# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:53:43 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (2S,3R,4S,5S)-2-methyl-5-(4-methylphenyl)pyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H]([C@H](O)[C@@H]1O)c2ccc(C)cc2
#
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
 K80  K80  (2S,3R,4S,5S)-2-methyl-5-(4-methylphenyl)pyrrolidine-3,4-diol  ligand  32  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_K80
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
 K80  CAJ  C  CR16  0  -0.310   1.7265   0.9436   0.9433
 K80  CAK  C  CR16  0  -0.286   3.1009   0.8418   0.7669
 K80  CAL  C  CR6   0   0.083   3.6460  -0.1218  -0.0752
 K80  CAO  C  CH3   0  -0.722   5.1313  -0.2650  -0.2378
 K80  CAM  C  CR16  0  -0.282   2.7670  -0.9737  -0.7456
 K80  CAN  C  CR16  0  -0.307   1.3963  -0.8708  -0.5715
 K80  CAI  C  CR6   0   0.124   0.8530   0.0911   0.2797
 K80  CAC  C  CH1   0  -0.127  -0.6341   0.2232   0.4710
 K80  NAD  N  NH1   0  -0.632  -1.3227  -1.0343   0.7552
 K80  CAE  C  CH1   0  -0.071  -2.4318  -1.2253  -0.1855
 K80  CAF  C  CH3   0  -0.660  -3.5814  -1.9936   0.4387
 K80  CAA  C  CH1   0  -0.005  -2.7582   0.1919  -0.6340
 K80  OAH  O  OH1   0  -0.675  -3.4930   0.8617   0.3612
 K80  CAB  C  CH1   0  -0.001  -1.3536   0.7805  -0.7678
 K80  OAG  O  OH1   0  -0.662  -1.3003   2.1819  -0.7714
 K80  H1   H  HCR6  0   0.246   1.3282   1.6990   1.6110
 K80  H2   H  HCR6  0   0.245   3.7574   1.5205   1.2992
 K80  H3   H  HCH3  0   0.247   5.5152  -1.0800   0.3802
 K80  H4   H  HCH3  0   0.243   5.4019  -0.4912  -1.2692
 K80  H5   H  HCH3  0   0.243   5.6564   0.6422   0.0591
 K80  H6   H  HCR6  0   0.245   3.1629  -1.7300  -1.4140
 K80  H7   H  HCR6  0   0.247   0.7452  -1.5485  -1.1132
 K80  H8   H  HCH1  0   0.228  -0.7969   0.9329   1.2935
 K80  H9   H  HNH1  0   0.352  -0.6981  -1.8272   0.7681
 K80  H11  H  HCH1  0   0.216  -2.1095  -1.7667  -1.0877
 K80  H12  H  HCH3  0   0.223  -3.9414  -1.5002   1.3402
 K80  H13  H  HCH3  0   0.220  -4.4129  -2.0897  -0.2613
 K80  H14  H  HCH3  0   0.228  -3.2625  -3.0012   0.7093
 K80  H15  H  HCH1  0   0.224  -3.2972   0.1884  -1.5922
 K80  H16  H  HOH1  0   0.443  -3.3364   1.8065   0.2495
 K80  H17  H  HCH1  0   0.225  -0.8956   0.3619  -1.6746
 K80  H18  H  HOH1  0   0.460  -1.5644   2.4969  -1.6417

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
 K80  OAH  CAA  single    1.407  0.020  1.407
 K80  OAG  CAB  single    1.402  0.020  1.402
 K80  CAA  CAB  single    1.529  0.020  1.529
 K80  CAA  CAE  single    1.522  0.020  1.522
 K80  CAB  CAC  single    1.537  0.020  1.537
 K80  CAF  CAE  single    1.517  0.020  1.517
 K80  CAC  NAD  single    1.462  0.020  1.462
 K80  CAC  CAI  single    1.505  0.020  1.505
 K80  NAD  CAE  single    1.467  0.020  1.467
 K80  CAJ  CAI  aromatic  1.389  0.020  1.389
 K80  CAJ  CAK  aromatic  1.389  0.020  1.389
 K80  CAI  CAN  aromatic  1.395  0.020  1.395
 K80  CAK  CAL  aromatic  1.391  0.020  1.391
 K80  CAN  CAM  aromatic  1.386  0.020  1.386
 K80  CAL  CAM  aromatic  1.396  0.020  1.396
 K80  CAL  CAO  single    1.501  0.020  1.501
 K80  CAJ  H1   single    0.930  0.020  1.080
 K80  CAK  H2   single    0.930  0.020  1.080
 K80  CAO  H3   single    0.970  0.020  1.090
 K80  CAO  H4   single    0.970  0.020  1.090
 K80  CAO  H5   single    0.970  0.020  1.090
 K80  CAM  H6   single    0.930  0.020  1.080
 K80  CAN  H7   single    0.930  0.020  1.080
 K80  CAC  H8   single    0.970  0.020  1.090
 K80  NAD  H9   single    0.890  0.020  1.040
 K80  CAE  H11  single    0.970  0.020  1.090
 K80  CAF  H12  single    0.970  0.020  1.090
 K80  CAF  H13  single    0.970  0.020  1.090
 K80  CAF  H14  single    0.970  0.020  1.090
 K80  CAA  H15  single    0.970  0.020  1.090
 K80  OAH  H16  single    0.850  0.020  0.980
 K80  CAB  H17  single    0.970  0.020  1.090
 K80  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
 K80  H1   CAJ  CAI  119.39  3.000
 K80  H1   CAJ  CAK  119.52  3.000
 K80  CAI  CAJ  CAK  121.09  3.000
 K80  H2   CAK  CAL  119.58  3.000
 K80  H2   CAK  CAJ  119.40  3.000
 K80  CAL  CAK  CAJ  121.01  3.000
 K80  CAM  CAL  CAO  120.86  3.000
 K80  CAO  CAL  CAK  121.29  3.000
 K80  CAM  CAL  CAK  117.83  3.000
 K80  H5   CAO  H4   108.12  3.000
 K80  H5   CAO  H3   107.32  3.000
 K80  H4   CAO  H3   107.05  3.000
 K80  H5   CAO  CAL  111.59  3.000
 K80  H4   CAO  CAL  111.59  3.000
 K80  H3   CAO  CAL  110.95  3.000
 K80  H6   CAM  CAN  119.37  3.000
 K80  H6   CAM  CAL  119.47  3.000
 K80  CAN  CAM  CAL  121.16  3.000
 K80  H7   CAN  CAI  120.13  3.000
 K80  H7   CAN  CAM  118.99  3.000
 K80  CAI  CAN  CAM  120.88  3.000
 K80  CAC  CAI  CAN  121.53  3.000
 K80  CAN  CAI  CAJ  118.03  3.000
 K80  CAC  CAI  CAJ  120.44  3.000
 K80  H8   CAC  CAB  107.45  3.000
 K80  H8   CAC  NAD  109.91  3.000
 K80  CAB  CAC  NAD  104.37  3.000
 K80  H8   CAC  CAI  107.35  3.000
 K80  NAD  CAC  CAI  114.50  3.000
 K80  CAB  CAC  CAI  113.07  3.000
 K80  H9   NAD  CAE  111.95  3.000
 K80  H9   NAD  CAC  112.75  3.000
 K80  CAE  NAD  CAC  110.09  3.000
 K80  H11  CAE  CAA  106.22  3.000
 K80  H11  CAE  CAF  108.07  3.000
 K80  CAA  CAE  CAF  115.49  3.000
 K80  H11  CAE  NAD  111.61  3.000
 K80  CAF  CAE  NAD  112.03  3.000
 K80  CAA  CAE  NAD  103.29  3.000
 K80  H14  CAF  H13  107.50  3.000
 K80  H14  CAF  H12  108.04  3.000
 K80  H13  CAF  H12  108.61  3.000
 K80  H14  CAF  CAE  110.38  3.000
 K80  H13  CAF  CAE  110.99  3.000
 K80  H12  CAF  CAE  111.20  3.000
 K80  H15  CAA  CAB  112.05  3.000
 K80  H15  CAA  OAH  111.23  3.000
 K80  CAB  CAA  OAH  111.01  3.000
 K80  H15  CAA  CAE  111.04  3.000
 K80  CAB  CAA  CAE  100.79  3.000
 K80  OAH  CAA  CAE  110.30  3.000
 K80  H16  OAH  CAA  107.44  3.000
 K80  H17  CAB  OAG  111.27  3.000
 K80  H17  CAB  CAA  107.97  3.000
 K80  OAG  CAB  CAA  114.82  3.000
 K80  H17  CAB  CAC  109.38  3.000
 K80  CAA  CAB  CAC  102.71  3.000
 K80  OAG  CAB  CAC  110.28  3.000
 K80  H18  OAG  CAB  108.60  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
 K80  CONST_01  CAM  CAN  CAI  CAJ    0.00   0.0  0
 K80  CONST_02  CAM  CAL  CAK  CAJ    0.00   0.0  0
 K80  CONST_03  CAN  CAI  CAJ  CAK    0.00   0.0  0
 K80  CONST_04  CAN  CAM  CAL  CAK    0.00   0.0  0
 K80  CONST_05  CAI  CAJ  CAK  CAL    0.00   0.0  0
 K80  CONST_06  CAI  CAN  CAM  CAL    0.00   0.0  0
 K80  CONST_07  CAC  CAI  CAJ  CAK  180.00   0.0  0
 K80  CONST_08  CAC  CAI  CAN  CAM  180.00   0.0  0
 K80  CONST_09  CAO  CAL  CAK  CAJ  180.00   0.0  0
 K80  CONST_10  CAN  CAM  CAL  CAO  180.00   0.0  0
 K80  CONST_11  H7   CAN  CAI  CAJ  180.00   0.0  0
 K80  CONST_12  H6   CAM  CAL  CAK  180.00   0.0  0
 K80  CONST_13  H1   CAJ  CAK  CAL  180.00   0.0  0
 K80  CONST_14  H2   CAK  CAL  CAM  180.00   0.0  0
 K80  Var_01    H3   CAO  CAL  CAK   99.11  30.0  2

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
 K80  chir_01  CAC  CAB  NAD  CAI  negativ
 K80  chir_02  CAE  NAD  CAA  CAF  positiv
 K80  chir_03  CAA  OAH  CAE  CAB  positiv
 K80  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
 K80  plan-1  CAJ  0.020
 K80  plan-1  CAK  0.020
 K80  plan-1  CAL  0.020
 K80  plan-1  CAO  0.020
 K80  plan-1  CAM  0.020
 K80  plan-1  CAN  0.020
 K80  plan-1  CAI  0.020
 K80  plan-1  CAC  0.020
 K80  plan-1  H1   0.020
 K80  plan-1  H2   0.020
 K80  plan-1  H6   0.020
 K80  plan-1  H7   0.020

