# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:31:52 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: 5'-({[4-chloro-3-(trifluoromethyl)phenyl]carbamothioyl}amino)-2',5'-dideoxy-3,4-dihydrothymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CNC(=S)Nc3ccc(Cl)c(c3)C(F)(F)F)O2)C(=O)NC1=O
#
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
 74W  74W  5'-({[4-chloro-3-(trifluoromethyl)phenyl]carbamothioyl}amino)-2',5'-dideoxy-3,4-dihydrothymidine  ligand  49  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_74W
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
 74W  OAC   O   O     0  -0.473   4.8269   0.1968   1.7957
 74W  CAZ   C   CR6   0   0.742   5.3910   0.4460   0.7509
 74W  NAR   N   NR16  0  -0.734   6.3122   1.4561   0.6468
 74W  CAY   C   CR6   0   0.559   7.0294   1.8458  -0.4700
 74W  OAB   O   O     0  -0.455   7.8226   2.7675  -0.4074
 74W  CAU   C   CR6   0  -0.185   6.7430   1.0743  -1.6623
 74W  CAA   C   CH3   0  -0.706   7.4585   1.4078  -2.9299
 74W  CAM   C   CR16  0   0.059   5.8366   0.0864  -1.5679
 74W  NBD   N   NR6   0  -0.566   5.1733  -0.2486  -0.4159
 74W  CBC   C   CH1   0   0.218   4.1874  -1.3284  -0.4504
 74W  OAS   O   O2    0  -0.493   2.9168  -0.8055  -0.1902
 74W  CAO   C   CH2   0  -0.562   4.4213  -2.4827   0.5285
 74W  CBA   C   CH1   0   0.030   3.2618  -2.4003   1.5217
 74W  OAD   O   OH1   0  -0.667   2.7126  -3.6394   1.8918
 74W  CBB   C   CH1   0   0.050   2.2120  -1.6070   0.7429
 74W  CAN   C   CH2   0  -0.311   1.3607  -0.7170   1.6284
 74W  NAP   N   NH1   0  -0.612   0.3852   0.0530   0.8934
 74W  CAT   C   C     0   0.399  -0.8151  -0.3903   0.5113
 74W  SAE   S   S1    0  -0.389  -1.4016  -1.9032   0.9362
 74W  NAQ   N   NH1   0  -0.741  -1.5054   0.4941  -0.2565
 74W  CAV   C   CR6   0   0.401  -2.7933   0.3538  -0.7828
 74W  CAL   C   CR16  0  -0.324  -3.8656  -0.0893  -0.0140
 74W  CAJ   C   CR16  0  -0.317  -3.0161   0.7473  -2.0960
 74W  CAK   C   CR16  0  -0.194  -4.2868   0.6883  -2.6419
 74W  CAW   C   CR6   0  -0.082  -5.3441   0.2226  -1.8819
 74W  CL    CL  CL    0  -0.105  -6.9083   0.1483  -2.6138
 74W  CAX   C   CR6   0  -0.129  -5.1384  -0.1687  -0.5590
 74W  CBE   C   CT    0   1.073  -6.2794  -0.6486   0.2905
 74W  FAF   F   F     0  -0.310  -6.8634  -1.7361  -0.2260
 74W  FAG   F   F     0  -0.298  -5.8863  -0.9715   1.5246
 74W  FAH   F   F     0  -0.310  -7.2301   0.2850   0.4177
 74W  HAR   H   HNR6  0   0.425   6.4817   1.9743   1.5006
 74W  HAA1  H   HCH3  0   0.247   7.2690   2.4376  -3.2362
 74W  HAA2  H   HCH3  0   0.247   8.5380   1.2980  -2.8178
 74W  HAA3  H   HCH3  0   0.247   7.1386   0.7536  -3.7394
 74W  HAM   H   HCR6  0   0.317   5.5828  -0.5181  -2.4286
 74W  HBC   H   HCH1  0   0.255   4.2346  -1.6988  -1.4769
 74W  HAO1  H   HCH2  0   0.268   4.3528  -3.4221  -0.0233
 74W  HAO2  H   HCH2  0   0.276   5.4026  -2.4515   0.9994
 74W  HBB   H   HCH1  0   0.233   1.5618  -2.3129   0.2083
 74W  HBA   H   HCH1  0   0.232   3.5720  -1.8378   2.4067
 74W  HAD   H   HOH1  0   0.457   3.2855  -4.0366   2.5541
 74W  HAN1  H   HCH2  0   0.261   0.8496  -1.3378   2.3642
 74W  HAN2  H   HCH2  0   0.269   1.9984  -0.0114   2.1613
 74W  HAP   H   HNH1  0   0.409   0.6773   0.9723   0.5966
 74W  HAQ   H   HNH1  0   0.415  -0.9829   1.2750  -0.6299
 74W  HAL   H   HCR6  0   0.287  -3.6974  -0.3594   1.0163
 74W  HAJ   H   HCR6  0   0.291  -2.1936   1.1021  -2.7041
 74W  HAK   H   HCR6  0   0.295  -4.4491   0.9954  -3.6656

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
 74W  OAC  CAZ   double    1.213  0.020  1.213
 74W  CAZ  NAR   single    1.371  0.020  1.371
 74W  CAZ  NBD   single    1.375  0.020  1.375
 74W  NAR  CAY   single    1.383  0.020  1.383
 74W  CAY  OAB   double    1.218  0.020  1.218
 74W  CAY  CAU   single    1.449  0.020  1.449
 74W  CAU  CAA   single    1.493  0.020  1.493
 74W  CAU  CAM   double    1.344  0.020  1.344
 74W  CAM  NBD   single    1.371  0.020  1.371
 74W  NBD  CBC   single    1.463  0.020  1.463
 74W  CBC  OAS   single    1.398  0.020  1.398
 74W  CBC  CAO   single    1.531  0.020  1.531
 74W  OAS  CBB   single    1.418  0.020  1.418
 74W  CAO  CBA   single    1.529  0.020  1.529
 74W  CBA  OAD   single    1.405  0.020  1.405
 74W  CBA  CBB   single    1.529  0.020  1.529
 74W  CBB  CAN   single    1.517  0.020  1.517
 74W  CAN  NAP   single    1.444  0.020  1.444
 74W  NAP  CAT   single    1.335  0.020  1.335
 74W  CAT  SAE   double    1.677  0.020  1.677
 74W  CAT  NAQ   single    1.359  0.020  1.359
 74W  NAQ  CAV   single    1.398  0.020  1.398
 74W  CAV  CAL   aromatic  1.392  0.020  1.392
 74W  CAV  CAJ   aromatic  1.389  0.020  1.389
 74W  CAL  CAX   aromatic  1.387  0.020  1.387
 74W  CAJ  CAK   aromatic  1.384  0.020  1.384
 74W  CAK  CAW   aromatic  1.383  0.020  1.383
 74W  CAW  CL    single    1.729  0.020  1.729
 74W  CAW  CAX   aromatic  1.395  0.020  1.395
 74W  CAX  CBE   single    1.501  0.020  1.501
 74W  CBE  FAG   single    1.335  0.020  1.335
 74W  CBE  FAH   single    1.338  0.020  1.338
 74W  CBE  FAF   single    1.338  0.020  1.338
 74W  NAR  HAR   single    0.860  0.020  1.020
 74W  CAA  HAA1  single    0.970  0.020  1.090
 74W  CAA  HAA2  single    0.970  0.020  1.090
 74W  CAA  HAA3  single    0.970  0.020  1.090
 74W  CAM  HAM   single    0.930  0.020  1.080
 74W  CBC  HBC   single    0.970  0.020  1.090
 74W  CAO  HAO1  single    0.970  0.020  1.090
 74W  CAO  HAO2  single    0.970  0.020  1.090
 74W  CBB  HBB   single    0.970  0.020  1.090
 74W  CBA  HBA   single    0.970  0.020  1.090
 74W  OAD  HAD   single    0.850  0.020  0.980
 74W  CAN  HAN1  single    0.970  0.020  1.090
 74W  CAN  HAN2  single    0.970  0.020  1.090
 74W  NAP  HAP   single    0.860  0.020  1.020
 74W  NAQ  HAQ   single    0.860  0.020  1.020
 74W  CAL  HAL   single    0.930  0.020  1.080
 74W  CAJ  HAJ   single    0.930  0.020  1.080
 74W  CAK  HAK   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
 74W  NBD   CAZ  NAR   114.46  3.000
 74W  NBD   CAZ  OAC   123.60  3.000
 74W  NAR   CAZ  OAC   121.94  3.000
 74W  HAR   NAR  CAY   116.72  3.000
 74W  HAR   NAR  CAZ   115.17  3.000
 74W  CAY   NAR  CAZ   128.11  3.000
 74W  CAU   CAY  OAB   125.05  3.000
 74W  CAU   CAY  NAR   114.33  3.000
 74W  OAB   CAY  NAR   120.63  3.000
 74W  CAM   CAU  CAA   123.15  3.000
 74W  CAM   CAU  CAY   117.84  3.000
 74W  CAA   CAU  CAY   119.01  3.000
 74W  HAA3  CAA  HAA2  107.86  3.000
 74W  HAA3  CAA  HAA1  107.90  3.000
 74W  HAA2  CAA  HAA1  107.20  3.000
 74W  HAA3  CAA  CAU   110.86  3.000
 74W  HAA2  CAA  CAU   111.37  3.000
 74W  HAA1  CAA  CAU   111.46  3.000
 74W  HAM   CAM  NBD   114.74  3.000
 74W  HAM   CAM  CAU   120.87  3.000
 74W  NBD   CAM  CAU   124.40  3.000
 74W  CBC   NBD  CAM   119.13  3.000
 74W  CBC   NBD  CAZ   119.97  3.000
 74W  CAM   NBD  CAZ   120.86  3.000
 74W  HBC   CBC  CAO   109.78  3.000
 74W  HBC   CBC  OAS   109.93  3.000
 74W  CAO   CBC  OAS   107.56  3.000
 74W  HBC   CBC  NBD   104.09  3.000
 74W  CAO   CBC  NBD   116.01  3.000
 74W  OAS   CBC  NBD   109.39  3.000
 74W  CBB   OAS  CBC   111.27  3.000
 74W  HAO2  CAO  HAO1  107.45  3.000
 74W  HAO2  CAO  CBA   113.64  3.000
 74W  HAO1  CAO  CBA   109.10  3.000
 74W  HAO2  CAO  CBC   113.11  3.000
 74W  HAO1  CAO  CBC   108.42  3.000
 74W  CBA   CAO  CBC   104.99  3.000
 74W  HBA   CBA  CBB   109.89  3.000
 74W  HBA   CBA  OAD   110.57  3.000
 74W  CBB   CBA  OAD   108.87  3.000
 74W  HBA   CBA  CAO   109.78  3.000
 74W  CBB   CBA  CAO   102.58  3.000
 74W  OAD   CBA  CAO   114.83  3.000
 74W  HAD   OAD  CBA   108.23  3.000
 74W  HBB   CBB  CAN   109.20  3.000
 74W  HBB   CBB  CBA   108.72  3.000
 74W  CAN   CBB  CBA   113.10  3.000
 74W  HBB   CBB  OAS   109.71  3.000
 74W  CAN   CBB  OAS   109.36  3.000
 74W  CBA   CBB  OAS   106.69  3.000
 74W  HAN2  CAN  HAN1  108.23  3.000
 74W  HAN2  CAN  NAP   107.39  3.000
 74W  HAN1  CAN  NAP   109.31  3.000
 74W  HAN2  CAN  CBB   109.68  3.000
 74W  HAN1  CAN  CBB   108.85  3.000
 74W  NAP   CAN  CBB   113.26  3.000
 74W  HAP   NAP  CAT   118.58  3.000
 74W  HAP   NAP  CAN   116.10  3.000
 74W  CAT   NAP  CAN   125.16  3.000
 74W  NAQ   CAT  SAE   123.53  3.000
 74W  NAQ   CAT  NAP   113.70  3.000
 74W  SAE   CAT  NAP   122.77  3.000
 74W  HAQ   NAQ  CAV   114.48  3.000
 74W  HAQ   NAQ  CAT   116.66  3.000
 74W  CAV   NAQ  CAT   127.95  3.000
 74W  CAJ   CAV  CAL   119.27  3.000
 74W  CAJ   CAV  NAQ   118.37  3.000
 74W  CAL   CAV  NAQ   122.25  3.000
 74W  HAL   CAL  CAX   120.28  3.000
 74W  HAL   CAL  CAV   119.17  3.000
 74W  CAX   CAL  CAV   120.55  3.000
 74W  HAJ   CAJ  CAK   119.33  3.000
 74W  HAJ   CAJ  CAV   120.13  3.000
 74W  CAK   CAJ  CAV   120.53  3.000
 74W  HAK   CAK  CAW   120.09  3.000
 74W  HAK   CAK  CAJ   119.94  3.000
 74W  CAW   CAK  CAJ   119.97  3.000
 74W  CAX   CAW  CL    121.53  3.000
 74W  CAX   CAW  CAK   120.20  3.000
 74W  CL    CAW  CAK   118.27  3.000
 74W  CBE   CAX  CAW   120.95  3.000
 74W  CBE   CAX  CAL   119.57  3.000
 74W  CAW   CAX  CAL   119.47  3.000
 74W  FAH   CBE  FAG   106.86  3.000
 74W  FAH   CBE  FAF   107.07  3.000
 74W  FAG   CBE  FAF   106.79  3.000
 74W  FAF   CBE  CAX   111.90  3.000
 74W  FAH   CBE  CAX   111.76  3.000
 74W  FAG   CBE  CAX   112.13  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
 74W  CONST_01  CAW   CAX  CAL  CAV    0.00   0.0  0
 74W  CONST_02  CAW   CAK  CAJ  CAV    0.00   0.0  0
 74W  CONST_03  CAK   CAJ  CAV  CAL    0.00   0.0  0
 74W  CONST_04  CAK   CAW  CAX  CAL    0.00   0.0  0
 74W  CONST_05  CAX   CAL  CAV  CAJ    0.00   0.0  0
 74W  CONST_06  CAX   CAW  CAK  CAJ    0.00   0.0  0
 74W  CONST_07  CAM   NBD  CAZ  NAR    0.00   0.0  0
 74W  CONST_08  CBC   NBD  CAZ  NAR  180.00   0.0  0
 74W  CONST_09  NBD   CAZ  NAR  CAY    0.00   0.0  0
 74W  CONST_10  CAX   CAL  CAV  NAQ  180.00   0.0  0
 74W  CONST_11  CAK   CAJ  CAV  NAQ  180.00   0.0  0
 74W  CONST_12  CBE   CAX  CAL  CAV  180.00   0.0  0
 74W  CONST_13  CL    CAW  CAX  CAL  180.00   0.0  0
 74W  CONST_14  CL    CAW  CAK  CAJ  180.00   0.0  0
 74W  CONST_15  CBE   CAX  CAW  CAK  180.00   0.0  0
 74W  CONST_16  CAY   NAR  CAZ  OAC  180.00   0.0  0
 74W  CONST_17  CAM   NBD  CAZ  OAC  180.00   0.0  0
 74W  CONST_18  CBC   NBD  CAZ  OAC    0.00   0.0  0
 74W  CONST_19  HAK   CAK  CAJ  CAV  180.00   0.0  0
 74W  CONST_20  HAJ   CAJ  CAV  CAL  180.00   0.0  0
 74W  CONST_21  HAL   CAL  CAV  CAJ  180.00   0.0  0
 74W  CONST_22  HAR   NAR  CAZ  NBD  180.00   0.0  0
 74W  CONST_26  CAV   NAQ  CAT  NAP  180.00   0.0  0
 74W  CONST_27  CAV   NAQ  CAT  SAE    0.00   0.0  0
 74W  CONST_28  SAE   CAT  NAP  CAN    0.00   0.0  0
 74W  CONST_29  NAQ   CAT  NAP  CAN  180.00   0.0  0
 74W  CONST_30  HAP   NAP  CAT  SAE  180.00   0.0  0
 74W  Var_01    FAG   CBE  CAX  CAL   -0.95  30.0  2
 74W  Var_02    HAA1  CAA  CAU  CAY  -59.36  30.0  3
 74W  Var_03    CAT   NAP  CAN  CBB   83.52  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
 74W  chir_01  CBC  NBD  OAS  CAO  positiv
 74W  chir_02  CBA  OAD  CBB  CAO  positiv
 74W  chir_03  CBB  OAS  CBA  CAN  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
 74W  plan-1  OAC  0.020
 74W  plan-1  CAZ  0.020
 74W  plan-1  NAR  0.020
 74W  plan-1  CAY  0.020
 74W  plan-1  OAB  0.020
 74W  plan-1  CAU  0.020
 74W  plan-1  CAA  0.020
 74W  plan-1  CAM  0.020
 74W  plan-1  NBD  0.020
 74W  plan-1  CBC  0.020
 74W  plan-1  HAR  0.020
 74W  plan-1  HAM  0.020
 74W  plan-2  NAQ  0.020
 74W  plan-2  CAV  0.020
 74W  plan-2  CAL  0.020
 74W  plan-2  CAJ  0.020
 74W  plan-2  CAK  0.020
 74W  plan-2  CAW  0.020
 74W  plan-2  CL   0.020
 74W  plan-2  CAX  0.020
 74W  plan-2  CBE  0.020
 74W  plan-2  HAL  0.020
 74W  plan-2  HAJ  0.020
 74W  plan-2  HAK  0.020
 74W  plan-3  CAN  0.020
 74W  plan-3  NAP  0.020
 74W  plan-3  CAT  0.020
 74W  plan-3  SAE  0.020
 74W  plan-3  NAQ  0.020
 74W  plan-3  CAV  0.020
 74W  plan-3  HAP  0.020
 74W  plan-3  HAQ  0.020

