# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:05:24 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 1-cyclohexyl-2-[(5~{S})-6-fluoranyl-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc2c3cncn3[C@@H](CC(=O)C4CCCCC4)c12
#
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
 5PJ  5PJ  1-cyclohexyl-2-[(5~{S})-6-fluoranyl-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanone  ligand  41  22  .  2022-07-23  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_5PJ
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
 5PJ  CAB  C  CH2   0  -0.433   3.3519  -1.3517  -0.2519
 5PJ  CAC  C  CH2   0  -0.430   4.5845  -1.9069   0.4546
 5PJ  CAD  C  CH2   0  -0.430   5.7130  -0.8837   0.5034
 5PJ  CAE  C  CH2   0  -0.438   5.2464   0.4181   1.1455
 5PJ  CAF  C  CH2   0  -0.416   4.0211   0.9836   0.4348
 5PJ  CAA  C  CH1   0  -0.361   2.8866  -0.0373   0.4034
 5PJ  CAG  C  C     0   0.435   1.6597   0.4772  -0.3123
 5PJ  OAJ  O  O     0  -0.403   1.7039   1.3797  -1.1181
 5PJ  CAH  C  CH2   0  -0.566   0.3623  -0.2291   0.0072
 5PJ  CAI  C  CR15  0  -0.103  -0.8636   0.3645  -0.6762
 5PJ  CAN  C  CR56  0  -0.120  -2.1067  -0.4661  -0.4541
 5PJ  CAU  C  CR6   0   0.531  -2.3862  -1.7503  -0.8567
 5PJ  FAV  F  F     0  -0.305  -1.4746  -2.4294  -1.5699
 5PJ  CAT  C  CR16  0  -0.417  -3.5917  -2.3553  -0.5416
 5PJ  CAS  C  CR16  0  -0.240  -4.5336  -1.6417   0.1906
 5PJ  CAR  C  CR16  0  -0.377  -4.2896  -0.3373   0.6039
 5PJ  CAM  C  CR56  0   0.020  -3.0740   0.2395   0.2718
 5PJ  CAL  C  CR55  0   0.395  -2.5323   1.5579   0.5144
 5PJ  NAK  N  N     0  -0.499  -1.2911   1.6186  -0.0606
 5PJ  CAO  C  CR15  0   0.099  -0.8074   2.8579   0.1449
 5PJ  NAP  N  N     0  -0.449  -1.6678   3.5893   0.8175
 5PJ  CAQ  C  CR15  0  -0.287  -2.7517   2.7941   1.0580
 5PJ  H1   H  HCH2  0   0.229   3.5856  -1.1651  -1.3053
 5PJ  H2   H  HCH2  0   0.244   2.5514  -2.0948  -0.2318
 5PJ  H3   H  HCH2  0   0.216   4.3119  -2.1981   1.4744
 5PJ  H4   H  HCH2  0   0.235   4.9138  -2.8171  -0.0515
 5PJ  H5   H  HCH2  0   0.230   6.5671  -1.2898   1.0503
 5PJ  H6   H  HCH2  0   0.211   6.0634  -0.6803  -0.5147
 5PJ  H7   H  HCH2  0   0.213   5.0065   0.2392   2.1992
 5PJ  H8   H  HCH2  0   0.232   6.0514   1.1562   1.1333
 5PJ  H9   H  HCH2  0   0.237   3.6891   1.8983   0.9319
 5PJ  H10  H  HCH2  0   0.220   4.2925   1.2618  -0.5874
 5PJ  H11  H  HCH1  0   0.254   2.5893  -0.2763   1.4325
 5PJ  H12  H  HCH2  0   0.298   0.4774  -1.2749  -0.2913
 5PJ  H13  H  HCH2  0   0.300   0.2191  -0.2511   1.0912
 5PJ  H14  H  HCR5  0   0.312  -0.6731   0.5174  -1.7410
 5PJ  H15  H  HCR6  0   0.285  -3.7923  -3.3666  -0.8690
 5PJ  H16  H  HCR6  0   0.274  -5.4750  -2.1141   0.4364
 5PJ  H17  H  HCR6  0   0.259  -5.0336   0.2113   1.1653
 5PJ  H18  H  HCR5  0   0.286   0.1535   3.1888  -0.2120
 5PJ  H19  H  HCR5  0   0.260  -3.6171   3.1495   1.5955

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
 5PJ  CAD  CAE  single    1.525  0.020  1.525
 5PJ  CAD  CAC  single    1.524  0.020  1.524
 5PJ  CAE  CAF  single    1.525  0.020  1.525
 5PJ  CAC  CAB  single    1.525  0.020  1.525
 5PJ  CAF  CAA  single    1.527  0.020  1.527
 5PJ  CAB  CAA  single    1.541  0.020  1.541
 5PJ  CAA  CAG  single    1.511  0.020  1.511
 5PJ  CAG  OAJ  double    1.211  0.020  1.211
 5PJ  CAG  CAH  single    1.511  0.020  1.511
 5PJ  CAH  CAI  single    1.524  0.020  1.524
 5PJ  CAO  NAK  aromatic  1.346  0.020  1.346
 5PJ  CAO  NAP  aromatic  1.314  0.020  1.314
 5PJ  CAI  NAK  single    1.461  0.020  1.461
 5PJ  CAI  CAN  single    1.511  0.020  1.511
 5PJ  NAK  CAL  aromatic  1.369  0.020  1.369
 5PJ  FAV  CAU  single    1.342  0.020  1.342
 5PJ  NAP  CAQ  aromatic  1.366  0.020  1.366
 5PJ  CAN  CAU  aromatic  1.375  0.020  1.375
 5PJ  CAN  CAM  aromatic  1.400  0.020  1.400
 5PJ  CAU  CAT  aromatic  1.385  0.020  1.385
 5PJ  CAL  CAQ  aromatic  1.368  0.020  1.368
 5PJ  CAL  CAM  aromatic  1.446  0.020  1.446
 5PJ  CAM  CAR  aromatic  1.386  0.020  1.386
 5PJ  CAT  CAS  aromatic  1.390  0.020  1.390
 5PJ  CAR  CAS  aromatic  1.390  0.020  1.390
 5PJ  CAB  H1   single    0.970  0.020  1.090
 5PJ  CAB  H2   single    0.970  0.020  1.090
 5PJ  CAC  H3   single    0.970  0.020  1.090
 5PJ  CAC  H4   single    0.970  0.020  1.090
 5PJ  CAD  H5   single    0.970  0.020  1.090
 5PJ  CAD  H6   single    0.970  0.020  1.090
 5PJ  CAE  H7   single    0.970  0.020  1.090
 5PJ  CAE  H8   single    0.970  0.020  1.090
 5PJ  CAF  H9   single    0.970  0.020  1.090
 5PJ  CAF  H10  single    0.970  0.020  1.090
 5PJ  CAA  H11  single    0.970  0.020  1.090
 5PJ  CAH  H12  single    0.970  0.020  1.090
 5PJ  CAH  H13  single    0.970  0.020  1.090
 5PJ  CAI  H14  single    0.970  0.020  1.090
 5PJ  CAT  H15  single    0.930  0.020  1.080
 5PJ  CAS  H16  single    0.930  0.020  1.080
 5PJ  CAR  H17  single    0.930  0.020  1.080
 5PJ  CAO  H18  single    0.930  0.020  1.080
 5PJ  CAQ  H19  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
 5PJ  H2   CAB  H1   106.86  3.000
 5PJ  H2   CAB  CAA  110.56  3.000
 5PJ  H1   CAB  CAA  109.16  3.000
 5PJ  H2   CAB  CAC  109.63  3.000
 5PJ  H1   CAB  CAC  109.59  3.000
 5PJ  CAA  CAB  CAC  110.95  3.000
 5PJ  H4   CAC  H3   106.56  3.000
 5PJ  H4   CAC  CAD  110.55  3.000
 5PJ  H3   CAC  CAD  109.46  3.000
 5PJ  H4   CAC  CAB  109.40  3.000
 5PJ  H3   CAC  CAB  109.09  3.000
 5PJ  CAD  CAC  CAB  111.64  3.000
 5PJ  H6   CAD  H5   106.51  3.000
 5PJ  H6   CAD  CAE  109.31  3.000
 5PJ  H5   CAD  CAE  110.23  3.000
 5PJ  H6   CAD  CAC  109.37  3.000
 5PJ  H5   CAD  CAC  110.20  3.000
 5PJ  CAE  CAD  CAC  111.10  3.000
 5PJ  H8   CAE  H7   106.41  3.000
 5PJ  H8   CAE  CAF  109.65  3.000
 5PJ  H7   CAE  CAF  109.44  3.000
 5PJ  H8   CAE  CAD  110.28  3.000
 5PJ  H7   CAE  CAD  109.43  3.000
 5PJ  CAF  CAE  CAD  111.48  3.000
 5PJ  H10  CAF  H9   106.72  3.000
 5PJ  H10  CAF  CAA  109.59  3.000
 5PJ  H9   CAF  CAA  110.08  3.000
 5PJ  H10  CAF  CAE  109.30  3.000
 5PJ  H9   CAF  CAE  110.03  3.000
 5PJ  CAA  CAF  CAE  111.02  3.000
 5PJ  H11  CAA  CAG  107.36  3.000
 5PJ  H11  CAA  CAF  109.12  3.000
 5PJ  CAG  CAA  CAF  112.68  3.000
 5PJ  H11  CAA  CAB  107.15  3.000
 5PJ  CAG  CAA  CAB  109.54  3.000
 5PJ  CAF  CAA  CAB  110.78  3.000
 5PJ  CAH  CAG  OAJ  121.36  3.000
 5PJ  CAH  CAG  CAA  115.97  3.000
 5PJ  OAJ  CAG  CAA  122.65  3.000
 5PJ  H13  CAH  H12  105.37  3.000
 5PJ  H13  CAH  CAI  110.31  3.000
 5PJ  H12  CAH  CAI  109.56  3.000
 5PJ  H13  CAH  CAG  109.35  3.000
 5PJ  H12  CAH  CAG  107.39  3.000
 5PJ  CAI  CAH  CAG  114.44  3.000
 5PJ  H14  CAI  NAK  109.97  3.000
 5PJ  H14  CAI  CAN  111.32  3.000
 5PJ  NAK  CAI  CAN   99.73  3.000
 5PJ  H14  CAI  CAH  110.57  3.000
 5PJ  CAN  CAI  CAH  112.44  3.000
 5PJ  NAK  CAI  CAH  112.38  3.000
 5PJ  CAM  CAN  CAU  118.83  3.000
 5PJ  CAM  CAN  CAI  111.56  3.000
 5PJ  CAU  CAN  CAI  129.61  3.000
 5PJ  CAT  CAU  FAV  119.41  3.000
 5PJ  CAT  CAU  CAN  121.22  3.000
 5PJ  FAV  CAU  CAN  119.36  3.000
 5PJ  H15  CAT  CAS  120.91  3.000
 5PJ  H15  CAT  CAU  120.06  3.000
 5PJ  CAS  CAT  CAU  119.03  3.000
 5PJ  H16  CAS  CAR  119.68  3.000
 5PJ  H16  CAS  CAT  119.03  3.000
 5PJ  CAR  CAS  CAT  121.30  3.000
 5PJ  H17  CAR  CAM  121.11  3.000
 5PJ  H17  CAR  CAS  120.64  3.000
 5PJ  CAM  CAR  CAS  118.24  3.000
 5PJ  CAL  CAM  CAR  131.90  3.000
 5PJ  CAR  CAM  CAN  121.36  3.000
 5PJ  CAL  CAM  CAN  106.72  3.000
 5PJ  CAQ  CAL  NAK  105.79  3.000
 5PJ  CAQ  CAL  CAM  146.15  3.000
 5PJ  NAK  CAL  CAM  108.04  3.000
 5PJ  CAO  NAK  CAL  107.61  3.000
 5PJ  CAL  NAK  CAI  113.84  3.000
 5PJ  CAO  NAK  CAI  138.54  3.000
 5PJ  H18  CAO  NAP  125.63  3.000
 5PJ  H18  CAO  NAK  123.56  3.000
 5PJ  NAP  CAO  NAK  110.80  3.000
 5PJ  CAQ  NAP  CAO  106.60  3.000
 5PJ  H19  CAQ  NAP  122.18  3.000
 5PJ  H19  CAQ  CAL  128.62  3.000
 5PJ  NAP  CAQ  CAL  109.20  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
 5PJ  CONST_01  CAS  CAT  CAU  CAN    0.00   0.0  0
 5PJ  CONST_02  NAK  CAL  CAM  CAN    0.00   0.0  0
 5PJ  CONST_03  CAQ  CAL  CAM  CAN  180.00   0.0  0
 5PJ  CONST_04  CAS  CAR  CAM  CAN    0.00   0.0  0
 5PJ  CONST_05  CAL  CAM  CAN  CAU  180.00   0.0  0
 5PJ  CONST_06  CAR  CAM  CAN  CAU    0.00   0.0  0
 5PJ  CONST_07  CAR  CAS  CAT  CAU    0.00   0.0  0
 5PJ  CONST_08  CAM  CAN  CAU  CAT    0.00   0.0  0
 5PJ  CONST_09  CAM  CAR  CAS  CAT    0.00   0.0  0
 5PJ  CONST_10  CAL  CAM  CAR  CAS  180.00   0.0  0
 5PJ  CONST_11  NAK  CAL  CAM  CAR  180.00   0.0  0
 5PJ  CONST_12  CAQ  CAL  CAM  CAR    0.00   0.0  0
 5PJ  CONST_13  CAO  NAK  CAL  CAM  180.00   0.0  0
 5PJ  CONST_14  NAP  CAQ  CAL  CAM  180.00   0.0  0
 5PJ  CONST_15  NAP  CAO  NAK  CAL    0.00   0.0  0
 5PJ  CONST_16  CAO  NAP  CAQ  CAL    0.00   0.0  0
 5PJ  CONST_17  CAQ  NAP  CAO  NAK    0.00   0.0  0
 5PJ  CONST_18  NAP  CAQ  CAL  NAK    0.00   0.0  0
 5PJ  CONST_19  CAQ  CAL  NAK  CAO    0.00   0.0  0
 5PJ  CONST_20  FAV  CAU  CAN  CAI    0.00   0.0  0
 5PJ  CONST_21  CAM  CAN  CAU  FAV  180.00   0.0  0
 5PJ  CONST_22  CAS  CAT  CAU  FAV  180.00   0.0  0
 5PJ  CONST_23  H18  CAO  NAK  CAI    0.00   0.0  0
 5PJ  CONST_24  H15  CAT  CAU  CAN  180.00   0.0  0
 5PJ  CONST_25  H17  CAR  CAM  CAN  180.00   0.0  0
 5PJ  CONST_26  H16  CAS  CAT  CAU  180.00   0.0  0
 5PJ  CONST_27  H19  CAQ  CAL  CAM    0.00   0.0  0
 5PJ  Var_01    CAE  CAD  CAC  CAB   55.13  30.0  1
 5PJ  Var_02    CAF  CAE  CAD  CAC  -55.43  30.0  1
 5PJ  Var_03    CAA  CAF  CAE  CAD   56.18  30.0  1
 5PJ  Var_04    CAA  CAB  CAC  CAD  -55.27  30.0  1
 5PJ  Var_05    CAI  CAH  CAG  CAA  176.91  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
 5PJ  chir_01  CAA  CAF  CAB  CAG  positiv
 5PJ  chir_02  CAI  NAK  CAH  CAN  negativ

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
 5PJ  plan-1  CAA  0.020
 5PJ  plan-1  CAG  0.020
 5PJ  plan-1  OAJ  0.020
 5PJ  plan-1  CAH  0.020
 5PJ  plan-2  CAI  0.020
 5PJ  plan-2  CAN  0.020
 5PJ  plan-2  CAU  0.020
 5PJ  plan-2  FAV  0.020
 5PJ  plan-2  CAT  0.020
 5PJ  plan-2  CAS  0.020
 5PJ  plan-2  CAR  0.020
 5PJ  plan-2  CAM  0.020
 5PJ  plan-2  CAL  0.020
 5PJ  plan-2  NAK  0.020
 5PJ  plan-2  CAO  0.020
 5PJ  plan-2  NAP  0.020
 5PJ  plan-2  CAQ  0.020
 5PJ  plan-2  H15  0.020
 5PJ  plan-2  H16  0.020
 5PJ  plan-2  H17  0.020
 5PJ  plan-2  H18  0.020
 5PJ  plan-2  H19  0.020

