# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 02:10:25 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)NCCS
#
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
 PNY  PNY  (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide  ligand  40  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PNY
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
 PNY  CAA   C  CH2   0  -0.132  -4.3169  -1.0837   1.1861
 PNY  CAB   C  CH3   0  -0.665  -3.0372  -1.6770  -0.8910
 PNY  OAC   O  O     0  -0.499   2.7065   0.6641   1.0939
 PNY  OAD   O  O     0  -0.498  -2.3087   1.4035   1.4103
 PNY  OAE   O  OH1   0  -0.673  -4.8020  -2.4045   1.2910
 PNY  CAF   C  CT    0  -0.146  -4.0955  -0.7480  -0.2902
 PNY  SAG   S  S2    0  -0.258   7.2082  -0.7322   0.2619
 PNY  CAH   C  CH2   0  -0.553   5.4416  -1.0134  -0.0957
 PNY  CAI   C  CH3   0  -0.644  -5.4014  -0.9174  -1.0735
 PNY  CAJ   C  CH2   0  -0.283   4.8580   0.2753  -0.6640
 PNY  CAK   C  CH2   0  -0.257   0.1239   1.1723  -0.0505
 PNY  CAL   C  CH2   0  -0.599   1.0720   0.0935  -0.5598
 PNY  NAM   N  NH1   0  -0.631   3.4538   0.1439  -0.9695
 PNY  CAO   C  C     0   0.561   2.4819   0.3302  -0.0613
 PNY  CAP   C  C     0   0.516  -2.3194   1.0487   0.2369
 PNY  CAQ   C  CH1   0  -0.037  -3.6479   0.7313  -0.4524
 PNY  OAR   O  OH1   0  -0.663  -4.6101   1.6446   0.0054
 PNY  HAA   H  HCH2  0   0.196  -5.0329  -0.3735   1.6207
 PNY  HAAA  H  HCH2  0   0.205  -3.3763  -0.9727   1.7393
 PNY  HAB   H  HCH3  0   0.243  -3.4082  -2.7001  -0.9353
 PNY  HABA  H  HCH3  0   0.226  -2.7877  -1.3799  -1.9125
 PNY  HABB  H  HCH3  0   0.229  -2.1145  -1.6912  -0.3088
 PNY  HOAE  H  HOH1  0   0.454  -4.9003  -2.6089   2.2249
 PNY  HSAG  H  HSH1  0   0.229   7.4868  -1.9548   0.7250
 PNY  HAH   H  HCH2  0   0.271   5.3384  -1.8241  -0.8162
 PNY  HAHA  H  HCH2  0   0.274   4.9232  -1.2903   0.8212
 PNY  HAI   H  HCH3  0   0.230  -6.2048  -0.3048  -0.6643
 PNY  HAIA  H  HCH3  0   0.223  -5.2617  -0.6330  -2.1191
 PNY  HAIB  H  HCH3  0   0.234  -5.7328  -1.9550  -1.0586
 PNY  HAJ   H  HCH2  0   0.255   4.9959   1.0942   0.0427
 PNY  HAJA  H  HCH2  0   0.265   5.3764   0.5474  -1.5834
 PNY  HAK   H  HCH2  0   0.258   0.1157   1.1841   1.0363
 PNY  HAKA  H  HCH2  0   0.253   0.4617   2.1565  -0.3865
 PNY  HAL   H  HCH2  0   0.281   0.7439  -0.8827  -0.1910
 PNY  HALA  H  HCH2  0   0.263   1.0412   0.0462  -1.6510
 PNY  HNAM  H  HNH1  0   0.406   3.2010  -0.1564  -1.8962
 PNY  HNAN  H  HNH1  0   0.404  -1.3422   0.7316  -1.4991
 PNY  HAQ   H  HCH1  0   0.250  -3.5342   0.9010  -1.5300
 PNY  HOAR  H  HOH1  0   0.444  -4.4336   1.8158   0.9390
 PNY  NAN   N  NH1   0  -0.631  -1.2227   0.9292  -0.5178

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
 PNY  CAA  OAE   single  1.411  0.020  1.411
 PNY  CAA  CAF   single  1.530  0.020  1.530
 PNY  CAB  CAF   single  1.531  0.020  1.531
 PNY  OAC  CAO   double  1.223  0.020  1.223
 PNY  OAD  CAP   double  1.226  0.020  1.226
 PNY  CAF  CAI   single  1.532  0.020  1.532
 PNY  CAF  CAQ   single  1.554  0.020  1.554
 PNY  SAG  CAH   single  1.824  0.020  1.824
 PNY  CAH  CAJ   single  1.525  0.020  1.525
 PNY  CAJ  NAM   single  1.443  0.020  1.443
 PNY  CAK  CAL   single  1.524  0.020  1.524
 PNY  CAK  NAN   single  1.446  0.020  1.446
 PNY  CAL  CAO   single  1.514  0.020  1.514
 PNY  NAM  CAO   single  1.343  0.020  1.343
 PNY  NAN  CAP   single  1.337  0.020  1.337
 PNY  CAP  CAQ   single  1.530  0.020  1.530
 PNY  CAQ  OAR   single  1.403  0.020  1.403
 PNY  CAA  HAA   single  0.970  0.020  1.090
 PNY  CAA  HAAA  single  0.970  0.020  1.090
 PNY  CAB  HAB   single  0.970  0.020  1.090
 PNY  CAB  HABA  single  0.970  0.020  1.090
 PNY  CAB  HABB  single  0.970  0.020  1.090
 PNY  OAE  HOAE  single  0.850  0.020  0.980
 PNY  SAG  HSAG  single  1.200  0.020  1.300
 PNY  CAH  HAH   single  0.970  0.020  1.090
 PNY  CAH  HAHA  single  0.970  0.020  1.090
 PNY  CAI  HAI   single  0.970  0.020  1.090
 PNY  CAI  HAIA  single  0.970  0.020  1.090
 PNY  CAI  HAIB  single  0.970  0.020  1.090
 PNY  CAJ  HAJ   single  0.970  0.020  1.090
 PNY  CAJ  HAJA  single  0.970  0.020  1.090
 PNY  CAK  HAK   single  0.970  0.020  1.090
 PNY  CAK  HAKA  single  0.970  0.020  1.090
 PNY  CAL  HAL   single  0.970  0.020  1.090
 PNY  CAL  HALA  single  0.970  0.020  1.090
 PNY  NAM  HNAM  single  0.860  0.020  1.020
 PNY  NAN  HNAN  single  0.860  0.020  1.020
 PNY  CAQ  HAQ   single  0.970  0.020  1.090
 PNY  OAR  HOAR  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
 PNY  HAAA  CAA  HAA   107.10  3.000
 PNY  HAAA  CAA  CAF   109.90  3.000
 PNY  HAA   CAA  CAF   109.53  3.000
 PNY  HAAA  CAA  OAE   110.61  3.000
 PNY  HAA   CAA  OAE   110.60  3.000
 PNY  CAF   CAA  OAE   109.08  3.000
 PNY  HABB  CAB  HABA  108.01  3.000
 PNY  HABB  CAB  HAB   107.31  3.000
 PNY  HABA  CAB  HAB   107.17  3.000
 PNY  HABB  CAB  CAF   112.52  3.000
 PNY  HABA  CAB  CAF   111.08  3.000
 PNY  HAB   CAB  CAF   110.52  3.000
 PNY  HOAE  OAE  CAA   107.85  3.000
 PNY  CAQ   CAF  CAI   107.30  3.000
 PNY  CAQ   CAF  CAB   109.73  3.000
 PNY  CAI   CAF  CAB   108.75  3.000
 PNY  CAQ   CAF  CAA   110.56  3.000
 PNY  CAI   CAF  CAA   110.22  3.000
 PNY  CAB   CAF  CAA   110.21  3.000
 PNY  HSAG  SAG  CAH    97.40  3.000
 PNY  HAHA  CAH  HAH   108.81  3.000
 PNY  HAHA  CAH  CAJ   110.28  3.000
 PNY  HAH   CAH  CAJ   110.25  3.000
 PNY  HAHA  CAH  SAG   109.58  3.000
 PNY  HAH   CAH  SAG   109.63  3.000
 PNY  CAJ   CAH  SAG   108.27  3.000
 PNY  HAIB  CAI  HAIA  107.45  3.000
 PNY  HAIB  CAI  HAI   107.81  3.000
 PNY  HAIA  CAI  HAI   107.89  3.000
 PNY  HAIB  CAI  CAF   110.95  3.000
 PNY  HAIA  CAI  CAF   110.58  3.000
 PNY  HAI   CAI  CAF   111.97  3.000
 PNY  HAJA  CAJ  HAJ   107.40  3.000
 PNY  HAJA  CAJ  NAM   107.88  3.000
 PNY  HAJ   CAJ  NAM   109.19  3.000
 PNY  HAJA  CAJ  CAH   110.08  3.000
 PNY  HAJ   CAJ  CAH   110.17  3.000
 PNY  NAM   CAJ  CAH   111.99  3.000
 PNY  HAKA  CAK  HAK   107.45  3.000
 PNY  HAKA  CAK  NAN   109.86  3.000
 PNY  HAK   CAK  NAN   108.53  3.000
 PNY  HAKA  CAK  CAL   110.02  3.000
 PNY  HAK   CAK  CAL   110.28  3.000
 PNY  NAN   CAK  CAL   110.63  3.000
 PNY  HALA  CAL  HAL   106.83  3.000
 PNY  HALA  CAL  CAO   111.21  3.000
 PNY  HAL   CAL  CAO   107.93  3.000
 PNY  HALA  CAL  CAK   110.30  3.000
 PNY  HAL   CAL  CAK   109.42  3.000
 PNY  CAO   CAL  CAK   111.02  3.000
 PNY  HNAM  NAM  CAO   118.83  3.000
 PNY  HNAM  NAM  CAJ   117.81  3.000
 PNY  CAO   NAM  CAJ   123.25  3.000
 PNY  NAM   CAO  CAL   115.44  3.000
 PNY  NAM   CAO  OAC   122.93  3.000
 PNY  CAL   CAO  OAC   121.63  3.000
 PNY  CAQ   CAP  NAN   116.07  3.000
 PNY  CAQ   CAP  OAD   119.92  3.000
 PNY  NAN   CAP  OAD   124.00  3.000
 PNY  HAQ   CAQ  OAR   106.91  3.000
 PNY  HAQ   CAQ  CAP   108.70  3.000
 PNY  OAR   CAQ  CAP   108.26  3.000
 PNY  HAQ   CAQ  CAF   106.24  3.000
 PNY  OAR   CAQ  CAF   112.83  3.000
 PNY  CAP   CAQ  CAF   113.61  3.000
 PNY  HOAR  OAR  CAQ   107.79  3.000
 PNY  HNAN  NAN  CAP   118.02  3.000
 PNY  HNAN  NAN  CAK   117.26  3.000
 PNY  CAP   NAN  CAK   124.51  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
 PNY  CONST_01  CAJ   NAM  CAO  OAC     0.00   0.0  0
 PNY  CONST_02  CAK   NAN  CAP  OAD     0.00   0.0  0
 PNY  CONST_03  CAL   CAO  NAM  CAJ   180.00   0.0  0
 PNY  CONST_04  CAQ   CAP  NAN  CAK   180.00   0.0  0
 PNY  CONST_05  HNAM  NAM  CAO  OAC   180.00   0.0  0
 PNY  CONST_06  HNAN  NAN  CAP  OAD   180.00   0.0  0
 PNY  Var_01    OAE   CAA  CAF  CAB   -62.17  30.0  1
 PNY  Var_02    CAK   CAL  CAO  OAC    42.84  30.0  1
 PNY  Var_03    NAM   CAJ  CAH  SAG  -179.65  30.0  3
 PNY  Var_04    CAO   NAM  CAJ  CAH    85.33  30.0  3
 PNY  Var_05    CAP   NAN  CAK  CAL   136.87  30.0  3
 PNY  Var_06    CAO   CAL  CAK  NAN  -179.30  30.0  3
 PNY  Var_07    HAB   CAB  CAF  CAA    67.44  30.0  3
 PNY  Var_08    HAI   CAI  CAF  CAA    56.93  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
 PNY  chir_01  CAQ  CAF  CAP  OAR  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
 PNY  plan-1  OAC   0.020
 PNY  plan-1  CAJ   0.020
 PNY  plan-1  CAL   0.020
 PNY  plan-1  NAM   0.020
 PNY  plan-1  CAO   0.020
 PNY  plan-1  HNAM  0.020
 PNY  plan-2  OAD   0.020
 PNY  plan-2  CAK   0.020
 PNY  plan-2  CAP   0.020
 PNY  plan-2  CAQ   0.020
 PNY  plan-2  HNAN  0.020
 PNY  plan-2  NAN   0.020

