# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:24:11 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (4R)-5-[(S)-(3,4-difluorophenyl)(hydroxy)methyl]-4-(3-hydroxyphenyl)-1,6-dimethyl-3,4-dihydropyrimidine-2(1H)-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=C([C@@H](O)c2ccc(F)c(F)c2)[C@H](NC1=S)c3cccc(O)c3)C
#
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
 X7E  X7E  (4R)-5-[(S)-(3,4-difluorophenyl)(hydroxy)methyl]-4-(3-hydroxyphenyl)-1,6-dimethyl-3,4-dihydropyrimidine-2(1H)-thione  ligand  44  26  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X7E
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
 X7E  CAN   C  CR16  0  -0.425  -2.7654  -0.9231  -0.0976
 X7E  CAW   C  CR6   0   0.413  -3.7714  -0.4896  -0.9304
 X7E  FAG   F  F     0  -0.306  -4.4501  -1.3613  -1.6838
 X7E  CAV   C  CR6   0   0.383  -4.0999   0.8552  -0.9996
 X7E  FAF   F  F     0  -0.306  -5.0809   1.2443  -1.8214
 X7E  CAL   C  CR16  0  -0.392  -3.4223   1.7725  -0.2293
 X7E  CAJ   C  CR16  0  -0.298  -2.4074   1.3390   0.6172
 X7E  CAU   C  CR6   0   0.051  -2.0677  -0.0041   0.6846
 X7E  CAQ   C  CH1   0  -0.057  -0.9507  -0.5179   1.5738
 X7E  OAC   O  OH1   0  -0.653  -0.5741   0.4190   2.5583
 X7E  CAS   C  C     0  -0.033   0.2394  -0.9883   0.7641
 X7E  CAP   C  C     0   0.299   1.0737  -1.9494   1.1893
 X7E  CAA   C  CH3   0  -0.764   0.8691  -2.7370   2.4467
 X7E  NAZ   N  NT    0  -0.520   2.2357  -2.2677   0.4538
 X7E  CAB   C  CH3   0  -0.530   3.2515  -3.1359   1.0341
 X7E  CAR   C  C     0   0.384   2.3622  -1.8833  -0.8435
 X7E  SAE   S  S1    0  -0.412   3.5379  -2.4935  -1.8790
 X7E  NAO   N  NH1   0  -0.593   1.4669  -1.0056  -1.2943
 X7E  CAY   C  CH1   0  -0.201   0.5741  -0.2124  -0.4757
 X7E  CAX   C  CR6   0   0.146   1.1430   1.1647  -0.1719
 X7E  CAM   C  CR16  0  -0.439   0.6419   2.2690  -0.8498
 X7E  CAK   C  CR16  0  -0.332   2.1650   1.3306   0.7595
 X7E  CAH   C  CR16  0  -0.227   2.6773   2.6000   0.9935
 X7E  CAI   C  CR16  0  -0.342   2.1810   3.7050   0.3210
 X7E  CAT   C  CR6   0   0.376   1.1535   3.5413  -0.6052
 X7E  OAD   O  OH1   0  -0.629   0.6909   4.6407  -1.2295
 X7E  HAN   H  HCR6  0   0.285  -2.5214  -1.9790  -0.0647
 X7E  HAL   H  HCR6  0   0.292  -3.6859   2.8205  -0.2866
 X7E  HAJ   H  HCR6  0   0.262  -1.8890   2.0699   1.2213
 X7E  HAQ   H  HCH1  0   0.267  -1.3703  -1.3646   2.1212
 X7E  HAC   H  HOH1  0   0.455   0.0869   1.0157   2.1895
 X7E  HAY   H  HCH1  0   0.291  -0.3298  -0.0689  -1.0727
 X7E  HAA1  H  HCH3  0   0.273  -0.1486  -2.6479   2.8122
 X7E  HAA2  H  HCH3  0   0.270   1.0659  -3.7972   2.2930
 X7E  HAA3  H  HCH3  0   0.271   1.5254  -2.3895   3.2462
 X7E  HAB1  H  HCH3  0   0.252   3.0648  -4.1873   0.8150
 X7E  HAB2  H  HCH3  0   0.268   4.2226  -2.8679   0.6323
 X7E  HAB3  H  HCH3  0   0.265   3.2838  -2.9963   2.1092
 X7E  HAO   H  HNH1  0   0.411   1.5654  -0.7392  -2.2615
 X7E  HAM   H  HCR6  0   0.273  -0.1600   2.1359  -1.5691
 X7E  HAK   H  HCR6  0   0.265   2.5652   0.4838   1.3027
 X7E  HAH   H  HCR6  0   0.263   3.4743   2.7312   1.7137
 X7E  HAI   H  HCR6  0   0.268   2.5812   4.6928   0.5120
 X7E  HAD   H  HOH1  0   0.476  -0.0139   4.4124  -1.8459

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
 X7E  CAN  CAW   aromatic  1.376  0.020  1.376
 X7E  CAN  CAU   aromatic  1.394  0.020  1.394
 X7E  CAW  FAG   single    1.337  0.020  1.337
 X7E  CAW  CAV   aromatic  1.386  0.020  1.386
 X7E  CAV  FAF   single    1.338  0.020  1.338
 X7E  CAV  CAL   aromatic  1.376  0.020  1.376
 X7E  CAL  CAJ   aromatic  1.391  0.020  1.391
 X7E  CAJ  CAU   aromatic  1.387  0.020  1.387
 X7E  CAU  CAQ   single    1.517  0.020  1.517
 X7E  CAQ  OAC   single    1.410  0.020  1.410
 X7E  CAQ  CAS   single    1.514  0.020  1.514
 X7E  CAS  CAP   double    1.342  0.020  1.342
 X7E  CAS  CAY   single    1.500  0.020  1.500
 X7E  CAP  CAA   single    1.498  0.020  1.498
 X7E  CAP  NAZ   single    1.412  0.020  1.412
 X7E  NAZ  CAB   single    1.457  0.020  1.457
 X7E  NAZ  CAR   single    1.359  0.020  1.359
 X7E  CAR  SAE   double    1.681  0.020  1.681
 X7E  CAR  NAO   single    1.332  0.020  1.332
 X7E  NAO  CAY   single    1.448  0.020  1.448
 X7E  CAY  CAX   single    1.521  0.020  1.521
 X7E  CAX  CAM   aromatic  1.389  0.020  1.389
 X7E  CAX  CAK   aromatic  1.393  0.020  1.393
 X7E  CAM  CAT   aromatic  1.393  0.020  1.393
 X7E  CAK  CAH   aromatic  1.389  0.020  1.389
 X7E  CAH  CAI   aromatic  1.386  0.020  1.386
 X7E  CAI  CAT   aromatic  1.393  0.020  1.393
 X7E  CAT  OAD   single    1.346  0.020  1.346
 X7E  CAN  HAN   single    0.930  0.020  1.080
 X7E  CAL  HAL   single    0.930  0.020  1.080
 X7E  CAJ  HAJ   single    0.930  0.020  1.080
 X7E  CAQ  HAQ   single    0.970  0.020  1.090
 X7E  OAC  HAC   single    0.850  0.020  0.980
 X7E  CAY  HAY   single    0.970  0.020  1.090
 X7E  CAA  HAA1  single    0.970  0.020  1.090
 X7E  CAA  HAA2  single    0.970  0.020  1.090
 X7E  CAA  HAA3  single    0.970  0.020  1.090
 X7E  CAB  HAB1  single    0.970  0.020  1.090
 X7E  CAB  HAB2  single    0.970  0.020  1.090
 X7E  CAB  HAB3  single    0.970  0.020  1.090
 X7E  NAO  HAO   single    0.860  0.020  1.020
 X7E  CAM  HAM   single    0.930  0.020  1.080
 X7E  CAK  HAK   single    0.930  0.020  1.080
 X7E  CAH  HAH   single    0.930  0.020  1.080
 X7E  CAI  HAI   single    0.930  0.020  1.080
 X7E  OAD  HAD   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
 X7E  HAN   CAN  CAU   120.82  3.000
 X7E  HAN   CAN  CAW   119.32  3.000
 X7E  CAU   CAN  CAW   119.86  3.000
 X7E  CAV   CAW  FAG   118.95  3.000
 X7E  CAV   CAW  CAN   120.60  3.000
 X7E  FAG   CAW  CAN   120.44  3.000
 X7E  CAL   CAV  FAF   120.74  3.000
 X7E  CAL   CAV  CAW   120.14  3.000
 X7E  FAF   CAV  CAW   119.12  3.000
 X7E  HAL   CAL  CAJ   120.79  3.000
 X7E  HAL   CAL  CAV   119.73  3.000
 X7E  CAJ   CAL  CAV   119.48  3.000
 X7E  HAJ   CAJ  CAU   120.68  3.000
 X7E  HAJ   CAJ  CAL   118.65  3.000
 X7E  CAU   CAJ  CAL   120.67  3.000
 X7E  CAQ   CAU  CAJ   122.46  3.000
 X7E  CAQ   CAU  CAN   118.30  3.000
 X7E  CAJ   CAU  CAN   119.24  3.000
 X7E  HAQ   CAQ  CAS   109.22  3.000
 X7E  HAQ   CAQ  OAC   105.53  3.000
 X7E  CAS   CAQ  OAC   111.70  3.000
 X7E  HAQ   CAQ  CAU   105.87  3.000
 X7E  CAS   CAQ  CAU   111.74  3.000
 X7E  OAC   CAQ  CAU   112.38  3.000
 X7E  HAC   OAC  CAQ   109.11  3.000
 X7E  CAY   CAS  CAP   119.57  3.000
 X7E  CAY   CAS  CAQ   117.16  3.000
 X7E  CAP   CAS  CAQ   122.80  3.000
 X7E  NAZ   CAP  CAA   115.55  3.000
 X7E  NAZ   CAP  CAS   120.54  3.000
 X7E  CAA   CAP  CAS   123.90  3.000
 X7E  HAA3  CAA  HAA2  107.74  3.000
 X7E  HAA3  CAA  HAA1  106.93  3.000
 X7E  HAA2  CAA  HAA1  107.27  3.000
 X7E  HAA3  CAA  CAP   111.44  3.000
 X7E  HAA2  CAA  CAP   111.63  3.000
 X7E  HAA1  CAA  CAP   111.58  3.000
 X7E  CAR   NAZ  CAB   118.94  3.000
 X7E  CAR   NAZ  CAP   120.69  3.000
 X7E  CAB   NAZ  CAP   120.05  3.000
 X7E  HAB3  CAB  HAB2  107.99  3.000
 X7E  HAB3  CAB  HAB1  109.17  3.000
 X7E  HAB2  CAB  HAB1  108.50  3.000
 X7E  HAB3  CAB  NAZ   109.81  3.000
 X7E  HAB2  CAB  NAZ   109.23  3.000
 X7E  HAB1  CAB  NAZ   112.04  3.000
 X7E  NAO   CAR  SAE   120.04  3.000
 X7E  NAO   CAR  NAZ   116.53  3.000
 X7E  SAE   CAR  NAZ   123.40  3.000
 X7E  HAO   NAO  CAY   117.26  3.000
 X7E  HAO   NAO  CAR   115.66  3.000
 X7E  CAY   NAO  CAR   125.73  3.000
 X7E  HAY   CAY  CAX   107.44  3.000
 X7E  HAY   CAY  NAO   105.85  3.000
 X7E  CAX   CAY  NAO   112.24  3.000
 X7E  HAY   CAY  CAS   109.56  3.000
 X7E  CAX   CAY  CAS   112.75  3.000
 X7E  NAO   CAY  CAS   108.75  3.000
 X7E  CAK   CAX  CAM   119.76  3.000
 X7E  CAK   CAX  CAY   121.07  3.000
 X7E  CAM   CAX  CAY   119.17  3.000
 X7E  HAM   CAM  CAT   119.98  3.000
 X7E  HAM   CAM  CAX   119.49  3.000
 X7E  CAT   CAM  CAX   120.52  3.000
 X7E  HAK   CAK  CAH   119.60  3.000
 X7E  HAK   CAK  CAX   120.90  3.000
 X7E  CAH   CAK  CAX   119.49  3.000
 X7E  HAH   CAH  CAI   119.35  3.000
 X7E  HAH   CAH  CAK   119.65  3.000
 X7E  CAI   CAH  CAK   121.00  3.000
 X7E  HAI   CAI  CAT   119.81  3.000
 X7E  HAI   CAI  CAH   120.64  3.000
 X7E  CAT   CAI  CAH   119.55  3.000
 X7E  OAD   CAT  CAI   117.77  3.000
 X7E  OAD   CAT  CAM   122.56  3.000
 X7E  CAI   CAT  CAM   119.67  3.000
 X7E  HAD   OAD  CAT   110.76  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
 X7E  CONST_01  CAL   CAV  CAW  CAN    0.00   0.0  0
 X7E  CONST_02  CAL   CAJ  CAU  CAN    0.00   0.0  0
 X7E  CONST_03  CAJ   CAU  CAN  CAW    0.00   0.0  0
 X7E  CONST_04  CAJ   CAL  CAV  CAW    0.00   0.0  0
 X7E  CONST_05  CAU   CAN  CAW  CAV    0.00   0.0  0
 X7E  CONST_06  CAU   CAJ  CAL  CAV    0.00   0.0  0
 X7E  CONST_07  CAI   CAT  CAM  CAX    0.00   0.0  0
 X7E  CONST_08  CAI   CAH  CAK  CAX    0.00   0.0  0
 X7E  CONST_09  CAH   CAK  CAX  CAM    0.00   0.0  0
 X7E  CONST_10  CAH   CAI  CAT  CAM    0.00   0.0  0
 X7E  CONST_11  CAT   CAM  CAX  CAK    0.00   0.0  0
 X7E  CONST_12  CAT   CAI  CAH  CAK    0.00   0.0  0
 X7E  CONST_13  CAT   CAM  CAX  CAY  180.00   0.0  0
 X7E  CONST_14  CAH   CAK  CAX  CAY  180.00   0.0  0
 X7E  CONST_15  NAO   CAR  NAZ  CAP    0.00   0.0  0
 X7E  CONST_16  CAY   NAO  CAR  NAZ    0.00   0.0  0
 X7E  CONST_17  FAF   CAV  CAW  CAN  180.00   0.0  0
 X7E  CONST_18  CAQ   CAU  CAN  CAW  180.00   0.0  0
 X7E  CONST_19  CAU   CAN  CAW  FAG  180.00   0.0  0
 X7E  CONST_20  CAL   CAV  CAW  FAG  180.00   0.0  0
 X7E  CONST_21  CAJ   CAL  CAV  FAF  180.00   0.0  0
 X7E  CONST_22  CAQ   CAU  CAJ  CAL  180.00   0.0  0
 X7E  CONST_23  OAD   CAT  CAM  CAX  180.00   0.0  0
 X7E  CONST_24  OAD   CAT  CAI  CAH  180.00   0.0  0
 X7E  CONST_25  SAE   CAR  NAZ  CAP  180.00   0.0  0
 X7E  CONST_26  NAO   CAR  NAZ  CAB  180.00   0.0  0
 X7E  CONST_27  CAY   NAO  CAR  SAE  180.00   0.0  0
 X7E  CONST_28  HAJ   CAJ  CAU  CAN  180.00   0.0  0
 X7E  CONST_29  HAL   CAL  CAV  CAW  180.00   0.0  0
 X7E  CONST_30  HAN   CAN  CAW  CAV  180.00   0.0  0
 X7E  CONST_31  HAM   CAM  CAX  CAY    0.00   0.0  0
 X7E  CONST_32  HAK   CAK  CAX  CAY    0.00   0.0  0
 X7E  CONST_33  HAH   CAH  CAK  CAX  180.00   0.0  0
 X7E  CONST_34  HAI   CAI  CAT  CAM  180.00   0.0  0
 X7E  CONST_35  HAO   NAO  CAR  NAZ  180.00   0.0  0
 X7E  CONST_36  SAE   CAR  NAZ  CAB    0.00   0.0  0
 X7E  Var_01    CAR   NAZ  CAP  CAS  -17.46  30.0  1
 X7E  Var_02    CAY   CAS  CAP  NAZ   -2.32  30.0  1
 X7E  Var_03    HAA1  CAA  CAP  CAS   16.42  30.0  3
 X7E  Var_04    HAB1  CAB  NAZ  CAP   89.52  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
 X7E  chir_01  CAQ  CAU  OAC  CAS  positiv
 X7E  chir_02  CAY  NAO  CAS  CAX  negativ

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
 X7E  plan-1  CAN  0.020
 X7E  plan-1  CAW  0.020
 X7E  plan-1  FAG  0.020
 X7E  plan-1  CAV  0.020
 X7E  plan-1  FAF  0.020
 X7E  plan-1  CAL  0.020
 X7E  plan-1  CAJ  0.020
 X7E  plan-1  CAU  0.020
 X7E  plan-1  CAQ  0.020
 X7E  plan-1  HAN  0.020
 X7E  plan-1  HAL  0.020
 X7E  plan-1  HAJ  0.020
 X7E  plan-2  CAY  0.020
 X7E  plan-2  CAX  0.020
 X7E  plan-2  CAM  0.020
 X7E  plan-2  CAK  0.020
 X7E  plan-2  CAH  0.020
 X7E  plan-2  CAI  0.020
 X7E  plan-2  CAT  0.020
 X7E  plan-2  OAD  0.020
 X7E  plan-2  HAM  0.020
 X7E  plan-2  HAK  0.020
 X7E  plan-2  HAH  0.020
 X7E  plan-2  HAI  0.020
 X7E  plan-3  CAP  0.020
 X7E  plan-3  NAZ  0.020
 X7E  plan-3  CAB  0.020
 X7E  plan-3  CAR  0.020
 X7E  plan-3  SAE  0.020
 X7E  plan-3  NAO  0.020
 X7E  plan-3  CAY  0.020
 X7E  plan-3  HAO  0.020

