# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 14:53:01 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-(6-chloro-1H-indazol-4-yl)cyclohexan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1(CCCCC1)c2cc(Cl)cc3[nH]ncc23
#
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
 9R9  9R9  1-(6-chloro-1H-indazol-4-yl)cyclohexan-1-ol  ligand  32  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9R9
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
 9R9  CAK  C   CH2   0  -0.439  -2.0873  -0.3076  -1.2618
 9R9  CAL  C   CH2   0  -0.432  -3.5653  -0.6845  -1.2580
 9R9  CAM  C   CH2   0  -0.436  -4.2627  -0.1637  -0.0072
 9R9  CAN  C   CH2   0  -0.427  -3.5767  -0.6699   1.2557
 9R9  CAO  C   CH2   0  -0.476  -2.1005  -0.2857   1.2677
 9R9  CAJ  C   CT    0   0.162  -1.3575  -0.7654   0.0091
 9R9  OAP  O   OH1   0  -0.668  -1.3649  -2.1762  -0.0341
 9R9  CAF  C   CR6   0   0.113   0.0694  -0.2312   0.0060
 9R9  CAE  C   CR56  0  -0.121   0.3580   1.1520   0.0285
 9R9  CAI  C   CR15  0  -0.152  -0.3886   2.3661   0.0424
 9R9  NAH  N   N     0  -0.227   0.4036   3.4070   0.0540
 9R9  NAG  N   NR15  0  -0.546   1.6518   2.9404   0.0482
 9R9  CAD  C   CR56  0   0.433   1.6953   1.5909   0.0304
 9R9  CAC  C   CR16  0  -0.280   2.7889   0.7199   0.0110
 9R9  CAB  C   CR6   0  -0.026   2.4691  -0.6120  -0.0188
 9R9  CLA  CL  CL    0  -0.128   3.7516  -1.7815  -0.0520
 9R9  CAA  C   CR16  0  -0.330   1.1452  -1.0918  -0.0257
 9R9  H1   H   HCH2  0   0.242  -1.5805  -0.7327  -2.1326
 9R9  H2   H   HCH2  0   0.233  -1.9969   0.7764  -1.3586
 9R9  H3   H   HCH2  0   0.230  -4.0384  -0.2739  -2.1532
 9R9  H4   H   HCH2  0   0.220  -3.6770  -1.7699  -1.3206
 9R9  H5   H   HCH2  0   0.210  -4.2388   0.9321  -0.0128
 9R9  H6   H   HCH2  0   0.232  -5.3164  -0.4516  -0.0100
 9R9  H7   H   HCH2  0   0.232  -4.0588  -0.2527   2.1428
 9R9  H8   H   HCH2  0   0.217  -3.6871  -1.7552   1.3294
 9R9  H9   H   HCH2  0   0.234  -2.0181   0.7990   1.3580
 9R9  H10  H   HCH2  0   0.245  -1.6014  -0.6930   2.1536
 9R9  H11  H   HOH1  0   0.449  -1.1593  -2.5199   0.8426
 9R9  H12  H   HCR5  0   0.262  -1.4581   2.5103   0.0398
 9R9  H14  H   HCR6  0   0.291   3.8108   1.0730   0.0161
 9R9  H15  H   HCR6  0   0.265   0.9874  -2.1597  -0.0637
 9R9  H13  H   HNR5  0   0.420   2.4269   3.5828   0.0553

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
 9R9  OAP  CAJ  single    1.411  0.020  1.411
 9R9  CAL  CAM  single    1.524  0.020  1.524
 9R9  CAL  CAK  single    1.525  0.020  1.525
 9R9  CAN  CAM  single    1.524  0.020  1.524
 9R9  CAN  CAO  single    1.525  0.020  1.525
 9R9  CAK  CAJ  single    1.535  0.020  1.535
 9R9  CAJ  CAO  single    1.538  0.020  1.538
 9R9  CAJ  CAF  single    1.524  0.020  1.524
 9R9  CAA  CAF  aromatic  1.378  0.020  1.378
 9R9  CAA  CAB  aromatic  1.408  0.020  1.408
 9R9  CAF  CAE  aromatic  1.413  0.020  1.413
 9R9  CLA  CAB  single    1.736  0.020  1.736
 9R9  CAB  CAC  aromatic  1.370  0.020  1.370
 9R9  CAE  CAI  aromatic  1.425  0.020  1.425
 9R9  CAE  CAD  aromatic  1.407  0.020  1.407
 9R9  CAI  NAH  aromatic  1.308  0.020  1.308
 9R9  CAC  CAD  aromatic  1.398  0.020  1.398
 9R9  CAD  NAG  aromatic  1.350  0.020  1.350
 9R9  NAH  NAG  aromatic  1.333  0.020  1.333
 9R9  CAK  H1   single    0.970  0.020  1.090
 9R9  CAK  H2   single    0.970  0.020  1.090
 9R9  CAL  H3   single    0.970  0.020  1.090
 9R9  CAL  H4   single    0.970  0.020  1.090
 9R9  CAM  H5   single    0.970  0.020  1.090
 9R9  CAM  H6   single    0.970  0.020  1.090
 9R9  CAN  H7   single    0.970  0.020  1.090
 9R9  CAN  H8   single    0.970  0.020  1.090
 9R9  CAO  H9   single    0.970  0.020  1.090
 9R9  CAO  H10  single    0.970  0.020  1.090
 9R9  OAP  H11  single    0.850  0.020  0.980
 9R9  CAI  H12  single    0.930  0.020  1.080
 9R9  CAC  H14  single    0.930  0.020  1.080
 9R9  CAA  H15  single    0.930  0.020  1.080
 9R9  NAG  H13  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
 9R9  H2   CAK  H1   106.08  3.000
 9R9  H2   CAK  CAJ  109.27  3.000
 9R9  H1   CAK  CAJ  108.85  3.000
 9R9  H2   CAK  CAL  109.01  3.000
 9R9  H1   CAK  CAL  110.79  3.000
 9R9  CAJ  CAK  CAL  112.63  3.000
 9R9  H4   CAL  H3   106.38  3.000
 9R9  H4   CAL  CAM  109.86  3.000
 9R9  H3   CAL  CAM  110.24  3.000
 9R9  H4   CAL  CAK  110.14  3.000
 9R9  H3   CAL  CAK  108.95  3.000
 9R9  CAM  CAL  CAK  111.17  3.000
 9R9  H6   CAM  H5   106.54  3.000
 9R9  H6   CAM  CAN  110.42  3.000
 9R9  H5   CAM  CAN  109.06  3.000
 9R9  H6   CAM  CAL  110.44  3.000
 9R9  H5   CAM  CAL  109.11  3.000
 9R9  CAN  CAM  CAL  111.14  3.000
 9R9  H8   CAN  H7   106.25  3.000
 9R9  H8   CAN  CAO  110.31  3.000
 9R9  H7   CAN  CAO  108.94  3.000
 9R9  H8   CAN  CAM  109.88  3.000
 9R9  H7   CAN  CAM  110.33  3.000
 9R9  CAO  CAN  CAM  111.01  3.000
 9R9  H10  CAO  H9   105.56  3.000
 9R9  H10  CAO  CAJ  109.01  3.000
 9R9  H9   CAO  CAJ  109.94  3.000
 9R9  H10  CAO  CAN  110.71  3.000
 9R9  H9   CAO  CAN  108.90  3.000
 9R9  CAJ  CAO  CAN  112.49  3.000
 9R9  CAF  CAJ  OAP  110.81  3.000
 9R9  CAF  CAJ  CAO  110.17  3.000
 9R9  OAP  CAJ  CAO  109.52  3.000
 9R9  CAF  CAJ  CAK  109.81  3.000
 9R9  CAO  CAJ  CAK  110.78  3.000
 9R9  OAP  CAJ  CAK  105.68  3.000
 9R9  H11  OAP  CAJ  109.12  3.000
 9R9  CAA  CAF  CAE  116.89  3.000
 9R9  CAE  CAF  CAJ  122.30  3.000
 9R9  CAA  CAF  CAJ  120.81  3.000
 9R9  CAD  CAE  CAI  103.42  3.000
 9R9  CAD  CAE  CAF  119.95  3.000
 9R9  CAI  CAE  CAF  136.63  3.000
 9R9  H12  CAI  NAH  119.59  3.000
 9R9  H12  CAI  CAE  129.27  3.000
 9R9  NAH  CAI  CAE  111.14  3.000
 9R9  NAG  NAH  CAI  106.77  3.000
 9R9  H13  NAG  CAD  127.80  3.000
 9R9  H13  NAG  NAH  119.85  3.000
 9R9  CAD  NAG  NAH  112.35  3.000
 9R9  CAC  CAD  NAG  130.39  3.000
 9R9  NAG  CAD  CAE  106.32  3.000
 9R9  CAC  CAD  CAE  123.29  3.000
 9R9  H14  CAC  CAB  122.56  3.000
 9R9  H14  CAC  CAD  122.39  3.000
 9R9  CAB  CAC  CAD  115.05  3.000
 9R9  CAA  CAB  CLA  117.70  3.000
 9R9  CLA  CAB  CAC  118.88  3.000
 9R9  CAA  CAB  CAC  123.42  3.000
 9R9  H15  CAA  CAB  118.32  3.000
 9R9  H15  CAA  CAF  120.27  3.000
 9R9  CAB  CAA  CAF  121.40  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
 9R9  CONST_01  CAC  CAB  CAA  CAF    0.00   0.0  0
 9R9  CONST_02  NAH  CAI  CAE  CAF  180.00   0.0  0
 9R9  CONST_03  CAC  CAD  CAE  CAF    0.00   0.0  0
 9R9  CONST_04  NAG  CAD  CAE  CAF  180.00   0.0  0
 9R9  CONST_05  CAB  CAA  CAF  CAE    0.00   0.0  0
 9R9  CONST_06  NAG  NAH  CAI  CAE    0.00   0.0  0
 9R9  CONST_07  CAB  CAC  CAD  CAE    0.00   0.0  0
 9R9  CONST_08  NAH  NAG  CAD  CAE    0.00   0.0  0
 9R9  CONST_09  CAA  CAF  CAE  CAI  180.00   0.0  0
 9R9  CONST_10  CAC  CAD  CAE  CAI  180.00   0.0  0
 9R9  CONST_11  NAG  CAD  CAE  CAI    0.00   0.0  0
 9R9  CONST_12  CAD  NAG  NAH  CAI    0.00   0.0  0
 9R9  CONST_13  CAD  CAE  CAI  NAH    0.00   0.0  0
 9R9  CONST_14  CAC  CAD  NAG  NAH  180.00   0.0  0
 9R9  CONST_15  CAB  CAC  CAD  NAG  180.00   0.0  0
 9R9  CONST_16  CAA  CAF  CAE  CAD    0.00   0.0  0
 9R9  CONST_17  CAA  CAB  CAC  CAD    0.00   0.0  0
 9R9  CONST_18  CAB  CAA  CAF  CAJ  180.00   0.0  0
 9R9  CONST_19  CAI  CAE  CAF  CAJ    0.00   0.0  0
 9R9  CONST_20  CAD  CAE  CAF  CAJ  180.00   0.0  0
 9R9  CONST_21  CLA  CAB  CAA  CAF  180.00   0.0  0
 9R9  CONST_22  CLA  CAB  CAC  CAD  180.00   0.0  0
 9R9  CONST_23  H15  CAA  CAF  CAJ    0.00   0.0  0
 9R9  CONST_24  H12  CAI  CAE  CAF    0.00   0.0  0
 9R9  CONST_25  H14  CAC  CAD  CAE  180.00   0.0  0
 9R9  CONST_26  H13  NAG  CAD  CAE  180.00   0.0  0
 9R9  Var_01    CAN  CAM  CAL  CAK  -56.32  30.0  1
 9R9  Var_02    CAO  CAN  CAM  CAL   56.56  30.0  1
 9R9  Var_03    CAJ  CAK  CAL  CAM   54.57  30.0  1
 9R9  Var_04    CAJ  CAO  CAN  CAM  -55.04  30.0  1

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
 9R9  chir_01  CAJ  CAK  CAO  CAF  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
 9R9  plan-1  CAJ  0.020
 9R9  plan-1  CAF  0.020
 9R9  plan-1  CAE  0.020
 9R9  plan-1  CAI  0.020
 9R9  plan-1  NAH  0.020
 9R9  plan-1  NAG  0.020
 9R9  plan-1  CAD  0.020
 9R9  plan-1  CAC  0.020
 9R9  plan-1  CAB  0.020
 9R9  plan-1  CLA  0.020
 9R9  plan-1  CAA  0.020
 9R9  plan-1  H12  0.020
 9R9  plan-1  H14  0.020
 9R9  plan-1  H15  0.020
 9R9  plan-1  H13  0.020

