# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 16:41:37 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: (3~{S},3~{a}~{S},6~{a}~{R})-2-[3-[3,5-bis(fluoranyl)phenyl]propanoyl]-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(F)cc(CCC(=O)N2C[C@@H]3CCC[C@@H]3[C@H]2C(=O)N[C@@H](C[C@@H]4CCNC4=O)C=O)c1
#
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
 GQU  GQU  (3~{S},3~{a}~{S},6~{a}~{R})-2-[3-[3,5-bis(fluoranyl)phenyl]propanoyl]-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide  ligand  62  33  .  2022-03-18  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GQU
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
 GQU  C10  C  CR15  0  -0.191  -15.8746  -25.9488   0.2005
 GQU  C15  C  C1    0   0.196  -12.1840  -28.6853   1.0311
 GQU  C17  C  CH2   0  -0.434  -12.0533  -26.8072   2.7378
 GQU  C20  C  CH2   0  -0.260  -11.6364  -23.0802   3.0587
 GQU  C22  C  CR5   0   0.570  -12.0208  -24.9368   4.4417
 GQU  C26  C  CR6   0   0.161  -14.7655  -20.3432  -1.1904
 GQU  C28  C  CR6   0   0.560  -14.5992  -17.9728  -0.9477
 GQU  C02  C  C     0   0.547  -15.8031  -23.5703   0.5787
 GQU  N03  N  NR5   0  -0.453  -16.2187  -24.5981  -0.1857
 GQU  C04  C  CH2   0  -0.284  -16.7241  -24.5428  -1.5480
 GQU  C05  C  C     0  -0.249  -17.3675  -25.9068  -1.7377
 GQU  C06  C  CH2   0  -0.440  -18.8141  -26.0314  -1.2034
 GQU  C07  C  CH2   0  -0.455  -18.7511  -26.9675   0.0097
 GQU  C08  C  CH2   0  -0.438  -17.5305  -27.8421  -0.2653
 GQU  C09  C  C     0  -0.289  -16.5262  -26.8635  -0.8662
 GQU  C11  C  C     0   0.580  -14.3610  -26.1166   0.1958
 GQU  O12  O  O     0  -0.473  -13.6604  -25.5340  -0.6131
 GQU  N13  N  NH1   0  -0.644  -13.8929  -26.9958   1.1033
 GQU  C14  C  CH1   0  -0.215  -12.4895  -27.2359   1.3404
 GQU  C18  C  CR15  0  -0.425  -12.4009  -25.3573   3.0304
 GQU  C19  C  CH2   0  -0.470  -11.7102  -24.3119   2.1561
 GQU  N21  N  NR15  0  -0.630  -11.5783  -23.6710   4.3798
 GQU  C25  C  CH2   0  -0.524  -14.6428  -21.7288  -0.6255
 GQU  C27  C  CR16  0  -0.477  -14.4318  -19.2362  -0.4156
 GQU  F29  F  F     0  -0.310  -14.2764  -16.9085  -0.2007
 GQU  C30  C  CR16  0  -0.573  -15.0860  -17.7531  -2.2219
 GQU  C31  C  CR6   0   0.559  -15.4076  -18.8748  -2.9622
 GQU  F32  F  F     0  -0.310  -15.8805  -18.7017  -4.2039
 GQU  C33  C  CR16  0  -0.474  -15.2600  -20.1595  -2.4789
 GQU  H1   H  HCR5  0   0.281  -16.2698  -26.1665   1.1969
 GQU  H2   H  H     0   0.210  -12.7121  -29.0698   0.1397
 GQU  H4   H  HCH2  0   0.249  -12.5243  -27.4533   3.4833
 GQU  H5   H  HCH2  0   0.253  -10.9743  -26.9537   2.8278
 GQU  H6   H  HCH2  0   0.249  -10.7593  -22.4631   2.8662
 GQU  H7   H  HCH2  0   0.233  -12.5238  -22.4496   2.9471
 GQU  H8   H  HCH2  0   0.277  -16.1870  -21.5060   0.8688
 GQU  H9   H  HCH2  0   0.266  -16.7777  -22.0832  -0.6801
 GQU  H10  H  HCH2  0   0.247  -15.9078  -24.3959  -2.2623
 GQU  H11  H  HCH2  0   0.259  -17.4393  -23.7325  -1.6804
 GQU  H12  H  H     0   0.265  -17.3245  -26.1926  -2.7890
 GQU  H13  H  HCH2  0   0.235  -19.2459  -25.0608  -0.9519
 GQU  H14  H  HCH2  0   0.236  -19.4496  -26.4660  -1.9771
 GQU  H15  H  HCH2  0   0.227  -18.6041  -26.3952   0.9298
 GQU  H16  H  HCH2  0   0.240  -19.6658  -27.5466   0.1412
 GQU  H17  H  HCH2  0   0.238  -17.7727  -28.6100  -1.0046
 GQU  H18  H  HCH2  0   0.238  -17.1507  -28.3546   0.6209
 GQU  H19  H  H     0   0.270  -15.7594  -27.3723  -1.4536
 GQU  H20  H  HNH1  0   0.407  -14.5416  -27.3726   1.7782
 GQU  H21  H  HCH1  0   0.305  -11.9404  -26.6615   0.5847
 GQU  H23  H  HCR5  0   0.294  -13.4869  -25.2219   2.9575
 GQU  H24  H  HCH2  0   0.263  -12.2417  -24.1053   1.2304
 GQU  H25  H  HCH2  0   0.241  -10.7016  -24.6493   1.9021
 GQU  H26  H  HNR5  0   0.396  -11.3834  -23.1312   5.2089
 GQU  H27  H  HCH2  0   0.268  -14.3714  -22.4274  -1.4200
 GQU  H28  H  HCH2  0   0.267  -13.8411  -21.7640   0.1145
 GQU  H29  H  HCR6  0   0.277  -14.0442  -19.3572   0.5882
 GQU  H30  H  HCR6  0   0.302  -15.2083  -16.7545  -2.6199
 GQU  H31  H  HCR6  0   0.275  -15.5222  -21.0080  -3.0991
 GQU  O16  O  O     0  -0.367  -11.4351  -29.3777   1.6684
 GQU  C24  C  CH2   0  -0.565  -15.9592  -22.1708   0.0341
 GQU  O01  O  O     0  -0.492  -15.2709  -23.7624   1.6662
 GQU  O23  O  O     0  -0.498  -12.1188  -25.6184   5.4504

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
 GQU  F32  C31  single    1.340  0.020  1.340
 GQU  C31  C33  aromatic  1.381  0.020  1.381
 GQU  C31  C30  aromatic  1.382  0.020  1.382
 GQU  C33  C26  aromatic  1.392  0.020  1.392
 GQU  C05  C06  single    1.547  0.020  1.547
 GQU  C05  C04  single    1.520  0.020  1.520
 GQU  C05  C09  single    1.544  0.020  1.544
 GQU  C06  C07  single    1.534  0.020  1.534
 GQU  C04  N03  single    1.454  0.020  1.454
 GQU  C30  C28  aromatic  1.382  0.020  1.382
 GQU  C26  C25  single    1.501  0.020  1.501
 GQU  C26  C27  aromatic  1.392  0.020  1.392
 GQU  C09  C08  single    1.526  0.020  1.526
 GQU  C09  C10  single    1.549  0.020  1.549
 GQU  C25  C24  single    1.537  0.020  1.537
 GQU  C07  C08  single    1.527  0.020  1.527
 GQU  C28  C27  aromatic  1.381  0.020  1.381
 GQU  C28  F29  single    1.340  0.020  1.340
 GQU  N03  C10  single    1.446  0.020  1.446
 GQU  N03  C02  single    1.347  0.020  1.347
 GQU  C24  C02  single    1.510  0.020  1.510
 GQU  O12  C11  double    1.218  0.020  1.218
 GQU  C10  C11  single    1.523  0.020  1.523
 GQU  C02  O01  double    1.226  0.020  1.226
 GQU  C11  N13  single    1.347  0.020  1.347
 GQU  N13  C14  single    1.443  0.020  1.443
 GQU  C19  C20  single    1.529  0.020  1.529
 GQU  C19  C18  single    1.528  0.020  1.528
 GQU  C14  C15  single    1.513  0.020  1.513
 GQU  C14  C17  single    1.525  0.020  1.525
 GQU  C20  N21  single    1.448  0.020  1.448
 GQU  C15  O16  double    1.203  0.020  1.203
 GQU  C18  C17  single    1.519  0.020  1.519
 GQU  C18  C22  single    1.521  0.020  1.521
 GQU  N21  C22  single    1.342  0.020  1.342
 GQU  C22  O23  double    1.221  0.020  1.221
 GQU  C10  H1   single    0.970  0.020  1.090
 GQU  C15  H2   single    0.930  0.020  1.080
 GQU  C17  H4   single    0.970  0.020  1.090
 GQU  C17  H5   single    0.970  0.020  1.090
 GQU  C20  H6   single    0.970  0.020  1.090
 GQU  C20  H7   single    0.970  0.020  1.090
 GQU  C24  H8   single    0.970  0.020  1.090
 GQU  C24  H9   single    0.970  0.020  1.090
 GQU  C04  H10  single    0.970  0.020  1.090
 GQU  C04  H11  single    0.970  0.020  1.090
 GQU  C05  H12  single    0.970  0.020  1.090
 GQU  C06  H13  single    0.970  0.020  1.090
 GQU  C06  H14  single    0.970  0.020  1.090
 GQU  C07  H15  single    0.970  0.020  1.090
 GQU  C07  H16  single    0.970  0.020  1.090
 GQU  C08  H17  single    0.970  0.020  1.090
 GQU  C08  H18  single    0.970  0.020  1.090
 GQU  C09  H19  single    0.970  0.020  1.090
 GQU  N13  H20  single    0.860  0.020  1.020
 GQU  C14  H21  single    0.970  0.020  1.090
 GQU  C18  H23  single    0.970  0.020  1.090
 GQU  C19  H24  single    0.970  0.020  1.090
 GQU  C19  H25  single    0.970  0.020  1.090
 GQU  N21  H26  single    0.860  0.020  1.020
 GQU  C25  H27  single    0.970  0.020  1.090
 GQU  C25  H28  single    0.970  0.020  1.090
 GQU  C27  H29  single    0.930  0.020  1.080
 GQU  C30  H30  single    0.930  0.020  1.080
 GQU  C33  H31  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
 GQU  H1   C10  C11  109.87  3.000
 GQU  H1   C10  C09  110.97  3.000
 GQU  C11  C10  C09  110.54  3.000
 GQU  H1   C10  N03  110.07  3.000
 GQU  C11  C10  N03  109.79  3.000
 GQU  C09  C10  N03  105.52  3.000
 GQU  H2   C15  O16  121.65  3.000
 GQU  H2   C15  C14  113.68  3.000
 GQU  O16  C15  C14  124.67  3.000
 GQU  H5   C17  H4   106.86  3.000
 GQU  H5   C17  C18  109.75  3.000
 GQU  H4   C17  C18  109.52  3.000
 GQU  H5   C17  C14  108.67  3.000
 GQU  H4   C17  C14  109.60  3.000
 GQU  C18  C17  C14  112.28  3.000
 GQU  H7   C20  H6   107.96  3.000
 GQU  H7   C20  N21  111.13  3.000
 GQU  H6   C20  N21  111.09  3.000
 GQU  H7   C20  C19  111.40  3.000
 GQU  H6   C20  C19  113.01  3.000
 GQU  N21  C20  C19  102.23  3.000
 GQU  O23  C22  N21  126.21  3.000
 GQU  O23  C22  C18  126.31  3.000
 GQU  N21  C22  C18  107.48  3.000
 GQU  C33  C26  C27  119.70  3.000
 GQU  C27  C26  C25  120.33  3.000
 GQU  C33  C26  C25  119.93  3.000
 GQU  C30  C28  F29  118.22  3.000
 GQU  F29  C28  C27  118.86  3.000
 GQU  C30  C28  C27  122.92  3.000
 GQU  N03  C02  O01  121.20  3.000
 GQU  O01  C02  C24  120.67  3.000
 GQU  N03  C02  C24  118.09  3.000
 GQU  C04  N03  C02  127.59  3.000
 GQU  C02  N03  C10  119.20  3.000
 GQU  C04  N03  C10  111.61  3.000
 GQU  H11  C04  H10  108.10  3.000
 GQU  H11  C04  C05  111.99  3.000
 GQU  H10  C04  C05  110.77  3.000
 GQU  H11  C04  N03  111.75  3.000
 GQU  H10  C04  N03  110.94  3.000
 GQU  C05  C04  N03  103.30  3.000
 GQU  H12  C05  C09  111.13  3.000
 GQU  H12  C05  C06  110.41  3.000
 GQU  C09  C05  C06  105.35  3.000
 GQU  H12  C05  C04  109.81  3.000
 GQU  C09  C05  C04  104.77  3.000
 GQU  C06  C05  C04  115.15  3.000
 GQU  H14  C06  H13  106.68  3.000
 GQU  H14  C06  C07  109.97  3.000
 GQU  H13  C06  C07  112.13  3.000
 GQU  H14  C06  C05  109.37  3.000
 GQU  H13  C06  C05  112.19  3.000
 GQU  C07  C06  C05  106.50  3.000
 GQU  H16  C07  H15  106.81  3.000
 GQU  H16  C07  C08  112.83  3.000
 GQU  H15  C07  C08  110.12  3.000
 GQU  H16  C07  C06  112.65  3.000
 GQU  H15  C07  C06  110.59  3.000
 GQU  C08  C07  C06  103.89  3.000
 GQU  H18  C08  H17  107.23  3.000
 GQU  H18  C08  C09  113.06  3.000
 GQU  H17  C08  C09  109.28  3.000
 GQU  H18  C08  C07  113.63  3.000
 GQU  H17  C08  C07  110.31  3.000
 GQU  C09  C08  C07  103.29  3.000
 GQU  H19  C09  C08  112.04  3.000
 GQU  H19  C09  C05  111.59  3.000
 GQU  C08  C09  C05  105.14  3.000
 GQU  H19  C09  C10  110.51  3.000
 GQU  C08  C09  C10  112.61  3.000
 GQU  C05  C09  C10  104.60  3.000
 GQU  N13  C11  O12  124.02  3.000
 GQU  N13  C11  C10  114.53  3.000
 GQU  O12  C11  C10  121.39  3.000
 GQU  H20  N13  C14  116.94  3.000
 GQU  H20  N13  C11  118.08  3.000
 GQU  C14  N13  C11  123.84  3.000
 GQU  H21  C14  N13  106.65  3.000
 GQU  H21  C14  C17  109.93  3.000
 GQU  N13  C14  C17  112.44  3.000
 GQU  H21  C14  C15  105.06  3.000
 GQU  C17  C14  C15  113.50  3.000
 GQU  N13  C14  C15  108.78  3.000
 GQU  H23  C18  C19  108.97  3.000
 GQU  H23  C18  C22  105.96  3.000
 GQU  C19  C18  C22  103.23  3.000
 GQU  H23  C18  C17  109.35  3.000
 GQU  C22  C18  C17  112.66  3.000
 GQU  C19  C18  C17  116.06  3.000
 GQU  H25  C19  H24  108.17  3.000
 GQU  H25  C19  C18  109.80  3.000
 GQU  H24  C19  C18  113.34  3.000
 GQU  H25  C19  C20  109.95  3.000
 GQU  H24  C19  C20  111.92  3.000
 GQU  C18  C19  C20  103.61  3.000
 GQU  H26  N21  C22  122.05  3.000
 GQU  H26  N21  C20  122.64  3.000
 GQU  C22  N21  C20  114.42  3.000
 GQU  H28  C25  H27  106.86  3.000
 GQU  H28  C25  C26  110.17  3.000
 GQU  H27  C25  C26  109.69  3.000
 GQU  H28  C25  C24  109.19  3.000
 GQU  H27  C25  C24  109.94  3.000
 GQU  C26  C25  C24  110.91  3.000
 GQU  H29  C27  C28  120.19  3.000
 GQU  H29  C27  C26  120.86  3.000
 GQU  C28  C27  C26  118.95  3.000
 GQU  H30  C30  C31  121.73  3.000
 GQU  H30  C30  C28  121.72  3.000
 GQU  C31  C30  C28  116.55  3.000
 GQU  C33  C31  F32  118.84  3.000
 GQU  C33  C31  C30  122.88  3.000
 GQU  F32  C31  C30  118.27  3.000
 GQU  H31  C33  C31  120.17  3.000
 GQU  H31  C33  C26  120.83  3.000
 GQU  C31  C33  C26  119.00  3.000
 GQU  H9   C24  H8   107.19  3.000
 GQU  H9   C24  C25  109.81  3.000
 GQU  H8   C24  C25  109.38  3.000
 GQU  H9   C24  C02  112.86  3.000
 GQU  H8   C24  C02  108.08  3.000
 GQU  C25  C24  C02  109.44  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
 GQU  CONST_01  C30  C31  C33  C26    0.00   0.0  0
 GQU  CONST_02  C30  C28  C27  C26    0.00   0.0  0
 GQU  CONST_03  C33  C31  C30  C28    0.00   0.0  0
 GQU  CONST_04  C33  C26  C27  C28    0.00   0.0  0
 GQU  CONST_05  C31  C33  C26  C27    0.00   0.0  0
 GQU  CONST_06  C31  C30  C28  C27    0.00   0.0  0
 GQU  CONST_07  C18  C22  N21  C20    0.00   0.0  0
 GQU  CONST_08  F32  C31  C33  C26  180.00   0.0  0
 GQU  CONST_09  F29  C28  C27  C26  180.00   0.0  0
 GQU  CONST_10  F32  C31  C30  C28  180.00   0.0  0
 GQU  CONST_11  C25  C26  C27  C28  180.00   0.0  0
 GQU  CONST_12  C31  C33  C26  C25  180.00   0.0  0
 GQU  CONST_13  C31  C30  C28  F29  180.00   0.0  0
 GQU  CONST_14  O23  C22  N21  C20  180.00   0.0  0
 GQU  CONST_15  H31  C33  C26  C27  180.00   0.0  0
 GQU  CONST_16  H30  C30  C28  C27  180.00   0.0  0
 GQU  CONST_17  H29  C27  C28  C30  180.00   0.0  0
 GQU  CONST_18  H26  N21  C22  C18  180.00   0.0  0
 GQU  CONST_19  C24  C02  N03  C10  180.00   0.0  0
 GQU  CONST_20  O01  C02  N03  C10    0.00   0.0  0
 GQU  CONST_21  C04  N03  C02  C24    0.00   0.0  0
 GQU  CONST_22  C04  N03  C02  O01  180.00   0.0  0
 GQU  CONST_23  C14  N13  C11  C10  180.00   0.0  0
 GQU  CONST_24  H20  N13  C11  C10    0.00   0.0  0
 GQU  CONST_25  C14  N13  C11  O12    0.00   0.0  0
 GQU  Var_01    C05  C04  N03  C10   29.35  30.0  1
 GQU  Var_02    C19  C20  N21  C22  -20.03  30.0  1
 GQU  Var_03    C08  C07  C06  C05  -26.66  30.0  1
 GQU  Var_04    C09  C08  C07  C06   39.29  30.0  1
 GQU  Var_05    N21  C20  C19  C18   28.75  30.0  1
 GQU  Var_06    C33  C26  C25  C24  -86.66  30.0  3
 GQU  Var_07    C02  C24  C25  C26  179.49  30.0  3
 GQU  Var_08    C25  C24  C02  N03  -95.76  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
 GQU  chir_01  C10  C09  N03  C11  positiv
 GQU  chir_02  C05  C06  C04  C09  negativ
 GQU  chir_03  C09  C10  C08  C05  negativ
 GQU  chir_04  C14  N13  C15  C17  positiv
 GQU  chir_05  C18  C22  C17  C19  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
 GQU  plan-1  C15  0.020
 GQU  plan-1  C14  0.020
 GQU  plan-1  H2   0.020
 GQU  plan-1  O16  0.020
 GQU  plan-2  C26  0.020
 GQU  plan-2  C28  0.020
 GQU  plan-2  C25  0.020
 GQU  plan-2  C27  0.020
 GQU  plan-2  F29  0.020
 GQU  plan-2  C30  0.020
 GQU  plan-2  C31  0.020
 GQU  plan-2  F32  0.020
 GQU  plan-2  C33  0.020
 GQU  plan-2  H29  0.020
 GQU  plan-2  H30  0.020
 GQU  plan-2  H31  0.020
 GQU  plan-3  C10  0.020
 GQU  plan-3  C11  0.020
 GQU  plan-3  O12  0.020
 GQU  plan-3  N13  0.020
 GQU  plan-3  C14  0.020
 GQU  plan-3  H20  0.020
 GQU  plan-4  C10  0.020
 GQU  plan-4  C02  0.020
 GQU  plan-4  N03  0.020
 GQU  plan-4  C04  0.020
 GQU  plan-4  C24  0.020
 GQU  plan-4  O01  0.020
 GQU  plan-5  C20  0.020
 GQU  plan-5  C22  0.020
 GQU  plan-5  C18  0.020
 GQU  plan-5  N21  0.020
 GQU  plan-5  H26  0.020
 GQU  plan-5  O23  0.020

