# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 20:05:47 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 1-[5-(cyclopropylsulfamoyl)-2-thiophen-3-yl-phenyl]-3-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(NC(=O)Nc2cc(ccc2c3cscc3)[S](=O)(=O)NC4CC4)c1
#
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
 1K9  1K9  1-[5-(cyclopropylsulfamoyl)-2-thiophen-3-yl-phenyl]-3-[3-(trifluoromethyl)phenyl]urea  ligand  50  32  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1K9
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
 1K9  FAD  F  F     0  -0.314  -7.4974   0.2720  -0.8315
 1K9  CBE  C  CT    0   1.054  -6.8647   0.4169   0.3419
 1K9  FAE  F  F     0  -0.301  -6.6655   1.7258   0.5189
 1K9  FAF  F  F     0  -0.314  -7.7282   0.0205   1.2881
 1K9  CAZ  C  CR6   0  -0.179  -5.5982  -0.3793   0.3849
 1K9  CAO  C  CR16  0  -0.394  -4.3745   0.2402   0.5692
 1K9  CAJ  C  CR16  0  -0.288  -5.6767  -1.7587   0.2216
 1K9  CAG  C  CR16  0  -0.237  -4.5097  -2.5005   0.2609
 1K9  CAI  C  CR16  0  -0.296  -3.2751  -1.8980   0.4566
 1K9  CAX  C  CR6   0   0.409  -3.1993  -0.5143   0.6057
 1K9  NAS  N  NH1   0  -0.794  -2.0116   0.1807   0.8343
 1K9  CAW  C  C     0   0.724  -0.7493  -0.2085   0.4750
 1K9  OAA  O  O     0  -0.487  -0.4904  -1.2634  -0.0716
 1K9  NAT  N  NH1   0  -0.795   0.1989   0.7254   0.8003
 1K9  CBB  C  CR6   0   0.324   1.5606   0.6140   0.5094
 1K9  CAP  C  CR16  0  -0.244   2.2376  -0.5816   0.7201
 1K9  CBA  C  CR6   0  -0.225   3.6010  -0.6457   0.4836
 1K9  SBF  S  S     0   1.384   4.4280  -2.1875   0.7597
 1K9  OAB  O  OS    0  -0.644   5.8551  -1.9096   0.8309
 1K9  OAC  O  OS    0  -0.665   3.8015  -2.8847   1.8742
 1K9  NAU  N  NC1   0  -0.741   3.9991  -3.0324  -0.5901
 1K9  CBD  C  CH1   0  -0.100   4.5244  -2.6273  -1.8637
 1K9  CAQ  C  CH2   0  -0.505   4.9123  -3.6909  -2.8369
 1K9  CAR  C  CH2   0  -0.475   5.9665  -2.8221  -2.2246
 1K9  CAL  C  CR16  0  -0.230   4.3219   0.4604   0.0656
 1K9  CAM  C  CR16  0  -0.306   3.6410   1.6491  -0.1310
 1K9  CBC  C  CR6   0   0.069   2.2658   1.7478   0.0676
 1K9  CAY  C  CR5   0   0.110   1.6070   3.0430  -0.1714
 1K9  CAK  C  CR15  0  -0.204   2.1427   4.2859   0.2874
 1K9  CAH  C  CR15  0  -0.463   1.3919   5.3547  -0.0873
 1K9  SAV  S  S2    0   0.245   0.0294   4.8739  -1.0063
 1K9  CAN  C  CR15  0  -0.540   0.4540   3.2245  -0.8872
 1K9  H1   H  HCR6  0   0.284  -4.3085   1.3149   0.6823
 1K9  H2   H  HCR6  0   0.274  -6.6261  -2.2549   0.0690
 1K9  H3   H  HCR6  0   0.271  -4.5556  -3.5752   0.1474
 1K9  H4   H  HCR6  0   0.284  -2.3904  -2.5118   0.4997
 1K9  H5   H  HNH1  0   0.416  -2.1289   1.1158   1.1946
 1K9  H6   H  HNH1  0   0.414  -0.1071   1.6291   1.1302
 1K9  H7   H  HCR6  0   0.293   1.7077  -1.4442   1.0952
 1K9  H8   H  HNC1  0   0.420   3.9485  -4.0302  -0.4144
 1K9  H9   H  HCH1  0   0.278   4.0248  -1.7546  -2.2695
 1K9  H10  H  HCH2  0   0.264   4.8544  -4.7202  -2.5035
 1K9  H11  H  HCH2  0   0.268   4.6409  -3.5423  -3.8733
 1K9  H12  H  HCH2  0   0.259   6.4369  -2.0627  -2.8352
 1K9  H13  H  HCH2  0   0.261   6.6128  -3.2688  -1.4811
 1K9  H14  H  HCR6  0   0.285   5.3869   0.4080  -0.1089
 1K9  H15  H  HCR6  0   0.272   4.1870   2.5191  -0.4714
 1K9  H16  H  HCR5  0   0.272   3.0394   4.3684   0.8854
 1K9  H17  H  HCR5  0   0.302   1.5626   6.3959   0.1372
 1K9  H18  H  HCR5  0   0.303  -0.1460   2.4761  -1.3824

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
 1K9  CAH  SAV  aromatic  1.712  0.020  1.712
 1K9  CAH  CAK  aromatic  1.359  0.020  1.359
 1K9  SAV  CAN  aromatic  1.707  0.020  1.707
 1K9  CAK  CAY  aromatic  1.429  0.020  1.429
 1K9  CAY  CAN  aromatic  1.369  0.020  1.369
 1K9  CAY  CBC  single    1.473  0.020  1.473
 1K9  CAI  CAG  aromatic  1.388  0.020  1.388
 1K9  CAI  CAX  aromatic  1.394  0.020  1.394
 1K9  CAG  CAJ  aromatic  1.383  0.020  1.383
 1K9  NAS  CAX  single    1.395  0.020  1.395
 1K9  NAS  CAW  single    1.369  0.020  1.369
 1K9  NAT  CAW  single    1.370  0.020  1.370
 1K9  NAT  CBB  single    1.397  0.020  1.397
 1K9  CAX  CAO  aromatic  1.397  0.020  1.397
 1K9  CBC  CBB  aromatic  1.406  0.020  1.406
 1K9  CBC  CAM  aromatic  1.393  0.020  1.393
 1K9  CAJ  CAZ  aromatic  1.391  0.020  1.391
 1K9  CAW  OAA  double    1.216  0.020  1.216
 1K9  CBB  CAP  aromatic  1.390  0.020  1.390
 1K9  CAM  CAL  aromatic  1.384  0.020  1.384
 1K9  CAO  CAZ  aromatic  1.384  0.020  1.384
 1K9  CAZ  CBE  single    1.497  0.020  1.497
 1K9  CAP  CBA  aromatic  1.385  0.020  1.385
 1K9  CAL  CBA  aromatic  1.385  0.020  1.385
 1K9  FAD  CBE  single    1.341  0.020  1.341
 1K9  CBE  FAE  single    1.336  0.020  1.336
 1K9  CBE  FAF  single    1.341  0.020  1.341
 1K9  CBA  SBF  single    1.771  0.020  1.771
 1K9  OAC  SBF  double    1.456  0.020  1.456
 1K9  SBF  OAB  double    1.456  0.020  1.456
 1K9  SBF  NAU  single    1.649  0.020  1.649
 1K9  NAU  CBD  single    1.436  0.020  1.436
 1K9  CBD  CAQ  single    1.493  0.020  1.493
 1K9  CBD  CAR  single    1.499  0.020  1.499
 1K9  CAQ  CAR  single    1.497  0.020  1.497
 1K9  CAO  H1   single    0.930  0.020  1.080
 1K9  CAJ  H2   single    0.930  0.020  1.080
 1K9  CAG  H3   single    0.930  0.020  1.080
 1K9  CAI  H4   single    0.930  0.020  1.080
 1K9  NAS  H5   single    0.860  0.020  1.020
 1K9  NAT  H6   single    0.860  0.020  1.020
 1K9  CAP  H7   single    0.930  0.020  1.080
 1K9  NAU  H8   single    0.890  0.020  1.040
 1K9  CBD  H9   single    0.970  0.020  1.090
 1K9  CAQ  H10  single    0.970  0.020  1.090
 1K9  CAQ  H11  single    0.970  0.020  1.090
 1K9  CAR  H12  single    0.970  0.020  1.090
 1K9  CAR  H13  single    0.970  0.020  1.090
 1K9  CAL  H14  single    0.930  0.020  1.080
 1K9  CAM  H15  single    0.930  0.020  1.080
 1K9  CAK  H16  single    0.930  0.020  1.080
 1K9  CAH  H17  single    0.930  0.020  1.080
 1K9  CAN  H18  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
 1K9  CAZ  CBE  FAF  111.56  3.000
 1K9  FAF  CBE  FAE  106.99  3.000
 1K9  CAZ  CBE  FAE  113.04  3.000
 1K9  FAF  CBE  FAD  106.36  3.000
 1K9  FAE  CBE  FAD  106.99  3.000
 1K9  CAZ  CBE  FAD  111.52  3.000
 1K9  CAJ  CAZ  CAO  120.62  3.000
 1K9  CAO  CAZ  CBE  120.93  3.000
 1K9  CAJ  CAZ  CBE  118.45  3.000
 1K9  H1   CAO  CAX  118.82  3.000
 1K9  H1   CAO  CAZ  120.81  3.000
 1K9  CAX  CAO  CAZ  120.37  3.000
 1K9  H2   CAJ  CAG  119.89  3.000
 1K9  H2   CAJ  CAZ  121.38  3.000
 1K9  CAG  CAJ  CAZ  118.73  3.000
 1K9  H3   CAG  CAI  118.95  3.000
 1K9  H3   CAG  CAJ  119.60  3.000
 1K9  CAI  CAG  CAJ  121.45  3.000
 1K9  H4   CAI  CAX  121.11  3.000
 1K9  H4   CAI  CAG  119.25  3.000
 1K9  CAX  CAI  CAG  119.64  3.000
 1K9  NAS  CAX  CAI  123.95  3.000
 1K9  NAS  CAX  CAO  116.84  3.000
 1K9  CAI  CAX  CAO  119.18  3.000
 1K9  H5   NAS  CAW  117.67  3.000
 1K9  H5   NAS  CAX  114.92  3.000
 1K9  CAW  NAS  CAX  126.90  3.000
 1K9  NAT  CAW  OAA  123.42  3.000
 1K9  OAA  CAW  NAS  124.12  3.000
 1K9  NAT  CAW  NAS  112.46  3.000
 1K9  H6   NAT  CBB  115.78  3.000
 1K9  H6   NAT  CAW  118.55  3.000
 1K9  CBB  NAT  CAW  124.81  3.000
 1K9  CBC  CBB  CAP  119.79  3.000
 1K9  CAP  CBB  NAT  120.78  3.000
 1K9  CBC  CBB  NAT  119.34  3.000
 1K9  H7   CAP  CBA  120.36  3.000
 1K9  H7   CAP  CBB  120.06  3.000
 1K9  CBA  CAP  CBB  119.56  3.000
 1K9  CAL  CBA  SBF  119.95  3.000
 1K9  SBF  CBA  CAP  118.24  3.000
 1K9  CAL  CBA  CAP  121.79  3.000
 1K9  NAU  SBF  OAC  105.62  3.000
 1K9  NAU  SBF  OAB  113.13  3.000
 1K9  OAC  SBF  OAB  118.41  3.000
 1K9  NAU  SBF  CBA  101.36  3.000
 1K9  OAB  SBF  CBA  107.41  3.000
 1K9  OAC  SBF  CBA  109.59  3.000
 1K9  H8   NAU  CBD  116.70  3.000
 1K9  H8   NAU  SBF  112.04  3.000
 1K9  CBD  NAU  SBF  119.09  3.000
 1K9  H9   CBD  CAR  117.24  3.000
 1K9  H9   CBD  CAQ  116.69  3.000
 1K9  CAR  CBD  CAQ   60.04  3.000
 1K9  H9   CBD  NAU  112.98  3.000
 1K9  CAR  CBD  NAU  121.91  3.000
 1K9  CAQ  CBD  NAU  118.17  3.000
 1K9  H11  CAQ  H10  114.33  3.000
 1K9  H11  CAQ  CAR  119.26  3.000
 1K9  H10  CAQ  CAR  117.59  3.000
 1K9  H11  CAQ  CBD  117.48  3.000
 1K9  H10  CAQ  CBD  117.54  3.000
 1K9  CAR  CAQ  CBD   60.19  3.000
 1K9  H13  CAR  H12  114.71  3.000
 1K9  H13  CAR  CAQ  117.53  3.000
 1K9  H12  CAR  CAQ  118.86  3.000
 1K9  H13  CAR  CBD  117.58  3.000
 1K9  H12  CAR  CBD  117.56  3.000
 1K9  CAQ  CAR  CBD   59.77  3.000
 1K9  H14  CAL  CAM  120.25  3.000
 1K9  H14  CAL  CBA  121.53  3.000
 1K9  CAM  CAL  CBA  118.22  3.000
 1K9  H15  CAM  CBC  119.08  3.000
 1K9  H15  CAM  CAL  119.14  3.000
 1K9  CBC  CAM  CAL  121.76  3.000
 1K9  CAY  CBC  CAM  118.74  3.000
 1K9  CAM  CBC  CBB  118.86  3.000
 1K9  CAY  CBC  CBB  122.39  3.000
 1K9  CAN  CAY  CAK  111.61  3.000
 1K9  CAN  CAY  CBC  125.32  3.000
 1K9  CAK  CAY  CBC  123.03  3.000
 1K9  H16  CAK  CAH  123.42  3.000
 1K9  H16  CAK  CAY  123.71  3.000
 1K9  CAH  CAK  CAY  112.86  3.000
 1K9  H17  CAH  SAV  120.57  3.000
 1K9  H17  CAH  CAK  127.91  3.000
 1K9  SAV  CAH  CAK  111.52  3.000
 1K9  CAN  SAV  CAH   92.06  3.000
 1K9  H18  CAN  SAV  119.97  3.000
 1K9  H18  CAN  CAY  128.02  3.000
 1K9  SAV  CAN  CAY  111.96  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
 1K9  CONST_01  CAI  CAG  CAJ  CAZ     0.00   0.0  0
 1K9  CONST_02  CAI  CAX  CAO  CAZ     0.00   0.0  0
 1K9  CONST_03  CAG  CAI  CAX  CAO     0.00   0.0  0
 1K9  CONST_04  CAG  CAJ  CAZ  CAO     0.00   0.0  0
 1K9  CONST_05  CAX  CAI  CAG  CAJ     0.00   0.0  0
 1K9  CONST_06  CAX  CAO  CAZ  CAJ     0.00   0.0  0
 1K9  CONST_09  CAL  CAM  CBC  CBB     0.00   0.0  0
 1K9  CONST_10  CAL  CBA  CAP  CBB     0.00   0.0  0
 1K9  CONST_11  CAY  CBC  CBB  CAP   180.00   0.0  0
 1K9  CONST_12  CAM  CBC  CBB  CAP     0.00   0.0  0
 1K9  CONST_13  CAM  CAL  CBA  CAP     0.00   0.0  0
 1K9  CONST_14  CBC  CBB  CAP  CBA     0.00   0.0  0
 1K9  CONST_15  CBC  CAM  CAL  CBA     0.00   0.0  0
 1K9  CONST_16  CAY  CBC  CAM  CAL   180.00   0.0  0
 1K9  CONST_19  CAH  CAK  CAY  CBC   180.00   0.0  0
 1K9  CONST_20  SAV  CAN  CAY  CBC   180.00   0.0  0
 1K9  CONST_21  SAV  CAH  CAK  CAY     0.00   0.0  0
 1K9  CONST_22  CAH  SAV  CAN  CAY     0.00   0.0  0
 1K9  CONST_23  CAN  SAV  CAH  CAK     0.00   0.0  0
 1K9  CONST_24  SAV  CAN  CAY  CAK     0.00   0.0  0
 1K9  CONST_25  CAN  CAY  CAK  CAH     0.00   0.0  0
 1K9  CONST_26  CAG  CAJ  CAZ  CBE   180.00   0.0  0
 1K9  CONST_27  CAX  CAO  CAZ  CBE   180.00   0.0  0
 1K9  CONST_28  NAS  CAX  CAO  CAZ   180.00   0.0  0
 1K9  CONST_29  NAS  CAX  CAI  CAG   180.00   0.0  0
 1K9  CONST_30  CAY  CBC  CBB  NAT     0.00   0.0  0
 1K9  CONST_31  CAM  CBC  CBB  NAT   180.00   0.0  0
 1K9  CONST_32  CBA  CAP  CBB  NAT   180.00   0.0  0
 1K9  CONST_33  SBF  CBA  CAP  CBB   180.00   0.0  0
 1K9  CONST_34  CAM  CAL  CBA  SBF   180.00   0.0  0
 1K9  CONST_35  H3   CAG  CAJ  CAZ   180.00   0.0  0
 1K9  CONST_36  H4   CAI  CAX  CAO   180.00   0.0  0
 1K9  CONST_37  H2   CAJ  CAZ  CAO   180.00   0.0  0
 1K9  CONST_38  H1   CAO  CAZ  CAJ   180.00   0.0  0
 1K9  CONST_39  H15  CAM  CBC  CBB   180.00   0.0  0
 1K9  CONST_40  H14  CAL  CBA  CAP   180.00   0.0  0
 1K9  CONST_41  H7   CAP  CBA  CAL   180.00   0.0  0
 1K9  CONST_42  H16  CAK  CAY  CBC     0.00   0.0  0
 1K9  CONST_43  H18  CAN  CAY  CBC     0.00   0.0  0
 1K9  CONST_44  H17  CAH  CAK  CAY   180.00   0.0  0
 1K9  CONST_51  OAA  CAW  NAS  CAX     0.00   0.0  0
 1K9  CONST_52  CBB  NAT  CAW  OAA     0.00   0.0  0
 1K9  CONST_53  NAT  CAW  NAS  CAX   180.00   0.0  0
 1K9  CONST_54  CBB  NAT  CAW  NAS   180.00   0.0  0
 1K9  Var_01    CAR  CAQ  CBD  NAU  -112.55  30.0  1
 1K9  Var_02    H12  CAR  CAQ  CBD  -106.88  30.0  1
 1K9  Var_03    CAJ  CAZ  CBE  FAD   -59.81  30.0  2
 1K9  Var_04    OAC  SBF  CBA  CAP   -33.70  30.0  2
 1K9  Var_05    CBD  NAU  SBF  CBA    68.87  30.0  3
 1K9  Var_06    CAQ  CBD  NAU  SBF   141.33  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
 1K9  chir_01  CBD  NAU  CAQ  CAR  both

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
 1K9  plan-1  CBC  0.020
 1K9  plan-1  CAY  0.020
 1K9  plan-1  CAK  0.020
 1K9  plan-1  CAH  0.020
 1K9  plan-1  SAV  0.020
 1K9  plan-1  CAN  0.020
 1K9  plan-1  H16  0.020
 1K9  plan-1  H17  0.020
 1K9  plan-1  H18  0.020
 1K9  plan-2  CBE  0.020
 1K9  plan-2  CAZ  0.020
 1K9  plan-2  CAO  0.020
 1K9  plan-2  CAJ  0.020
 1K9  plan-2  CAG  0.020
 1K9  plan-2  CAI  0.020
 1K9  plan-2  CAX  0.020
 1K9  plan-2  NAS  0.020
 1K9  plan-2  H1   0.020
 1K9  plan-2  H2   0.020
 1K9  plan-2  H3   0.020
 1K9  plan-2  H4   0.020
 1K9  plan-3  NAT  0.020
 1K9  plan-3  CBB  0.020
 1K9  plan-3  CAP  0.020
 1K9  plan-3  CBA  0.020
 1K9  plan-3  SBF  0.020
 1K9  plan-3  CAL  0.020
 1K9  plan-3  CAM  0.020
 1K9  plan-3  CBC  0.020
 1K9  plan-3  CAY  0.020
 1K9  plan-3  H7   0.020
 1K9  plan-3  H14  0.020
 1K9  plan-3  H15  0.020
 1K9  plan-4  CAX  0.020
 1K9  plan-4  NAS  0.020
 1K9  plan-4  CAW  0.020
 1K9  plan-4  OAA  0.020
 1K9  plan-4  NAT  0.020
 1K9  plan-4  CBB  0.020
 1K9  plan-4  H5   0.020
 1K9  plan-4  H6   0.020

