CAD  CAE  -179.99  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
 Y39  plan-1  H1   0.020

