# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:07:41 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 1-[(9bR)-5-oxo-2,3,5,9b-tetrahydro-1H-pyrrolo[2,1-a]isoindol-9-yl]-3-pyridin-2-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccccn1)Nc2cccc3C(=O)N4CCC[C@@H]4c23
#
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
 1PU  1PU  1-[(9bR)-5-oxo-2,3,5,9b-tetrahydro-1H-pyrrolo[2,1-a]isoindol-9-yl]-3-pyridin-2-ylurea  ligand  39  23  .  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_1PU
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
 1PU  C1    C  CR56  0   0.097  -0.4110   0.3487  -2.0167
 1PU  C2    C  C     0  -0.117   1.0480   0.3333  -2.3420
 1PU  C3    C  CR56  0  -0.099  -1.1401   0.1966  -3.1848
 1PU  C7    C  CR5   0   0.525  -0.1938  -0.0045  -4.3075
 1PU  C6    C  CH2   0  -0.436   1.9190  -0.8317  -1.8761
 1PU  C4    C  CR6   0   0.302  -1.0484   0.5115  -0.7939
 1PU  N5    N  N     0  -0.491   1.0474   0.1679  -3.7887
 1PU  C8    C  CR16  0  -0.318  -2.5239   0.1590  -3.1887
 1PU  C9    C  CR16  0  -0.284  -2.4442   0.4905  -0.7871
 1PU  N10   N  NH1   0  -0.799  -0.2775   0.7224   0.3526
 1PU  C11   C  CH2   0  -0.268   2.2498  -0.5016  -4.2639
 1PU  C12   C  CH2   0  -0.500   2.9951  -0.8638  -2.9663
 1PU  O13   O  O     0  -0.471  -0.4591  -0.3045  -5.4586
 1PU  C14   C  CR16  0  -0.266  -3.1631   0.3101  -1.9659
 1PU  C15   C  C     0   0.714  -0.5332   0.1702   1.5825
 1PU  N16   N  NH1   0  -0.772   0.3833   0.5774   2.5236
 1PU  O17   O  O     0  -0.473  -1.4638  -0.5765   1.7976
 1PU  C18   C  CR6   0   0.517   0.4712   0.1550   3.8450
 1PU  C19   C  CR16  0  -0.399   1.1057   1.0028   4.7603
 1PU  N20   N  N     0  -0.425  -0.0041  -1.0322   4.1780
 1PU  C21   C  CR16  0  -0.144   1.2315   0.5782   6.0668
 1PU  C22   C  CR16  0  -0.066   0.1101  -1.4182   5.4458
 1PU  C23   C  CR16  0  -0.344   0.7171  -0.6617   6.4312
 1PU  H2    H  H     0   0.284   1.5215   1.2839  -2.0652
 1PU  H61   H  HCH2  0   0.246   1.3335  -1.7541  -1.8714
 1PU  H62   H  HCH2  0   0.254   2.3312  -0.6835  -0.8789
 1PU  H8    H  HCR6  0   0.262  -3.0850   0.0235  -4.1039
 1PU  H9    H  HCR6  0   0.275  -2.9853   0.6284   0.1375
 1PU  H10   H  HNH1  0   0.414   0.6049   1.1923   0.2155
 1PU  H111  H  HCH2  0   0.246   1.9716  -1.3872  -4.8378
 1PU  H112  H  HCH2  0   0.252   2.8450   0.1437  -4.9101
 1PU  H121  H  HCH2  0   0.263   3.4916  -1.8303  -3.0394
 1PU  H122  H  HCH2  0   0.248   3.7607  -0.1161  -2.7530
 1PU  H14   H  HCR6  0   0.267  -4.2439   0.3006  -1.9178
 1PU  H16   H  HNH1  0   0.419   0.9630   1.3701   2.2904
 1PU  H19   H  HCR6  0   0.280   1.4828   1.9681   4.4482
 1PU  H21   H  HCR6  0   0.277   1.7189   1.2112   6.7966
 1PU  H22   H  HCR6  0   0.263  -0.3000  -2.3939   5.6818
 1PU  H23   H  HCR6  0   0.269   0.7870  -1.0296   7.4450

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
 1PU  C1   C2    single    1.495  0.020  1.495
 1PU  C1   C3    aromatic  1.385  0.020  1.385
 1PU  C1   C4    aromatic  1.389  0.020  1.389
 1PU  C2   C6    single    1.527  0.020  1.527
 1PU  C2   N5    single    1.456  0.020  1.456
 1PU  C2   H2    single    0.970  0.020  1.090
 1PU  C3   C7    single    1.482  0.020  1.482
 1PU  C3   C8    aromatic  1.384  0.020  1.384
 1PU  C7   N5    single    1.356  0.020  1.356
 1PU  C7   O13   double    1.219  0.020  1.219
 1PU  C6   C12   single    1.532  0.020  1.532
 1PU  C6   H61   single    0.970  0.020  1.090
 1PU  C6   H62   single    0.970  0.020  1.090
 1PU  C4   C9    aromatic  1.396  0.020  1.396
 1PU  C4   N10   single    1.398  0.020  1.398
 1PU  N5   C11   single    1.456  0.020  1.456
 1PU  C8   C14   aromatic  1.388  0.020  1.388
 1PU  C8   H8    single    0.930  0.020  1.080
 1PU  C9   C14   aromatic  1.392  0.020  1.392
 1PU  C9   H9    single    0.930  0.020  1.080
 1PU  N10  C15   single    1.372  0.020  1.372
 1PU  N10  H10   single    0.860  0.020  1.020
 1PU  C11  C12   single    1.540  0.020  1.540
 1PU  C11  H111  single    0.970  0.020  1.090
 1PU  C11  H112  single    0.970  0.020  1.090
 1PU  C12  H121  single    0.970  0.020  1.090
 1PU  C12  H122  single    0.970  0.020  1.090
 1PU  C14  H14   single    0.930  0.020  1.080
 1PU  C15  N16   single    1.375  0.020  1.375
 1PU  C15  O17   double    1.212  0.020  1.212
 1PU  N16  C18   single    1.390  0.020  1.390
 1PU  N16  H16   single    0.860  0.020  1.020
 1PU  C18  C19   aromatic  1.400  0.020  1.400
 1PU  C18  N20   aromatic  1.321  0.020  1.321
 1PU  C19  C21   aromatic  1.380  0.020  1.380
 1PU  C19  H19   single    0.930  0.020  1.080
 1PU  N20  C22   aromatic  1.330  0.020  1.330
 1PU  C21  C23   aromatic  1.391  0.020  1.391
 1PU  C21  H21   single    0.930  0.020  1.080
 1PU  C22  C23   aromatic  1.383  0.020  1.383
 1PU  C22  H22   single    0.930  0.020  1.080
 1PU  C23  H23   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
 1PU  C4    C1   C3    120.92  3.000
 1PU  C4    C1   C2    129.86  3.000
 1PU  C3    C1   C2    109.21  3.000
 1PU  H2    C2   N5    110.44  3.000
 1PU  H2    C2   C6    109.73  3.000
 1PU  N5    C2   C6    102.52  3.000
 1PU  H2    C2   C1    110.93  3.000
 1PU  N5    C2   C1    102.53  3.000
 1PU  C6    C2   C1    119.87  3.000
 1PU  C8    C3   C7    129.23  3.000
 1PU  C8    C3   C1    122.10  3.000
 1PU  C7    C3   C1    108.52  3.000
 1PU  O13   C7   N5    126.28  3.000
 1PU  O13   C7   C3    127.59  3.000
 1PU  N5    C7   C3    106.10  3.000
 1PU  H62   C6   H61   108.29  3.000
 1PU  H62   C6   C12   112.86  3.000
 1PU  H61   C6   C12   111.21  3.000
 1PU  H62   C6   C2    113.04  3.000
 1PU  H61   C6   C2    109.85  3.000
 1PU  C12   C6   C2    101.50  3.000
 1PU  N10   C4   C9    123.36  3.000
 1PU  N10   C4   C1    119.14  3.000
 1PU  C9    C4   C1    117.48  3.000
 1PU  C11   N5   C7    124.93  3.000
 1PU  C11   N5   C2    112.10  3.000
 1PU  C7    N5   C2    113.25  3.000
 1PU  H8    C8   C14   121.33  3.000
 1PU  H8    C8   C3    121.61  3.000
 1PU  C14   C8   C3    117.06  3.000
 1PU  H9    C9   C14   118.86  3.000
 1PU  H9    C9   C4    120.20  3.000
 1PU  C14   C9   C4    120.94  3.000
 1PU  H10   N10  C15   118.17  3.000
 1PU  H10   N10  C4    116.18  3.000
 1PU  C15   N10  C4    124.87  3.000
 1PU  H112  C11  H111  107.93  3.000
 1PU  H112  C11  C12   112.00  3.000
 1PU  H111  C11  C12   112.06  3.000
 1PU  H112  C11  N5    111.85  3.000
 1PU  H111  C11  N5    109.53  3.000
 1PU  C12   C11  N5    103.47  3.000
 1PU  H122  C12  H121  107.54  3.000
 1PU  H122  C12  C11   110.07  3.000
 1PU  H121  C12  C11   111.90  3.000
 1PU  H122  C12  C6    109.84  3.000
 1PU  H121  C12  C6    112.74  3.000
 1PU  C11   C12  C6    104.76  3.000
 1PU  H14   C14  C9    118.63  3.000
 1PU  H14   C14  C8    119.89  3.000
 1PU  C9    C14  C8    121.47  3.000
 1PU  O17   C15  N16   124.92  3.000
 1PU  O17   C15  N10   123.37  3.000
 1PU  N16   C15  N10   111.71  3.000
 1PU  H16   N16  C18   114.96  3.000
 1PU  H16   N16  C15   117.20  3.000
 1PU  C18   N16  C15   127.06  3.000
 1PU  N20   C18  C19   122.85  3.000
 1PU  N20   C18  N16   119.33  3.000
 1PU  C19   C18  N16   117.79  3.000
 1PU  H19   C19  C21   121.05  3.000
 1PU  H19   C19  C18   120.64  3.000
 1PU  C21   C19  C18   118.31  3.000
 1PU  C22   N20  C18   118.04  3.000
 1PU  H21   C21  C23   120.76  3.000
 1PU  H21   C21  C19   119.98  3.000
 1PU  C23   C21  C19   119.26  3.000
 1PU  H22   C22  C23   120.21  3.000
 1PU  H22   C22  N20   115.85  3.000
 1PU  C23   C22  N20   123.93  3.000
 1PU  H23   C23  C22   120.71  3.000
 1PU  H23   C23  C21   121.69  3.000
 1PU  C22   C23  C21   117.60  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
 1PU  CONST_01  C14  C8   C3   C1     0.00   0.0  0
 1PU  CONST_02  C14  C9   C4   C1     0.00   0.0  0
 1PU  CONST_03  C9   C4   C1   C3     0.00   0.0  0
 1PU  CONST_04  C9   C14  C8   C3     0.00   0.0  0
 1PU  CONST_05  C8   C3   C1   C4     0.00   0.0  0
 1PU  CONST_06  C8   C14  C9   C4     0.00   0.0  0
 1PU  CONST_07  C23  C21  C19  C18    0.00   0.0  0
 1PU  CONST_08  C23  C22  N20  C18    0.00   0.0  0
 1PU  CONST_09  C22  N20  C18  C19    0.00   0.0  0
 1PU  CONST_10  C22  C23  C21  C19    0.00   0.0  0
 1PU  CONST_11  C21  C19  C18  N20    0.00   0.0  0
 1PU  CONST_12  C21  C23  C22  N20    0.00   0.0  0
 1PU  CONST_13  C3   C7   N5   C2     0.00   0.0  0
 1PU  CONST_15  N10  C4   C1   C2     0.00   0.0  0
 1PU  CONST_16  N10  C4   C1   C3   180.00   0.0  0
 1PU  CONST_17  C14  C9   C4   N10  180.00   0.0  0
 1PU  CONST_18  C21  C19  C18  N16  180.00   0.0  0
 1PU  CONST_19  C22  N20  C18  N16  180.00   0.0  0
 1PU  CONST_20  O13  C7   N5   C2   180.00   0.0  0
 1PU  CONST_22  H8   C8   C3   C1   180.00   0.0  0
 1PU  CONST_23  H9   C9   C4   C1   180.00   0.0  0
 1PU  CONST_24  H14  C14  C8   C3   180.00   0.0  0
 1PU  CONST_25  H21  C21  C19  C18  180.00   0.0  0
 1PU  CONST_26  H22  C22  N20  C18  180.00   0.0  0
 1PU  CONST_27  H23  C23  C21  C19  180.00   0.0  0
 1PU  CONST_28  H19  C19  C18  N20  180.00   0.0  0
 1PU  CONST_34  H16  N16  C18  C19    0.00   0.0  0
 1PU  CONST_35  O17  C15  N10  C4     0.00   0.0  0
 1PU  CONST_36  C18  N16  C15  O17    0.00   0.0  0
 1PU  CONST_37  N16  C15  N10  C4   180.00   0.0  0
 1PU  CONST_38  C18  N16  C15  N10  180.00   0.0  0
 1PU  Var_01    C11  C12  C6   C2   -36.33  30.0  1
 1PU  Var_02    C12  C11  N5   C2     4.40  30.0  1
 1PU  Var_03    N5   C11  C12  C6    20.44  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
 1PU  chir_01  C2  C1  C6  N5  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
 1PU  plan-1  N16  0.020
 1PU  plan-1  C18  0.020
 1PU  plan-1  C19  0.020
 1PU  plan-1  N20  0.020
 1PU  plan-1  C21  0.020
 1PU  plan-1  C22  0.020
 1PU  plan-1  C23  0.020
 1PU  plan-1  H19  0.020
 1PU  plan-1  H21  0.020
 1PU  plan-1  H22  0.020
 1PU  plan-1  H23  0.020
 1PU  plan-2  C1   0.020
 1PU  plan-2  C2   0.020
 1PU  plan-2  C3   0.020
 1PU  plan-2  C7   0.020
 1PU  plan-2  C4   0.020
 1PU  plan-2  N5   0.020
 1PU  plan-2  C8   0.020
 1PU  plan-2  C9   0.020
 1PU  plan-2  N10  0.020
 1PU  plan-2  C11  0.020
 1PU  plan-2  O13  0.020
 1PU  plan-2  C14  0.020
 1PU  plan-2  H8   0.020
 1PU  plan-2  H9   0.020
 1PU  plan-2  H14  0.020
 1PU  plan-3  C4   0.020
 1PU  plan-3  N10  0.020
 1PU  plan-3  C15  0.020
 1PU  plan-3  N16  0.020
 1PU  plan-3  O17  0.020
 1PU  plan-3  C18  0.020
 1PU  plan-3  H10  0.020
 1PU  plan-3  H16  0.020

