# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 06:57:54 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Nc2ccc(cc2[C@@]13CCCN3C(=O)C4CC4)c5ccc6nccnc6c5
#
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
 P5V  P5V  (3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one  ligand  49  29  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P5V
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
 P5V  C2   C  CR5   0   0.576  -3.5677  -1.5141   0.1636
 P5V  C4   C  CR56  0   0.365  -1.4188  -2.0830   0.6572
 P5V  C5   C  CR16  0  -0.294  -0.3121  -2.6829   1.2253
 P5V  C6   C  CR16  0  -0.317   0.9386  -2.1675   0.9021
 P5V  C7   C  CR6   0   0.085   1.0934  -1.0874   0.0318
 P5V  C8   C  CR16  0  -0.408  -0.0506  -0.5150  -0.5438
 P5V  C11  C  CH2   0  -0.475  -2.8787  -0.9204  -2.2010
 P5V  C12  C  CH2   0  -0.470  -3.9251   0.0999  -2.6267
 P5V  C17  C  CH1   0  -0.432  -3.3128   2.8087   0.6982
 P5V  C18  C  CH2   0  -0.463  -4.1833   3.2673   1.8436
 P5V  C19  C  CH2   0  -0.459  -2.7359   3.5911   1.8492
 P5V  C21  C  CR16  0  -0.387   3.4107  -0.4988   0.6972
 P5V  C24  C  CR16  0  -0.115   6.7907   0.5511   1.0564
 P5V  C27  C  CR66  0   0.215   4.9753   0.4871  -0.8980
 P5V  O1   O  O     0  -0.439  -4.7767  -1.4834   0.1955
 P5V  N3   N  NR15  0  -0.741  -2.7613  -2.3825   0.8309
 P5V  C9   C  CR56  0   0.183  -1.2892  -1.0137  -0.2236
 P5V  C10  C  CR5   0  -0.085  -2.6563  -0.6210  -0.7041
 P5V  C13  C  CH2   0  -0.282  -3.5330   1.3390  -1.8357
 P5V  N14  N  NT    0  -0.508  -3.0005   0.7810  -0.5936
 P5V  O16  O  O     0  -0.501  -2.7313   0.7009   1.6236
 P5V  C20  C  CR6   0   0.095   2.4332  -0.5512  -0.2695
 P5V  C22  C  CR66  0   0.260   4.6892   0.0140   0.4045
 P5V  N23  N  N     0  -0.384   5.6283   0.0601   1.3799
 P5V  C25  C  CR16  0  -0.118   7.0773   1.0189  -0.2493
 P5V  N26  N  N     0  -0.377   6.1928   0.9888  -1.2059
 P5V  C28  C  CR16  0  -0.289   3.9664   0.4293  -1.8825
 P5V  C29  C  CR16  0  -0.303   2.7354  -0.0748  -1.5732
 P5V  H1   H  HCR6  0   0.272  -0.4033  -3.5222   1.9016
 P5V  H2   H  HCR6  0   0.261   1.8154  -2.6377   1.3288
 P5V  H3   H  HCR6  0   0.258   0.0336   0.3347  -1.2119
 P5V  H4   H  HCH2  0   0.275  -3.1698  -1.9550  -2.3795
 P5V  H5   H  HCH2  0   0.264  -1.9434  -0.7477  -2.7370
 P5V  H6   H  HCH2  0   0.260  -3.9188   0.2792  -3.7009
 P5V  H7   H  HCH2  0   0.251  -4.9255  -0.2265  -2.3418
 P5V  H8   H  HCH1  0   0.290  -3.4215   3.3477  -0.2333
 P5V  H9   H  HCH2  0   0.264  -4.8947   4.0541   1.6322
 P5V  H10  H  HCH2  0   0.259  -4.5380   2.5068   2.5268
 P5V  H11  H  HCH2  0   0.258  -2.0949   3.0606   2.5407
 P5V  H12  H  HCH2  0   0.263  -2.4328   4.6070   1.6341
 P5V  H13  H  HCR6  0   0.265   3.2156  -0.8270   1.7106
 P5V  H14  H  HCR6  0   0.278   7.5548   0.5963   1.8238
 P5V  H15  H  HNR5  0   0.412  -3.1112  -3.0844   1.4658
 P5V  H16  H  HCH2  0   0.249  -2.7698   1.9212  -2.3590
 P5V  H17  H  HCH2  0   0.264  -4.3838   1.9897  -1.6425
 P5V  H18  H  HCR6  0   0.278   8.0590   1.4187  -0.4756
 P5V  H19  H  HCR6  0   0.271   4.1909   0.7809  -2.8814
 P5V  H20  H  HCR6  0   0.265   1.9810  -0.1322  -2.3471
 P5V  C15  C  C     0   0.610  -2.9959   1.3608   0.6246

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
 P5V  C19  C18  single    1.483  0.020  1.483
 P5V  C19  C17  single    1.507  0.020  1.507
 P5V  C18  C17  single    1.510  0.020  1.510
 P5V  C24  C25  aromatic  1.416  0.020  1.416
 P5V  C24  N23  aromatic  1.303  0.020  1.303
 P5V  C25  N26  aromatic  1.303  0.020  1.303
 P5V  C17  C15  single    1.484  0.020  1.484
 P5V  N23  C22  aromatic  1.355  0.020  1.355
 P5V  N26  C27  aromatic  1.352  0.020  1.352
 P5V  C22  C27  aromatic  1.415  0.020  1.415
 P5V  C22  C21  aromatic  1.408  0.020  1.408
 P5V  C27  C28  aromatic  1.411  0.020  1.411
 P5V  C21  C20  aromatic  1.376  0.020  1.376
 P5V  C15  O16  double    1.226  0.020  1.226
 P5V  C15  N14  single    1.349  0.020  1.349
 P5V  C28  C29  aromatic  1.366  0.020  1.366
 P5V  C20  C29  aromatic  1.421  0.020  1.421
 P5V  C20  C7   single    1.474  0.020  1.474
 P5V  C13  N14  single    1.462  0.020  1.462
 P5V  C13  C12  single    1.522  0.020  1.522
 P5V  N14  C10  single    1.448  0.020  1.448
 P5V  C7   C8   aromatic  1.403  0.020  1.403
 P5V  C7   C6   aromatic  1.396  0.020  1.396
 P5V  C8   C9   aromatic  1.373  0.020  1.373
 P5V  C6   C5   aromatic  1.391  0.020  1.391
 P5V  C9   C10  single    1.501  0.020  1.501
 P5V  C9   C4   aromatic  1.391  0.020  1.391
 P5V  C5   C4   aromatic  1.381  0.020  1.381
 P5V  C10  C2   single    1.543  0.020  1.543
 P5V  C10  C11  single    1.543  0.020  1.543
 P5V  C12  C11  single    1.522  0.020  1.522
 P5V  C4   N3   single    1.386  0.020  1.386
 P5V  N3   C2   single    1.360  0.020  1.360
 P5V  C2   O1   double    1.210  0.020  1.210
 P5V  C5   H1   single    0.930  0.020  1.080
 P5V  C6   H2   single    0.930  0.020  1.080
 P5V  C8   H3   single    0.930  0.020  1.080
 P5V  C11  H4   single    0.970  0.020  1.090
 P5V  C11  H5   single    0.970  0.020  1.090
 P5V  C12  H6   single    0.970  0.020  1.090
 P5V  C12  H7   single    0.970  0.020  1.090
 P5V  C17  H8   single    0.970  0.020  1.090
 P5V  C18  H9   single    0.970  0.020  1.090
 P5V  C18  H10  single    0.970  0.020  1.090
 P5V  C19  H11  single    0.970  0.020  1.090
 P5V  C19  H12  single    0.970  0.020  1.090
 P5V  C21  H13  single    0.930  0.020  1.080
 P5V  C24  H14  single    0.930  0.020  1.080
 P5V  N3   H15  single    0.860  0.020  1.020
 P5V  C13  H16  single    0.970  0.020  1.090
 P5V  C13  H17  single    0.970  0.020  1.090
 P5V  C25  H18  single    0.930  0.020  1.080
 P5V  C28  H19  single    0.930  0.020  1.080
 P5V  C29  H20  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
 P5V  C10  C2   N3   107.17  3.000
 P5V  N3   C2   O1   126.57  3.000
 P5V  C10  C2   O1   126.19  3.000
 P5V  C9   C4   N3   109.60  3.000
 P5V  N3   C4   C5   129.09  3.000
 P5V  C9   C4   C5   121.31  3.000
 P5V  H1   C5   C6   120.57  3.000
 P5V  H1   C5   C4   121.78  3.000
 P5V  C6   C5   C4   117.65  3.000
 P5V  H2   C6   C7   119.47  3.000
 P5V  H2   C6   C5   118.41  3.000
 P5V  C7   C6   C5   122.10  3.000
 P5V  C20  C7   C8   120.60  3.000
 P5V  C8   C7   C6   118.76  3.000
 P5V  C20  C7   C6   120.64  3.000
 P5V  H3   C8   C9   119.90  3.000
 P5V  H3   C8   C7   120.62  3.000
 P5V  C9   C8   C7   119.46  3.000
 P5V  H5   C11  H4   107.38  3.000
 P5V  H5   C11  C10  108.80  3.000
 P5V  H4   C11  C10  112.44  3.000
 P5V  H5   C11  C12  110.22  3.000
 P5V  H4   C11  C12  114.01  3.000
 P5V  C10  C11  C12  103.91  3.000
 P5V  H7   C12  H6   108.20  3.000
 P5V  H7   C12  C13  110.15  3.000
 P5V  H6   C12  C13  112.16  3.000
 P5V  H7   C12  C11  110.92  3.000
 P5V  H6   C12  C11  112.47  3.000
 P5V  C13  C12  C11  102.90  3.000
 P5V  H8   C17  C19  115.95  3.000
 P5V  H8   C17  C18  116.36  3.000
 P5V  C19  C17  C18   58.90  3.000
 P5V  H8   C17  C15  117.71  3.000
 P5V  C18  C17  C15  117.19  3.000
 P5V  C19  C17  C15  117.56  3.000
 P5V  H10  C18  H9   114.77  3.000
 P5V  H10  C18  C19  118.10  3.000
 P5V  H9   C18  C19  118.93  3.000
 P5V  H10  C18  C17  117.03  3.000
 P5V  H9   C18  C17  116.86  3.000
 P5V  C19  C18  C17   60.43  3.000
 P5V  H12  C19  H11  114.93  3.000
 P5V  H12  C19  C18  118.54  3.000
 P5V  H11  C19  C18  118.27  3.000
 P5V  H12  C19  C17  116.30  3.000
 P5V  H11  C19  C17  117.43  3.000
 P5V  C18  C19  C17   60.66  3.000
 P5V  H13  C21  C22  117.93  3.000
 P5V  H13  C21  C20  121.20  3.000
 P5V  C22  C21  C20  120.86  3.000
 P5V  H14  C24  C25  119.75  3.000
 P5V  H14  C24  N23  117.97  3.000
 P5V  C25  C24  N23  122.28  3.000
 P5V  C28  C27  N26  120.01  3.000
 P5V  C28  C27  C22  118.95  3.000
 P5V  N26  C27  C22  121.04  3.000
 P5V  H15  N3   C4   124.40  3.000
 P5V  H15  N3   C2   123.18  3.000
 P5V  C4   N3   C2   112.01  3.000
 P5V  C10  C9   C8   130.67  3.000
 P5V  C10  C9   C4   108.60  3.000
 P5V  C8   C9   C4   120.71  3.000
 P5V  N14  C10  C9   116.45  3.000
 P5V  C9   C10  C11  113.02  3.000
 P5V  N14  C10  C11  103.16  3.000
 P5V  C11  C10  C2   110.37  3.000
 P5V  C9   C10  C2   101.92  3.000
 P5V  N14  C10  C2   112.15  3.000
 P5V  H17  C13  H16  108.20  3.000
 P5V  H17  C13  N14  111.23  3.000
 P5V  H16  C13  N14  110.83  3.000
 P5V  H17  C13  C12  112.19  3.000
 P5V  H16  C13  C12  111.39  3.000
 P5V  N14  C13  C12  102.98  3.000
 P5V  C13  N14  C10  113.04  3.000
 P5V  C10  N14  C15  118.96  3.000
 P5V  C13  N14  C15  127.18  3.000
 P5V  C29  C20  C21  118.75  3.000
 P5V  C29  C20  C7   120.19  3.000
 P5V  C21  C20  C7   121.06  3.000
 P5V  N23  C22  C27  120.74  3.000
 P5V  C27  C22  C21  119.78  3.000
 P5V  N23  C22  C21  119.48  3.000
 P5V  C22  N23  C24  116.91  3.000
 P5V  H18  C25  N26  118.03  3.000
 P5V  H18  C25  C24  119.84  3.000
 P5V  N26  C25  C24  122.13  3.000
 P5V  C25  N26  C27  116.90  3.000
 P5V  H19  C28  C29  121.05  3.000
 P5V  H19  C28  C27  118.84  3.000
 P5V  C29  C28  C27  120.11  3.000
 P5V  H20  C29  C28  119.07  3.000
 P5V  H20  C29  C20  119.35  3.000
 P5V  C28  C29  C20  121.56  3.000
 P5V  O16  C15  N14  120.34  3.000
 P5V  N14  C15  C17  117.60  3.000
 P5V  O16  C15  C17  122.06  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
 P5V  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 P5V  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 P5V  CONST_03  C20  C7   C6   C5    180.00   0.0  0
 P5V  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 P5V  CONST_05  C8   C9   C4   C5      0.00   0.0  0
 P5V  CONST_08  C9   C8   C7   C6      0.00   0.0  0
 P5V  CONST_09  C9   C4   C5   C6      0.00   0.0  0
 P5V  CONST_10  C22  C21  C20  C7    180.00   0.0  0
 P5V  CONST_11  C28  C29  C20  C7    180.00   0.0  0
 P5V  CONST_14  C24  N23  C22  C21   180.00   0.0  0
 P5V  CONST_15  N26  C27  C22  C21   180.00   0.0  0
 P5V  CONST_16  C28  C27  C22  C21     0.00   0.0  0
 P5V  CONST_17  C28  C29  C20  C21     0.00   0.0  0
 P5V  CONST_18  C27  N26  C25  C24     0.00   0.0  0
 P5V  CONST_19  C27  C22  N23  C24     0.00   0.0  0
 P5V  CONST_20  C20  C21  C22  C27     0.00   0.0  0
 P5V  CONST_21  C20  C29  C28  C27     0.00   0.0  0
 P5V  CONST_22  C20  C7   C8   C9    180.00   0.0  0
 P5V  CONST_23  N23  C22  C21  C20   180.00   0.0  0
 P5V  CONST_24  C25  C24  N23  C22     0.00   0.0  0
 P5V  CONST_25  C25  N26  C27  C22     0.00   0.0  0
 P5V  CONST_26  C29  C28  C27  C22     0.00   0.0  0
 P5V  CONST_27  C29  C20  C21  C22     0.00   0.0  0
 P5V  CONST_28  N26  C25  C24  N23     0.00   0.0  0
 P5V  CONST_29  N26  C27  C22  N23     0.00   0.0  0
 P5V  CONST_30  C28  C27  C22  N23   180.00   0.0  0
 P5V  CONST_31  C28  C27  N26  C25   180.00   0.0  0
 P5V  CONST_32  C29  C28  C27  N26   180.00   0.0  0
 P5V  CONST_33  C10  C2   N3   C4      0.00   0.0  0
 P5V  CONST_34  C13  N14  C15  C17     0.00   0.0  0
 P5V  CONST_35  C10  N14  C15  C17   180.00   0.0  0
 P5V  CONST_36  O1   C2   N3   C4    180.00   0.0  0
 P5V  CONST_37  H3   C8   C9   C4    180.00   0.0  0
 P5V  CONST_38  H2   C6   C5   C4    180.00   0.0  0
 P5V  CONST_39  H13  C21  C20  C7      0.00   0.0  0
 P5V  CONST_40  H20  C29  C20  C7      0.00   0.0  0
 P5V  CONST_41  H1   C5   C6   C7    180.00   0.0  0
 P5V  CONST_42  H18  C25  N26  C27   180.00   0.0  0
 P5V  CONST_43  H19  C28  C29  C20   180.00   0.0  0
 P5V  CONST_44  H14  C24  N23  C22   180.00   0.0  0
 P5V  CONST_45  H15  N3   C2   C10   180.00   0.0  0
 P5V  CONST_46  O16  C15  N14  C10     0.00   0.0  0
 P5V  CONST_47  O16  C15  N14  C13   180.00   0.0  0
 P5V  Var_01    N14  C13  C12  C11   -33.29  30.0  1
 P5V  Var_02    C10  N14  C13  C12    17.55  30.0  1
 P5V  Var_03    C13  C12  C11  C10    37.23  30.0  1
 P5V  Var_04    C18  C19  C17  C15  -106.69  30.0  1
 P5V  Var_05    N14  C15  C17  C18   139.77  30.0  3
 P5V  Var_06    H9   C18  C19  C17  -106.26  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
 P5V  chir_02  C10  C9   C2   C11  positiv
 P5V  chir_03  C17  C19  C18  C15  both

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
 P5V  plan-1  C17  0.020
 P5V  plan-1  C10  0.020
 P5V  plan-1  C13  0.020
 P5V  plan-1  N14  0.020
 P5V  plan-1  O16  0.020
 P5V  plan-1  C15  0.020
 P5V  plan-2  C7   0.020
 P5V  plan-2  C21  0.020
 P5V  plan-2  C24  0.020
 P5V  plan-2  C27  0.020
 P5V  plan-2  C20  0.020
 P5V  plan-2  C22  0.020
 P5V  plan-2  N23  0.020
 P5V  plan-2  C25  0.020
 P5V  plan-2  N26  0.020
 P5V  plan-2  C28  0.020
 P5V  plan-2  C29  0.020
 P5V  plan-2  H13  0.020
 P5V  plan-2  H14  0.020
 P5V  plan-2  H18  0.020
 P5V  plan-2  H19  0.020
 P5V  plan-2  H20  0.020
 P5V  plan-3  C2   0.020
 P5V  plan-3  C4   0.020
 P5V  plan-3  C5   0.020
 P5V  plan-3  C6   0.020
 P5V  plan-3  C7   0.020
 P5V  plan-3  C8   0.020
 P5V  plan-3  O1   0.020
 P5V  plan-3  N3   0.020
 P5V  plan-3  C9   0.020
 P5V  plan-3  C10  0.020
 P5V  plan-3  C20  0.020
 P5V  plan-3  H1   0.020
 P5V  plan-3  H2   0.020
 P5V  plan-3  H3   0.020
 P5V  plan-3  H15  0.020

