# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 09:53:32 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-{[(4-cyano-3-cyclopropylphenyl)acetyl]amino}cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1(CCCCC1)NC(=O)Cc2ccc(C#N)c(c2)C3CC3
#
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
 L6P  L6P  '1-{[(4-cyano-3-cyclopropylphenyl)acetyl]amino}cyclohexane-1-carboxylic acid'  ligand  46  24  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L6P
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
 L6P  CAA  C  CR6   0   0.292  -2.8637   0.6233   0.0135
 L6P  CAB  C  CR6   0  -0.051  -3.6518  -0.4437  -0.4438
 L6P  CAC  C  CR16  0  -0.216  -3.3224  -1.7687  -0.1472
 L6P  CAD  C  CR16  0  -0.324  -2.1993  -2.0511   0.6019
 L6P  CAE  C  CR6   0   0.173  -1.4022  -1.0105   1.0737
 L6P  CAF  C  CR16  0  -0.412  -1.7445   0.3017   0.7769
 L6P  CAG  C  CSP   0   0.016  -4.8219  -0.2020  -1.2233
 L6P  CAI  C  CH1   0  -0.391  -3.2154   2.0252  -0.3005
 L6P  CAJ  C  CH2   0  -0.471  -2.1611   3.0976  -0.3730
 L6P  CAK  C  CH2   0  -0.467  -3.1213   3.0922   0.7627
 L6P  CAL  C  CH2   0  -0.666  -0.1373  -1.2975   1.8332
 L6P  CAM  C  C     0   0.567   1.0068  -1.3672   0.8365
 L6P  CAO  C  CT    0  -0.008   3.0148  -0.2370  -0.0049
 L6P  CAQ  C  CH2   0  -0.428   2.8917   2.6689  -0.6371
 L6P  CAR  C  CH2   0  -0.452   3.4433   2.1784   0.6954
 L6P  CAS  C  CH2   0  -0.459   4.0244   0.7706   0.5832
 L6P  CAT  C  CH2   0  -0.412   2.4994   0.2898  -1.3520
 L6P  CAU  C  CH2   0  -0.444   1.8865   1.6777  -1.2113
 L6P  CAV  C  C     0   0.574   3.7504  -1.5631  -0.1874
 L6P  NAH  N  NS    0  -0.252  -5.7730  -0.0257  -1.8509
 L6P  NAN  N  NH1   0  -0.650   1.9292  -0.3997   0.9441
 L6P  OAP  O  O     0  -0.482   1.0524  -2.2317  -0.0250
 L6P  OAW  O  O     0  -0.433   4.1852  -1.9553  -1.2404
 L6P  OAX  O  OH1   0  -0.591   3.9440  -2.1932   0.9614
 L6P  H1   H  HCR6  0   0.280  -3.9511  -2.5705  -0.5105
 L6P  H2   H  HCR6  0   0.266  -1.9438  -3.0781   0.8254
 L6P  H3   H  HCR6  0   0.252  -1.1173   1.0993   1.1586
 L6P  H4   H  HCH1  0   0.272  -4.0344   2.1449  -0.9990
 L6P  H5   H  HCH2  0   0.254  -1.1332   2.8168  -0.1803
 L6P  H6   H  HCH2  0   0.272  -2.2758   3.8432  -1.1483
 L6P  H7   H  HCH2  0   0.270  -3.9062   3.8363   0.7868
 L6P  H8   H  HCH2  0   0.262  -2.7595   2.7888   1.7373
 L6P  H9   H  HCH2  0   0.287   0.0351  -0.5332   2.5915
 L6P  H10  H  HCH2  0   0.302  -0.2059  -2.2597   2.3430
 L6P  H11  H  HCH2  0   0.236   2.4326   3.6523  -0.5152
 L6P  H12  H  HCH2  0   0.217   3.7167   2.7937  -1.3468
 L6P  H13  H  HCH2  0   0.250   4.2269   2.8472   1.0568
 L6P  H14  H  HCH2  0   0.220   2.6547   2.2124   1.4550
 L6P  H15  H  HCH2  0   0.264   4.3744   0.4241   1.5583
 L6P  H16  H  HCH2  0   0.254   4.8958   0.7977  -0.0768
 L6P  H17  H  HCH2  0   0.236   3.3376   0.3436  -2.0501
 L6P  H18  H  HCH2  0   0.250   1.7787  -0.4078  -1.7799
 L6P  H19  H  HCH2  0   0.210   1.0010   1.6339  -0.5681
 L6P  H20  H  HCH2  0   0.241   1.5354   2.0159  -2.1882
 L6P  H21  H  HNH1  0   0.407   1.8568   0.2548   1.7061
 L6P  H22  H  HOH1  0   0.483   4.4558  -3.0017   0.8094

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
 L6P  CAJ  CAI  single    1.506  0.020  1.506
 L6P  CAJ  CAK  single    1.487  0.020  1.487
 L6P  OAW  CAV  double    1.205  0.020  1.205
 L6P  CAI  CAK  single    1.509  0.020  1.509
 L6P  CAI  CAA  single    1.479  0.020  1.479
 L6P  CAF  CAA  aromatic  1.392  0.020  1.392
 L6P  CAF  CAE  aromatic  1.388  0.020  1.388
 L6P  CAL  CAE  single    1.503  0.020  1.503
 L6P  CAL  CAM  single    1.519  0.020  1.519
 L6P  CAA  CAB  aromatic  1.403  0.020  1.403
 L6P  CAV  OAX  single    1.325  0.020  1.325
 L6P  CAV  CAO  single    1.527  0.020  1.527
 L6P  CAE  CAD  aromatic  1.393  0.020  1.393
 L6P  CAM  NAN  single    1.341  0.020  1.341
 L6P  CAM  OAP  double    1.221  0.020  1.221
 L6P  NAN  CAO  single    1.451  0.020  1.451
 L6P  CAT  CAO  single    1.535  0.020  1.535
 L6P  CAT  CAU  single    1.524  0.020  1.524
 L6P  CAO  CAS  single    1.543  0.020  1.543
 L6P  CAB  CAG  single    1.427  0.020  1.427
 L6P  CAB  CAC  aromatic  1.397  0.020  1.397
 L6P  CAD  CAC  aromatic  1.379  0.020  1.379
 L6P  CAU  CAQ  single    1.524  0.020  1.524
 L6P  CAG  NAH  triple    1.153  0.020  1.153
 L6P  CAS  CAR  single    1.527  0.020  1.527
 L6P  CAQ  CAR  single    1.523  0.020  1.523
 L6P  CAC  H1   single    0.930  0.020  1.080
 L6P  CAD  H2   single    0.930  0.020  1.080
 L6P  CAF  H3   single    0.930  0.020  1.080
 L6P  CAI  H4   single    0.970  0.020  1.090
 L6P  CAJ  H5   single    0.970  0.020  1.090
 L6P  CAJ  H6   single    0.970  0.020  1.090
 L6P  CAK  H7   single    0.970  0.020  1.090
 L6P  CAK  H8   single    0.970  0.020  1.090
 L6P  CAL  H9   single    0.970  0.020  1.090
 L6P  CAL  H10  single    0.970  0.020  1.090
 L6P  CAQ  H11  single    0.970  0.020  1.090
 L6P  CAQ  H12  single    0.970  0.020  1.090
 L6P  CAR  H13  single    0.970  0.020  1.090
 L6P  CAR  H14  single    0.970  0.020  1.090
 L6P  CAS  H15  single    0.970  0.020  1.090
 L6P  CAS  H16  single    0.970  0.020  1.090
 L6P  CAT  H17  single    0.970  0.020  1.090
 L6P  CAT  H18  single    0.970  0.020  1.090
 L6P  CAU  H19  single    0.970  0.020  1.090
 L6P  CAU  H20  single    0.970  0.020  1.090
 L6P  NAN  H21  single    0.860  0.020  1.020
 L6P  OAX  H22  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
 L6P  CAI  CAA  CAF  121.76  3.000
 L6P  CAF  CAA  CAB  117.04  3.000
 L6P  CAI  CAA  CAB  121.20  3.000
 L6P  CAG  CAB  CAC  118.04  3.000
 L6P  CAC  CAB  CAA  121.30  3.000
 L6P  CAG  CAB  CAA  120.66  3.000
 L6P  H1   CAC  CAD  120.26  3.000
 L6P  H1   CAC  CAB  119.64  3.000
 L6P  CAD  CAC  CAB  120.10  3.000
 L6P  H2   CAD  CAE  120.27  3.000
 L6P  H2   CAD  CAC  119.93  3.000
 L6P  CAE  CAD  CAC  119.80  3.000
 L6P  CAL  CAE  CAF  119.74  3.000
 L6P  CAL  CAE  CAD  120.67  3.000
 L6P  CAF  CAE  CAD  119.51  3.000
 L6P  H3   CAF  CAE  118.52  3.000
 L6P  H3   CAF  CAA  119.22  3.000
 L6P  CAE  CAF  CAA  122.26  3.000
 L6P  NAH  CAG  CAB  180.00  3.000
 L6P  H4   CAI  CAK  115.05  3.000
 L6P  H4   CAI  CAJ  114.82  3.000
 L6P  CAK  CAI  CAJ   59.12  3.000
 L6P  H4   CAI  CAA  114.93  3.000
 L6P  CAK  CAI  CAA  120.38  3.000
 L6P  CAJ  CAI  CAA  121.26  3.000
 L6P  H6   CAJ  H5   114.01  3.000
 L6P  H6   CAJ  CAK  118.78  3.000
 L6P  H5   CAJ  CAK  118.43  3.000
 L6P  H6   CAJ  CAI  116.83  3.000
 L6P  H5   CAJ  CAI  118.13  3.000
 L6P  CAK  CAJ  CAI   60.56  3.000
 L6P  H8   CAK  H7   114.52  3.000
 L6P  H8   CAK  CAJ  118.20  3.000
 L6P  H7   CAK  CAJ  118.88  3.000
 L6P  H8   CAK  CAI  117.18  3.000
 L6P  H7   CAK  CAI  117.18  3.000
 L6P  CAJ  CAK  CAI   60.32  3.000
 L6P  H10  CAL  H9   107.65  3.000
 L6P  H10  CAL  CAM  108.27  3.000
 L6P  H9   CAL  CAM  111.68  3.000
 L6P  H10  CAL  CAE  110.58  3.000
 L6P  H9   CAL  CAE  110.53  3.000
 L6P  CAM  CAL  CAE  108.12  3.000
 L6P  OAP  CAM  NAN  122.79  3.000
 L6P  OAP  CAM  CAL  121.57  3.000
 L6P  NAN  CAM  CAL  115.61  3.000
 L6P  NAN  CAO  CAV  109.94  3.000
 L6P  NAN  CAO  CAT  111.17  3.000
 L6P  CAV  CAO  CAT  110.77  3.000
 L6P  CAT  CAO  CAS  109.27  3.000
 L6P  NAN  CAO  CAS  108.27  3.000
 L6P  CAV  CAO  CAS  107.30  3.000
 L6P  H12  CAQ  H11  106.64  3.000
 L6P  H12  CAQ  CAU  109.07  3.000
 L6P  H11  CAQ  CAU  110.51  3.000
 L6P  H12  CAQ  CAR  109.31  3.000
 L6P  H11  CAQ  CAR  110.15  3.000
 L6P  CAU  CAQ  CAR  111.04  3.000
 L6P  H14  CAR  H13  105.55  3.000
 L6P  H14  CAR  CAS  110.71  3.000
 L6P  H13  CAR  CAS  108.42  3.000
 L6P  H14  CAR  CAQ  109.63  3.000
 L6P  H13  CAR  CAQ  110.62  3.000
 L6P  CAS  CAR  CAQ  111.74  3.000
 L6P  H16  CAS  H15  106.93  3.000
 L6P  H16  CAS  CAR  108.95  3.000
 L6P  H15  CAS  CAR  110.41  3.000
 L6P  H16  CAS  CAO  107.91  3.000
 L6P  H15  CAS  CAO  110.05  3.000
 L6P  CAR  CAS  CAO  112.40  3.000
 L6P  H18  CAT  H17  106.74  3.000
 L6P  H18  CAT  CAU  110.67  3.000
 L6P  H17  CAT  CAU  108.83  3.000
 L6P  H18  CAT  CAO  110.28  3.000
 L6P  H17  CAT  CAO  108.67  3.000
 L6P  CAU  CAT  CAO  111.50  3.000
 L6P  H20  CAU  H19  106.13  3.000
 L6P  H20  CAU  CAT  109.20  3.000
 L6P  H19  CAU  CAT  110.05  3.000
 L6P  H20  CAU  CAQ  110.36  3.000
 L6P  H19  CAU  CAQ  109.75  3.000
 L6P  CAT  CAU  CAQ  111.22  3.000
 L6P  OAX  CAV  OAW  123.39  3.000
 L6P  OAX  CAV  CAO  112.32  3.000
 L6P  OAW  CAV  CAO  124.12  3.000
 L6P  H21  NAN  CAO  118.41  3.000
 L6P  H21  NAN  CAM  118.69  3.000
 L6P  CAO  NAN  CAM  122.89  3.000
 L6P  H22  OAX  CAV  109.76  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
 L6P  CONST_01  CAD  CAE  CAF  CAA     0.00   0.0  0
 L6P  CONST_02  CAD  CAC  CAB  CAA     0.00   0.0  0
 L6P  CONST_03  CAE  CAF  CAA  CAB     0.00   0.0  0
 L6P  CONST_04  CAE  CAD  CAC  CAB     0.00   0.0  0
 L6P  CONST_05  CAF  CAA  CAB  CAC     0.00   0.0  0
 L6P  CONST_06  CAF  CAE  CAD  CAC     0.00   0.0  0
 L6P  CONST_07  CAI  CAA  CAB  CAC   180.00   0.0  0
 L6P  CONST_08  CAI  CAA  CAF  CAE   180.00   0.0  0
 L6P  CONST_09  CAL  CAE  CAF  CAA   180.00   0.0  0
 L6P  CONST_10  CAL  CAE  CAD  CAC   180.00   0.0  0
 L6P  CONST_11  CAG  CAB  CAC  CAD   180.00   0.0  0
 L6P  CONST_12  CAG  CAB  CAA  CAF   180.00   0.0  0
 L6P  CONST_13  CAI  CAA  CAB  CAG     0.00   0.0  0
 L6P  CONST_14  H1   CAC  CAB  CAA   180.00   0.0  0
 L6P  CONST_15  H3   CAF  CAA  CAB   180.00   0.0  0
 L6P  CONST_16  H2   CAD  CAC  CAB   180.00   0.0  0
 L6P  CONST_17  CAO  NAN  CAM  CAL   180.00   0.0  0
 L6P  CONST_18  OAP  CAM  NAN  CAO     0.00   0.0  0
 L6P  CONST_19  H22  OAX  CAV  CAO   180.00   0.0  0
 L6P  CONST_20  H21  NAN  CAM  CAL     0.00   0.0  0
 L6P  Var_01    CAK  CAJ  CAI  CAA  -109.05  30.0  1
 L6P  Var_02    CAJ  CAI  CAA  CAB  -152.82  30.0  2
 L6P  Var_03    CAQ  CAU  CAT  CAO    57.85  30.0  1
 L6P  Var_04    CAQ  CAR  CAS  CAO   -54.30  30.0  1
 L6P  Var_05    CAT  CAU  CAQ  CAR   -55.87  30.0  1
 L6P  Var_06    CAU  CAQ  CAR  CAS    54.03  30.0  1
 L6P  Var_07    CAM  CAL  CAE  CAD    91.10  30.0  1
 L6P  Var_08    NAN  CAM  CAL  CAE   113.90  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
 L6P  chir_02  CAO  NAN  CAT  CAS  negativ
 L6P  chir_03  CAI  CAJ  CAK  CAA  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
 L6P  plan-1  CAA  0.020
 L6P  plan-1  CAB  0.020
 L6P  plan-1  CAC  0.020
 L6P  plan-1  CAD  0.020
 L6P  plan-1  CAE  0.020
 L6P  plan-1  CAF  0.020
 L6P  plan-1  CAG  0.020
 L6P  plan-1  CAI  0.020
 L6P  plan-1  CAL  0.020
 L6P  plan-1  NAH  0.020
 L6P  plan-1  H1   0.020
 L6P  plan-1  H2   0.020
 L6P  plan-1  H3   0.020
 L6P  plan-2  CAL  0.020
 L6P  plan-2  CAM  0.020
 L6P  plan-2  CAO  0.020
 L6P  plan-2  NAN  0.020
 L6P  plan-2  OAP  0.020
 L6P  plan-2  H21  0.020
 L6P  plan-3  CAO  0.020
 L6P  plan-3  CAV  0.020
 L6P  plan-3  OAW  0.020
 L6P  plan-3  OAX  0.020
 L6P  plan-3  H22  0.020

