# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:20:09 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-[(9bS)-5-oxo-2,3,5,9b-tetrahydro-1H-pyrrolo[2,1-a]isoindol-9-yl]-3-{5-[(2S)-pyrrolidin-2-yl]-1H-pyrazol-3-yl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cc([nH]n1)[C@@H]2CCCN2)Nc3cccc4C(=O)N5CCC[C@H]5c34
#
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
 2PU  2PU  1-[(9bS)-5-oxo-2,3,5,9b-tetrahydro-1H-pyrrolo[2,1-a]isoindol-9-yl]-3-{5-[(2S)-pyrrolidin-2-yl]-1H-pyrazol-3-yl}urea  ligand  49  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2PU
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
 2PU  C1    C  CR56  0   0.097  -0.4622  -0.3079  -3.4868
 2PU  C2    C  C     0  -0.120   0.9958  -0.2526  -3.8106
 2PU  C3    C  CR56  0  -0.098  -1.1938  -0.0276  -4.6292
 2PU  C4    C  CR6   0   0.300  -1.0954  -0.6103  -2.2885
 2PU  N5    N  N     0  -0.490   0.9929   0.0586  -5.2323
 2PU  C6    C  CH2   0  -0.434   1.8597   0.8659  -3.2303
 2PU  C7    C  CR5   0   0.525  -0.2494   0.2896  -5.7266
 2PU  C8    C  CR16  0  -0.319  -2.5770   0.0074  -4.6259
 2PU  C9    C  CR16  0  -0.284  -2.4918  -0.5940  -2.2774
 2PU  N10   N  NH1   0  -0.801  -0.3192  -0.9487  -1.1773
 2PU  C11   C  CH2   0  -0.268   2.1982   0.7672  -5.6382
 2PU  C12   C  CH2   0  -0.500   2.9380   1.0083  -4.3093
 2PU  O13   O  O     0  -0.471  -0.5159   0.7100  -6.8387
 2PU  C14   C  CR16  0  -0.265  -3.2131  -0.2813  -3.4266
 2PU  C15   C  C     0   0.727  -0.5846  -0.5699   0.1148
 2PU  N16   N  NH1   0  -0.772   0.3456  -1.0200   1.0015
 2PU  O17   O  O     0  -0.495  -1.5520   0.0986   0.4295
 2PU  C18   C  CR5   0   0.471   0.3465  -0.7717   2.3673
 2PU  C19   C  CR15  0  -0.565  -0.5921  -0.1060   3.1811
 2PU  N20   N  N     0  -0.326   1.3690  -1.2256   3.0676
 2PU  C21   C  CR5   0   0.444  -0.0493  -0.1891   4.4469
 2PU  N22   N  NR15  0  -0.482   1.1043  -0.8544   4.3225
 2PU  C23   C  CH1   0  -0.139  -0.5048   0.3573   5.7568
 2PU  C24   C  CH2   0  -0.459   0.0054   1.7934   6.0306
 2PU  N25   N  NH1   0  -0.617   0.0467  -0.4147   6.8605
 2PU  C26   C  CH2   0  -0.449   0.4136   1.7931   7.5154
 2PU  C27   C  CH2   0  -0.293  -0.0606   0.4380   8.0335
 2PU  H2    H  H     0   0.282   1.4758  -1.2231  -3.6308
 2PU  H61   H  HCH2  0   0.253   2.2697   0.6251  -2.2503
 2PU  H62   H  HCH2  0   0.246   1.2683   1.7799  -3.1409
 2PU  H8    H  HCR6  0   0.261  -3.1399   0.2437  -5.5193
 2PU  H9    H  HCR6  0   0.275  -3.0299  -0.8368  -1.3734
 2PU  H10   H  HNH1  0   0.411   0.5603  -1.4030  -1.3707
 2PU  H111  H  HCH2  0   0.252   2.7957   0.1814  -6.3371
 2PU  H112  H  HCH2  0   0.247   1.9240   1.7011  -6.1318
 2PU  H121  H  HCH2  0   0.248   3.7078   0.2485  -4.1648
 2PU  H122  H  HCH2  0   0.262   3.4291   1.9800  -4.2889
 2PU  H14   H  HCR6  0   0.266  -4.2938  -0.2789  -3.3754
 2PU  H16   H  HNH1  0   0.409   1.1232  -1.5718   0.6705
 2PU  H19   H  HCR5  0   0.268  -1.5196   0.3585   2.9017
 2PU  H22   H  HNR5  0   0.408   1.7246  -1.1070   5.0755
 2PU  H23   H  HCH1  0   0.242  -1.6038   0.3690   5.7605
 2PU  H241  H  HCH2  0   0.244   0.8536   2.0362   5.3902
 2PU  H242  H  HCH2  0   0.244  -0.7780   2.5183   5.8135
 2PU  H25   H  HNH1  0   0.355  -0.4509  -1.2879   6.9840
 2PU  H261  H  HCH2  0   0.235   1.4960   1.8794   7.6133
 2PU  H262  H  HCH2  0   0.238  -0.0306   2.6168   8.0730
 2PU  H271  H  HCH2  0   0.234   0.5526   0.0556   8.8512
 2PU  H272  H  HCH2  0   0.202  -1.0926   0.5164   8.4035

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
 2PU  C1   C2    single    1.495  0.020  1.495
 2PU  C1   C3    aromatic  1.385  0.020  1.385
 2PU  C1   C4    aromatic  1.389  0.020  1.389
 2PU  C2   N5    single    1.455  0.020  1.455
 2PU  C2   C6    single    1.528  0.020  1.528
 2PU  C2   H2    single    0.970  0.020  1.090
 2PU  C3   C7    single    1.482  0.020  1.482
 2PU  C3   C8    aromatic  1.384  0.020  1.384
 2PU  C4   C9    aromatic  1.397  0.020  1.397
 2PU  C4   N10   single    1.397  0.020  1.397
 2PU  N5   C7    single    1.357  0.020  1.357
 2PU  N5   C11   single    1.456  0.020  1.456
 2PU  C6   C12   single    1.532  0.020  1.532
 2PU  C6   H61   single    0.970  0.020  1.090
 2PU  C6   H62   single    0.970  0.020  1.090
 2PU  C7   O13   double    1.218  0.020  1.218
 2PU  C8   C14   aromatic  1.388  0.020  1.388
 2PU  C8   H8    single    0.930  0.020  1.080
 2PU  C9   C14   aromatic  1.392  0.020  1.392
 2PU  C9   H9    single    0.930  0.020  1.080
 2PU  N10  C15   single    1.372  0.020  1.372
 2PU  N10  H10   single    0.860  0.020  1.020
 2PU  C11  C12   single    1.540  0.020  1.540
 2PU  C11  H111  single    0.970  0.020  1.090
 2PU  C11  H112  single    0.970  0.020  1.090
 2PU  C12  H121  single    0.970  0.020  1.090
 2PU  C12  H122  single    0.970  0.020  1.090
 2PU  C14  H14   single    0.930  0.020  1.080
 2PU  C15  N16   single    1.362  0.020  1.362
 2PU  C15  O17   double    1.217  0.020  1.217
 2PU  N16  C18   single    1.388  0.020  1.388
 2PU  N16  H16   single    0.860  0.020  1.020
 2PU  C18  C19   aromatic  1.409  0.020  1.409
 2PU  C18  N20   aromatic  1.320  0.020  1.320
 2PU  C19  C21   aromatic  1.380  0.020  1.380
 2PU  C19  H19   single    0.930  0.020  1.080
 2PU  N20  N22   aromatic  1.335  0.020  1.335
 2PU  C21  N22   aromatic  1.338  0.020  1.338
 2PU  C21  C23   single    1.491  0.020  1.491
 2PU  N22  H22   single    0.860  0.020  1.020
 2PU  C23  C24   single    1.548  0.020  1.548
 2PU  C23  N25   single    1.455  0.020  1.455
 2PU  C23  H23   single    0.970  0.020  1.090
 2PU  C24  C26   single    1.540  0.020  1.540
 2PU  C24  H241  single    0.970  0.020  1.090
 2PU  C24  H242  single    0.970  0.020  1.090
 2PU  N25  C27   single    1.454  0.020  1.454
 2PU  N25  H25   single    0.890  0.020  1.040
 2PU  C26  C27   single    1.526  0.020  1.526
 2PU  C26  H261  single    0.970  0.020  1.090
 2PU  C26  H262  single    0.970  0.020  1.090
 2PU  C27  H271  single    0.970  0.020  1.090
 2PU  C27  H272  single    0.970  0.020  1.090

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
 2PU  C4    C1   C3    120.99  3.000
 2PU  C4    C1   C2    129.78  3.000
 2PU  C3    C1   C2    109.21  3.000
 2PU  H2    C2   C6    109.75  3.000
 2PU  H2    C2   N5    110.48  3.000
 2PU  C6    C2   N5    102.46  3.000
 2PU  H2    C2   C1    111.00  3.000
 2PU  C6    C2   C1    119.76  3.000
 2PU  N5    C2   C1    102.57  3.000
 2PU  C8    C3   C7    129.29  3.000
 2PU  C8    C3   C1    122.08  3.000
 2PU  C7    C3   C1    108.51  3.000
 2PU  N10   C4   C9    123.51  3.000
 2PU  N10   C4   C1    119.06  3.000
 2PU  C9    C4   C1    117.40  3.000
 2PU  C11   N5   C7    125.00  3.000
 2PU  C11   N5   C2    112.01  3.000
 2PU  C7    N5   C2    113.21  3.000
 2PU  H62   C6   H61   108.37  3.000
 2PU  H62   C6   C12   111.15  3.000
 2PU  H61   C6   C12   112.91  3.000
 2PU  H62   C6   C2    109.73  3.000
 2PU  H61   C6   C2    113.13  3.000
 2PU  C12   C6   C2    101.45  3.000
 2PU  O13   C7   N5    126.27  3.000
 2PU  O13   C7   C3    127.61  3.000
 2PU  N5    C7   C3    106.09  3.000
 2PU  H8    C8   C14   121.36  3.000
 2PU  H8    C8   C3    121.58  3.000
 2PU  C14   C8   C3    117.06  3.000
 2PU  H9    C9   C14   118.91  3.000
 2PU  H9    C9   C4    120.15  3.000
 2PU  C14   C9   C4    120.93  3.000
 2PU  H10   N10  C15   118.26  3.000
 2PU  H10   N10  C4    116.18  3.000
 2PU  C15   N10  C4    125.07  3.000
 2PU  H112  C11  H111  107.91  3.000
 2PU  H112  C11  C12   112.14  3.000
 2PU  H111  C11  C12   111.96  3.000
 2PU  H112  C11  N5    109.55  3.000
 2PU  H111  C11  N5    111.77  3.000
 2PU  C12   C11  N5    103.49  3.000
 2PU  H122  C12  H121  107.50  3.000
 2PU  H122  C12  C11   111.87  3.000
 2PU  H121  C12  C11   110.13  3.000
 2PU  H122  C12  C6    112.78  3.000
 2PU  H121  C12  C6    109.79  3.000
 2PU  C11   C12  C6    104.78  3.000
 2PU  H14   C14  C9    118.61  3.000
 2PU  H14   C14  C8    119.88  3.000
 2PU  C9    C14  C8    121.50  3.000
 2PU  O17   C15  N16   123.79  3.000
 2PU  O17   C15  N10   123.27  3.000
 2PU  N16   C15  N10   112.94  3.000
 2PU  H16   N16  C18   114.83  3.000
 2PU  H16   N16  C15   119.57  3.000
 2PU  C18   N16  C15   125.60  3.000
 2PU  N20   C18  C19   111.84  3.000
 2PU  N20   C18  N16   117.46  3.000
 2PU  C19   C18  N16   130.70  3.000
 2PU  H19   C19  C21   127.18  3.000
 2PU  H19   C19  C18   128.97  3.000
 2PU  C21   C19  C18   103.84  3.000
 2PU  N22   N20  C18   104.45  3.000
 2PU  C23   C21  N22   121.84  3.000
 2PU  C23   C21  C19   131.60  3.000
 2PU  N22   C21  C19   106.50  3.000
 2PU  H22   N22  C21   125.88  3.000
 2PU  H22   N22  N20   120.70  3.000
 2PU  C21   N22  N20   113.37  3.000
 2PU  H23   C23  N25   112.46  3.000
 2PU  H23   C23  C24   108.60  3.000
 2PU  N25   C23  C24   103.47  3.000
 2PU  H23   C23  C21   108.20  3.000
 2PU  N25   C23  C21   110.87  3.000
 2PU  C24   C23  C21   113.25  3.000
 2PU  H242  C24  H241  107.12  3.000
 2PU  H242  C24  C26   112.52  3.000
 2PU  H241  C24  C26   111.12  3.000
 2PU  H242  C24  C23   110.18  3.000
 2PU  H241  C24  C23   111.04  3.000
 2PU  C26   C24  C23   104.93  3.000
 2PU  H25   N25  C27   111.78  3.000
 2PU  H25   N25  C23   111.33  3.000
 2PU  C27   N25  C23   105.83  3.000
 2PU  H262  C26  H261  107.39  3.000
 2PU  H262  C26  C27   111.77  3.000
 2PU  H261  C26  C27   110.38  3.000
 2PU  H262  C26  C24   112.66  3.000
 2PU  H261  C26  C24   110.47  3.000
 2PU  C27   C26  C24   104.19  3.000
 2PU  H272  C27  H271  107.48  3.000
 2PU  H272  C27  C26   110.04  3.000
 2PU  H271  C27  C26   113.01  3.000
 2PU  H272  C27  N25   112.50  3.000
 2PU  H271  C27  N25   110.95  3.000
 2PU  C26   C27  N25   102.93  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
 2PU  CONST_01  C14  C8   C3   C1     0.00   0.0  0
 2PU  CONST_02  C14  C9   C4   C1     0.00   0.0  0
 2PU  CONST_03  C9   C4   C1   C3     0.00   0.0  0
 2PU  CONST_04  C9   C14  C8   C3     0.00   0.0  0
 2PU  CONST_05  C8   C3   C1   C4     0.00   0.0  0
 2PU  CONST_06  C8   C14  C9   C4     0.00   0.0  0
 2PU  CONST_07  N22  C21  C19  C18    0.00   0.0  0
 2PU  CONST_08  C21  N22  N20  C18    0.00   0.0  0
 2PU  CONST_09  N22  N20  C18  C19    0.00   0.0  0
 2PU  CONST_10  N20  N22  C21  C19    0.00   0.0  0
 2PU  CONST_11  C21  C19  C18  N20    0.00   0.0  0
 2PU  CONST_12  C23  C21  C19  C18  180.00   0.0  0
 2PU  CONST_13  C23  C21  N22  N20  180.00   0.0  0
 2PU  CONST_14  C3   C7   N5   C2     0.00   0.0  0
 2PU  CONST_16  N10  C4   C1   C2     0.00   0.0  0
 2PU  CONST_17  N10  C4   C1   C3   180.00   0.0  0
 2PU  CONST_18  C14  C9   C4   N10  180.00   0.0  0
 2PU  CONST_19  C21  C19  C18  N16  180.00   0.0  0
 2PU  CONST_20  N22  N20  C18  N16  180.00   0.0  0
 2PU  CONST_21  O13  C7   N5   C2   180.00   0.0  0
 2PU  CONST_23  H8   C8   C3   C1   180.00   0.0  0
 2PU  CONST_24  H9   C9   C4   C1   180.00   0.0  0
 2PU  CONST_25  H14  C14  C8   C3   180.00   0.0  0
 2PU  CONST_26  H22  N22  N20  C18  180.00   0.0  0
 2PU  CONST_27  H19  C19  C18  N20  180.00   0.0  0
 2PU  CONST_30  C19  C18  N16  C15    0.00   0.0  0
 2PU  CONST_31  N20  C18  N16  C15  180.00   0.0  0
 2PU  CONST_33  H16  N16  C18  C19  180.00   0.0  0
 2PU  CONST_34  O17  C15  N10  C4     0.00   0.0  0
 2PU  CONST_35  C18  N16  C15  O17    0.00   0.0  0
 2PU  CONST_36  N16  C15  N10  C4   180.00   0.0  0
 2PU  CONST_37  C18  N16  C15  N10  180.00   0.0  0
 2PU  Var_01    C12  C11  N5   C2    -5.12  30.0  1
 2PU  Var_02    C11  C12  C6   C2    36.20  30.0  1
 2PU  Var_03    C6   C12  C11  N5   -19.95  30.0  1
 2PU  Var_04    C27  C26  C24  C23   -7.42  30.0  1
 2PU  Var_05    C26  C27  N25  C23  -44.25  30.0  1
 2PU  Var_06    N25  C27  C26  C24   30.64  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
 2PU  chir_01  C2   C1   N5   C6   negativ
 2PU  chir_02  C23  C21  C24  N25  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
 2PU  plan-1  N16  0.020
 2PU  plan-1  C18  0.020
 2PU  plan-1  C19  0.020
 2PU  plan-1  N20  0.020
 2PU  plan-1  C21  0.020
 2PU  plan-1  N22  0.020
 2PU  plan-1  C23  0.020
 2PU  plan-1  H19  0.020
 2PU  plan-1  H22  0.020
 2PU  plan-2  C1   0.020
 2PU  plan-2  C2   0.020
 2PU  plan-2  C3   0.020
 2PU  plan-2  C4   0.020
 2PU  plan-2  N5   0.020
 2PU  plan-2  C7   0.020
 2PU  plan-2  C8   0.020
 2PU  plan-2  C9   0.020
 2PU  plan-2  N10  0.020
 2PU  plan-2  C11  0.020
 2PU  plan-2  O13  0.020
 2PU  plan-2  C14  0.020
 2PU  plan-2  H8   0.020
 2PU  plan-2  H9   0.020
 2PU  plan-2  H14  0.020
 2PU  plan-3  C4   0.020
 2PU  plan-3  N10  0.020
 2PU  plan-3  C15  0.020
 2PU  plan-3  N16  0.020
 2PU  plan-3  O17  0.020
 2PU  plan-3  C18  0.020
 2PU  plan-3  H10  0.020
 2PU  plan-3  H16  0.020

