# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 00:27:58 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (S)-cyclopropyl(4-methoxyphenyl)pyrimidin-5-ylmethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@@](O)(C2CC2)c3cncnc3
#
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
 P3Z  P3Z  (S)-cyclopropyl(4-methoxyphenyl)pyrimidin-5-ylmethanol  ligand  35  19  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P3Z
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
 P3Z  CAA   C  CH3   0  -0.437   5.4877  -0.8120  -0.6763
 P3Z  OAB   O  OH1   0  -0.658  -0.8941   1.6142   1.4362
 P3Z  CAC   C  CR16  0  -0.367   2.9034   0.2922  -0.7241
 P3Z  CAD   C  CR16  0  -0.328   2.2996  -1.2595   1.0081
 P3Z  CAE   C  CR16  0  -0.303   1.6065   0.7954  -0.7048
 P3Z  CAF   C  CR16  0  -0.282   1.0169  -0.7499   1.0086
 P3Z  CAG   C  CR16  0   0.045  -3.6735  -2.1498   0.0543
 P3Z  CAH   C  CR16  0  -0.048  -2.9310  -0.2484   1.0180
 P3Z  CAI   C  CR16  0  -0.029  -1.7140  -1.3129  -0.6805
 P3Z  CAJ   C  CH2   0  -0.491  -2.1800   2.8105  -0.7937
 P3Z  CAK   C  CH2   0  -0.478  -0.7472   3.2426  -0.8996
 P3Z  NAL   N  N     0  -0.389  -3.8647  -1.1919   0.9452
 P3Z  NAM   N  N     0  -0.392  -2.6397  -2.2580  -0.7675
 P3Z  OAN   O  O2    0  -0.469   4.4852  -1.2936   0.1976
 P3Z  CAO   C  CR6   0   0.374   3.2610  -0.7401   0.1370
 P3Z  CAP   C  CR6   0   0.093   0.6412   0.2887   0.1517
 P3Z  CAQ   C  CR6   0  -0.047  -1.8010  -0.2529   0.2140
 P3Z  CAR   C  CH1   0  -0.265  -1.0953   1.7876  -0.9122
 P3Z  CAS   C  CT    0   0.133  -0.7665   0.8633   0.2493
 P3Z  HAA   H  HCH3  0   0.261   6.3827  -1.3930  -0.4686
 P3Z  HAAA  H  HCH3  0   0.229   5.2141  -0.9483  -1.7258
 P3Z  HAAB  H  HCH3  0   0.229   5.7067   0.2450  -0.5039
 P3Z  HOAB  H  HOH1  0   0.456  -0.5161   1.1182   2.1705
 P3Z  HAC   H  HCR6  0   0.279   3.6133   0.7242  -1.4157
 P3Z  HAD   H  HCR6  0   0.264   2.5650  -2.0673   1.6787
 P3Z  HAE   H  HCR6  0   0.268   1.3676   1.6021  -1.3843
 P3Z  HAF   H  HCR6  0   0.260   0.2944  -1.1883   1.6886
 P3Z  HAH   H  HCR6  0   0.274  -3.0911   0.5336   1.7506
 P3Z  HAI   H  HCR6  0   0.272  -0.8640  -1.4039  -1.3499
 P3Z  HAJ   H  HCH2  0   0.249  -2.6743   2.9318   0.1618
 P3Z  HAJA  H  HCH2  0   0.251  -2.8263   2.9562  -1.6495
 P3Z  HAK   H  HCH2  0   0.252  -0.4101   3.6852  -1.8286
 P3Z  HAKA  H  HCH2  0   0.250  -0.2746   3.6511  -0.0164
 P3Z  HAR   H  HCH1  0   0.280  -1.0249   1.2923  -1.8757
 P3Z  HAG   H  HCR6  0   0.263  -4.4340  -2.9199  -0.0106

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
 P3Z  CAA  OAN   single    1.414  0.020  1.414
 P3Z  CAA  HAA   single    0.970  0.020  1.090
 P3Z  CAA  HAAA  single    0.970  0.020  1.090
 P3Z  CAA  HAAB  single    0.970  0.020  1.090
 P3Z  OAB  CAS   single    1.410  0.020  1.410
 P3Z  OAB  HOAB  single    0.850  0.020  0.980
 P3Z  CAO  CAC   aromatic  1.391  0.020  1.391
 P3Z  CAC  CAE   aromatic  1.391  0.020  1.391
 P3Z  CAC  HAC   single    0.930  0.020  1.080
 P3Z  CAD  CAF   aromatic  1.380  0.020  1.380
 P3Z  CAD  CAO   aromatic  1.397  0.020  1.397
 P3Z  CAD  HAD   single    0.930  0.020  1.080
 P3Z  CAP  CAE   aromatic  1.386  0.020  1.386
 P3Z  CAE  HAE   single    0.930  0.020  1.080
 P3Z  CAF  CAP   aromatic  1.398  0.020  1.398
 P3Z  CAF  HAF   single    0.930  0.020  1.080
 P3Z  NAL  CAG   aromatic  1.322  0.020  1.322
 P3Z  NAM  CAG   aromatic  1.325  0.020  1.325
 P3Z  CAG  HAG   single    0.930  0.020  1.080
 P3Z  CAQ  CAH   aromatic  1.387  0.020  1.387
 P3Z  CAH  NAL   aromatic  1.329  0.020  1.329
 P3Z  CAH  HAH   single    0.930  0.020  1.080
 P3Z  CAQ  CAI   aromatic  1.390  0.020  1.390
 P3Z  CAI  NAM   aromatic  1.326  0.020  1.326
 P3Z  CAI  HAI   single    0.930  0.020  1.080
 P3Z  CAK  CAJ   single    1.500  0.020  1.500
 P3Z  CAR  CAJ   single    1.496  0.020  1.496
 P3Z  CAJ  HAJ   single    0.970  0.020  1.090
 P3Z  CAJ  HAJA  single    0.970  0.020  1.090
 P3Z  CAK  CAR   single    1.496  0.020  1.496
 P3Z  CAK  HAK   single    0.970  0.020  1.090
 P3Z  CAK  HAKA  single    0.970  0.020  1.090
 P3Z  OAN  CAO   single    1.345  0.020  1.345
 P3Z  CAP  CAS   single    1.524  0.020  1.524
 P3Z  CAS  CAQ   single    1.522  0.020  1.522
 P3Z  CAR  CAS   single    1.520  0.020  1.520
 P3Z  CAR  HAR   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
 P3Z  HAAB  CAA  HAAA  108.80  3.000
 P3Z  HAAB  CAA  HAA   108.77  3.000
 P3Z  HAAA  CAA  HAA   108.83  3.000
 P3Z  HAAB  CAA  OAN   111.95  3.000
 P3Z  HAAA  CAA  OAN   111.92  3.000
 P3Z  HAA   CAA  OAN   106.47  3.000
 P3Z  HOAB  OAB  CAS   109.38  3.000
 P3Z  HAC   CAC  CAO   121.58  3.000
 P3Z  HAC   CAC  CAE   118.45  3.000
 P3Z  CAO   CAC  CAE   119.97  3.000
 P3Z  HAD   CAD  CAO   119.65  3.000
 P3Z  HAD   CAD  CAF   120.19  3.000
 P3Z  CAO   CAD  CAF   120.16  3.000
 P3Z  HAE   CAE  CAP   120.46  3.000
 P3Z  HAE   CAE  CAC   117.84  3.000
 P3Z  CAP   CAE  CAC   121.70  3.000
 P3Z  HAF   CAF  CAP   120.37  3.000
 P3Z  HAF   CAF  CAD   118.04  3.000
 P3Z  CAP   CAF  CAD   121.59  3.000
 P3Z  HAG   CAG  NAM   116.88  3.000
 P3Z  HAG   CAG  NAL   116.97  3.000
 P3Z  NAM   CAG  NAL   126.15  3.000
 P3Z  HAH   CAH  CAQ   120.98  3.000
 P3Z  HAH   CAH  NAL   116.46  3.000
 P3Z  CAQ   CAH  NAL   122.56  3.000
 P3Z  HAI   CAI  CAQ   120.64  3.000
 P3Z  HAI   CAI  NAM   116.52  3.000
 P3Z  CAQ   CAI  NAM   122.84  3.000
 P3Z  HAJA  CAJ  HAJ   114.22  3.000
 P3Z  HAJA  CAJ  CAR   117.55  3.000
 P3Z  HAJ   CAJ  CAR   118.53  3.000
 P3Z  HAJA  CAJ  CAK   118.40  3.000
 P3Z  HAJ   CAJ  CAK   117.78  3.000
 P3Z  CAR   CAJ  CAK    59.92  3.000
 P3Z  HAKA  CAK  HAK   114.21  3.000
 P3Z  HAKA  CAK  CAR   118.41  3.000
 P3Z  HAK   CAK  CAR   117.56  3.000
 P3Z  HAKA  CAK  CAJ   117.93  3.000
 P3Z  HAK   CAK  CAJ   118.40  3.000
 P3Z  CAR   CAK  CAJ    59.89  3.000
 P3Z  CAH   NAL  CAG   116.71  3.000
 P3Z  CAI   NAM  CAG   116.48  3.000
 P3Z  CAO   OAN  CAA   118.50  3.000
 P3Z  OAN   CAO  CAD   116.44  3.000
 P3Z  OAN   CAO  CAC   124.57  3.000
 P3Z  CAD   CAO  CAC   119.00  3.000
 P3Z  CAS   CAP  CAF   119.29  3.000
 P3Z  CAS   CAP  CAE   123.03  3.000
 P3Z  CAF   CAP  CAE   117.59  3.000
 P3Z  CAS   CAQ  CAI   122.12  3.000
 P3Z  CAS   CAQ  CAH   122.54  3.000
 P3Z  CAI   CAQ  CAH   115.25  3.000
 P3Z  HAR   CAR  CAS   112.74  3.000
 P3Z  HAR   CAR  CAK   115.85  3.000
 P3Z  CAS   CAR  CAK   122.31  3.000
 P3Z  HAR   CAR  CAJ   115.43  3.000
 P3Z  CAS   CAR  CAJ   120.81  3.000
 P3Z  CAK   CAR  CAJ    60.20  3.000
 P3Z  CAR   CAS  CAQ   106.33  3.000
 P3Z  CAR   CAS  CAP   112.34  3.000
 P3Z  CAQ   CAS  CAP   110.48  3.000
 P3Z  CAR   CAS  OAB   107.44  3.000
 P3Z  CAQ   CAS  OAB   110.39  3.000
 P3Z  CAP   CAS  OAB   109.78  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
 P3Z  CONST_01  CAF  CAD  CAO  CAC     0.00   0.0  0
 P3Z  CONST_02  CAF  CAP  CAE  CAC     0.00   0.0  0
 P3Z  CONST_03  CAE  CAP  CAF  CAD     0.00   0.0  0
 P3Z  CONST_04  CAE  CAC  CAO  CAD     0.00   0.0  0
 P3Z  CONST_05  CAQ  CAH  NAL  CAG     0.00   0.0  0
 P3Z  CONST_06  CAQ  CAI  NAM  CAG     0.00   0.0  0
 P3Z  CONST_07  NAM  CAI  CAQ  CAH     0.00   0.0  0
 P3Z  CONST_08  NAM  CAG  NAL  CAH     0.00   0.0  0
 P3Z  CONST_09  NAL  CAH  CAQ  CAI     0.00   0.0  0
 P3Z  CONST_10  NAL  CAG  NAM  CAI     0.00   0.0  0
 P3Z  CONST_11  CAP  CAE  CAC  CAO     0.00   0.0  0
 P3Z  CONST_12  CAP  CAF  CAD  CAO     0.00   0.0  0
 P3Z  CONST_13  CAS  CAP  CAE  CAC   180.00   0.0  0
 P3Z  CONST_14  CAS  CAP  CAF  CAD   180.00   0.0  0
 P3Z  CONST_15  OAN  CAO  CAC  CAE   180.00   0.0  0
 P3Z  CONST_16  OAN  CAO  CAD  CAF   180.00   0.0  0
 P3Z  CONST_17  CAS  CAQ  CAH  NAL   180.00   0.0  0
 P3Z  CONST_18  CAS  CAQ  CAI  NAM   180.00   0.0  0
 P3Z  CONST_19  HAD  CAD  CAO  CAC   180.00   0.0  0
 P3Z  CONST_20  HAC  CAC  CAO  CAD   180.00   0.0  0
 P3Z  CONST_21  HAF  CAF  CAP  CAE   180.00   0.0  0
 P3Z  CONST_22  HAE  CAE  CAP  CAF   180.00   0.0  0
 P3Z  CONST_23  HAH  CAH  NAL  CAG   180.00   0.0  0
 P3Z  CONST_24  HAI  CAI  NAM  CAG   180.00   0.0  0
 P3Z  CONST_25  HAG  CAG  NAL  CAH   180.00   0.0  0
 P3Z  Var_01    CAS  CAR  CAK  CAJ  -109.64  30.0  1
 P3Z  Var_02    CAC  CAO  OAN  CAA    -0.56  30.0  2
 P3Z  Var_03    HAA  CAA  OAN  CAO  -179.59  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
 P3Z  chir_02  CAS  CAP  CAQ  CAR  positiv
 P3Z  chir_03  CAR  CAJ  CAK  CAS  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
 P3Z  plan-1  CAG  0.020
 P3Z  plan-1  CAH  0.020
 P3Z  plan-1  CAI  0.020
 P3Z  plan-1  NAL  0.020
 P3Z  plan-1  NAM  0.020
 P3Z  plan-1  CAQ  0.020
 P3Z  plan-1  CAS  0.020
 P3Z  plan-1  HAH  0.020
 P3Z  plan-1  HAI  0.020
 P3Z  plan-1  HAG  0.020
 P3Z  plan-2  CAC  0.020
 P3Z  plan-2  CAD  0.020
 P3Z  plan-2  CAE  0.020
 P3Z  plan-2  CAF  0.020
 P3Z  plan-2  OAN  0.020
 P3Z  plan-2  CAO  0.020
 P3Z  plan-2  CAP  0.020
 P3Z  plan-2  CAS  0.020
 P3Z  plan-2  HAC  0.020
 P3Z  plan-2  HAD  0.020
 P3Z  plan-2  HAE  0.020
 P3Z  plan-2  HAF  0.020

