# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 10:18:33 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@](CNC2CCCCC2)(C[C@@H]1O)[S](O)(=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
 OPX  OPX  '(1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid'  ligand  41  19  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OPX
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
 OPX  CAF  C  CH2    0  -0.428  -5.3830   0.4865  -0.3766
 OPX  CAG  C  CH2    0  -0.434  -4.7885   1.0150   0.9244
 OPX  CAH  C  CH2    0  -0.433  -4.3981   0.6410  -1.5303
 OPX  CAI  C  CH2    0  -0.448  -3.4479   0.3543   1.2303
 OPX  CAJ  C  CH2    0  -0.433  -3.0585  -0.0153  -1.2127
 OPX  CAK  C  CH2    0  -0.233  -0.1309   0.1787  -0.5074
 OPX  CAL  C  CH2    0  -0.453   2.3062   0.1832  -1.0760
 OPX  CAM  C  CH2    0  -0.468   1.6699   0.8120   1.2125
 OPX  CAO  C  CR15   0   0.017   3.4110   0.9740  -0.3908
 OPX  CAP  C  CR15   0   0.010   2.6552   1.8166   0.6397
 OPX  CAQ  C  CH1    0  -0.033  -2.4574   0.5266   0.0826
 OPX  CAR  C  CR5    0  -0.306   1.2699  -0.1097   0.0302
 OPX  NAN  N  NH1    0  -0.602  -1.2105  -0.1480   0.3988
 OPX  OAC  O  OH1    0  -0.670   4.1332   1.7372  -1.3300
 OPX  OAD  O  OH1    0  -0.673   1.9541   2.8680   0.0123
 OPX  SAS  S  S      0   1.438   1.4231  -1.8535   0.5470
 OPX  H1   H  HCH2   0   0.208  -5.6344  -0.5728  -0.2556
 OPX  H2   H  HCH2   0   0.225  -6.3186   1.0031  -0.6055
 OPX  H3   H  HCH2   0   0.209  -4.6511   2.0988   0.8449
 OPX  H4   H  HCH2   0   0.228  -5.4816   0.8535   1.7534
 OPX  H5   H  HCH2   0   0.227  -4.8140   0.2133  -2.4456
 OPX  H6   H  HCH2   0   0.208  -4.2419   1.7063  -1.7327
 OPX  H7   H  HCH2   0   0.225  -3.0235   0.7712   2.1494
 OPX  H8   H  HCH2   0   0.210  -3.5971  -0.7163   1.4099
 OPX  H9   H  HCH2   0   0.206  -3.1907  -1.0980  -1.1050
 OPX  H10  H  HCH2   0   0.231  -2.3680   0.1335  -2.0470
 OPX  H11  H  HCH2   0   0.200  -0.1373   1.2466  -0.7816
 OPX  H12  H  HCH2   0   0.228  -0.2594  -0.3757  -1.4408
 OPX  H13  H  HCH2   0   0.242   1.8460   0.8037  -1.8501
 OPX  H14  H  HCH2   0   0.253   2.6764  -0.7128  -1.5735
 OPX  H15  H  HCH2   0   0.253   2.1704   0.2553   2.0059
 OPX  H16  H  HCH2   0   0.244   0.8093   1.2998   1.6751
 OPX  H17  H  HCR5   0   0.221   4.0676   0.2830   0.1506
 OPX  H18  H  HCR5   0   0.216   3.3276   2.2090   1.4158
 OPX  H19  H  HCH1   0   0.173  -2.2945   1.6128  -0.0582
 OPX  H20  H  HNH1   0   0.338  -0.9419   0.0800   1.3481
 OPX  H22  H  HOH1   0   0.455   4.9400   2.0541  -0.9120
 OPX  H23  H  HOH1   0   0.439   2.5418   3.2502  -0.6502
 OPX  OAA  O  OS     0  -0.764   0.8720  -2.6565  -0.5640
 OPX  OAB  O  OS     0  -0.766   2.8750  -2.0733   0.7416
 OPX  OAE  O  OS    -1  -0.760   0.6719  -2.0006   1.8100

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
 OPX  CAF  CAG  single  1.525  0.020  1.525
 OPX  CAF  CAH  single  1.525  0.020  1.525
 OPX  CAG  CAI  single  1.526  0.020  1.526
 OPX  CAI  CAQ  single  1.526  0.020  1.526
 OPX  CAH  CAJ  single  1.525  0.020  1.525
 OPX  CAJ  CAQ  single  1.527  0.020  1.527
 OPX  CAQ  NAN  single  1.453  0.020  1.453
 OPX  NAN  CAK  single  1.447  0.020  1.447
 OPX  OAA  SAS  deloc   1.477  0.020  1.477
 OPX  CAL  CAR  single  1.544  0.020  1.544
 OPX  CAL  CAO  single  1.522  0.020  1.522
 OPX  OAC  CAO  single  1.409  0.020  1.409
 OPX  CAK  CAR  single  1.528  0.020  1.528
 OPX  CAR  SAS  single  1.825  0.020  1.825
 OPX  CAR  CAM  single  1.552  0.020  1.552
 OPX  CAO  CAP  single  1.531  0.020  1.531
 OPX  SAS  OAB  deloc   1.481  0.020  1.481
 OPX  SAS  OAE  deloc   1.477  0.020  1.477
 OPX  OAD  CAP  single  1.411  0.020  1.411
 OPX  CAP  CAM  single  1.519  0.020  1.519
 OPX  CAF  H1   single  0.970  0.020  1.090
 OPX  CAF  H2   single  0.970  0.020  1.090
 OPX  CAG  H3   single  0.970  0.020  1.090
 OPX  CAG  H4   single  0.970  0.020  1.090
 OPX  CAH  H5   single  0.970  0.020  1.090
 OPX  CAH  H6   single  0.970  0.020  1.090
 OPX  CAI  H7   single  0.970  0.020  1.090
 OPX  CAI  H8   single  0.970  0.020  1.090
 OPX  CAJ  H9   single  0.970  0.020  1.090
 OPX  CAJ  H10  single  0.970  0.020  1.090
 OPX  CAK  H11  single  0.970  0.020  1.090
 OPX  CAK  H12  single  0.970  0.020  1.090
 OPX  CAL  H13  single  0.970  0.020  1.090
 OPX  CAL  H14  single  0.970  0.020  1.090
 OPX  CAM  H15  single  0.970  0.020  1.090
 OPX  CAM  H16  single  0.970  0.020  1.090
 OPX  CAO  H17  single  0.970  0.020  1.090
 OPX  CAP  H18  single  0.970  0.020  1.090
 OPX  CAQ  H19  single  0.970  0.020  1.090
 OPX  NAN  H20  single  0.890  0.020  1.040
 OPX  OAC  H22  single  0.850  0.020  0.980
 OPX  OAD  H23  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
 OPX  H2   CAF  H1   106.48  3.000
 OPX  H2   CAF  CAH  110.28  3.000
 OPX  H1   CAF  CAH  109.26  3.000
 OPX  H2   CAF  CAG  110.40  3.000
 OPX  H1   CAF  CAG  109.29  3.000
 OPX  CAH  CAF  CAG  111.01  3.000
 OPX  H4   CAG  H3   106.31  3.000
 OPX  H4   CAG  CAI  109.96  3.000
 OPX  H3   CAG  CAI  109.44  3.000
 OPX  H4   CAG  CAF  110.42  3.000
 OPX  H3   CAG  CAF  109.27  3.000
 OPX  CAI  CAG  CAF  111.32  3.000
 OPX  H6   CAH  H5   106.27  3.000
 OPX  H6   CAH  CAJ  109.38  3.000
 OPX  H5   CAH  CAJ  109.90  3.000
 OPX  H6   CAH  CAF  109.29  3.000
 OPX  H5   CAH  CAF  110.38  3.000
 OPX  CAJ  CAH  CAF  111.48  3.000
 OPX  H8   CAI  H7   106.69  3.000
 OPX  H8   CAI  CAQ  108.79  3.000
 OPX  H7   CAI  CAQ  109.69  3.000
 OPX  H8   CAI  CAG  109.65  3.000
 OPX  H7   CAI  CAG  110.12  3.000
 OPX  CAQ  CAI  CAG  111.76  3.000
 OPX  H10  CAJ  H9   106.60  3.000
 OPX  H10  CAJ  CAQ  110.51  3.000
 OPX  H9   CAJ  CAQ  108.34  3.000
 OPX  H10  CAJ  CAH  109.71  3.000
 OPX  H9   CAJ  CAH  109.86  3.000
 OPX  CAQ  CAJ  CAH  111.69  3.000
 OPX  H12  CAK  H11  106.15  3.000
 OPX  H12  CAK  NAN  109.42  3.000
 OPX  H11  CAK  NAN  111.72  3.000
 OPX  H12  CAK  CAR  108.21  3.000
 OPX  H11  CAK  CAR  106.00  3.000
 OPX  NAN  CAK  CAR  114.91  3.000
 OPX  H14  CAL  H13  106.64  3.000
 OPX  H14  CAL  CAR  113.53  3.000
 OPX  H13  CAL  CAR  109.41  3.000
 OPX  H14  CAL  CAO  112.72  3.000
 OPX  H13  CAL  CAO  109.23  3.000
 OPX  CAR  CAL  CAO  105.27  3.000
 OPX  H16  CAM  H15  106.34  3.000
 OPX  H16  CAM  CAR  112.64  3.000
 OPX  H15  CAM  CAR  111.68  3.000
 OPX  H16  CAM  CAP  112.05  3.000
 OPX  H15  CAM  CAP  108.31  3.000
 OPX  CAR  CAM  CAP  105.83  3.000
 OPX  H17  CAO  OAC  111.32  3.000
 OPX  H17  CAO  CAP  108.07  3.000
 OPX  OAC  CAO  CAP  113.81  3.000
 OPX  H17  CAO  CAL  109.25  3.000
 OPX  CAP  CAO  CAL  103.34  3.000
 OPX  OAC  CAO  CAL  110.70  3.000
 OPX  H18  CAP  OAD  110.60  3.000
 OPX  H18  CAP  CAO  111.70  3.000
 OPX  OAD  CAP  CAO  110.86  3.000
 OPX  H18  CAP  CAM  111.51  3.000
 OPX  OAD  CAP  CAM  109.76  3.000
 OPX  CAO  CAP  CAM  102.13  3.000
 OPX  H19  CAQ  NAN  110.91  3.000
 OPX  H19  CAQ  CAJ  107.35  3.000
 OPX  NAN  CAQ  CAJ  110.96  3.000
 OPX  H19  CAQ  CAI  107.57  3.000
 OPX  NAN  CAQ  CAI  109.94  3.000
 OPX  CAJ  CAQ  CAI  110.02  3.000
 OPX  SAS  CAR  CAM  109.28  3.000
 OPX  CAM  CAR  CAL  105.08  3.000
 OPX  SAS  CAR  CAL  109.13  3.000
 OPX  CAM  CAR  CAK  113.10  3.000
 OPX  SAS  CAR  CAK  110.91  3.000
 OPX  CAL  CAR  CAK  109.12  3.000
 OPX  H20  NAN  CAQ  109.10  3.000
 OPX  H20  NAN  CAK  109.77  3.000
 OPX  CAQ  NAN  CAK  113.54  3.000
 OPX  H22  OAC  CAO  108.57  3.000
 OPX  H23  OAD  CAP  107.33  3.000
 OPX  OAE  SAS  OAB  111.81  3.000
 OPX  OAE  SAS  OAA  113.53  3.000
 OPX  OAB  SAS  OAA  112.57  3.000
 OPX  OAE  SAS  CAR  107.13  3.000
 OPX  OAB  SAS  CAR  105.14  3.000
 OPX  OAA  SAS  CAR  105.96  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
 OPX  Var_01  CAQ  CAI  CAG  CAF   55.96  30.0  1
 OPX  Var_02  CAQ  CAJ  CAH  CAF  -55.74  30.0  1
 OPX  Var_03  CAJ  CAH  CAF  CAG   54.68  30.0  1
 OPX  Var_04  CAI  CAG  CAF  CAH  -54.71  30.0  1
 OPX  Var_05  CAR  CAK  NAN  CAQ  160.35  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
 OPX  chir_01  CAO  CAL  OAC  CAP  negativ
 OPX  chir_02  CAP  OAD  CAO  CAM  positiv
 OPX  chir_03  CAQ  NAN  CAI  CAJ  positiv
 OPX  chir_04  CAR  CAL  CAK  CAM  positiv

