# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:24:13 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: N-{[(4-cyanophenyl)methyl]sulfonyl}-1-(thiophen-3-yl)cyclohexane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N[S](=O)(=O)Cc1ccc(cc1)C#N)C2(CCCCC2)c3cscc3
#
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
 L6V  L6V  N-{[(4-cyanophenyl)methyl]sulfonyl}-1-(thiophen-3-yl)cyclohexane-1-carboxamide  ligand  46  26  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_L6V
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
 L6V  CAA  C  CR16  0  -0.265  -3.8764  -0.0209   1.1531
 L6V  CAB  C  CR6   0   0.120  -3.3711   0.3232  -0.0972
 L6V  CAC  C  CR16  0  -0.263  -4.1788   0.2042  -1.2250
 L6V  CAD  C  CR16  0  -0.224  -5.4836  -0.2391  -1.1076
 L6V  CAE  C  CR6   0  -0.000  -5.9833  -0.5721   0.1506
 L6V  CAF  C  CR16  0  -0.224  -5.1799  -0.4626   1.2849
 L6V  CAG  C  CSP   0   0.060  -7.3322  -1.0216   0.2808
 L6V  CAI  C  CH2   0  -0.719  -1.9565   0.7928  -0.2274
 L6V  CAL  C  C     0   0.639   1.3199   0.5778   0.3536
 L6V  CAO  C  CT    0  -0.309   2.7663   0.9775   0.0465
 L6V  CAP  C  CR5   0   0.248   3.5450  -0.3275   0.0796
 L6V  CAR  C  CR15  0  -0.465   4.8342  -2.0887  -0.7200
 L6V  CAS  C  CR15  0  -0.230   4.2198  -0.9153  -1.0322
 L6V  CAT  C  CR15  0  -0.534   3.6705  -1.0947   1.2040
 L6V  CAU  C  CH2   0  -0.428   2.7128   3.9575  -0.2614
 L6V  CAV  C  CH2   0  -0.447   2.6141   3.3059   1.1118
 L6V  CAW  C  CH2   0  -0.394   3.2809   1.9326   1.1386
 L6V  CAX  C  CH2   0  -0.468   2.8994   1.6855  -1.3127
 L6V  CAY  C  CH2   0  -0.429   2.1789   3.0288  -1.3441
 L6V  NAH  N  NS    0  -0.247  -8.4208  -1.3833   0.3863
 L6V  NAK  N  NC1   0  -0.819   0.6240   0.0393  -0.7053
 L6V  OAM  O  OS    0  -0.625  -0.9582  -1.5402   0.5431
 L6V  OAN  O  OS    0  -0.645  -1.2081  -1.1118  -1.9118
 L6V  OAZ  O  O     0  -0.424   0.8100   0.6729   1.4456
 L6V  SAJ  S  S     0   1.385  -0.9099  -0.6258  -0.5774
 L6V  SAQ  S  S2    0   0.231   4.5982  -2.5022   0.9231
 L6V  H1   H  HCR6  0   0.277  -3.2543   0.0714   2.0335
 L6V  H2   H  HCR6  0   0.280  -3.7941   0.4707  -2.2001
 L6V  H3   H  HCR6  0   0.288  -6.1114  -0.3263  -1.9834
 L6V  H4   H  HCR6  0   0.288  -5.5735  -0.7195   2.2584
 L6V  H5   H  HCH2  0   0.341  -1.8201   1.4902  -1.0543
 L6V  H6   H  HCH2  0   0.339  -1.5900   1.2466   0.6928
 L6V  H7   H  HCR5  0   0.297   5.4138  -2.7258  -1.3697
 L6V  H8   H  HCR5  0   0.269   4.2547  -0.4854  -2.0224
 L6V  H9   H  HCR5  0   0.295   3.2635  -0.9054   2.1857
 L6V  H10  H  HCH2  0   0.234   2.1689   4.9044  -0.2706
 L6V  H11  H  HCH2  0   0.215   3.7597   4.1927  -0.4804
 L6V  H12  H  HCH2  0   0.237   3.0872   3.9406   1.8648
 L6V  H13  H  HCH2  0   0.223   1.5640   3.2194   1.4033
 L6V  H14  H  HCH2  0   0.245   3.1700   1.4812   2.1251
 L6V  H15  H  HCH2  0   0.237   4.3561   2.0510   0.9729
 L6V  H16  H  HCH2  0   0.259   3.9664   1.8509  -1.4882
 L6V  H17  H  HCH2  0   0.245   2.5652   1.0597  -2.1451
 L6V  H18  H  HCH2  0   0.216   1.0998   2.8854  -1.2149
 L6V  H19  H  HCH2  0   0.244   2.3096   3.4771  -2.3308
 L6V  H20  H  HNC1  0   0.444   1.0276  -0.0030  -1.6326

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
 L6V  SAQ  CAT  aromatic  1.709  0.020  1.709
 L6V  SAQ  CAR  aromatic  1.711  0.020  1.711
 L6V  CAT  CAP  aromatic  1.367  0.020  1.367
 L6V  CAR  CAS  aromatic  1.361  0.020  1.361
 L6V  OAM  SAJ  double    1.447  0.020  1.447
 L6V  CAI  SAJ  single    1.797  0.020  1.797
 L6V  CAI  CAB  single    1.496  0.020  1.496
 L6V  CAC  CAB  aromatic  1.392  0.020  1.392
 L6V  CAC  CAD  aromatic  1.383  0.020  1.383
 L6V  CAP  CAS  aromatic  1.427  0.020  1.427
 L6V  CAP  CAO  single    1.520  0.020  1.520
 L6V  SAJ  NAK  single    1.677  0.020  1.677
 L6V  SAJ  OAN  double    1.451  0.020  1.451
 L6V  CAB  CAA  aromatic  1.392  0.020  1.392
 L6V  NAK  CAL  single    1.377  0.020  1.377
 L6V  CAD  CAE  aromatic  1.394  0.020  1.394
 L6V  CAL  CAO  single    1.532  0.020  1.532
 L6V  CAL  OAZ  double    1.209  0.020  1.209
 L6V  CAX  CAO  single    1.538  0.020  1.538
 L6V  CAX  CAY  single    1.525  0.020  1.525
 L6V  CAO  CAW  single    1.539  0.020  1.539
 L6V  CAA  CAF  aromatic  1.383  0.020  1.383
 L6V  CAE  CAF  aromatic  1.394  0.020  1.394
 L6V  CAE  CAG  single    1.428  0.020  1.428
 L6V  CAY  CAU  single    1.523  0.020  1.523
 L6V  CAG  NAH  triple    1.152  0.020  1.152
 L6V  CAW  CAV  single    1.527  0.020  1.527
 L6V  CAU  CAV  single    1.523  0.020  1.523
 L6V  CAA  H1   single    0.930  0.020  1.080
 L6V  CAC  H2   single    0.930  0.020  1.080
 L6V  CAD  H3   single    0.930  0.020  1.080
 L6V  CAF  H4   single    0.930  0.020  1.080
 L6V  CAI  H5   single    0.970  0.020  1.090
 L6V  CAI  H6   single    0.970  0.020  1.090
 L6V  CAR  H7   single    0.930  0.020  1.080
 L6V  CAS  H8   single    0.930  0.020  1.080
 L6V  CAT  H9   single    0.930  0.020  1.080
 L6V  CAU  H10  single    0.970  0.020  1.090
 L6V  CAU  H11  single    0.970  0.020  1.090
 L6V  CAV  H12  single    0.970  0.020  1.090
 L6V  CAV  H13  single    0.970  0.020  1.090
 L6V  CAW  H14  single    0.970  0.020  1.090
 L6V  CAW  H15  single    0.970  0.020  1.090
 L6V  CAX  H16  single    0.970  0.020  1.090
 L6V  CAX  H17  single    0.970  0.020  1.090
 L6V  CAY  H18  single    0.970  0.020  1.090
 L6V  CAY  H19  single    0.970  0.020  1.090
 L6V  NAK  H20  single    0.860  0.020  1.020

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
 L6V  H1   CAA  CAF  119.46  3.000
 L6V  H1   CAA  CAB  120.08  3.000
 L6V  CAF  CAA  CAB  120.46  3.000
 L6V  CAI  CAB  CAC  120.32  3.000
 L6V  CAC  CAB  CAA  119.73  3.000
 L6V  CAI  CAB  CAA  119.93  3.000
 L6V  H2   CAC  CAD  119.41  3.000
 L6V  H2   CAC  CAB  120.19  3.000
 L6V  CAD  CAC  CAB  120.40  3.000
 L6V  H3   CAD  CAE  120.24  3.000
 L6V  H3   CAD  CAC  120.33  3.000
 L6V  CAE  CAD  CAC  119.43  3.000
 L6V  CAG  CAE  CAF  119.67  3.000
 L6V  CAG  CAE  CAD  119.74  3.000
 L6V  CAF  CAE  CAD  120.59  3.000
 L6V  H4   CAF  CAE  120.28  3.000
 L6V  H4   CAF  CAA  120.33  3.000
 L6V  CAE  CAF  CAA  119.39  3.000
 L6V  NAH  CAG  CAE  180.00  3.000
 L6V  H6   CAI  H5   109.40  3.000
 L6V  H6   CAI  SAJ  107.29  3.000
 L6V  H5   CAI  SAJ  106.52  3.000
 L6V  H6   CAI  CAB  112.04  3.000
 L6V  H5   CAI  CAB  112.64  3.000
 L6V  SAJ  CAI  CAB  108.65  3.000
 L6V  OAZ  CAL  NAK  120.82  3.000
 L6V  OAZ  CAL  CAO  123.97  3.000
 L6V  NAK  CAL  CAO  115.16  3.000
 L6V  CAX  CAO  CAW  108.21  3.000
 L6V  CAW  CAO  CAP  110.24  3.000
 L6V  CAX  CAO  CAP  111.72  3.000
 L6V  CAW  CAO  CAL  109.59  3.000
 L6V  CAX  CAO  CAL  112.27  3.000
 L6V  CAP  CAO  CAL  104.79  3.000
 L6V  CAT  CAP  CAS  111.48  3.000
 L6V  CAS  CAP  CAO  125.37  3.000
 L6V  CAT  CAP  CAO  123.15  3.000
 L6V  H7   CAR  SAQ  120.65  3.000
 L6V  H7   CAR  CAS  127.85  3.000
 L6V  SAQ  CAR  CAS  111.50  3.000
 L6V  H8   CAS  CAR  122.61  3.000
 L6V  H8   CAS  CAP  124.44  3.000
 L6V  CAR  CAS  CAP  112.95  3.000
 L6V  H9   CAT  SAQ  119.91  3.000
 L6V  H9   CAT  CAP  127.95  3.000
 L6V  SAQ  CAT  CAP  112.14  3.000
 L6V  H11  CAU  H10  106.75  3.000
 L6V  H11  CAU  CAY  108.90  3.000
 L6V  H10  CAU  CAY  110.37  3.000
 L6V  H11  CAU  CAV  109.52  3.000
 L6V  H10  CAU  CAV  110.26  3.000
 L6V  CAY  CAU  CAV  110.94  3.000
 L6V  H13  CAV  H12  106.15  3.000
 L6V  H13  CAV  CAW  110.10  3.000
 L6V  H12  CAV  CAW  108.74  3.000
 L6V  H13  CAV  CAU  109.66  3.000
 L6V  H12  CAV  CAU  110.17  3.000
 L6V  CAW  CAV  CAU  111.86  3.000
 L6V  H15  CAW  H14  106.36  3.000
 L6V  H15  CAW  CAV  109.21  3.000
 L6V  H14  CAW  CAV  110.11  3.000
 L6V  H15  CAW  CAO  106.75  3.000
 L6V  H14  CAW  CAO  110.55  3.000
 L6V  CAV  CAW  CAO  113.55  3.000
 L6V  H17  CAX  H16  105.21  3.000
 L6V  H17  CAX  CAY  110.12  3.000
 L6V  H16  CAX  CAY  108.93  3.000
 L6V  H17  CAX  CAO  112.50  3.000
 L6V  H16  CAX  CAO  107.20  3.000
 L6V  CAY  CAX  CAO  112.51  3.000
 L6V  H19  CAY  H18  106.15  3.000
 L6V  H19  CAY  CAX  108.90  3.000
 L6V  H18  CAY  CAX  110.34  3.000
 L6V  H19  CAY  CAU  110.49  3.000
 L6V  H18  CAY  CAU  109.94  3.000
 L6V  CAX  CAY  CAU  110.91  3.000
 L6V  H20  NAK  SAJ  114.72  3.000
 L6V  H20  NAK  CAL  121.29  3.000
 L6V  SAJ  NAK  CAL  123.98  3.000
 L6V  OAN  SAJ  OAM  119.57  3.000
 L6V  OAN  SAJ  NAK  104.51  3.000
 L6V  OAM  SAJ  NAK  109.89  3.000
 L6V  OAN  SAJ  CAI  108.89  3.000
 L6V  NAK  SAJ  CAI  103.56  3.000
 L6V  OAM  SAJ  CAI  109.18  3.000
 L6V  CAT  SAQ  CAR   91.93  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
 L6V  CONST_01  CAD  CAC  CAB  CAA    0.00   0.0  0
 L6V  CONST_02  CAD  CAE  CAF  CAA    0.00   0.0  0
 L6V  CONST_03  CAE  CAD  CAC  CAB    0.00   0.0  0
 L6V  CONST_04  CAE  CAF  CAA  CAB    0.00   0.0  0
 L6V  CONST_05  CAF  CAA  CAB  CAC    0.00   0.0  0
 L6V  CONST_06  CAF  CAE  CAD  CAC    0.00   0.0  0
 L6V  CONST_07  CAR  SAQ  CAT  CAP    0.00   0.0  0
 L6V  CONST_08  SAQ  CAR  CAS  CAP    0.00   0.0  0
 L6V  CONST_09  CAT  CAP  CAS  CAR    0.00   0.0  0
 L6V  CONST_10  CAT  SAQ  CAR  CAS    0.00   0.0  0
 L6V  CONST_11  SAQ  CAT  CAP  CAS    0.00   0.0  0
 L6V  CONST_12  SAQ  CAT  CAP  CAO  180.00   0.0  0
 L6V  CONST_13  CAR  CAS  CAP  CAO  180.00   0.0  0
 L6V  CONST_14  CAG  CAE  CAF  CAA  180.00   0.0  0
 L6V  CONST_15  CAG  CAE  CAD  CAC  180.00   0.0  0
 L6V  CONST_16  CAI  CAB  CAC  CAD  180.00   0.0  0
 L6V  CONST_17  CAI  CAB  CAA  CAF  180.00   0.0  0
 L6V  CONST_18  H2   CAC  CAB  CAA  180.00   0.0  0
 L6V  CONST_19  H3   CAD  CAC  CAB  180.00   0.0  0
 L6V  CONST_20  H4   CAF  CAA  CAB  180.00   0.0  0
 L6V  CONST_21  H1   CAA  CAB  CAC  180.00   0.0  0
 L6V  CONST_22  H9   CAT  CAP  CAO    0.00   0.0  0
 L6V  CONST_23  H8   CAS  CAP  CAO    0.00   0.0  0
 L6V  CONST_24  H7   CAR  CAS  CAP  180.00   0.0  0
 L6V  CONST_25  SAJ  NAK  CAL  CAO  180.00   0.0  0
 L6V  CONST_26  H20  NAK  CAL  CAO    0.00   0.0  0
 L6V  CONST_27  SAJ  NAK  CAL  OAZ    0.00   0.0  0
 L6V  Var_01    CAU  CAY  CAX  CAO   58.27  30.0  1
 L6V  Var_02    CAU  CAV  CAW  CAO  -53.90  30.0  1
 L6V  Var_03    CAX  CAY  CAU  CAV  -55.64  30.0  1
 L6V  Var_04    CAY  CAU  CAV  CAW   53.48  30.0  1
 L6V  Var_05    SAJ  CAI  CAB  CAA   92.21  30.0  2
 L6V  Var_06    OAM  SAJ  CAI  CAB  -63.28  30.0  3
 L6V  Var_07    CAL  NAK  SAJ  CAI   68.52  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
 L6V  chir_01  CAO  CAP  CAX  CAW  positiv

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
 L6V  plan-1  CAO  0.020
 L6V  plan-1  CAP  0.020
 L6V  plan-1  CAR  0.020
 L6V  plan-1  CAS  0.020
 L6V  plan-1  CAT  0.020
 L6V  plan-1  SAQ  0.020
 L6V  plan-1  H7   0.020
 L6V  plan-1  H8   0.020
 L6V  plan-1  H9   0.020
 L6V  plan-2  CAA  0.020
 L6V  plan-2  CAB  0.020
 L6V  plan-2  CAC  0.020
 L6V  plan-2  CAD  0.020
 L6V  plan-2  CAE  0.020
 L6V  plan-2  CAF  0.020
 L6V  plan-2  CAG  0.020
 L6V  plan-2  CAI  0.020
 L6V  plan-2  NAH  0.020
 L6V  plan-2  H1   0.020
 L6V  plan-2  H2   0.020
 L6V  plan-2  H3   0.020
 L6V  plan-2  H4   0.020
 L6V  plan-3  CAL  0.020
 L6V  plan-3  CAO  0.020
 L6V  plan-3  NAK  0.020
 L6V  plan-3  OAZ  0.020
 L6V  plan-3  SAJ  0.020
 L6V  plan-3  H20  0.020

