# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:00:59 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](C[C@@H]1n2cncc2c3ccccc13)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
 5PK  5PK  (1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol  ligand  43  21  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5PK
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
 5PK  CAA  C  CH2   0  -0.434  -2.8417  -0.4953   1.3536
 5PK  CAF  C  CH2   0  -0.426  -4.1994  -0.9593   1.8750
 5PK  CAE  C  CH2   0  -0.429  -5.3423  -0.1441   1.2836
 5PK  CAD  C  CH2   0  -0.432  -5.2933  -0.1750  -0.2388
 5PK  CAC  C  CH2   0  -0.409  -3.9404   0.2976  -0.7601
 5PK  CAB  C  CH1   0  -0.267  -2.7788  -0.5118  -0.1763
 5PK  CAG  C  CH1   0   0.074  -1.4332   0.0018  -0.7032
 5PK  OAI  O  OH1   0  -0.671  -1.4045   0.0504  -2.1172
 5PK  CAH  C  CH2   0  -0.482  -0.2507  -0.7981  -0.1607
 5PK  CAJ  C  CR15  0  -0.103   1.0950  -0.4560  -0.8089
 5PK  CAK  C  CR56  0   0.104   1.6103   0.9431  -0.5387
 5PK  CAR  C  CR16  0  -0.317   1.1005   2.1563  -0.9621
 5PK  CAS  C  CR16  0  -0.255   1.7480   3.3280  -0.5764
 5PK  CAT  C  CR16  0  -0.255   2.8938   3.2818   0.2100
 5PK  CAU  C  CR16  0  -0.360   3.4270   2.0645   0.6174
 5PK  CAL  C  CR56  0  -0.017   2.7813   0.8997   0.2328
 5PK  CAM  C  CR55  0   0.399   3.1053  -0.4939   0.4502
 5PK  NAN  N  N     0  -0.495   2.1560  -1.2418  -0.1862
 5PK  CAQ  C  CR15  0   0.094   2.4530  -2.5380   0.0049
 5PK  NAP  N  N     0  -0.453   3.5485  -2.6645   0.7213
 5PK  CAO  C  CR15  0  -0.296   3.9708  -1.3968   1.0092
 5PK  H1   H  HCH2  0   0.210  -2.6408   0.5221   1.7115
 5PK  H2   H  HCH2  0   0.235  -2.0630  -1.1317   1.7790
 5PK  H3   H  HCH2  0   0.209  -4.3382  -2.0152   1.6181
 5PK  H4   H  HCH2  0   0.227  -4.2142  -0.9023   2.9662
 5PK  H5   H  HCH2  0   0.226  -6.3032  -0.5189   1.6445
 5PK  H6   H  HCH2  0   0.207  -5.2629   0.8939   1.6253
 5PK  H7   H  HCH2  0   0.208  -5.4822  -1.1962  -0.5881
 5PK  H8   H  HCH2  0   0.225  -6.0888   0.4458  -0.6587
 5PK  H9   H  HCH2  0   0.229  -3.9272   0.2470  -1.8501
 5PK  H10  H  HCH2  0   0.204  -3.8032   1.3538  -0.4963
 5PK  H11  H  HCH1  0   0.211  -2.8896  -1.5576  -0.5025
 5PK  H12  H  HCH1  0   0.228  -1.3253   1.0431  -0.3809
 5PK  H13  H  HOH1  0   0.444  -1.5458  -0.8406  -2.4566
 5PK  H14  H  HCH2  0   0.254  -0.1594  -0.6410   0.9159
 5PK  H15  H  HCH2  0   0.248  -0.4338  -1.8691  -0.3080
 5PK  H16  H  HCR5  0   0.294   1.0661  -0.6644  -1.8801
 5PK  H17  H  HCR6  0   0.261   0.2241   2.2059  -1.5945
 5PK  H18  H  HCR6  0   0.260   1.3558   4.2842  -0.8962
 5PK  H19  H  HCR6  0   0.261   3.3835   4.2031   0.4970
 5PK  H20  H  HCR6  0   0.252   4.3299   2.0302   1.2133
 5PK  H21  H  HCR5  0   0.284   1.8589  -3.3474  -0.3907
 5PK  H22  H  HCR5  0   0.256   4.8597  -1.2083   1.5911

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
 5PK  CAU  CAT  aromatic  1.390  0.020  1.390
 5PK  CAU  CAL  aromatic  1.386  0.020  1.386
 5PK  CAT  CAS  aromatic  1.390  0.020  1.390
 5PK  CAO  CAM  aromatic  1.370  0.020  1.370
 5PK  CAO  NAP  aromatic  1.367  0.020  1.367
 5PK  CAL  CAM  aromatic  1.447  0.020  1.447
 5PK  CAL  CAK  aromatic  1.403  0.020  1.403
 5PK  CAM  NAN  aromatic  1.366  0.020  1.366
 5PK  NAP  CAQ  aromatic  1.315  0.020  1.315
 5PK  CAS  CAR  aromatic  1.393  0.020  1.393
 5PK  CAK  CAR  aromatic  1.382  0.020  1.382
 5PK  CAK  CAJ  single    1.515  0.020  1.515
 5PK  NAN  CAQ  aromatic  1.343  0.020  1.343
 5PK  NAN  CAJ  single    1.460  0.020  1.460
 5PK  CAJ  CAH  single    1.532  0.020  1.532
 5PK  CAH  CAG  single    1.527  0.020  1.527
 5PK  OAI  CAG  single    1.415  0.020  1.415
 5PK  CAG  CAB  single    1.534  0.020  1.534
 5PK  CAC  CAB  single    1.531  0.020  1.531
 5PK  CAC  CAD  single    1.525  0.020  1.525
 5PK  CAB  CAA  single    1.531  0.020  1.531
 5PK  CAD  CAE  single    1.523  0.020  1.523
 5PK  CAA  CAF  single    1.527  0.020  1.527
 5PK  CAE  CAF  single    1.523  0.020  1.523
 5PK  CAA  H1   single    0.970  0.020  1.090
 5PK  CAA  H2   single    0.970  0.020  1.090
 5PK  CAF  H3   single    0.970  0.020  1.090
 5PK  CAF  H4   single    0.970  0.020  1.090
 5PK  CAE  H5   single    0.970  0.020  1.090
 5PK  CAE  H6   single    0.970  0.020  1.090
 5PK  CAD  H7   single    0.970  0.020  1.090
 5PK  CAD  H8   single    0.970  0.020  1.090
 5PK  CAC  H9   single    0.970  0.020  1.090
 5PK  CAC  H10  single    0.970  0.020  1.090
 5PK  CAB  H11  single    0.970  0.020  1.090
 5PK  CAG  H12  single    0.970  0.020  1.090
 5PK  OAI  H13  single    0.850  0.020  0.980
 5PK  CAH  H14  single    0.970  0.020  1.090
 5PK  CAH  H15  single    0.970  0.020  1.090
 5PK  CAJ  H16  single    0.970  0.020  1.090
 5PK  CAR  H17  single    0.930  0.020  1.080
 5PK  CAS  H18  single    0.930  0.020  1.080
 5PK  CAT  H19  single    0.930  0.020  1.080
 5PK  CAU  H20  single    0.930  0.020  1.080
 5PK  CAQ  H21  single    0.930  0.020  1.080
 5PK  CAO  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
 5PK  H2   CAA  H1   106.43  3.000
 5PK  H2   CAA  CAB  110.71  3.000
 5PK  H1   CAA  CAB  109.17  3.000
 5PK  H2   CAA  CAF  108.90  3.000
 5PK  H1   CAA  CAF  109.47  3.000
 5PK  CAB  CAA  CAF  112.00  3.000
 5PK  H4   CAF  H3   106.42  3.000
 5PK  H4   CAF  CAE  110.46  3.000
 5PK  H3   CAF  CAE  109.24  3.000
 5PK  H4   CAF  CAA  109.72  3.000
 5PK  H3   CAF  CAA  109.00  3.000
 5PK  CAE  CAF  CAA  111.84  3.000
 5PK  H6   CAE  H5   106.60  3.000
 5PK  H6   CAE  CAD  109.18  3.000
 5PK  H5   CAE  CAD  110.57  3.000
 5PK  H6   CAE  CAF  109.35  3.000
 5PK  H5   CAE  CAF  110.36  3.000
 5PK  CAD  CAE  CAF  110.67  3.000
 5PK  H8   CAD  H7   106.35  3.000
 5PK  H8   CAD  CAC  109.77  3.000
 5PK  H7   CAD  CAC  109.44  3.000
 5PK  H8   CAD  CAE  110.43  3.000
 5PK  H7   CAD  CAE  109.39  3.000
 5PK  CAC  CAD  CAE  111.34  3.000
 5PK  H10  CAC  H9   106.46  3.000
 5PK  H10  CAC  CAB  108.80  3.000
 5PK  H9   CAC  CAB  110.31  3.000
 5PK  H10  CAC  CAD  109.09  3.000
 5PK  H9   CAC  CAD  109.75  3.000
 5PK  CAB  CAC  CAD  112.26  3.000
 5PK  H11  CAB  CAG  107.73  3.000
 5PK  H11  CAB  CAC  108.23  3.000
 5PK  CAG  CAB  CAC  110.95  3.000
 5PK  H11  CAB  CAA  107.58  3.000
 5PK  CAC  CAB  CAA  110.12  3.000
 5PK  CAG  CAB  CAA  112.07  3.000
 5PK  H12  CAG  CAH  108.48  3.000
 5PK  H12  CAG  OAI  105.03  3.000
 5PK  CAH  CAG  OAI  110.93  3.000
 5PK  H12  CAG  CAB  107.68  3.000
 5PK  OAI  CAG  CAB  111.88  3.000
 5PK  CAH  CAG  CAB  112.45  3.000
 5PK  H13  OAI  CAG  108.49  3.000
 5PK  H15  CAH  H14  106.68  3.000
 5PK  H15  CAH  CAJ  107.93  3.000
 5PK  H14  CAH  CAJ  108.16  3.000
 5PK  H15  CAH  CAG  109.54  3.000
 5PK  H14  CAH  CAG  109.86  3.000
 5PK  CAJ  CAH  CAG  114.38  3.000
 5PK  H16  CAJ  NAN  109.57  3.000
 5PK  H16  CAJ  CAK  111.12  3.000
 5PK  NAN  CAJ  CAK  100.01  3.000
 5PK  H16  CAJ  CAH  110.44  3.000
 5PK  NAN  CAJ  CAH  109.73  3.000
 5PK  CAK  CAJ  CAH  115.42  3.000
 5PK  CAL  CAK  CAR  120.22  3.000
 5PK  CAR  CAK  CAJ  129.07  3.000
 5PK  CAL  CAK  CAJ  110.69  3.000
 5PK  H17  CAR  CAS  119.99  3.000
 5PK  H17  CAR  CAK  121.19  3.000
 5PK  CAS  CAR  CAK  118.81  3.000
 5PK  H18  CAS  CAT  119.69  3.000
 5PK  H18  CAS  CAR  119.54  3.000
 5PK  CAT  CAS  CAR  120.77  3.000
 5PK  H19  CAT  CAU  119.62  3.000
 5PK  H19  CAT  CAS  119.64  3.000
 5PK  CAU  CAT  CAS  120.73  3.000
 5PK  H20  CAU  CAL  120.98  3.000
 5PK  H20  CAU  CAT  120.60  3.000
 5PK  CAL  CAU  CAT  118.42  3.000
 5PK  CAM  CAL  CAU  131.54  3.000
 5PK  CAM  CAL  CAK  107.42  3.000
 5PK  CAU  CAL  CAK  121.02  3.000
 5PK  CAO  CAM  NAN  105.56  3.000
 5PK  NAN  CAM  CAL  107.56  3.000
 5PK  CAO  CAM  CAL  146.87  3.000
 5PK  CAQ  NAN  CAM  107.96  3.000
 5PK  CAQ  NAN  CAJ  137.79  3.000
 5PK  CAM  NAN  CAJ  114.15  3.000
 5PK  H21  CAQ  NAP  125.88  3.000
 5PK  H21  CAQ  NAN  123.36  3.000
 5PK  NAP  CAQ  NAN  110.76  3.000
 5PK  CAO  NAP  CAQ  106.43  3.000
 5PK  H22  CAO  NAP  122.02  3.000
 5PK  H22  CAO  CAM  128.71  3.000
 5PK  NAP  CAO  CAM  109.27  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
 5PK  CONST_01  CAT  CAU  CAL  CAK    0.00   0.0  0
 5PK  CONST_02  CAO  CAM  CAL  CAK  180.00   0.0  0
 5PK  CONST_03  NAN  CAM  CAL  CAK    0.00   0.0  0
 5PK  CONST_04  CAT  CAS  CAR  CAK    0.00   0.0  0
 5PK  CONST_05  CAU  CAT  CAS  CAR    0.00   0.0  0
 5PK  CONST_06  CAU  CAL  CAK  CAR    0.00   0.0  0
 5PK  CONST_07  CAM  CAL  CAK  CAR  180.00   0.0  0
 5PK  CONST_08  CAL  CAU  CAT  CAS    0.00   0.0  0
 5PK  CONST_09  CAL  CAK  CAR  CAS    0.00   0.0  0
 5PK  CONST_10  CAM  CAL  CAU  CAT  180.00   0.0  0
 5PK  CONST_11  CAO  CAM  CAL  CAU    0.00   0.0  0
 5PK  CONST_12  NAN  CAM  CAL  CAU  180.00   0.0  0
 5PK  CONST_13  NAP  CAO  CAM  CAL  180.00   0.0  0
 5PK  CONST_14  CAQ  NAN  CAM  CAL  180.00   0.0  0
 5PK  CONST_15  CAQ  NAP  CAO  CAM    0.00   0.0  0
 5PK  CONST_16  NAP  CAQ  NAN  CAM    0.00   0.0  0
 5PK  CONST_17  NAP  CAO  CAM  NAN    0.00   0.0  0
 5PK  CONST_18  CAO  NAP  CAQ  NAN    0.00   0.0  0
 5PK  CONST_19  CAO  CAM  NAN  CAQ    0.00   0.0  0
 5PK  CONST_20  H17  CAR  CAK  CAJ    0.00   0.0  0
 5PK  CONST_21  H21  CAQ  NAN  CAJ    0.00   0.0  0
 5PK  CONST_22  H20  CAU  CAL  CAK  180.00   0.0  0
 5PK  CONST_23  H18  CAS  CAR  CAK  180.00   0.0  0
 5PK  CONST_24  H19  CAT  CAS  CAR  180.00   0.0  0
 5PK  CONST_25  H22  CAO  CAM  CAL    0.00   0.0  0
 5PK  Var_01    CAD  CAE  CAF  CAA   55.24  30.0  1
 5PK  Var_02    CAC  CAD  CAE  CAF  -55.35  30.0  1
 5PK  Var_03    CAB  CAC  CAD  CAE   55.87  30.0  1
 5PK  Var_04    CAB  CAA  CAF  CAE  -55.24  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
 5PK  chir_01  CAB  CAG  CAC  CAA  positiv
 5PK  chir_02  CAG  OAI  CAB  CAH  negativ
 5PK  chir_03  CAJ  NAN  CAK  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
 5PK  plan-1  CAJ  0.020
 5PK  plan-1  CAK  0.020
 5PK  plan-1  CAR  0.020
 5PK  plan-1  CAS  0.020
 5PK  plan-1  CAT  0.020
 5PK  plan-1  CAU  0.020
 5PK  plan-1  CAL  0.020
 5PK  plan-1  CAM  0.020
 5PK  plan-1  NAN  0.020
 5PK  plan-1  CAQ  0.020
 5PK  plan-1  NAP  0.020
 5PK  plan-1  CAO  0.020
 5PK  plan-1  H17  0.020
 5PK  plan-1  H18  0.020
 5PK  plan-1  H19  0.020
 5PK  plan-1  H20  0.020
 5PK  plan-1  H21  0.020
 5PK  plan-1  H22  0.020

