# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:06:38 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (2S,3S,4R,5S)-2-(4-methoxyphenyl)-5-methylpyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@@H]2N[C@@H](C)[C@@H](O)[C@H]2O
#
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
 1KN  1KN  (2S,3S,4R,5S)-2-(4-methoxyphenyl)-5-methylpyrrolidine-3,4-diol  ligand  33  16  .  2022-03-10  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1KN
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
 1KN  CAP  C  CH3   0  -0.437   5.5147   0.3202   0.3175
 1KN  OAO  O  O2    0  -0.471   4.5576  -0.4011  -0.4315
 1KN  CAL  C  CR6   0   0.368   3.2515  -0.1830  -0.1831
 1KN  CAM  C  CR16  0  -0.329   2.3441  -0.9151  -0.9553
 1KN  CAN  C  CR16  0  -0.296   0.9853  -0.7610  -0.7650
 1KN  CAK  C  CR16  0  -0.369   2.7669   0.7015   0.7744
 1KN  CAJ  C  CR16  0  -0.316   1.3930   0.8395   0.9503
 1KN  CAI  C  CR6   0   0.124   0.4802   0.1236   0.1917
 1KN  CAC  C  CH1   0  -0.141  -0.9996   0.2822   0.4112
 1KN  NAD  N  NH1   0  -0.627  -1.6787  -0.9631   0.7798
 1KN  CAE  C  CH1   0  -0.072  -2.8410  -1.1745  -0.0939
 1KN  CAF  C  CH3   0  -0.660  -3.9672  -1.8983   0.6189
 1KN  CAA  C  CH1   0  -0.013  -3.1687   0.2259  -0.5907
 1KN  OAH  O  OH1   0  -0.674  -3.8397   0.9492   0.4123
 1KN  CAB  C  CH1   0   0.006  -1.7629   0.7795  -0.8238
 1KN  OAG  O  OH1   0  -0.663  -1.6836   2.1760  -0.9204
 1KN  H1   H  HCH3  0   0.228   5.4440   0.1063   1.3871
 1KN  H2   H  HCH3  0   0.259   6.4913   0.0012  -0.0382
 1KN  H3   H  HCH3  0   0.228   5.4220   1.3992   0.1688
 1KN  H4   H  HCR6  0   0.261   2.7170  -1.6037  -1.7036
 1KN  H5   H  HCR6  0   0.250   0.3084  -1.3431  -1.3806
 1KN  H6   H  HCR6  0   0.276   3.4343   1.2847   1.3941
 1KN  H7   H  HCR6  0   0.253   1.0324   1.5261   1.7074
 1KN  H8   H  HCH1  0   0.226  -1.1360   1.0277   1.2063
 1KN  H9   H  HNH1  0   0.352  -1.0530  -1.7555   0.7589
 1KN  H11  H  HCH1  0   0.218  -2.5654  -1.7579  -0.9840
 1KN  H12  H  HCH3  0   0.223  -4.2669  -1.3683   1.5220
 1KN  H13  H  HCH3  0   0.219  -4.8394  -2.0004  -0.0287
 1KN  H14  H  HCH3  0   0.228  -3.6519  -2.9020   0.9072
 1KN  H15  H  HCH1  0   0.226  -3.7580   0.1909  -1.5180
 1KN  H16  H  HOH1  0   0.444  -3.7592   1.8855   0.1984
 1KN  H17  H  HCH1  0   0.221  -1.3592   0.2934  -1.7226
 1KN  H18  H  HOH1  0   0.458  -1.9703   2.4399  -1.8005

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
 1KN  OAH  CAA  single    1.407  0.020  1.407
 1KN  OAG  CAB  single    1.402  0.020  1.402
 1KN  CAA  CAB  single    1.529  0.020  1.529
 1KN  CAA  CAE  single    1.522  0.020  1.522
 1KN  CAB  CAC  single    1.535  0.020  1.535
 1KN  CAC  NAD  single    1.466  0.020  1.466
 1KN  CAC  CAI  single    1.504  0.020  1.504
 1KN  CAF  CAE  single    1.517  0.020  1.517
 1KN  NAD  CAE  single    1.469  0.020  1.469
 1KN  CAJ  CAI  aromatic  1.386  0.020  1.386
 1KN  CAJ  CAK  aromatic  1.392  0.020  1.392
 1KN  CAI  CAN  aromatic  1.397  0.020  1.397
 1KN  CAK  CAL  aromatic  1.391  0.020  1.391
 1KN  CAN  CAM  aromatic  1.381  0.020  1.381
 1KN  CAL  CAM  aromatic  1.398  0.020  1.398
 1KN  CAL  OAO  single    1.347  0.020  1.347
 1KN  OAO  CAP  single    1.413  0.020  1.413
 1KN  CAP  H1   single    0.970  0.020  1.090
 1KN  CAP  H2   single    0.970  0.020  1.090
 1KN  CAP  H3   single    0.970  0.020  1.090
 1KN  CAM  H4   single    0.930  0.020  1.080
 1KN  CAN  H5   single    0.930  0.020  1.080
 1KN  CAK  H6   single    0.930  0.020  1.080
 1KN  CAJ  H7   single    0.930  0.020  1.080
 1KN  CAC  H8   single    0.970  0.020  1.090
 1KN  NAD  H9   single    0.890  0.020  1.040
 1KN  CAE  H11  single    0.970  0.020  1.090
 1KN  CAF  H12  single    0.970  0.020  1.090
 1KN  CAF  H13  single    0.970  0.020  1.090
 1KN  CAF  H14  single    0.970  0.020  1.090
 1KN  CAA  H15  single    0.970  0.020  1.090
 1KN  OAH  H16  single    0.850  0.020  0.980
 1KN  CAB  H17  single    0.970  0.020  1.090
 1KN  OAG  H18  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
 1KN  H3   CAP  H2   108.74  3.000
 1KN  H3   CAP  H1   108.71  3.000
 1KN  H2   CAP  H1   108.72  3.000
 1KN  H3   CAP  OAO  111.98  3.000
 1KN  H2   CAP  OAO  106.58  3.000
 1KN  H1   CAP  OAO  112.02  3.000
 1KN  CAL  OAO  CAP  118.44  3.000
 1KN  CAK  CAL  CAM  119.15  3.000
 1KN  CAM  CAL  OAO  116.26  3.000
 1KN  CAK  CAL  OAO  124.59  3.000
 1KN  H4   CAM  CAN  120.33  3.000
 1KN  H4   CAM  CAL  119.40  3.000
 1KN  CAN  CAM  CAL  120.27  3.000
 1KN  H5   CAN  CAI  120.18  3.000
 1KN  H5   CAN  CAM  118.43  3.000
 1KN  CAI  CAN  CAM  121.38  3.000
 1KN  H6   CAK  CAJ  118.90  3.000
 1KN  H6   CAK  CAL  121.50  3.000
 1KN  CAJ  CAK  CAL  119.60  3.000
 1KN  H7   CAJ  CAI  119.37  3.000
 1KN  H7   CAJ  CAK  118.65  3.000
 1KN  CAI  CAJ  CAK  121.98  3.000
 1KN  CAC  CAI  CAJ  120.89  3.000
 1KN  CAJ  CAI  CAN  117.62  3.000
 1KN  CAC  CAI  CAN  121.48  3.000
 1KN  H8   CAC  CAB  107.50  3.000
 1KN  H8   CAC  NAD  109.70  3.000
 1KN  CAB  CAC  NAD  104.31  3.000
 1KN  H8   CAC  CAI  107.42  3.000
 1KN  NAD  CAC  CAI  113.76  3.000
 1KN  CAB  CAC  CAI  113.95  3.000
 1KN  H9   NAD  CAE  111.40  3.000
 1KN  H9   NAD  CAC  111.99  3.000
 1KN  CAE  NAD  CAC  109.83  3.000
 1KN  H11  CAE  CAA  106.14  3.000
 1KN  H11  CAE  CAF  108.27  3.000
 1KN  CAA  CAE  CAF  115.64  3.000
 1KN  H11  CAE  NAD  111.07  3.000
 1KN  CAF  CAE  NAD  112.12  3.000
 1KN  CAA  CAE  NAD  103.42  3.000
 1KN  H14  CAF  H13  107.56  3.000
 1KN  H14  CAF  H12  107.95  3.000
 1KN  H13  CAF  H12  108.53  3.000
 1KN  H14  CAF  CAE  110.41  3.000
 1KN  H13  CAF  CAE  111.06  3.000
 1KN  H12  CAF  CAE  111.21  3.000
 1KN  H15  CAA  CAB  112.08  3.000
 1KN  H15  CAA  OAH  111.23  3.000
 1KN  CAB  CAA  OAH  111.16  3.000
 1KN  H15  CAA  CAE  111.20  3.000
 1KN  CAB  CAA  CAE  100.66  3.000
 1KN  OAH  CAA  CAE  110.07  3.000
 1KN  H16  OAH  CAA  107.54  3.000
 1KN  H17  CAB  OAG  111.32  3.000
 1KN  H17  CAB  CAA  107.60  3.000
 1KN  OAG  CAB  CAA  115.04  3.000
 1KN  H17  CAB  CAC  109.40  3.000
 1KN  CAA  CAB  CAC  102.55  3.000
 1KN  OAG  CAB  CAC  110.49  3.000
 1KN  H18  OAG  CAB  108.62  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
 1KN  CONST_01  CAI  CAJ  CAK  CAL    0.00   0.0  0
 1KN  CONST_02  CAI  CAN  CAM  CAL    0.00   0.0  0
 1KN  CONST_03  CAJ  CAI  CAN  CAM    0.00   0.0  0
 1KN  CONST_04  CAJ  CAK  CAL  CAM    0.00   0.0  0
 1KN  CONST_05  CAK  CAJ  CAI  CAN    0.00   0.0  0
 1KN  CONST_06  CAK  CAL  CAM  CAN    0.00   0.0  0
 1KN  CONST_07  CAC  CAI  CAN  CAM  180.00   0.0  0
 1KN  CONST_08  CAC  CAI  CAJ  CAK  180.00   0.0  0
 1KN  CONST_09  CAJ  CAK  CAL  OAO  180.00   0.0  0
 1KN  CONST_10  CAN  CAM  CAL  OAO  180.00   0.0  0
 1KN  CONST_11  H7   CAJ  CAK  CAL  180.00   0.0  0
 1KN  CONST_12  H5   CAN  CAM  CAL  180.00   0.0  0
 1KN  CONST_13  H6   CAK  CAL  CAM  180.00   0.0  0
 1KN  CONST_14  H4   CAM  CAL  CAK  180.00   0.0  0
 1KN  Var_01    CAK  CAL  OAO  CAP   -0.56  30.0  2
 1KN  Var_02    H1   CAP  OAO  CAL   61.41  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
 1KN  chir_01  CAC  CAB  NAD  CAI  negativ
 1KN  chir_02  CAE  NAD  CAA  CAF  positiv
 1KN  chir_03  CAA  OAH  CAE  CAB  positiv
 1KN  chir_04  CAB  OAG  CAA  CAC  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
 1KN  plan-1  OAO  0.020
 1KN  plan-1  CAL  0.020
 1KN  plan-1  CAM  0.020
 1KN  plan-1  CAN  0.020
 1KN  plan-1  CAK  0.020
 1KN  plan-1  CAJ  0.020
 1KN  plan-1  CAI  0.020
 1KN  plan-1  CAC  0.020
 1KN  plan-1  H4   0.020
 1KN  plan-1  H5   0.020
 1KN  plan-1  H6   0.020
 1KN  plan-1  H7   0.020

