# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:32:21 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=S)NCCCn2ccnc2)cc1OC
#
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
 PBD  PBD  1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea  ligand  42  22  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PBD
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
 PBD  CAA   C  CH3   0  -0.437   6.9725   1.6950   0.5285
 PBD  CAB   C  CH3   0  -0.439   4.8526  -3.1727  -0.4578
 PBD  SAC   S  S1    0  -0.423   0.1580   1.7747  -1.4001
 PBD  CAD   C  CR15  0  -0.218  -7.8406  -0.5627   1.3644
 PBD  CAE   C  CR16  0  -0.275   2.7867   1.2894   0.4977
 PBD  CAF   C  CR16  0  -0.390   4.1698   1.4542   0.5007
 PBD  CAG   C  CR15  0  -0.108  -6.7772   0.2786   1.2019
 PBD  CAH   C  CR15  0   0.095  -6.9949  -1.0339  -0.5284
 PBD  CAI   C  CR16  0  -0.452   3.0900  -1.0415  -0.0023
 PBD  CAJ   C  CH2   0  -0.491  -3.7835  -0.0285  -0.0209
 PBD  CAK   C  CH2   0  -0.223  -2.5623   0.6194  -0.6533
 PBD  CAL   C  CH2   0  -0.297  -5.0614   0.5464  -0.6145
 PBD  NAM   N  N     0  -0.457  -7.9681  -1.3783   0.2760
 PBD  NAN   N  NH1   0  -0.625  -1.3577   0.0688  -0.0735
 PBD  OAP   O  O2    0  -0.464   6.3644   0.4457   0.2752
 PBD  CAR   C  C     0   0.402  -0.1212   0.4950  -0.3494
 PBD  CAS   C  CR6   0   0.349   2.2453   0.0459   0.2364
 PBD  CAT   C  CR6   0   0.306   5.0193   0.3842   0.2740
 PBD  CAU   C  CR6   0   0.320   4.4656  -0.8876   0.0248
 PBD  NAV   N  NR5   0  -0.399  -6.2477  -0.0320  -0.0192
 PBD  HAA   H  HCH3  0   0.259   8.0464   1.5263   0.5075
 PBD  HAAA  H  HCH3  0   0.228   6.7187   2.4362  -0.2343
 PBD  HAAB  H  HCH3  0   0.227   6.6980   2.0941   1.5089
 PBD  HAB   H  HCH3  0   0.262   5.7188  -3.8155  -0.5924
 PBD  HABA  H  HCH3  0   0.229   4.2482  -3.5628   0.3656
 PBD  HABB  H  HCH3  0   0.229   4.2544  -3.1923  -1.3729
 PBD  HAE   H  HCR6  0   0.261   2.1491   2.1370   0.6996
 PBD  HAF   H  HCR6  0   0.283   4.5681   2.4390   0.7035
 PBD  HAG   H  HCR5  0   0.288  -6.3655   1.0547   1.8258
 PBD  HAH   H  HCR5  0   0.279  -6.7845  -1.4694  -1.4944
 PBD  HAI   H  HCR6  0   0.292   2.6474  -2.0070  -0.2107
 PBD  HAJ   H  HCH2  0   0.253  -3.7638  -1.1096  -0.1832
 PBD  HAJA  H  HCH2  0   0.254  -3.7726   0.1399   1.0593
 PBD  HAK   H  HCH2  0   0.240  -2.5664   0.4607  -1.7352
 PBD  HAKA  H  HCH2  0   0.242  -2.5836   1.6999  -0.4947
 PBD  HAL   H  HCH2  0   0.269  -5.0970   1.6275  -0.4740
 PBD  HALA  H  HCH2  0   0.270  -5.1020   0.3603  -1.6881
 PBD  HNAN  H  HNH1  0   0.405  -1.4708  -0.6940   0.5782
 PBD  NAO   N  NH1   0  -0.735   0.8593  -0.1994   0.2731
 PBD  OAQ   O  O2    0  -0.464   5.3508  -1.8796  -0.1816
 PBD  HAD   H  HCR5  0   0.250  -8.5168  -0.6179   2.2035
 PBD  HNAO  H  HNH1  0   0.407   0.5888  -1.0563   0.7357

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
 PBD  CAA  OAP   single    1.412  0.020  1.412
 PBD  CAB  OAQ   single    1.413  0.020  1.413
 PBD  SAC  CAR   double    1.679  0.020  1.679
 PBD  CAD  CAG   aromatic  1.366  0.020  1.366
 PBD  CAD  NAM   aromatic  1.366  0.020  1.366
 PBD  CAE  CAF   aromatic  1.393  0.020  1.393
 PBD  CAE  CAS   aromatic  1.381  0.020  1.381
 PBD  CAF  CAT   aromatic  1.385  0.020  1.385
 PBD  CAG  NAV   aromatic  1.367  0.020  1.367
 PBD  CAH  NAM   aromatic  1.309  0.020  1.309
 PBD  CAH  NAV   aromatic  1.350  0.020  1.350
 PBD  CAI  CAS   aromatic  1.398  0.020  1.398
 PBD  CAI  CAU   aromatic  1.384  0.020  1.384
 PBD  CAJ  CAK   single    1.520  0.020  1.520
 PBD  CAJ  CAL   single    1.522  0.020  1.522
 PBD  CAK  NAN   single    1.446  0.020  1.446
 PBD  CAL  NAV   single    1.448  0.020  1.448
 PBD  NAN  CAR   single    1.337  0.020  1.337
 PBD  NAO  CAR   single    1.353  0.020  1.353
 PBD  NAO  CAS   single    1.408  0.020  1.408
 PBD  OAP  CAT   single    1.347  0.020  1.347
 PBD  OAQ  CAU   single    1.345  0.020  1.345
 PBD  CAT  CAU   aromatic  1.409  0.020  1.409
 PBD  CAA  HAA   single    0.970  0.020  1.090
 PBD  CAA  HAAA  single    0.970  0.020  1.090
 PBD  CAA  HAAB  single    0.970  0.020  1.090
 PBD  CAB  HAB   single    0.970  0.020  1.090
 PBD  CAB  HABA  single    0.970  0.020  1.090
 PBD  CAB  HABB  single    0.970  0.020  1.090
 PBD  CAD  HAD   single    0.930  0.020  1.080
 PBD  CAE  HAE   single    0.930  0.020  1.080
 PBD  CAF  HAF   single    0.930  0.020  1.080
 PBD  CAG  HAG   single    0.930  0.020  1.080
 PBD  CAH  HAH   single    0.930  0.020  1.080
 PBD  CAI  HAI   single    0.930  0.020  1.080
 PBD  CAJ  HAJ   single    0.970  0.020  1.090
 PBD  CAJ  HAJA  single    0.970  0.020  1.090
 PBD  CAK  HAK   single    0.970  0.020  1.090
 PBD  CAK  HAKA  single    0.970  0.020  1.090
 PBD  CAL  HAL   single    0.970  0.020  1.090
 PBD  CAL  HALA  single    0.970  0.020  1.090
 PBD  NAN  HNAN  single    0.860  0.020  1.020
 PBD  NAO  HNAO  single    0.860  0.020  1.020

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
 PBD  HAAB  CAA  HAAA  108.65  3.000
 PBD  HAAB  CAA  HAA   108.78  3.000
 PBD  HAAA  CAA  HAA   108.72  3.000
 PBD  HAAB  CAA  OAP   112.06  3.000
 PBD  HAAA  CAA  OAP   112.00  3.000
 PBD  HAA   CAA  OAP   106.53  3.000
 PBD  HABB  CAB  HABA  108.75  3.000
 PBD  HABB  CAB  HAB   108.77  3.000
 PBD  HABA  CAB  HAB   108.82  3.000
 PBD  HABB  CAB  OAQ   111.90  3.000
 PBD  HABA  CAB  OAQ   111.97  3.000
 PBD  HAB   CAB  OAQ   106.52  3.000
 PBD  HAD   CAD  NAM   122.04  3.000
 PBD  HAD   CAD  CAG   127.74  3.000
 PBD  NAM   CAD  CAG   110.22  3.000
 PBD  HAE   CAE  CAS   120.70  3.000
 PBD  HAE   CAE  CAF   119.55  3.000
 PBD  CAS   CAE  CAF   119.75  3.000
 PBD  HAF   CAF  CAT   120.55  3.000
 PBD  HAF   CAF  CAE   118.28  3.000
 PBD  CAT   CAF  CAE   121.15  3.000
 PBD  HAG   CAG  NAV   122.21  3.000
 PBD  HAG   CAG  CAD   132.24  3.000
 PBD  NAV   CAG  CAD   105.55  3.000
 PBD  HAH   CAH  NAV   121.92  3.000
 PBD  HAH   CAH  NAM   126.04  3.000
 PBD  NAV   CAH  NAM   112.03  3.000
 PBD  HAI   CAI  CAU   120.61  3.000
 PBD  HAI   CAI  CAS   118.67  3.000
 PBD  CAU   CAI  CAS   120.72  3.000
 PBD  HAJA  CAJ  HAJ   107.39  3.000
 PBD  HAJA  CAJ  CAL   109.60  3.000
 PBD  HAJ   CAJ  CAL   109.32  3.000
 PBD  HAJA  CAJ  CAK   109.72  3.000
 PBD  HAJ   CAJ  CAK   110.19  3.000
 PBD  CAL   CAJ  CAK   110.56  3.000
 PBD  HAKA  CAK  HAK   106.69  3.000
 PBD  HAKA  CAK  NAN   109.56  3.000
 PBD  HAK   CAK  NAN   110.16  3.000
 PBD  HAKA  CAK  CAJ   110.22  3.000
 PBD  HAK   CAK  CAJ   110.28  3.000
 PBD  NAN   CAK  CAJ   109.88  3.000
 PBD  HALA  CAL  HAL   107.14  3.000
 PBD  HALA  CAL  NAV   107.83  3.000
 PBD  HAL   CAL  NAV   108.44  3.000
 PBD  HALA  CAL  CAJ   110.54  3.000
 PBD  HAL   CAL  CAJ   110.59  3.000
 PBD  NAV   CAL  CAJ   112.13  3.000
 PBD  CAH   NAM  CAD   105.26  3.000
 PBD  HNAN  NAN  CAR   118.54  3.000
 PBD  HNAN  NAN  CAK   116.95  3.000
 PBD  CAR   NAN  CAK   124.50  3.000
 PBD  CAT   OAP  CAA   118.08  3.000
 PBD  NAO   CAR  NAN   114.31  3.000
 PBD  NAO   CAR  SAC   123.95  3.000
 PBD  NAN   CAR  SAC   121.74  3.000
 PBD  NAO   CAS  CAI   117.64  3.000
 PBD  NAO   CAS  CAE   122.54  3.000
 PBD  CAI   CAS  CAE   119.73  3.000
 PBD  CAU   CAT  OAP   115.71  3.000
 PBD  CAU   CAT  CAF   119.03  3.000
 PBD  OAP   CAT  CAF   125.26  3.000
 PBD  CAT   CAU  OAQ   115.72  3.000
 PBD  CAT   CAU  CAI   119.61  3.000
 PBD  OAQ   CAU  CAI   124.66  3.000
 PBD  CAL   NAV  CAH   126.52  3.000
 PBD  CAL   NAV  CAG   126.44  3.000
 PBD  CAH   NAV  CAG   106.94  3.000
 PBD  HNAO  NAO  CAS   115.04  3.000
 PBD  HNAO  NAO  CAR   116.85  3.000
 PBD  CAS   NAO  CAR   127.72  3.000
 PBD  CAU   OAQ  CAB   118.21  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
 PBD  CONST_01  CAH   NAV  CAG  CAD     0.00   0.0  0
 PBD  CONST_02  NAV   CAH  NAM  CAD     0.00   0.0  0
 PBD  CONST_03  CAU   CAT  CAF  CAE     0.00   0.0  0
 PBD  CONST_04  CAU   CAI  CAS  CAE     0.00   0.0  0
 PBD  CONST_05  CAI   CAS  CAE  CAF     0.00   0.0  0
 PBD  CONST_06  CAI   CAU  CAT  CAF     0.00   0.0  0
 PBD  CONST_07  CAH   NAM  CAD  CAG     0.00   0.0  0
 PBD  CONST_08  NAM   CAH  NAV  CAG     0.00   0.0  0
 PBD  CONST_09  NAV   CAG  CAD  NAM     0.00   0.0  0
 PBD  CONST_10  CAT   CAF  CAE  CAS     0.00   0.0  0
 PBD  CONST_11  CAT   CAU  CAI  CAS     0.00   0.0  0
 PBD  CONST_12  CAL   NAV  CAG  CAD   180.00   0.0  0
 PBD  CONST_13  OAP   CAT  CAF  CAE   180.00   0.0  0
 PBD  CONST_14  NAO   CAS  CAE  CAF   180.00   0.0  0
 PBD  CONST_15  OAQ   CAU  CAT  CAF   180.00   0.0  0
 PBD  CONST_16  OAP   CAT  CAU  CAI   180.00   0.0  0
 PBD  CONST_17  NAM   CAH  NAV  CAL   180.00   0.0  0
 PBD  CONST_18  CAU   CAI  CAS  NAO   180.00   0.0  0
 PBD  CONST_19  CAS   CAI  CAU  OAQ   180.00   0.0  0
 PBD  CONST_20  HAH   CAH  NAM  CAD   180.00   0.0  0
 PBD  CONST_21  HAI   CAI  CAS  CAE   180.00   0.0  0
 PBD  CONST_22  HAD   CAD  NAM  CAH   180.00   0.0  0
 PBD  CONST_23  HAG   CAG  NAV  CAH   180.00   0.0  0
 PBD  CONST_24  HAE   CAE  CAS  CAI   180.00   0.0  0
 PBD  CONST_25  HAF   CAF  CAE  CAS   180.00   0.0  0
 PBD  CONST_29  CAS   NAO  CAR  SAC     0.00   0.0  0
 PBD  CONST_30  CAS   NAO  CAR  NAN   180.00   0.0  0
 PBD  CONST_31  CAK   NAN  CAR  SAC     0.00   0.0  0
 PBD  CONST_32  NAO   CAR  NAN  CAK   180.00   0.0  0
 PBD  CONST_33  HNAN  NAN  CAR  SAC   180.00   0.0  0
 PBD  Var_01    CAF   CAT  OAP  CAA     0.10  30.0  2
 PBD  Var_02    CAI   CAU  OAQ  CAB     0.57  30.0  2
 PBD  Var_03    CAJ   CAL  NAV  CAG    77.52  30.0  2
 PBD  Var_04    NAV   CAL  CAJ  CAK  -179.03  30.0  3
 PBD  Var_05    HAA   CAA  OAP  CAT   178.76  30.0  3
 PBD  Var_06    HAB   CAB  OAQ  CAU   179.89  30.0  3
 PBD  Var_07    CAR   NAN  CAK  CAJ  -175.18  30.0  3
 PBD  Var_08    NAN   CAK  CAJ  CAL   179.65  30.0  3

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
 PBD  plan-1  CAD   0.020
 PBD  plan-1  CAG   0.020
 PBD  plan-1  CAH   0.020
 PBD  plan-1  CAL   0.020
 PBD  plan-1  NAM   0.020
 PBD  plan-1  NAV   0.020
 PBD  plan-1  HAG   0.020
 PBD  plan-1  HAH   0.020
 PBD  plan-1  HAD   0.020
 PBD  plan-2  CAE   0.020
 PBD  plan-2  CAF   0.020
 PBD  plan-2  CAI   0.020
 PBD  plan-2  OAP   0.020
 PBD  plan-2  CAS   0.020
 PBD  plan-2  CAT   0.020
 PBD  plan-2  CAU   0.020
 PBD  plan-2  HAE   0.020
 PBD  plan-2  HAF   0.020
 PBD  plan-2  HAI   0.020
 PBD  plan-2  NAO   0.020
 PBD  plan-2  OAQ   0.020
 PBD  plan-3  SAC   0.020
 PBD  plan-3  CAK   0.020
 PBD  plan-3  NAN   0.020
 PBD  plan-3  CAR   0.020
 PBD  plan-3  CAS   0.020
 PBD  plan-3  HNAN  0.020
 PBD  plan-3  NAO   0.020
 PBD  plan-3  HNAO  0.020

