# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:39:01 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 1-(2-amino-4-phenyl-1H-imidazol-1-yl)-3-(2-fluorophenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(cn1NC(=O)Nc2ccccc2F)c3ccccc3
#
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
 34X  34X  1-(2-amino-4-phenyl-1H-imidazol-1-yl)-3-(2-fluorophenyl)urea  ligand  37  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_34X
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
 34X  FAP   F  F     0  -0.216   4.9422  -1.6060   1.0000
 34X  CAO   C  CR6   0   0.555   4.9375  -0.3686   0.4767
 34X  CAN   C  CR16  0  -0.493   6.1236   0.1798   0.0372
 34X  CAM   C  CR16  0  -0.203   6.1088   1.4534  -0.5137
 34X  CAA   C  CR16  0  -0.290   4.9143   2.1551  -0.5964
 34X  CAB   C  CR16  0  -0.286   3.7342   1.5965  -0.1276
 34X  CAC   C  CR6   0   0.064   3.7264   0.3125   0.4116
 34X  NAD   N  NH1   0  -0.737   2.5721  -0.2968   0.9171
 34X  CAE   C  C     0   0.793   1.3684  -0.2903   0.2814
 34X  OAQ   O  O     0  -0.387   1.1294   0.2894  -0.7556
 34X  NAF   N  NC1   0  -0.635   0.4178  -1.0503   0.9371
 34X  NAG   N  NR5   0  -0.372  -0.8655  -0.9665   0.5162
 34X  CAH   C  CR15  0  -0.066  -1.7596   0.0608   0.7574
 34X  CAR   C  CR5   0   0.553  -1.4757  -1.8659  -0.3032
 34X  NAW   N  NH2   0  -0.860  -0.8747  -3.0274  -0.6787
 34X  NAS   N  N     0  -0.417  -2.6925  -1.4894  -0.5811
 34X  CAI   C  CR5   0   0.066  -2.8834  -0.2900   0.0762
 34X  CAJ   C  CR6   0   0.232  -4.1530   0.4279  -0.0120
 34X  CAK   C  CR16  0  -0.355  -5.1974  -0.0792  -0.7870
 34X  CAL   C  CR16  0  -0.256  -6.4065   0.5961  -0.8791
 34X  CAV   C  CR16  0  -0.242  -6.5975   1.7906  -0.1982
 34X  CAU   C  CR16  0  -0.244  -5.5636   2.3043   0.5769
 34X  CAT   C  CR16  0  -0.405  -4.3564   1.6316   0.6696
 34X  HAN   H  HCR6  0   0.244   7.0410  -0.3886   0.1187
 34X  HAM   H  HCR6  0   0.276   7.0305   1.8939  -0.8682
 34X  HAA   H  HCR6  0   0.243   4.8974   3.1515  -1.0170
 34X  HAB   H  HCR6  0   0.302   2.8177   2.1659  -0.1741
 34X  HAD   H  HNH1  0   0.427   2.6897  -0.9188   1.7024
 34X  HAF   H  HNC1  0   0.413   0.5506  -1.3452   1.8948
 34X  HAH   H  HCR5  0   0.300  -1.4974   0.9018   1.3767
 34X  HAW1  H  HNH2  0   0.389   0.1326  -3.0194  -0.7194
 34X  HAW2  H  HNH2  0   0.363  -1.2902  -3.4636  -1.4863
 34X  HAK   H  HCR6  0   0.265  -5.0600  -1.0095  -1.3221
 34X  HAT   H  HCR6  0   0.225  -3.5677   2.0505   1.2824
 34X  HAL   H  HCR6  0   0.259  -7.2020   0.1850  -1.4874
 34X  HAV   H  HCR6  0   0.227  -7.5408   2.3164  -0.2677
 34X  HAU   H  HCR6  0   0.269  -5.6987   3.2347   1.1135

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
 34X  FAP  CAO   single    1.344  0.020  1.344
 34X  CAO  CAN   aromatic  1.379  0.020  1.379
 34X  CAO  CAC   aromatic  1.391  0.020  1.391
 34X  CAN  CAM   aromatic  1.388  0.020  1.388
 34X  CAM  CAA   aromatic  1.388  0.020  1.388
 34X  CAA  CAB   aromatic  1.387  0.020  1.387
 34X  CAB  CAC   aromatic  1.393  0.020  1.393
 34X  CAC  NAD   single    1.400  0.020  1.400
 34X  NAD  CAE   single    1.361  0.020  1.361
 34X  CAE  OAQ   double    1.212  0.020  1.212
 34X  CAE  NAF   single    1.382  0.020  1.382
 34X  NAF  NAG   single    1.353  0.020  1.353
 34X  NAG  CAH   aromatic  1.383  0.020  1.383
 34X  NAG  CAR   aromatic  1.361  0.020  1.361
 34X  CAH  CAI   aromatic  1.360  0.020  1.360
 34X  CAR  NAW   single    1.361  0.020  1.361
 34X  CAR  NAS   aromatic  1.304  0.020  1.304
 34X  NAS  CAI   aromatic  1.381  0.020  1.381
 34X  CAI  CAJ   single    1.461  0.020  1.461
 34X  CAJ  CAK   aromatic  1.396  0.020  1.396
 34X  CAJ  CAT   aromatic  1.398  0.020  1.398
 34X  CAK  CAL   aromatic  1.388  0.020  1.388
 34X  CAL  CAV   aromatic  1.388  0.020  1.388
 34X  CAV  CAU   aromatic  1.391  0.020  1.391
 34X  CAU  CAT   aromatic  1.385  0.020  1.385
 34X  CAN  HAN   single    0.930  0.020  1.080
 34X  CAM  HAM   single    0.930  0.020  1.080
 34X  CAA  HAA   single    0.930  0.020  1.080
 34X  CAB  HAB   single    0.930  0.020  1.080
 34X  NAD  HAD   single    0.860  0.020  1.020
 34X  NAF  HAF   single    0.890  0.020  1.040
 34X  CAH  HAH   single    0.930  0.020  1.080
 34X  NAW  HAW1  single    0.890  0.020  1.040
 34X  NAW  HAW2  single    0.890  0.020  1.040
 34X  CAK  HAK   single    0.930  0.020  1.080
 34X  CAT  HAT   single    0.930  0.020  1.080
 34X  CAL  HAL   single    0.930  0.020  1.080
 34X  CAV  HAV   single    0.930  0.020  1.080
 34X  CAU  HAU   single    0.930  0.020  1.080

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
 34X  CAC   CAO  CAN   122.64  3.000
 34X  CAC   CAO  FAP   118.18  3.000
 34X  CAN   CAO  FAP   119.18  3.000
 34X  HAN   CAN  CAM   121.40  3.000
 34X  HAN   CAN  CAO   119.76  3.000
 34X  CAM   CAN  CAO   118.84  3.000
 34X  HAM   CAM  CAA   120.54  3.000
 34X  HAM   CAM  CAN   119.67  3.000
 34X  CAA   CAM  CAN   119.79  3.000
 34X  HAA   CAA  CAB   119.28  3.000
 34X  HAA   CAA  CAM   120.16  3.000
 34X  CAB   CAA  CAM   120.56  3.000
 34X  HAB   CAB  CAC   119.86  3.000
 34X  HAB   CAB  CAA   119.68  3.000
 34X  CAC   CAB  CAA   120.46  3.000
 34X  NAD   CAC  CAB   123.08  3.000
 34X  NAD   CAC  CAO   119.21  3.000
 34X  CAB   CAC  CAO   117.69  3.000
 34X  HAD   NAD  CAE   118.01  3.000
 34X  HAD   NAD  CAC   116.96  3.000
 34X  CAE   NAD  CAC   123.95  3.000
 34X  NAF   CAE  OAQ   122.23  3.000
 34X  NAF   CAE  NAD   112.57  3.000
 34X  OAQ   CAE  NAD   125.19  3.000
 34X  HAF   NAF  NAG   115.93  3.000
 34X  HAF   NAF  CAE   121.29  3.000
 34X  NAG   NAF  CAE   118.07  3.000
 34X  CAR   NAG  CAH   107.82  3.000
 34X  CAR   NAG  NAF   124.85  3.000
 34X  CAH   NAG  NAF   127.22  3.000
 34X  HAH   CAH  CAI   133.68  3.000
 34X  HAH   CAH  NAG   121.53  3.000
 34X  CAI   CAH  NAG   104.79  3.000
 34X  NAS   CAR  NAW   126.87  3.000
 34X  NAS   CAR  NAG   110.85  3.000
 34X  NAW   CAR  NAG   122.15  3.000
 34X  HAW2  NAW  HAW1  112.53  3.000
 34X  HAW2  NAW  CAR   114.12  3.000
 34X  HAW1  NAW  CAR   116.47  3.000
 34X  CAI   NAS  CAR   106.17  3.000
 34X  CAJ   CAI  NAS   121.20  3.000
 34X  CAJ   CAI  CAH   128.42  3.000
 34X  NAS   CAI  CAH   110.37  3.000
 34X  CAT   CAJ  CAK   118.33  3.000
 34X  CAT   CAJ  CAI   121.33  3.000
 34X  CAK   CAJ  CAI   120.34  3.000
 34X  HAK   CAK  CAL   119.75  3.000
 34X  HAK   CAK  CAJ   119.47  3.000
 34X  CAL   CAK  CAJ   120.79  3.000
 34X  HAL   CAL  CAV   120.08  3.000
 34X  HAL   CAL  CAK   119.52  3.000
 34X  CAV   CAL  CAK   120.40  3.000
 34X  HAV   CAV  CAU   120.29  3.000
 34X  HAV   CAV  CAL   120.43  3.000
 34X  CAU   CAV  CAL   119.28  3.000
 34X  HAU   CAU  CAT   119.54  3.000
 34X  HAU   CAU  CAV   120.07  3.000
 34X  CAT   CAU  CAV   120.39  3.000
 34X  HAT   CAT  CAU   118.99  3.000
 34X  HAT   CAT  CAJ   120.19  3.000
 34X  CAU   CAT  CAJ   120.82  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
 34X  CONST_01  CAA  CAM  CAN  CAO    0.00  0.0  0
 34X  CONST_02  CAA  CAB  CAC  CAO    0.00  0.0  0
 34X  CONST_03  CAB  CAC  CAO  CAN    0.00  0.0  0
 34X  CONST_04  CAB  CAA  CAM  CAN    0.00  0.0  0
 34X  CONST_05  CAC  CAO  CAN  CAM    0.00  0.0  0
 34X  CONST_06  CAC  CAB  CAA  CAM    0.00  0.0  0
 34X  CONST_07  NAS  CAI  CAH  NAG    0.00  0.0  0
 34X  CONST_08  CAJ  CAI  CAH  NAG  180.00  0.0  0
 34X  CONST_09  CAI  NAS  CAR  NAG    0.00  0.0  0
 34X  CONST_10  NAS  CAR  NAG  CAH    0.00  0.0  0
 34X  CONST_11  CAR  NAS  CAI  CAH    0.00  0.0  0
 34X  CONST_12  CAK  CAJ  CAI  CAH  180.00  0.0  0
 34X  CONST_13  CAT  CAJ  CAI  CAH    0.00  0.0  0
 34X  CONST_14  CAI  CAH  NAG  CAR    0.00  0.0  0
 34X  CONST_15  CAJ  CAI  NAS  CAR  180.00  0.0  0
 34X  CONST_16  CAK  CAJ  CAI  NAS    0.00  0.0  0
 34X  CONST_17  CAT  CAJ  CAI  NAS  180.00  0.0  0
 34X  CONST_18  CAL  CAK  CAJ  CAI  180.00  0.0  0
 34X  CONST_19  CAU  CAT  CAJ  CAI  180.00  0.0  0
 34X  CONST_20  CAV  CAL  CAK  CAJ    0.00  0.0  0
 34X  CONST_21  CAV  CAU  CAT  CAJ    0.00  0.0  0
 34X  CONST_22  CAU  CAT  CAJ  CAK    0.00  0.0  0
 34X  CONST_23  CAU  CAV  CAL  CAK    0.00  0.0  0
 34X  CONST_24  CAT  CAJ  CAK  CAL    0.00  0.0  0
 34X  CONST_25  CAT  CAU  CAV  CAL    0.00  0.0  0
 34X  CONST_26  CAM  CAN  CAO  FAP  180.00  0.0  0
 34X  CONST_27  CAB  CAC  CAO  FAP  180.00  0.0  0
 34X  CONST_28  NAD  CAC  CAO  CAN  180.00  0.0  0
 34X  CONST_29  NAD  CAC  CAB  CAA  180.00  0.0  0
 34X  CONST_30  CAI  CAH  NAG  NAF  180.00  0.0  0
 34X  CONST_31  NAS  CAR  NAG  NAF  180.00  0.0  0
 34X  CONST_32  NAW  CAR  NAG  CAH  180.00  0.0  0
 34X  CONST_33  CAI  NAS  CAR  NAW  180.00  0.0  0
 34X  CONST_34  HAM  CAM  CAN  CAO  180.00  0.0  0
 34X  CONST_35  HAB  CAB  CAC  CAO  180.00  0.0  0
 34X  CONST_36  HAA  CAA  CAM  CAN  180.00  0.0  0
 34X  CONST_37  HAN  CAN  CAM  CAA  180.00  0.0  0
 34X  CONST_38  HAH  CAH  NAG  CAR  180.00  0.0  0
 34X  CONST_39  HAK  CAK  CAJ  CAI    0.00  0.0  0
 34X  CONST_40  HAT  CAT  CAJ  CAI    0.00  0.0  0
 34X  CONST_41  HAL  CAL  CAK  CAJ  180.00  0.0  0
 34X  CONST_42  HAU  CAU  CAT  CAJ  180.00  0.0  0
 34X  CONST_43  HAV  CAV  CAL  CAK  180.00  0.0  0
 34X  CONST_52  OAQ  CAE  NAD  CAC    0.00  0.0  0
 34X  CONST_53  NAG  NAF  CAE  OAQ    0.00  0.0  0
 34X  CONST_54  NAF  CAE  NAD  CAC  180.00  0.0  0
 34X  CONST_55  NAG  NAF  CAE  NAD  180.00  0.0  0

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
 34X  plan-1  NAF   0.020
 34X  plan-1  NAG   0.020
 34X  plan-1  CAH   0.020
 34X  plan-1  CAR   0.020
 34X  plan-1  NAW   0.020
 34X  plan-1  NAS   0.020
 34X  plan-1  CAI   0.020
 34X  plan-1  CAJ   0.020
 34X  plan-1  HAH   0.020
 34X  plan-2  FAP   0.020
 34X  plan-2  CAO   0.020
 34X  plan-2  CAN   0.020
 34X  plan-2  CAM   0.020
 34X  plan-2  CAA   0.020
 34X  plan-2  CAB   0.020
 34X  plan-2  CAC   0.020
 34X  plan-2  NAD   0.020
 34X  plan-2  HAN   0.020
 34X  plan-2  HAM   0.020
 34X  plan-2  HAA   0.020
 34X  plan-2  HAB   0.020
 34X  plan-3  CAI   0.020
 34X  plan-3  CAJ   0.020
 34X  plan-3  CAK   0.020
 34X  plan-3  CAL   0.020
 34X  plan-3  CAV   0.020
 34X  plan-3  CAU   0.020
 34X  plan-3  CAT   0.020
 34X  plan-3  HAK   0.020
 34X  plan-3  HAT   0.020
 34X  plan-3  HAL   0.020
 34X  plan-3  HAV   0.020
 34X  plan-3  HAU   0.020
 34X  plan-4  CAC   0.020
 34X  plan-4  NAD   0.020
 34X  plan-4  CAE   0.020
 34X  plan-4  OAQ   0.020
 34X  plan-4  NAF   0.020
 34X  plan-4  NAG   0.020
 34X  plan-4  HAD   0.020
 34X  plan-4  HAF   0.020
 34X  plan-5  CAR   0.020
 34X  plan-5  NAW   0.020
 34X  plan-5  HAW1  0.020
 34X  plan-5  HAW2  0.020

