# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 20:36:52 2020
#   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
 74X  74X  5'-({[4-chloro-3-(trifluoromethyl)phenyl]carbamothioyl}amino)-2',5'-dideoxy-3,4-dihydrothymidine  ligand  49  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_74X
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
 74X  OAC   O   O     0  -0.482   6.1139  -0.5000   2.5386
 74X  CAZ   C   CR6   0   0.732   6.0058   0.2855   1.6191
 74X  NAR   N   NR16  0  -0.735   6.6661   1.4861   1.6089
 74X  CAY   C   CR6   0   0.562   6.6279   2.4751   0.6427
 74X  OAB   O   O     0  -0.451   7.2684   3.5004   0.7810
 74X  CAU   C   CR6   0  -0.186   5.7809   2.1701  -0.4950
 74X  CAA   C   CH3   0  -0.708   5.6613   3.1711  -1.5964
 74X  CAM   C   CR16  0   0.071   5.1330   0.9942  -0.4953
 74X  NBD   N   NR6   0  -0.561   5.2292   0.0602   0.5052
 74X  CBC   C   CR15  0   0.190   4.4371  -1.1570   0.4122
 74X  OAS   O   O     0  -0.506   3.0764  -0.8045   0.2739
 74X  CAO   C   CH2   0  -0.557   4.7758  -2.0369  -0.7820
 74X  CBA   C   CR15  0   0.025   3.4271  -2.6785  -1.0905
 74X  OAD   O   OH1   0  -0.660   3.2472  -3.1126  -2.4075
 74X  CBB   C   CR15  0   0.018   2.4682  -1.5283  -0.7900
 74X  CAN   C   CH2   0  -0.269   1.0905  -1.9918  -0.3658
 74X  NAP   N   NH1   0  -0.625   0.2450  -0.8763  -0.0169
 74X  CAT   C   C     0   0.398  -1.0449  -0.7384  -0.3378
 74X  SAE   S   S1    0  -0.393  -1.8911  -1.8493  -1.2660
 74X  NAQ   N   NH1   0  -0.738  -1.6043   0.4020   0.1446
 74X  CAV   C   CR6   0   0.392  -2.9359   0.8137   0.0075
 74X  CAL   C   CR16  0  -0.318  -3.9971  -0.0254   0.3339
 74X  CAJ   C   CR16  0  -0.310  -3.1955   2.1173  -0.3903
 74X  CAK   C   CR16  0  -0.196  -4.4991   2.5780  -0.4753
 74X  CAW   C   CR6   0  -0.080  -5.5508   1.7329  -0.1743
 74X  CLA   CL  CL    0  -0.104  -7.1603   2.3473  -0.3147
 74X  CAX   C   CR6   0  -0.131  -5.3053   0.4216   0.2357
 74X  CBE   C   CT    0   1.074  -6.4350  -0.5007   0.5921
 74X  FAG   F   F     0  -0.298  -6.0002  -1.7036   0.9740
 74X  FAH   F   F     0  -0.310  -7.1728  -0.0183   1.5990
 74X  FAF   F   F     0  -0.310  -7.2610  -0.6980  -0.4421
 74X  HAR   H   HNR6  0   0.426   7.2478   1.6652   2.4186
 74X  HAA1  H   HCH3  0   0.249   5.2341   4.1086  -1.2379
 74X  HAA2  H   HCH3  0   0.248   6.6356   3.4038  -2.0279
 74X  HAA3  H   HCH3  0   0.248   5.0223   2.7972  -2.3949
 74X  HAM   H   HCR6  0   0.313   4.4826   0.7268  -1.3172
 74X  HBC   H   HCR5  0   0.281   4.5833  -1.6940   1.3485
 74X  HAO1  H   HCH2  0   0.268   5.1080  -1.4491  -1.6419
 74X  HAO2  H   HCH2  0   0.282   5.5589  -2.7562  -0.5451
 74X  HBB   H   HCR5  0   0.242   2.3831  -0.8829  -1.6756
 74X  HBA   H   HCR5  0   0.230   3.2444  -3.4916  -0.3738
 74X  HAD   H   HOH1  0   0.462   3.7502  -3.9229  -2.5321
 74X  HAN1  H   HCH2  0   0.267   0.6269  -2.5357  -1.1876
 74X  HAN2  H   HCH2  0   0.251   1.1750  -2.6796   0.4818
 74X  HAP   H   HNH1  0   0.407   0.6430  -0.2105   0.6305
 74X  HAQ   H   HNH1  0   0.415  -0.9739   1.1074   0.5020
 74X  HAL   H   HCR6  0   0.287  -3.7868  -1.0272   0.6743
 74X  HAJ   H   HCR6  0   0.291  -2.3790   2.7827  -0.6399
 74X  HAK   H   HCR6  0   0.295  -4.6931   3.5942  -0.7887

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
 74X  OAC  CAZ   double    1.214  0.020  1.214
 74X  CAZ  NAR   single    1.370  0.020  1.370
 74X  CAZ  NBD   single    1.376  0.020  1.376
 74X  NAR  CAY   single    1.383  0.020  1.383
 74X  CAY  OAB   double    1.217  0.020  1.217
 74X  CAY  CAU   single    1.451  0.020  1.451
 74X  CAU  CAA   single    1.493  0.020  1.493
 74X  CAU  CAM   double    1.343  0.020  1.343
 74X  CAM  NBD   single    1.372  0.020  1.372
 74X  NBD  CBC   single    1.455  0.020  1.455
 74X  CBC  OAS   single    1.412  0.020  1.412
 74X  CBC  CAO   single    1.522  0.020  1.522
 74X  OAS  CBB   single    1.423  0.020  1.423
 74X  CAO  CBA   single    1.525  0.020  1.525
 74X  CBA  OAD   single    1.398  0.020  1.398
 74X  CBA  CBB   single    1.527  0.020  1.527
 74X  CBB  CAN   single    1.514  0.020  1.514
 74X  CAN  NAP   single    1.443  0.020  1.443
 74X  NAP  CAT   single    1.336  0.020  1.336
 74X  CAT  SAE   double    1.677  0.020  1.677
 74X  CAT  NAQ   single    1.359  0.020  1.359
 74X  NAQ  CAV   single    1.401  0.020  1.401
 74X  CAV  CAL   aromatic  1.392  0.020  1.392
 74X  CAV  CAJ   aromatic  1.388  0.020  1.388
 74X  CAL  CAX   aromatic  1.386  0.020  1.386
 74X  CAJ  CAK   aromatic  1.385  0.020  1.385
 74X  CAK  CAW   aromatic  1.382  0.020  1.382
 74X  CAW  CLA   single    1.728  0.020  1.728
 74X  CAW  CAX   aromatic  1.396  0.020  1.396
 74X  CAX  CBE   single    1.501  0.020  1.501
 74X  CBE  FAG   single    1.335  0.020  1.335
 74X  CBE  FAH   single    1.338  0.020  1.338
 74X  CBE  FAF   single    1.338  0.020  1.338
 74X  NAR  HAR   single    0.860  0.020  1.020
 74X  CAA  HAA1  single    0.970  0.020  1.090
 74X  CAA  HAA2  single    0.970  0.020  1.090
 74X  CAA  HAA3  single    0.970  0.020  1.090
 74X  CAM  HAM   single    0.930  0.020  1.080
 74X  CBC  HBC   single    0.970  0.020  1.090
 74X  CAO  HAO1  single    0.970  0.020  1.090
 74X  CAO  HAO2  single    0.970  0.020  1.090
 74X  CBB  HBB   single    0.970  0.020  1.090
 74X  CBA  HBA   single    0.970  0.020  1.090
 74X  OAD  HAD   single    0.850  0.020  0.980
 74X  CAN  HAN1  single    0.970  0.020  1.090
 74X  CAN  HAN2  single    0.970  0.020  1.090
 74X  NAP  HAP   single    0.860  0.020  1.020
 74X  NAQ  HAQ   single    0.860  0.020  1.020
 74X  CAL  HAL   single    0.930  0.020  1.080
 74X  CAJ  HAJ   single    0.930  0.020  1.080
 74X  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
 74X  NBD   CAZ  NAR   114.16  3.000
 74X  NBD   CAZ  OAC   123.86  3.000
 74X  NAR   CAZ  OAC   121.98  3.000
 74X  HAR   NAR  CAY   116.61  3.000
 74X  HAR   NAR  CAZ   115.19  3.000
 74X  CAY   NAR  CAZ   128.20  3.000
 74X  CAU   CAY  OAB   125.00  3.000
 74X  CAU   CAY  NAR   114.43  3.000
 74X  OAB   CAY  NAR   120.57  3.000
 74X  CAM   CAU  CAA   123.25  3.000
 74X  CAM   CAU  CAY   117.78  3.000
 74X  CAA   CAU  CAY   118.97  3.000
 74X  HAA3  CAA  HAA2  107.90  3.000
 74X  HAA3  CAA  HAA1  107.83  3.000
 74X  HAA2  CAA  HAA1  107.25  3.000
 74X  HAA3  CAA  CAU   110.96  3.000
 74X  HAA2  CAA  CAU   111.31  3.000
 74X  HAA1  CAA  CAU   111.41  3.000
 74X  HAM   CAM  NBD   115.34  3.000
 74X  HAM   CAM  CAU   120.46  3.000
 74X  NBD   CAM  CAU   124.20  3.000
 74X  CBC   NBD  CAM   118.98  3.000
 74X  CBC   NBD  CAZ   119.72  3.000
 74X  CAM   NBD  CAZ   121.22  3.000
 74X  HBC   CBC  CAO   111.08  3.000
 74X  HBC   CBC  OAS   109.67  3.000
 74X  CAO   CBC  OAS   106.37  3.000
 74X  HBC   CBC  NBD   106.52  3.000
 74X  CAO   CBC  NBD   114.38  3.000
 74X  OAS   CBC  NBD   108.78  3.000
 74X  CBB   OAS  CBC   110.98  3.000
 74X  HAO2  CAO  HAO1  107.91  3.000
 74X  HAO2  CAO  CBA   113.70  3.000
 74X  HAO1  CAO  CBA   109.62  3.000
 74X  HAO2  CAO  CBC   111.78  3.000
 74X  HAO1  CAO  CBC   111.97  3.000
 74X  CBA   CAO  CBC   101.84  3.000
 74X  HBA   CBA  CBB   108.93  3.000
 74X  HBA   CBA  OAD   111.29  3.000
 74X  CBB   CBA  OAD   109.78  3.000
 74X  HBA   CBA  CAO   109.05  3.000
 74X  CBB   CBA  CAO   101.46  3.000
 74X  OAD   CBA  CAO   115.78  3.000
 74X  HAD   OAD  CBA   108.44  3.000
 74X  HBB   CBB  CAN   109.57  3.000
 74X  HBB   CBB  CBA   109.40  3.000
 74X  CAN   CBB  CBA   113.32  3.000
 74X  HBB   CBB  OAS   109.68  3.000
 74X  CAN   CBB  OAS   109.58  3.000
 74X  CBA   CBB  OAS   105.17  3.000
 74X  HAN2  CAN  HAN1  107.65  3.000
 74X  HAN2  CAN  NAP   110.11  3.000
 74X  HAN1  CAN  NAP   108.62  3.000
 74X  HAN2  CAN  CBB   109.81  3.000
 74X  HAN1  CAN  CBB   109.20  3.000
 74X  NAP   CAN  CBB   111.36  3.000
 74X  HAP   NAP  CAT   117.79  3.000
 74X  HAP   NAP  CAN   115.70  3.000
 74X  CAT   NAP  CAN   125.97  3.000
 74X  NAQ   CAT  SAE   123.02  3.000
 74X  NAQ   CAT  NAP   113.49  3.000
 74X  SAE   CAT  NAP   123.48  3.000
 74X  HAQ   NAQ  CAV   114.97  3.000
 74X  HAQ   NAQ  CAT   117.02  3.000
 74X  CAV   NAQ  CAT   127.11  3.000
 74X  CAJ   CAV  CAL   119.41  3.000
 74X  CAJ   CAV  NAQ   118.83  3.000
 74X  CAL   CAV  NAQ   121.66  3.000
 74X  HAL   CAL  CAX   120.39  3.000
 74X  HAL   CAL  CAV   119.03  3.000
 74X  CAX   CAL  CAV   120.58  3.000
 74X  HAJ   CAJ  CAK   119.42  3.000
 74X  HAJ   CAJ  CAV   120.17  3.000
 74X  CAK   CAJ  CAV   120.41  3.000
 74X  HAK   CAK  CAW   120.09  3.000
 74X  HAK   CAK  CAJ   119.96  3.000
 74X  CAW   CAK  CAJ   119.95  3.000
 74X  CAX   CAW  CLA   121.44  3.000
 74X  CAX   CAW  CAK   120.30  3.000
 74X  CLA   CAW  CAK   118.26  3.000
 74X  CBE   CAX  CAW   120.97  3.000
 74X  CBE   CAX  CAL   119.69  3.000
 74X  CAW   CAX  CAL   119.33  3.000
 74X  FAF   CBE  FAH   107.12  3.000
 74X  FAF   CBE  FAG   106.82  3.000
 74X  FAH   CBE  FAG   106.80  3.000
 74X  FAF   CBE  CAX   111.81  3.000
 74X  FAH   CBE  CAX   111.84  3.000
 74X  FAG   CBE  CAX   112.11  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
 74X  CONST_01  CAW   CAX  CAL  CAV    0.00   0.0  0
 74X  CONST_02  CAW   CAK  CAJ  CAV    0.00   0.0  0
 74X  CONST_03  CAK   CAJ  CAV  CAL    0.00   0.0  0
 74X  CONST_04  CAK   CAW  CAX  CAL    0.00   0.0  0
 74X  CONST_05  CAX   CAL  CAV  CAJ    0.00   0.0  0
 74X  CONST_06  CAX   CAW  CAK  CAJ    0.00   0.0  0
 74X  CONST_07  CAM   NBD  CAZ  NAR    0.00   0.0  0
 74X  CONST_08  CBC   NBD  CAZ  NAR  180.00   0.0  0
 74X  CONST_09  NBD   CAZ  NAR  CAY    0.00   0.0  0
 74X  CONST_10  CAX   CAL  CAV  NAQ  180.00   0.0  0
 74X  CONST_11  CAK   CAJ  CAV  NAQ  180.00   0.0  0
 74X  CONST_12  CBE   CAX  CAL  CAV  180.00   0.0  0
 74X  CONST_13  CLA   CAW  CAX  CAL  180.00   0.0  0
 74X  CONST_14  CLA   CAW  CAK  CAJ  180.00   0.0  0
 74X  CONST_15  CBE   CAX  CAW  CAK  180.00   0.0  0
 74X  CONST_16  CAY   NAR  CAZ  OAC  180.00   0.0  0
 74X  CONST_17  CAM   NBD  CAZ  OAC  180.00   0.0  0
 74X  CONST_18  CBC   NBD  CAZ  OAC    0.00   0.0  0
 74X  CONST_19  HAK   CAK  CAJ  CAV  180.00   0.0  0
 74X  CONST_20  HAJ   CAJ  CAV  CAL  180.00   0.0  0
 74X  CONST_21  HAL   CAL  CAV  CAJ  180.00   0.0  0
 74X  CONST_22  HAR   NAR  CAZ  NBD  180.00   0.0  0
 74X  CONST_26  CAV   NAQ  CAT  NAP  180.00   0.0  0
 74X  CONST_27  CAV   NAQ  CAT  SAE    0.00   0.0  0
 74X  CONST_28  SAE   CAT  NAP  CAN    0.00   0.0  0
 74X  CONST_29  NAQ   CAT  NAP  CAN  180.00   0.0  0
 74X  CONST_30  HAP   NAP  CAT  SAE  180.00   0.0  0
 74X  Var_01    FAG   CBE  CAX  CAL   -0.27  30.0  2
 74X  Var_02    HAA1  CAA  CAU  CAY  -61.67  30.0  3
 74X  Var_03    CAT   NAP  CAN  CBB  138.61  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
 74X  chir_01  CBC  NBD  OAS  CAO  negativ
 74X  chir_02  CBA  OAD  CBB  CAO  positiv
 74X  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
 74X  plan-1  OAC  0.020
 74X  plan-1  CAZ  0.020
 74X  plan-1  NAR  0.020
 74X  plan-1  CAY  0.020
 74X  plan-1  OAB  0.020
 74X  plan-1  CAU  0.020
 74X  plan-1  CAA  0.020
 74X  plan-1  CAM  0.020
 74X  plan-1  NBD  0.020
 74X  plan-1  CBC  0.020
 74X  plan-1  HAR  0.020
 74X  plan-1  HAM  0.020
 74X  plan-2  NAQ  0.020
 74X  plan-2  CAV  0.020
 74X  plan-2  CAL  0.020
 74X  plan-2  CAJ  0.020
 74X  plan-2  CAK  0.020
 74X  plan-2  CAW  0.020
 74X  plan-2  CLA  0.020
 74X  plan-2  CAX  0.020
 74X  plan-2  CBE  0.020
 74X  plan-2  HAL  0.020
 74X  plan-2  HAJ  0.020
 74X  plan-2  HAK  0.020
 74X  plan-3  CAN  0.020
 74X  plan-3  NAP  0.020
 74X  plan-3  CAT  0.020
 74X  plan-3  SAE  0.020
 74X  plan-3  NAQ  0.020
 74X  plan-3  CAV  0.020
 74X  plan-3  HAP  0.020
 74X  plan-3  HAQ  0.020

