# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 23:41:56 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)[C@H]2CN([C@@H]([C@@H]12)C(=O)N[C@H](CO)C[C@@H]3CCNC3=O)C(=O)OCc4ccccc4
#
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
 YHI  YHI  'benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate'  ligand  62  31  .  2022-08-11  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_YHI
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
 YHI  C10  C  CR16  0  -0.264   -5.1103  -23.6857  -23.2062
 YHI  C15  C  CH1   0  -0.268  -11.6080  -28.4853  -22.7519
 YHI  C17  C  CH3   0  -0.681  -13.8045  -27.0328  -22.5674
 YHI  C21  C  CH1   0  -0.132   -7.9069  -29.1271  -20.1773
 YHI  C22  C  CH2   0  -0.424   -7.3683  -28.4347  -18.9269
 YHI  C24  C  CH2   0  -0.467   -6.1623  -26.5308  -20.1905
 YHI  C01  C  CH1   0  -0.272  -11.8771  -27.9371  -24.1251
 YHI  C02  C  CH2   0  -0.261  -11.2597  -26.5652  -24.2137
 YHI  N03  N  NT    0  -0.509  -10.8005  -26.2949  -22.8552
 YHI  C04  C  C     0   0.775  -10.1499  -25.1852  -22.4643
 YHI  O05  O  O2    0  -0.482  -10.1247  -24.2621  -23.4329
 YHI  C06  C  CH2   0  -0.225   -9.3662  -23.0851  -23.1854
 YHI  C07  C  CR6   0   0.052   -7.8816  -23.3323  -23.1816
 YHI  C08  C  CR16  0  -0.300   -7.0609  -22.5480  -22.3777
 YHI  C09  C  CR16  0  -0.238   -5.6829  -22.7164  -22.3943
 YHI  C11  C  CR16  0  -0.239   -5.9243  -24.4751  -24.0086
 YHI  C12  C  CR16  0  -0.288   -7.3010  -24.2953  -24.0029
 YHI  O13  O  O     0  -0.506   -9.6560  -25.0309  -21.3650
 YHI  C14  C  CH1   0  -0.186  -10.8098  -27.4502  -21.9849
 YHI  C16  C  CT    0  -0.001  -13.0164  -28.1697  -23.1724
 YHI  C18  C  CH3   0  -0.656  -13.8727  -29.3787  -23.4741
 YHI  C19  C  C     0   0.562   -9.3872  -27.9730  -21.7809
 YHI  N20  N  NH1   0  -0.634   -9.1651  -28.5371  -20.5851
 YHI  C23  C  CR15  0  -0.415   -7.1655  -26.9401  -19.1119
 YHI  C25  C  CH2   0  -0.261   -5.6193  -25.1920  -19.6906
 YHI  N26  N  NR15  0  -0.629   -5.7455  -25.3280  -18.2553
 YHI  C27  C  CR5   0   0.567   -6.6265  -26.2629  -17.8602
 YHI  O28  O  O     0  -0.488   -6.9438  -26.5136  -16.7091
 YHI  C29  C  CH2   0  -0.128   -8.1129  -30.6250  -19.9743
 YHI  O30  O  OH1   0  -0.663   -6.8747  -31.2132  -19.6593
 YHI  O31  O  O     0  -0.482   -8.5627  -27.9056  -22.6784
 YHI  H1   H  HCR6  0   0.254   -4.0372  -23.8268  -23.2131
 YHI  H3   H  HCH3  0   0.231  -14.2786  -27.3557  -21.6384
 YHI  H4   H  HCH3  0   0.239  -13.2099  -26.1493  -22.3413
 YHI  H5   H  HCH3  0   0.232  -14.6009  -26.7246  -23.2479
 YHI  H6   H  HCH1  0   0.262   -7.2068  -28.9843  -21.0021
 YHI  H7   H  HCH2  0   0.234   -8.0580  -28.6109  -18.0953
 YHI  H8   H  HCH2  0   0.245   -6.4189  -28.8998  -18.6537
 YHI  H9   H  HCH2  0   0.252   -6.6028  -26.4510  -21.1824
 YHI  H10  H  HCH2  0   0.242   -5.3527  -27.2639  -20.2428
 YHI  H11  H  HCH1  0   0.264  -11.7989  -28.5692  -25.0015
 YHI  H12  H  HCH2  0   0.253  -10.4254  -26.5728  -24.9199
 YHI  H13  H  HCH2  0   0.249  -11.9709  -25.8046  -24.5419
 YHI  H14  H  HCH2  0   0.268   -9.6336  -22.4139  -24.0026
 YHI  H15  H  HCH2  0   0.251   -9.6777  -22.6071  -22.2544
 YHI  H16  H  HCR6  0   0.252   -7.5022  -21.8022  -21.7264
 YHI  H17  H  HCR6  0   0.256   -5.0582  -22.1000  -21.7606
 YHI  H18  H  HCR6  0   0.255   -5.4866  -25.2327  -24.6461
 YHI  H19  H  HCR6  0   0.255   -7.9182  -24.9132  -24.6435
 YHI  H20  H  HCH1  0   0.280  -11.2736  -27.2040  -21.0241
 YHI  H21  H  HCH3  0   0.229  -14.3404  -29.7607  -22.5645
 YHI  H22  H  HCH3  0   0.230  -14.6696  -29.1234  -24.1754
 YHI  H23  H  HCH3  0   0.229  -13.2907  -30.1895  -23.9147
 YHI  H24  H  HNH1  0   0.401   -9.9021  -28.5010  -19.8958
 YHI  H25  H  HCR5  0   0.278   -8.1308  -26.4631  -19.3241
 YHI  H26  H  HCH2  0   0.245   -4.5833  -25.0208  -19.9820
 YHI  H27  H  HCH2  0   0.193   -8.8532  -30.7765  -19.1760
 YHI  H28  H  HCH2  0   0.208   -8.5410  -31.0437  -20.8943
 YHI  H29  H  HOH1  0   0.456   -7.0194  -32.1451  -19.4733
 YHI  H30  H  HCH2  0   0.238   -6.2133  -24.3533  -20.0650
 YHI  H31  H  HNR5  0   0.392   -5.3458  -24.6649  -17.6093
 YHI  H2   H  HCH1  0   0.273  -11.3398  -29.5247  -22.5994

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
 YHI  C01  C02  single    1.507  0.020  1.507
 YHI  C01  C16  single    1.503  0.020  1.503
 YHI  C01  C15  single    1.503  0.020  1.503
 YHI  C02  N03  single    1.459  0.020  1.459
 YHI  C18  C16  single    1.512  0.020  1.512
 YHI  C11  C12  aromatic  1.388  0.020  1.388
 YHI  C11  C10  aromatic  1.389  0.020  1.389
 YHI  C12  C07  aromatic  1.393  0.020  1.393
 YHI  C16  C15  single    1.503  0.020  1.503
 YHI  C16  C17  single    1.510  0.020  1.510
 YHI  C10  C09  aromatic  1.388  0.020  1.388
 YHI  C15  C14  single    1.516  0.020  1.516
 YHI  O05  C06  single    1.422  0.020  1.422
 YHI  O05  C04  single    1.338  0.020  1.338
 YHI  C07  C06  single    1.505  0.020  1.505
 YHI  C07  C08  aromatic  1.391  0.020  1.391
 YHI  O31  C19  double    1.221  0.020  1.221
 YHI  N03  C04  single    1.344  0.020  1.344
 YHI  N03  C14  single    1.446  0.020  1.446
 YHI  C09  C08  aromatic  1.388  0.020  1.388
 YHI  C04  O13  double    1.215  0.020  1.215
 YHI  C14  C19  single    1.529  0.020  1.529
 YHI  C19  N20  single    1.341  0.020  1.341
 YHI  N20  C21  single    1.448  0.020  1.448
 YHI  C24  C25  single    1.529  0.020  1.529
 YHI  C24  C23  single    1.529  0.020  1.529
 YHI  C21  C29  single    1.526  0.020  1.526
 YHI  C21  C22  single    1.527  0.020  1.527
 YHI  C25  N26  single    1.447  0.020  1.447
 YHI  C29  O30  single    1.407  0.020  1.407
 YHI  C23  C22  single    1.520  0.020  1.520
 YHI  C23  C27  single    1.522  0.020  1.522
 YHI  N26  C27  single    1.344  0.020  1.344
 YHI  C27  O28  double    1.220  0.020  1.220
 YHI  C10  H1   single    0.930  0.020  1.080
 YHI  C15  H2   single    0.970  0.020  1.090
 YHI  C17  H3   single    0.970  0.020  1.090
 YHI  C17  H4   single    0.970  0.020  1.090
 YHI  C17  H5   single    0.970  0.020  1.090
 YHI  C21  H6   single    0.970  0.020  1.090
 YHI  C22  H7   single    0.970  0.020  1.090
 YHI  C22  H8   single    0.970  0.020  1.090
 YHI  C24  H9   single    0.970  0.020  1.090
 YHI  C24  H10  single    0.970  0.020  1.090
 YHI  C01  H11  single    0.970  0.020  1.090
 YHI  C02  H12  single    0.970  0.020  1.090
 YHI  C02  H13  single    0.970  0.020  1.090
 YHI  C06  H14  single    0.970  0.020  1.090
 YHI  C06  H15  single    0.970  0.020  1.090
 YHI  C08  H16  single    0.930  0.020  1.080
 YHI  C09  H17  single    0.930  0.020  1.080
 YHI  C11  H18  single    0.930  0.020  1.080
 YHI  C12  H19  single    0.930  0.020  1.080
 YHI  C14  H20  single    0.970  0.020  1.090
 YHI  C18  H21  single    0.970  0.020  1.090
 YHI  C18  H22  single    0.970  0.020  1.090
 YHI  C18  H23  single    0.970  0.020  1.090
 YHI  N20  H24  single    0.860  0.020  1.020
 YHI  C23  H25  single    0.970  0.020  1.090
 YHI  C25  H26  single    0.970  0.020  1.090
 YHI  C29  H27  single    0.970  0.020  1.090
 YHI  C29  H28  single    0.970  0.020  1.090
 YHI  O30  H29  single    0.850  0.020  0.980
 YHI  C25  H30  single    0.970  0.020  1.090
 YHI  N26  H31  single    0.860  0.020  1.020

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
 YHI  H1   C10  C11  120.21  3.000
 YHI  H1   C10  C09  120.25  3.000
 YHI  C11  C10  C09  119.54  3.000
 YHI  H2   C15  C16  118.18  3.000
 YHI  H2   C15  C14  116.96  3.000
 YHI  C16  C15  C14  119.45  3.000
 YHI  H2   C15  C01  121.50  3.000
 YHI  C14  C15  C01  107.92  3.000
 YHI  C16  C15  C01   60.01  3.000
 YHI  H5   C17  H4   107.38  3.000
 YHI  H5   C17  H3   107.28  3.000
 YHI  H4   C17  H3   107.48  3.000
 YHI  H5   C17  C16  110.09  3.000
 YHI  H4   C17  C16  114.16  3.000
 YHI  H3   C17  C16  110.17  3.000
 YHI  H6   C21  C29  108.40  3.000
 YHI  H6   C21  N20  106.94  3.000
 YHI  C29  C21  N20  108.67  3.000
 YHI  H6   C21  C22  109.46  3.000
 YHI  C29  C21  C22  112.56  3.000
 YHI  N20  C21  C22  110.62  3.000
 YHI  H8   C22  H7   106.81  3.000
 YHI  H8   C22  C23  109.47  3.000
 YHI  H7   C22  C23  109.57  3.000
 YHI  H8   C22  C21  108.56  3.000
 YHI  H7   C22  C21  109.07  3.000
 YHI  C23  C22  C21  113.16  3.000
 YHI  H10  C24  H9   107.77  3.000
 YHI  H10  C24  C25  109.87  3.000
 YHI  H9   C24  C25  112.18  3.000
 YHI  H10  C24  C23  109.88  3.000
 YHI  H9   C24  C23  113.39  3.000
 YHI  C25  C24  C23  103.70  3.000
 YHI  H11  C01  C16  118.50  3.000
 YHI  H11  C01  C02  117.00  3.000
 YHI  C16  C01  C02  119.25  3.000
 YHI  H11  C01  C15  120.90  3.000
 YHI  C16  C01  C15   60.01  3.000
 YHI  C02  C01  C15  108.20  3.000
 YHI  H13  C02  H12  107.93  3.000
 YHI  H13  C02  N03  110.84  3.000
 YHI  H12  C02  N03  111.26  3.000
 YHI  H13  C02  C01  112.64  3.000
 YHI  H12  C02  C01  110.14  3.000
 YHI  N03  C02  C01  104.05  3.000
 YHI  C14  N03  C04  119.17  3.000
 YHI  C14  N03  C02  114.22  3.000
 YHI  C04  N03  C02  125.16  3.000
 YHI  O13  C04  O05  124.03  3.000
 YHI  O13  C04  N03  124.38  3.000
 YHI  O05  C04  N03  111.59  3.000
 YHI  C06  O05  C04  117.07  3.000
 YHI  H15  C06  H14  107.42  3.000
 YHI  H15  C06  C07  110.56  3.000
 YHI  H14  C06  C07  110.17  3.000
 YHI  H15  C06  O05  111.01  3.000
 YHI  H14  C06  O05  104.37  3.000
 YHI  C07  C06  O05  113.00  3.000
 YHI  C12  C07  C08  119.00  3.000
 YHI  C08  C07  C06  119.40  3.000
 YHI  C12  C07  C06  121.56  3.000
 YHI  H16  C08  C09  119.64  3.000
 YHI  H16  C08  C07  119.66  3.000
 YHI  C09  C08  C07  120.69  3.000
 YHI  H17  C09  C08  119.78  3.000
 YHI  H17  C09  C10  120.14  3.000
 YHI  C08  C09  C10  120.07  3.000
 YHI  H18  C11  C12  119.60  3.000
 YHI  H18  C11  C10  120.06  3.000
 YHI  C12  C11  C10  120.34  3.000
 YHI  H19  C12  C11  119.26  3.000
 YHI  H19  C12  C07  120.39  3.000
 YHI  C11  C12  C07  120.36  3.000
 YHI  H20  C14  C19  110.72  3.000
 YHI  H20  C14  N03  110.55  3.000
 YHI  C19  C14  N03  110.32  3.000
 YHI  H20  C14  C15  112.00  3.000
 YHI  C19  C14  C15  108.90  3.000
 YHI  N03  C14  C15  104.14  3.000
 YHI  C18  C16  C01  115.25  3.000
 YHI  C18  C16  C17  112.73  3.000
 YHI  C01  C16  C17  122.21  3.000
 YHI  C17  C16  C15  122.34  3.000
 YHI  C18  C16  C15  114.74  3.000
 YHI  C01  C16  C15   59.98  3.000
 YHI  H23  C18  H22  107.68  3.000
 YHI  H23  C18  H21  107.75  3.000
 YHI  H22  C18  H21  107.71  3.000
 YHI  H23  C18  C16  111.89  3.000
 YHI  H22  C18  C16  110.77  3.000
 YHI  H21  C18  C16  110.87  3.000
 YHI  O31  C19  N20  124.56  3.000
 YHI  N20  C19  C14  114.64  3.000
 YHI  O31  C19  C14  120.76  3.000
 YHI  H24  N20  C19  118.23  3.000
 YHI  H24  N20  C21  117.16  3.000
 YHI  C19  N20  C21  124.50  3.000
 YHI  H25  C23  C27  106.09  3.000
 YHI  H25  C23  C24  108.93  3.000
 YHI  C27  C23  C24  103.22  3.000
 YHI  H25  C23  C22  109.49  3.000
 YHI  C27  C23  C22  112.63  3.000
 YHI  C24  C23  C22  115.90  3.000
 YHI  H30  C25  H26  107.72  3.000
 YHI  H30  C25  N26  111.36  3.000
 YHI  H26  C25  N26  111.27  3.000
 YHI  H30  C25  C24  111.51  3.000
 YHI  H26  C25  C24  112.82  3.000
 YHI  N26  C25  C24  102.18  3.000
 YHI  H31  N26  C27  121.94  3.000
 YHI  H31  N26  C25  122.61  3.000
 YHI  C27  N26  C25  114.46  3.000
 YHI  O28  C27  N26  126.21  3.000
 YHI  O28  C27  C23  126.33  3.000
 YHI  N26  C27  C23  107.45  3.000
 YHI  H28  C29  H27  107.07  3.000
 YHI  H28  C29  O30  111.80  3.000
 YHI  H27  C29  O30  111.87  3.000
 YHI  H28  C29  C21  108.40  3.000
 YHI  H27  C29  C21  108.84  3.000
 YHI  O30  C29  C21  108.76  3.000
 YHI  H29  O30  C29  108.44  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
 YHI  CONST_01  C07  C12  C11  C10    0.00   0.0  0
 YHI  CONST_02  C07  C08  C09  C10    0.00   0.0  0
 YHI  CONST_03  C11  C12  C07  C08    0.00   0.0  0
 YHI  CONST_04  C11  C10  C09  C08    0.00   0.0  0
 YHI  CONST_05  C12  C11  C10  C09    0.00   0.0  0
 YHI  CONST_06  C12  C07  C08  C09    0.00   0.0  0
 YHI  CONST_07  C25  N26  C27  C23    0.00   0.0  0
 YHI  CONST_08  C11  C12  C07  C06  180.00   0.0  0
 YHI  CONST_09  C09  C08  C07  C06  180.00   0.0  0
 YHI  CONST_10  O28  C27  N26  C25  180.00   0.0  0
 YHI  CONST_11  H19  C12  C11  C10  180.00   0.0  0
 YHI  CONST_12  H16  C08  C09  C10  180.00   0.0  0
 YHI  CONST_13  H18  C11  C12  C07  180.00   0.0  0
 YHI  CONST_14  H17  C09  C08  C07  180.00   0.0  0
 YHI  CONST_15  H1   C10  C09  C08  180.00   0.0  0
 YHI  CONST_16  H31  N26  C27  C23  180.00   0.0  0
 YHI  CONST_17  C14  C19  N20  C21  180.00   0.0  0
 YHI  CONST_18  H24  N20  C19  C14    0.00   0.0  0
 YHI  CONST_19  O31  C19  N20  C21    0.00   0.0  0
 YHI  Var_01    N03  C02  C01  C15   -6.68  30.0  1
 YHI  Var_02    C02  C01  C16  C15  -95.18  30.0  1
 YHI  Var_03    C27  N26  C25  C24  -20.53  30.0  1
 YHI  Var_04    C14  N03  C02  C01   12.22  30.0  1
 YHI  Var_05    C14  C15  C16  C01   94.71  30.0  1
 YHI  Var_06    N26  C25  C24  C23   28.82  30.0  1
 YHI  Var_07    O05  C04  N03  C02    8.41  30.0  2
 YHI  Var_08    C12  C07  C06  O05   33.09  30.0  2
 YHI  Var_09    H21  C18  C16  C15   86.34  30.0  3
 YHI  Var_10    H3   C17  C16  C15  -84.37  30.0  3
 YHI  Var_11    C07  C06  O05  C04   70.44  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
 YHI  chir_02  C21  N20  C29  C22  positiv
 YHI  chir_04  C14  C15  N03  C19  positiv
 YHI  chir_05  C23  C24  C22  C27  negativ
 YHI  chir_06  C15  C01  C16  C14  both
 YHI  chir_07  C01  C15  C16  C02  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
 YHI  plan-1  C10  0.020
 YHI  plan-1  C06  0.020
 YHI  plan-1  C07  0.020
 YHI  plan-1  C08  0.020
 YHI  plan-1  C09  0.020
 YHI  plan-1  C11  0.020
 YHI  plan-1  C12  0.020
 YHI  plan-1  H1   0.020
 YHI  plan-1  H16  0.020
 YHI  plan-1  H17  0.020
 YHI  plan-1  H18  0.020
 YHI  plan-1  H19  0.020
 YHI  plan-2  C21  0.020
 YHI  plan-2  C14  0.020
 YHI  plan-2  C19  0.020
 YHI  plan-2  N20  0.020
 YHI  plan-2  O31  0.020
 YHI  plan-2  H24  0.020
 YHI  plan-3  C23  0.020
 YHI  plan-3  C25  0.020
 YHI  plan-3  N26  0.020
 YHI  plan-3  C27  0.020
 YHI  plan-3  O28  0.020
 YHI  plan-3  H31  0.020
 YHI  plan-4  N03  0.020
 YHI  plan-4  C04  0.020
 YHI  plan-4  O05  0.020
 YHI  plan-4  O13  0.020

