# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 00:27:28 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-[(6-methyl-2-oxo-1H-quinolin-3-yl)methyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2NC(=O)C(=Cc2c1)CN(CCO)C(=O)Nc3ccccc3F
#
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
 Z78  Z78  3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-[(6-methyl-2-oxo-1H-quinolin-3-yl)methyl]urea  ligand  47  27  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z78
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
 Z78  N1    N  NR16  0  -0.750   3.2593  -0.9266  -1.3378
 Z78  N2    N  NT    0  -0.475  -0.7737  -1.7091   0.2825
 Z78  N3    N  NH1   0  -0.799  -2.6466  -0.4028  -0.1411
 Z78  CAA   C  CH3   0  -0.722   5.6218   3.5482   1.2417
 Z78  OAB   O  O     0  -0.509  -0.8719   0.4172   1.0381
 Z78  OAC   O  O     0  -0.485   1.7704  -2.6124  -1.4730
 Z78  OAD   O  OH1   0  -0.667  -3.3757  -3.1191   0.5908
 Z78  CAF   C  CR16  0  -0.260  -4.9063   3.1387  -0.2795
 Z78  CAG   C  CR16  0  -0.268  -3.5451   3.1776  -0.5487
 Z78  CAH   C  CR16  0  -0.407  -5.5044   1.9277   0.0382
 Z78  CAI   C  CR16  0  -0.290  -2.7798   2.0220  -0.5019
 Z78  CAJ   C  CR16  0  -0.296   5.4915   1.8942  -0.6590
 Z78  CAK   C  CR16  0  -0.298   4.9320   0.8154  -1.3082
 Z78  CAL   C  CR16  0  -0.379   3.9280   1.6915   1.1320
 Z78  CAM   C  CR16  0  -0.186   2.2124  -0.1111   1.0365
 Z78  CAN   C  CH2   0  -0.138  -2.1715  -3.7743   0.2573
 Z78  CAO   C  CH2   0  -0.396  -1.2884  -2.8133  -0.5122
 Z78  CAP   C  CH2   0  -0.393   0.4773  -1.9032   1.0023
 Z78  CAS   C  C     0   0.721  -1.3945  -0.5100   0.4379
 Z78  CAT   C  CR6   0   0.096   5.0022   2.3551   0.5745
 Z78  CAU   C  CR6   0   0.469  -4.7241   0.7927   0.0970
 Z78  CAV   C  CR6   0  -0.084   1.6506  -1.1690   0.4126
 Z78  CAW   C  CR6   0   0.214  -3.3560   0.7967  -0.1645
 Z78  CAX   C  CR6   0   0.523   2.1973  -1.6419  -0.8550
 Z78  CAY   C  CR66  0   0.060   3.3343   0.5919   0.4958
 Z78  CAZ   C  CR66  0   0.364   3.8446   0.1548  -0.7315
 Z78  HN1   H  HNR6  0   0.413   3.6450  -1.2427  -2.2181
 Z78  HN3   H  HNH1  0   0.420  -3.2057  -1.2468  -0.1492
 Z78  HAA   H  HCH3  0   0.249   5.2707   4.4776   0.7889
 Z78  HAAA  H  HCH3  0   0.245   5.3738   3.5873   2.3015
 Z78  HAAB  H  HCH3  0   0.244   6.7080   3.5370   1.1498
 Z78  HAF   H  HCR6  0   0.264  -5.5038   4.0391  -0.3214
 Z78  HAG   H  HCR6  0   0.260  -3.0708   4.1140  -0.8098
 Z78  HAH   H  HCR6  0   0.279  -6.5643   1.8605   0.2472
 Z78  HAI   H  HCR6  0   0.270  -1.7269   2.0719  -0.7366
 Z78  HAJ   H  HCR6  0   0.259   6.3351   2.3985  -1.1150
 Z78  HAK   H  HCR6  0   0.275   5.3309   0.4803  -2.2576
 Z78  HAL   H  HCR6  0   0.255   3.5244   2.0148   2.0851
 Z78  HAM   H  HCR6  0   0.266   1.8046   0.2258   1.9825
 Z78  HAN   H  HCH2  0   0.211  -1.6403  -4.1209   1.1516
 Z78  HAO   H  HCH2  0   0.260  -1.8188  -2.4281  -1.3863
 Z78  HAOA  H  HCH2  0   0.285  -0.4344  -3.3624  -0.9013
 Z78  HAP   H  HCH2  0   0.270   0.3591  -1.6019   2.0437
 Z78  HAPA  H  HCH2  0   0.271   0.6798  -2.9748   1.0125
 Z78  H19   H  HOH1  0   0.467  -3.8681  -3.6473   1.2251
 Z78  H20   H  HCH2  0   0.209  -2.3514  -4.6535  -0.3735
 Z78  FAE   F  F     0  -0.317  -5.3064  -0.3806   0.4101

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
 Z78  N1   CAX   single    1.368  0.020  1.368
 Z78  N1   CAZ   single    1.371  0.020  1.371
 Z78  N1   HN1   single    0.860  0.020  1.020
 Z78  N2   CAO   single    1.455  0.020  1.455
 Z78  N2   CAP   single    1.456  0.020  1.456
 Z78  N2   CAS   single    1.359  0.020  1.359
 Z78  N3   CAS   single    1.384  0.020  1.384
 Z78  N3   CAW   single    1.394  0.020  1.394
 Z78  N3   HN3   single    0.890  0.020  1.040
 Z78  CAA  CAT   single    1.501  0.020  1.501
 Z78  CAA  HAA   single    0.970  0.020  1.090
 Z78  CAA  HAAA  single    0.970  0.020  1.090
 Z78  CAA  HAAB  single    0.970  0.020  1.090
 Z78  OAB  CAS   double    1.222  0.020  1.222
 Z78  OAC  CAX   double    1.227  0.020  1.227
 Z78  OAD  CAN   single    1.411  0.020  1.411
 Z78  FAE  CAU   single    1.347  0.020  1.347
 Z78  CAF  CAG   aromatic  1.388  0.020  1.388
 Z78  CAF  CAH   aromatic  1.388  0.020  1.388
 Z78  CAF  HAF   single    0.930  0.020  1.080
 Z78  CAG  CAI   aromatic  1.387  0.020  1.387
 Z78  CAG  HAG   single    0.930  0.020  1.080
 Z78  CAH  CAU   aromatic  1.379  0.020  1.379
 Z78  CAH  HAH   single    0.930  0.020  1.080
 Z78  CAI  CAW   aromatic  1.395  0.020  1.395
 Z78  CAI  HAI   single    0.930  0.020  1.080
 Z78  CAJ  CAK   aromatic  1.378  0.020  1.378
 Z78  CAJ  CAT   aromatic  1.405  0.020  1.405
 Z78  CAJ  HAJ   single    0.930  0.020  1.080
 Z78  CAK  CAZ   aromatic  1.397  0.020  1.397
 Z78  CAK  HAK   single    0.930  0.020  1.080
 Z78  CAL  CAT   aromatic  1.380  0.020  1.380
 Z78  CAL  CAY   aromatic  1.402  0.020  1.402
 Z78  CAL  HAL   single    0.930  0.020  1.080
 Z78  CAM  CAV   double    1.351  0.020  1.351
 Z78  CAM  CAY   single    1.430  0.020  1.430
 Z78  CAM  HAM   single    0.930  0.020  1.080
 Z78  CAN  CAO   single    1.515  0.020  1.515
 Z78  CAN  HAN   single    0.970  0.020  1.090
 Z78  CAO  HAO   single    0.970  0.020  1.090
 Z78  CAO  HAOA  single    0.970  0.020  1.090
 Z78  CAP  CAV   single    1.504  0.020  1.504
 Z78  CAP  HAP   single    0.970  0.020  1.090
 Z78  CAP  HAPA  single    0.970  0.020  1.090
 Z78  CAU  CAW   aromatic  1.393  0.020  1.393
 Z78  CAV  CAX   single    1.459  0.020  1.459
 Z78  CAY  CAZ   aromatic  1.399  0.020  1.399
 Z78  OAD  H19   single    0.850  0.020  0.980
 Z78  CAN  H20   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
 Z78  HN1   N1   CAZ   117.94  3.000
 Z78  HN1   N1   CAX   116.07  3.000
 Z78  CAZ   N1   CAX   125.99  3.000
 Z78  CAS   N2   CAP   116.96  3.000
 Z78  CAS   N2   CAO   124.79  3.000
 Z78  CAP   N2   CAO   118.22  3.000
 Z78  HN3   N3   CAW   115.86  3.000
 Z78  HN3   N3   CAS   116.01  3.000
 Z78  CAW   N3   CAS   122.30  3.000
 Z78  HAAB  CAA  HAAA  108.01  3.000
 Z78  HAAB  CAA  HAA   107.12  3.000
 Z78  HAAA  CAA  HAA   107.44  3.000
 Z78  HAAB  CAA  CAT   111.45  3.000
 Z78  HAAA  CAA  CAT   111.53  3.000
 Z78  HAA   CAA  CAT   111.08  3.000
 Z78  H19   OAD  CAN   109.75  3.000
 Z78  HAF   CAF  CAH   119.83  3.000
 Z78  HAF   CAF  CAG   120.73  3.000
 Z78  CAH   CAF  CAG   119.44  3.000
 Z78  HAG   CAG  CAI   119.18  3.000
 Z78  HAG   CAG  CAF   120.07  3.000
 Z78  CAI   CAG  CAF   120.75  3.000
 Z78  HAH   CAH  CAU   119.67  3.000
 Z78  HAH   CAH  CAF   121.36  3.000
 Z78  CAU   CAH  CAF   118.97  3.000
 Z78  HAI   CAI  CAW   119.72  3.000
 Z78  HAI   CAI  CAG   119.48  3.000
 Z78  CAW   CAI  CAG   120.79  3.000
 Z78  HAJ   CAJ  CAT   119.21  3.000
 Z78  HAJ   CAJ  CAK   118.84  3.000
 Z78  CAT   CAJ  CAK   121.95  3.000
 Z78  HAK   CAK  CAZ   120.15  3.000
 Z78  HAK   CAK  CAJ   120.39  3.000
 Z78  CAZ   CAK  CAJ   119.46  3.000
 Z78  HAL   CAL  CAY   118.36  3.000
 Z78  HAL   CAL  CAT   120.09  3.000
 Z78  CAY   CAL  CAT   121.55  3.000
 Z78  HAM   CAM  CAY   118.19  3.000
 Z78  HAM   CAM  CAV   119.35  3.000
 Z78  CAY   CAM  CAV   122.46  3.000
 Z78  H20   CAN  HAN   107.17  3.000
 Z78  H20   CAN  CAO   108.17  3.000
 Z78  HAN   CAN  CAO   109.41  3.000
 Z78  H20   CAN  OAD   111.60  3.000
 Z78  HAN   CAN  OAD   111.56  3.000
 Z78  CAO   CAN  OAD   108.84  3.000
 Z78  HAOA  CAO  HAO   105.84  3.000
 Z78  HAOA  CAO  CAN   108.62  3.000
 Z78  HAO   CAO  CAN   110.30  3.000
 Z78  HAOA  CAO  N2    107.52  3.000
 Z78  HAO   CAO  N2    109.95  3.000
 Z78  CAN   CAO  N2    114.22  3.000
 Z78  HAPA  CAP  HAP   106.42  3.000
 Z78  HAPA  CAP  CAV   109.78  3.000
 Z78  HAP   CAP  CAV   108.91  3.000
 Z78  HAPA  CAP  N2    107.16  3.000
 Z78  HAP   CAP  N2    110.00  3.000
 Z78  CAV   CAP  N2    114.28  3.000
 Z78  OAB   CAS  N3    122.26  3.000
 Z78  OAB   CAS  N2    122.02  3.000
 Z78  N3    CAS  N2    115.71  3.000
 Z78  CAL   CAT  CAJ   117.90  3.000
 Z78  CAL   CAT  CAA   121.60  3.000
 Z78  CAJ   CAT  CAA   120.49  3.000
 Z78  CAW   CAU  CAH   123.06  3.000
 Z78  CAW   CAU  FAE   118.09  3.000
 Z78  CAH   CAU  FAE   118.85  3.000
 Z78  CAX   CAV  CAP   118.33  3.000
 Z78  CAX   CAV  CAM   119.95  3.000
 Z78  CAP   CAV  CAM   121.71  3.000
 Z78  CAU   CAW  CAI   116.97  3.000
 Z78  CAU   CAW  N3    119.63  3.000
 Z78  CAI   CAW  N3    123.33  3.000
 Z78  CAV   CAX  OAC   124.29  3.000
 Z78  CAV   CAX  N1    115.33  3.000
 Z78  OAC   CAX  N1    120.38  3.000
 Z78  CAZ   CAY  CAM   117.65  3.000
 Z78  CAZ   CAY  CAL   119.25  3.000
 Z78  CAM   CAY  CAL   123.10  3.000
 Z78  CAY   CAZ  CAK   119.89  3.000
 Z78  CAY   CAZ  N1    118.60  3.000
 Z78  CAK   CAZ  N1    121.52  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
 Z78  CONST_01  CAW  CAI  CAG  CAF    0.00   0.0  0
 Z78  CONST_02  CAW  CAU  CAH  CAF    0.00   0.0  0
 Z78  CONST_03  CAU  CAH  CAF  CAG    0.00   0.0  0
 Z78  CONST_04  CAU  CAW  CAI  CAG    0.00   0.0  0
 Z78  CONST_05  CAI  CAG  CAF  CAH    0.00   0.0  0
 Z78  CONST_06  CAI  CAW  CAU  CAH    0.00   0.0  0
 Z78  CONST_07  CAY  CAZ  CAK  CAJ    0.00   0.0  0
 Z78  CONST_08  CAY  CAL  CAT  CAJ    0.00   0.0  0
 Z78  CONST_09  CAL  CAT  CAJ  CAK    0.00   0.0  0
 Z78  CONST_10  CAL  CAY  CAZ  CAK    0.00   0.0  0
 Z78  CONST_11  CAZ  CAK  CAJ  CAT    0.00   0.0  0
 Z78  CONST_12  CAZ  CAY  CAL  CAT    0.00   0.0  0
 Z78  CONST_13  CAZ  N1   CAX  CAV    0.00   0.0  0
 Z78  CONST_14  CAG  CAI  CAW  N3   180.00   0.0  0
 Z78  CONST_15  CAH  CAU  CAW  N3   180.00   0.0  0
 Z78  CONST_16  CAK  CAJ  CAT  CAA  180.00   0.0  0
 Z78  CONST_17  CAY  CAL  CAT  CAA  180.00   0.0  0
 Z78  CONST_18  CAF  CAH  CAU  FAE  180.00   0.0  0
 Z78  CONST_19  CAI  CAW  CAU  FAE  180.00   0.0  0
 Z78  CONST_20  CAZ  N1   CAX  OAC  180.00   0.0  0
 Z78  CONST_21  HAK  CAK  CAZ  N1     0.00   0.0  0
 Z78  CONST_22  HAI  CAI  CAG  CAF  180.00   0.0  0
 Z78  CONST_23  HAH  CAH  CAF  CAG  180.00   0.0  0
 Z78  CONST_24  HAG  CAG  CAF  CAH  180.00   0.0  0
 Z78  CONST_25  HAF  CAF  CAG  CAI  180.00   0.0  0
 Z78  CONST_26  HAL  CAL  CAT  CAJ  180.00   0.0  0
 Z78  CONST_27  HAJ  CAJ  CAT  CAL  180.00   0.0  0
 Z78  CONST_28  HN1  N1   CAX  CAV  180.00   0.0  0
 Z78  CONST_32  CAW  N3   CAS  OAB    0.00   0.0  0
 Z78  CONST_33  CAW  N3   CAS  N2   180.00   0.0  0
 Z78  CONST_34  CAO  N2   CAS  OAB  180.00   0.0  0
 Z78  CONST_35  CAP  N2   CAS  OAB    0.00   0.0  0
 Z78  CONST_36  CAO  N2   CAS  N3     0.00   0.0  0
 Z78  CONST_37  CAP  N2   CAS  N3   180.00   0.0  0
 Z78  Var_01    CAM  CAV  CAP  N2   109.99  30.0  3
 Z78  Var_02    HAA  CAA  CAT  CAJ   78.87  30.0  2
 Z78  Var_03    CAV  CAP  N2   CAO  107.22  30.0  3
 Z78  Var_04    OAD  CAN  CAO  N2    68.79  30.0  2
 Z78  Var_05    CAP  N2   CAO  CAN   87.95  30.0  2

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
 Z78  plan-1  N3   0.020
 Z78  plan-1  CAF  0.020
 Z78  plan-1  CAG  0.020
 Z78  plan-1  CAH  0.020
 Z78  plan-1  CAI  0.020
 Z78  plan-1  CAU  0.020
 Z78  plan-1  CAW  0.020
 Z78  plan-1  HAF  0.020
 Z78  plan-1  HAG  0.020
 Z78  plan-1  HAH  0.020
 Z78  plan-1  HAI  0.020
 Z78  plan-1  FAE  0.020
 Z78  plan-2  N1   0.020
 Z78  plan-2  CAA  0.020
 Z78  plan-2  OAC  0.020
 Z78  plan-2  CAJ  0.020
 Z78  plan-2  CAK  0.020
 Z78  plan-2  CAL  0.020
 Z78  plan-2  CAM  0.020
 Z78  plan-2  CAP  0.020
 Z78  plan-2  CAT  0.020
 Z78  plan-2  CAV  0.020
 Z78  plan-2  CAX  0.020
 Z78  plan-2  CAY  0.020
 Z78  plan-2  CAZ  0.020
 Z78  plan-2  HN1  0.020
 Z78  plan-2  HAJ  0.020
 Z78  plan-2  HAK  0.020
 Z78  plan-2  HAL  0.020
 Z78  plan-2  HAM  0.020
 Z78  plan-3  N2   0.020
 Z78  plan-3  N3   0.020
 Z78  plan-3  OAB  0.020
 Z78  plan-3  CAO  0.020
 Z78  plan-3  CAP  0.020
 Z78  plan-3  CAS  0.020
 Z78  plan-3  CAW  0.020
 Z78  plan-3  HN3  0.020

