# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 14:54:07 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (1~{R})-1-cyclohexyl-2-pyrido[3,4-b]indol-9-yl-ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](Cn1c2ccccc2c3ccncc13)C4CCCCC4
#
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
 XNL  XNL  (1~{R})-1-cyclohexyl-2-pyrido[3,4-b]indol-9-yl-ethanol  ligand  44  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XNL
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
 XNL  CAA  C  CH2   0  -0.407  -3.7669  -0.5902   1.2335
 XNL  CAB  C  CH2   0  -0.432  -5.2304  -0.8168   0.8690
 XNL  CAC  C  CH2   0  -0.430  -5.7674   0.3059  -0.0101
 XNL  CAD  C  CH2   0  -0.425  -4.8983   0.4858  -1.2482
 XNL  CAE  C  CH2   0  -0.439  -3.4326   0.7083  -0.8858
 XNL  CAF  C  CH1   0  -0.291  -2.8843  -0.4201  -0.0068
 XNL  CAG  C  CH1   0   0.071  -1.4197  -0.1927   0.3817
 XNL  OAV  O  OH1   0  -0.657  -0.9298  -1.1921   1.2473
 XNL  CAH  C  CH2   0  -0.370  -0.5170  -0.0763  -0.8522
 XNL  NAI  N  NR5   0  -0.624   0.8802   0.0208  -0.5106
 XNL  CAM  C  CR56  0   0.381   1.7678  -1.0227  -0.4147
 XNL  CAU  C  CR16  0  -0.323   1.5769  -2.3772  -0.6839
 XNL  CAT  C  CR16  0  -0.264   2.6601  -3.2216  -0.5241
 XNL  CAS  C  CR16  0  -0.273   3.9106  -2.7487  -0.1039
 XNL  CAR  C  CR16  0  -0.359   4.0989  -1.4056   0.1601
 XNL  CAL  C  CR56  0   0.048   3.0226  -0.5338   0.0043
 XNL  CAK  C  CR56  0   0.162   2.8630   0.8825   0.1826
 XNL  CAJ  C  CR56  0   0.239   1.5241   1.1728  -0.1382
 XNL  CAN  C  CR16  0  -0.104   1.0587   2.4815  -0.0542
 XNL  NAO  N  N     0  -0.410   1.8603   3.4665   0.3142
 XNL  CAP  C  CR16  0  -0.100   3.1363   3.1975   0.6130
 XNL  CAQ  C  CR16  0  -0.429   3.6911   1.9307   0.5668
 XNL  H1   H  HCH2  0   0.207  -3.6831   0.3119   1.8518
 XNL  H2   H  HCH2  0   0.229  -3.4082  -1.4190   1.8454
 XNL  H3   H  HCH2  0   0.209  -5.3281  -1.7715   0.3407
 XNL  H4   H  HCH2  0   0.227  -5.8285  -0.9051   1.7792
 XNL  H5   H  HCH2  0   0.226  -6.8014   0.1030  -0.2996
 XNL  H6   H  HCH2  0   0.208  -5.7811   1.2396   0.5632
 XNL  H7   H  HCH2  0   0.211  -4.9783  -0.4057  -1.8793
 XNL  H8   H  HCH2  0   0.228  -5.2598   1.3235  -1.8491
 XNL  H9   H  HCH2  0   0.237  -2.8538   0.8038  -1.8070
 XNL  H10  H  HCH2  0   0.214  -3.3299   1.6608  -0.3519
 XNL  H11  H  HCH1  0   0.217  -2.9283  -1.3521  -0.5924
 XNL  H12  H  HCH1  0   0.226  -1.3532   0.7426   0.9513
 XNL  H13  H  HOH1  0   0.443  -1.1569  -2.0551   0.8839
 XNL  H14  H  HCH2  0   0.271  -0.6547  -0.9405  -1.5067
 XNL  H15  H  HCH2  0   0.274  -0.7838   0.7978  -1.4465
 XNL  H16  H  HCR6  0   0.263   0.6232  -2.7675  -1.0134
 XNL  H17  H  HCR6  0   0.260   2.5350  -4.2776  -0.7257
 XNL  H18  H  HCR6  0   0.255   4.7310  -3.4439   0.0123
 XNL  H19  H  HCR6  0   0.252   5.0642  -1.0359   0.4826
 XNL  H20  H  HCR6  0   0.263   0.0299   2.7380  -0.2856
 XNL  H21  H  HCR6  0   0.257   3.7461   4.0442   0.9059
 XNL  H22  H  HCR6  0   0.261   4.7317   1.7764   0.8206

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
 XNL  CAC  CAD  single    1.523  0.020  1.523
 XNL  CAC  CAB  single    1.524  0.020  1.524
 XNL  CAD  CAE  single    1.526  0.020  1.526
 XNL  CAB  CAA  single    1.525  0.020  1.525
 XNL  CAE  CAF  single    1.532  0.020  1.532
 XNL  CAA  CAF  single    1.532  0.020  1.532
 XNL  CAF  CAG  single    1.532  0.020  1.532
 XNL  CAG  OAV  single    1.410  0.020  1.410
 XNL  CAG  CAH  single    1.533  0.020  1.533
 XNL  CAH  NAI  single    1.442  0.020  1.442
 XNL  CAU  CAT  aromatic  1.383  0.020  1.383
 XNL  CAU  CAM  aromatic  1.394  0.020  1.394
 XNL  NAI  CAM  aromatic  1.373  0.020  1.373
 XNL  NAI  CAJ  aromatic  1.371  0.020  1.371
 XNL  CAT  CAS  aromatic  1.401  0.020  1.401
 XNL  CAM  CAL  aromatic  1.410  0.020  1.410
 XNL  CAJ  CAN  aromatic  1.391  0.020  1.391
 XNL  CAJ  CAK  aromatic  1.407  0.020  1.407
 XNL  CAN  NAO  aromatic  1.322  0.020  1.322
 XNL  CAS  CAR  aromatic  1.382  0.020  1.382
 XNL  CAL  CAK  aromatic  1.436  0.020  1.436
 XNL  CAL  CAR  aromatic  1.394  0.020  1.394
 XNL  CAK  CAQ  aromatic  1.390  0.020  1.390
 XNL  NAO  CAP  aromatic  1.338  0.020  1.338
 XNL  CAQ  CAP  aromatic  1.384  0.020  1.384
 XNL  CAA  H1   single    0.970  0.020  1.090
 XNL  CAA  H2   single    0.970  0.020  1.090
 XNL  CAB  H3   single    0.970  0.020  1.090
 XNL  CAB  H4   single    0.970  0.020  1.090
 XNL  CAC  H5   single    0.970  0.020  1.090
 XNL  CAC  H6   single    0.970  0.020  1.090
 XNL  CAD  H7   single    0.970  0.020  1.090
 XNL  CAD  H8   single    0.970  0.020  1.090
 XNL  CAE  H9   single    0.970  0.020  1.090
 XNL  CAE  H10  single    0.970  0.020  1.090
 XNL  CAF  H11  single    0.970  0.020  1.090
 XNL  CAG  H12  single    0.970  0.020  1.090
 XNL  OAV  H13  single    0.850  0.020  0.980
 XNL  CAH  H14  single    0.970  0.020  1.090
 XNL  CAH  H15  single    0.970  0.020  1.090
 XNL  CAU  H16  single    0.930  0.020  1.080
 XNL  CAT  H17  single    0.930  0.020  1.080
 XNL  CAS  H18  single    0.930  0.020  1.080
 XNL  CAR  H19  single    0.930  0.020  1.080
 XNL  CAN  H20  single    0.930  0.020  1.080
 XNL  CAP  H21  single    0.930  0.020  1.080
 XNL  CAQ  H22  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
 XNL  H2   CAA  H1   106.47  3.000
 XNL  H2   CAA  CAF  110.43  3.000
 XNL  H1   CAA  CAF  108.72  3.000
 XNL  H2   CAA  CAB  109.68  3.000
 XNL  H1   CAA  CAB  109.29  3.000
 XNL  CAF  CAA  CAB  112.08  3.000
 XNL  H4   CAB  H3   106.41  3.000
 XNL  H4   CAB  CAC  110.32  3.000
 XNL  H3   CAB  CAC  109.42  3.000
 XNL  H4   CAB  CAA  109.76  3.000
 XNL  H3   CAB  CAA  109.29  3.000
 XNL  CAC  CAB  CAA  111.51  3.000
 XNL  H6   CAC  H5   106.56  3.000
 XNL  H6   CAC  CAD  109.37  3.000
 XNL  H5   CAC  CAD  110.27  3.000
 XNL  H6   CAC  CAB  109.30  3.000
 XNL  H5   CAC  CAB  110.46  3.000
 XNL  CAD  CAC  CAB  110.79  3.000
 XNL  H8   CAD  H7   106.44  3.000
 XNL  H8   CAD  CAE  109.67  3.000
 XNL  H7   CAD  CAE  109.01  3.000
 XNL  H8   CAD  CAC  110.42  3.000
 XNL  H7   CAD  CAC  109.30  3.000
 XNL  CAE  CAD  CAC  111.85  3.000
 XNL  H10  CAE  H9   106.56  3.000
 XNL  H10  CAE  CAF  109.08  3.000
 XNL  H9   CAE  CAF  111.02  3.000
 XNL  H10  CAE  CAD  109.40  3.000
 XNL  H9   CAE  CAD  108.75  3.000
 XNL  CAF  CAE  CAD  111.88  3.000
 XNL  H11  CAF  CAG  107.37  3.000
 XNL  H11  CAF  CAE  107.69  3.000
 XNL  CAG  CAF  CAE  112.23  3.000
 XNL  H11  CAF  CAA  108.27  3.000
 XNL  CAG  CAF  CAA  111.22  3.000
 XNL  CAE  CAF  CAA  109.89  3.000
 XNL  H12  CAG  CAH  108.51  3.000
 XNL  H12  CAG  OAV  105.34  3.000
 XNL  CAH  CAG  OAV  110.08  3.000
 XNL  H12  CAG  CAF  108.43  3.000
 XNL  CAH  CAG  CAF  111.71  3.000
 XNL  OAV  CAG  CAF  112.49  3.000
 XNL  H13  OAV  CAG  108.75  3.000
 XNL  H15  CAH  H14  106.06  3.000
 XNL  H15  CAH  NAI  108.20  3.000
 XNL  H14  CAH  NAI  108.50  3.000
 XNL  H15  CAH  CAG  110.82  3.000
 XNL  H14  CAH  CAG  110.36  3.000
 XNL  NAI  CAH  CAG  112.64  3.000
 XNL  CAJ  NAI  CAM  108.42  3.000
 XNL  CAJ  NAI  CAH  125.17  3.000
 XNL  CAM  NAI  CAH  126.29  3.000
 XNL  CAL  CAM  CAU  121.06  3.000
 XNL  CAL  CAM  NAI  109.41  3.000
 XNL  CAU  CAM  NAI  129.52  3.000
 XNL  H16  CAU  CAT  120.36  3.000
 XNL  H16  CAU  CAM  122.00  3.000
 XNL  CAT  CAU  CAM  117.63  3.000
 XNL  H17  CAT  CAS  119.22  3.000
 XNL  H17  CAT  CAU  118.93  3.000
 XNL  CAS  CAT  CAU  121.85  3.000
 XNL  H18  CAS  CAR  120.06  3.000
 XNL  H18  CAS  CAT  119.48  3.000
 XNL  CAR  CAS  CAT  120.46  3.000
 XNL  H19  CAR  CAL  120.53  3.000
 XNL  H19  CAR  CAS  120.69  3.000
 XNL  CAL  CAR  CAS  118.78  3.000
 XNL  CAK  CAL  CAR  133.53  3.000
 XNL  CAR  CAL  CAM  120.22  3.000
 XNL  CAK  CAL  CAM  106.25  3.000
 XNL  CAQ  CAK  CAJ  118.32  3.000
 XNL  CAQ  CAK  CAL  135.37  3.000
 XNL  CAJ  CAK  CAL  106.31  3.000
 XNL  CAN  CAJ  CAK  119.90  3.000
 XNL  CAK  CAJ  NAI  109.60  3.000
 XNL  CAN  CAJ  NAI  130.50  3.000
 XNL  H20  CAN  NAO  117.26  3.000
 XNL  H20  CAN  CAJ  121.77  3.000
 XNL  NAO  CAN  CAJ  120.97  3.000
 XNL  CAP  NAO  CAN  119.38  3.000
 XNL  H21  CAP  CAQ  119.91  3.000
 XNL  H21  CAP  NAO  116.10  3.000
 XNL  CAQ  CAP  NAO  123.99  3.000
 XNL  H22  CAQ  CAP  120.55  3.000
 XNL  H22  CAQ  CAK  122.02  3.000
 XNL  CAP  CAQ  CAK  117.43  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
 XNL  CONST_01  CAT  CAU  CAM  NAI  180.00   0.0  0
 XNL  CONST_02  CAK  CAL  CAM  NAI    0.00   0.0  0
 XNL  CONST_03  CAR  CAL  CAM  NAI  180.00   0.0  0
 XNL  CONST_04  NAO  CAN  CAJ  NAI  180.00   0.0  0
 XNL  CONST_05  CAL  CAK  CAJ  NAI    0.00   0.0  0
 XNL  CONST_06  CAQ  CAK  CAJ  NAI  180.00   0.0  0
 XNL  CONST_07  CAS  CAT  CAU  CAM    0.00   0.0  0
 XNL  CONST_08  CAN  CAJ  NAI  CAM  180.00   0.0  0
 XNL  CONST_09  CAK  CAJ  NAI  CAM    0.00   0.0  0
 XNL  CONST_10  CAJ  CAK  CAL  CAM    0.00   0.0  0
 XNL  CONST_11  CAQ  CAK  CAL  CAM  180.00   0.0  0
 XNL  CONST_12  CAS  CAR  CAL  CAM    0.00   0.0  0
 XNL  CONST_13  CAR  CAS  CAT  CAU    0.00   0.0  0
 XNL  CONST_14  CAJ  NAI  CAM  CAU  180.00   0.0  0
 XNL  CONST_15  CAK  CAL  CAM  CAU  180.00   0.0  0
 XNL  CONST_16  CAR  CAL  CAM  CAU    0.00   0.0  0
 XNL  CONST_17  CAL  CAM  CAU  CAT    0.00   0.0  0
 XNL  CONST_18  CAL  CAR  CAS  CAT    0.00   0.0  0
 XNL  CONST_19  CAK  CAL  CAR  CAS  180.00   0.0  0
 XNL  CONST_20  CAJ  CAK  CAL  CAR  180.00   0.0  0
 XNL  CONST_21  CAQ  CAK  CAL  CAR    0.00   0.0  0
 XNL  CONST_22  CAJ  NAI  CAM  CAL    0.00   0.0  0
 XNL  CONST_23  CAN  CAJ  CAK  CAL  180.00   0.0  0
 XNL  CONST_24  CAP  CAQ  CAK  CAL  180.00   0.0  0
 XNL  CONST_25  NAO  CAN  CAJ  CAK    0.00   0.0  0
 XNL  CONST_26  NAO  CAP  CAQ  CAK    0.00   0.0  0
 XNL  CONST_27  CAP  NAO  CAN  CAJ    0.00   0.0  0
 XNL  CONST_28  CAP  CAQ  CAK  CAJ    0.00   0.0  0
 XNL  CONST_29  CAQ  CAK  CAJ  CAN    0.00   0.0  0
 XNL  CONST_30  CAQ  CAP  NAO  CAN    0.00   0.0  0
 XNL  CONST_31  CAU  CAM  NAI  CAH    0.00   0.0  0
 XNL  CONST_32  CAL  CAM  NAI  CAH  180.00   0.0  0
 XNL  CONST_33  CAN  CAJ  NAI  CAH    0.00   0.0  0
 XNL  CONST_34  CAK  CAJ  NAI  CAH  180.00   0.0  0
 XNL  CONST_35  H16  CAU  CAM  NAI    0.00   0.0  0
 XNL  CONST_36  H20  CAN  CAJ  NAI    0.00   0.0  0
 XNL  CONST_37  H17  CAT  CAU  CAM  180.00   0.0  0
 XNL  CONST_38  H19  CAR  CAL  CAM  180.00   0.0  0
 XNL  CONST_39  H18  CAS  CAT  CAU  180.00   0.0  0
 XNL  CONST_40  H22  CAQ  CAK  CAL    0.00   0.0  0
 XNL  CONST_41  H21  CAP  CAQ  CAK  180.00   0.0  0
 XNL  Var_01    CAD  CAC  CAB  CAA   54.84  30.0  1
 XNL  Var_02    CAE  CAD  CAC  CAB  -54.81  30.0  1
 XNL  Var_03    CAF  CAE  CAD  CAC   55.50  30.0  1
 XNL  Var_04    CAF  CAA  CAB  CAC  -55.87  30.0  1
 XNL  Var_05    CAM  NAI  CAH  CAG   92.99  30.0  2

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
 XNL  chir_01  CAF  CAE  CAA  CAG  positiv
 XNL  chir_02  CAG  OAV  CAF  CAH  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
 XNL  plan-1  CAH  0.020
 XNL  plan-1  NAI  0.020
 XNL  plan-1  CAM  0.020
 XNL  plan-1  CAU  0.020
 XNL  plan-1  CAT  0.020
 XNL  plan-1  CAS  0.020
 XNL  plan-1  CAR  0.020
 XNL  plan-1  CAL  0.020
 XNL  plan-1  CAK  0.020
 XNL  plan-1  CAJ  0.020
 XNL  plan-1  CAN  0.020
 XNL  plan-1  NAO  0.020
 XNL  plan-1  CAP  0.020
 XNL  plan-1  CAQ  0.020
 XNL  plan-1  H16  0.020
 XNL  plan-1  H17  0.020
 XNL  plan-1  H18  0.020
 XNL  plan-1  H19  0.020
 XNL  plan-1  H20  0.020
 XNL  plan-1  H21  0.020
 XNL  plan-1  H22  0.020

