# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:49:47 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: Nalpha-[(benzyloxy)carbonyl]-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-phenylalaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)OCc3ccccc3
#
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
 GHX  GHX  Nalpha-[(benzyloxy)carbonyl]-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-phenylalaninamide  ligand  59  32  .  2021-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GHX
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
 GHX  O1   O  O     0  -0.495   6.8486  -0.2422  -1.9416
 GHX  C34  C  C     0   0.572   6.1138  -1.1678  -1.6364
 GHX  N33  N  NH1   0  -0.629   6.2171  -2.4385  -2.0541
 GHX  C32  C  CH2   0  -0.258   5.1696  -3.3174  -1.5773
 GHX  C31  C  CH2   0  -0.473   4.6229  -2.5477  -0.3735
 GHX  C30  C  CH1   0  -0.404   4.9005  -1.0868  -0.7220
 GHX  C29  C  CH2   0  -0.470   5.1212  -0.1573   0.4616
 GHX  C26  C  CH1   0  -0.202   3.9202  -0.1353   1.4085
 GHX  C27  C  C1    0   0.196   4.2266   0.7201   2.6181
 GHX  O28  O  O     0  -0.360   3.5482   1.6424   2.9839
 GHX  N24  N  NH1   0  -0.634   2.7295   0.3004   0.7355
 GHX  C23  C  C     0   0.578   1.4962  -0.0019   1.1732
 GHX  O25  O  O     0  -0.480   1.2729  -0.7903   2.0761
 GHX  C15  C  CH1   0  -0.224   0.3726   0.7529   0.4764
 GHX  C16  C  CH2   0  -0.522   0.0834   2.0498   1.2650
 GHX  C17  C  CR6   0   0.136  -1.0474   2.8156   0.6430
 GHX  C22  C  CR16  0  -0.294  -0.8116   3.7052  -0.4018
 GHX  C21  C  CR16  0  -0.242  -1.8629   4.3611  -1.0259
 GHX  C20  C  CR16  0  -0.267  -3.1701   4.1297  -0.6173
 GHX  C19  C  CR16  0  -0.238  -3.4167   3.2471   0.4253
 GHX  C18  C  CR16  0  -0.305  -2.3608   2.5992   1.0524
 GHX  N13  N  NH1   0  -0.655  -0.7890  -0.0878   0.3919
 GHX  C12  C  C     0   0.770  -1.5818  -0.1120  -0.6999
 GHX  O14  O  O     0  -0.508  -1.3093   0.3669  -1.7794
 GHX  O11  O  O2    0  -0.479  -2.7171  -0.7669  -0.4380
 GHX  C10  C  CH2   0  -0.239  -3.6782  -0.8406  -1.4964
 GHX  C1   C  CR6   0   0.078  -4.9164  -1.4536  -0.9171
 GHX  C6   C  CR16  0  -0.291  -5.1248  -2.8276  -0.9833
 GHX  C5   C  CR16  0  -0.242  -6.2620  -3.3964  -0.4253
 GHX  C4   C  CR16  0  -0.262  -7.2010  -2.5922   0.2071
 GHX  C3   C  CR16  0  -0.242  -7.0002  -1.2193   0.2788
 GHX  C2   C  CR16  0  -0.286  -5.8622  -0.6549  -0.2802
 GHX  H1   H  HNH1  0   0.398   6.8856  -2.7203  -2.7547
 GHX  H2   H  HCH2  0   0.238   4.4020  -3.4686  -2.3419
 GHX  H3   H  HCH2  0   0.254   5.5699  -4.2929  -1.3043
 GHX  H4   H  HCH2  0   0.261   3.5695  -2.7576  -0.1962
 GHX  H5   H  HCH2  0   0.250   5.1758  -2.8295   0.5265
 GHX  H6   H  HCH1  0   0.288   4.0810  -0.6969  -1.3386
 GHX  H7   H  HCH2  0   0.265   5.9975  -0.4842   1.0268
 GHX  H8   H  HCH2  0   0.266   5.3324   0.8549   0.1066
 GHX  H9   H  HCH1  0   0.298   3.7650  -1.1503   1.7924
 GHX  H10  H  H     0   0.208   5.1408   0.4210   3.1608
 GHX  H13  H  HNH1  0   0.409   2.8284   1.0172   0.0330
 GHX  H14  H  HCH1  0   0.293   0.6726   1.0177  -0.5384
 GHX  H15  H  HCH2  0   0.264  -0.1573   1.7861   2.2980
 GHX  H16  H  HCH2  0   0.266   0.9928   2.6540   1.2920
 GHX  H17  H  HCR6  0   0.245   0.2051   3.8851  -0.7328
 GHX  H18  H  HCR6  0   0.252  -1.6636   5.0526  -1.8348
 GHX  H19  H  HCR6  0   0.253  -3.9907   4.6395  -1.1054
 GHX  H20  H  HCR6  0   0.249  -4.4320   3.0648   0.7544
 GHX  H21  H  HCR6  0   0.247  -2.5589   1.9180   1.8713
 GHX  H22  H  HNH1  0   0.397  -1.1446  -0.4765   1.2523
 GHX  H23  H  HCH2  0   0.246  -3.8871   0.1589  -1.8828
 GHX  H24  H  HCH2  0   0.247  -3.2904  -1.4481  -2.3172
 GHX  H25  H  HCR6  0   0.255  -4.3958  -3.4572  -1.4798
 GHX  H26  H  HCR6  0   0.258  -6.4164  -4.4659  -0.4869
 GHX  H27  H  HCR6  0   0.260  -8.0894  -3.0332   0.6402
 GHX  H28  H  HCR6  0   0.259  -7.7322  -0.5891   0.7668
 GHX  H29  H  HCR6  0   0.248  -5.7109   0.4172  -0.2262

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
 GHX  C27  O28  double    1.202  0.020  1.202
 GHX  C27  C26  single    1.513  0.020  1.513
 GHX  C26  C29  single    1.530  0.020  1.530
 GHX  C26  N24  single    1.435  0.020  1.435
 GHX  C29  C30  single    1.521  0.020  1.521
 GHX  O1   C34  double    1.221  0.020  1.221
 GHX  C34  C30  single    1.521  0.020  1.521
 GHX  C34  N33  single    1.342  0.020  1.342
 GHX  N24  C23  single    1.343  0.020  1.343
 GHX  C30  C31  single    1.527  0.020  1.527
 GHX  C31  C32  single    1.530  0.020  1.530
 GHX  N33  C32  single    1.448  0.020  1.448
 GHX  O25  C23  double    1.219  0.020  1.219
 GHX  C23  C15  single    1.522  0.020  1.522
 GHX  C16  C15  single    1.545  0.020  1.545
 GHX  C16  C17  single    1.501  0.020  1.501
 GHX  C15  N13  single    1.436  0.020  1.436
 GHX  C17  C18  aromatic  1.393  0.020  1.393
 GHX  C17  C22  aromatic  1.392  0.020  1.392
 GHX  C18  C19  aromatic  1.389  0.020  1.389
 GHX  O14  C12  double    1.212  0.020  1.212
 GHX  C22  C21  aromatic  1.387  0.020  1.387
 GHX  N13  C12  single    1.349  0.020  1.349
 GHX  C12  O11  single    1.337  0.020  1.337
 GHX  C19  C20  aromatic  1.388  0.020  1.388
 GHX  C21  C20  aromatic  1.389  0.020  1.389
 GHX  O11  C10  single    1.432  0.020  1.432
 GHX  C10  C1   single    1.498  0.020  1.498
 GHX  C6   C1   aromatic  1.391  0.020  1.391
 GHX  C6   C5   aromatic  1.389  0.020  1.389
 GHX  C1   C2   aromatic  1.392  0.020  1.392
 GHX  C5   C4   aromatic  1.389  0.020  1.389
 GHX  C2   C3   aromatic  1.388  0.020  1.388
 GHX  C4   C3   aromatic  1.389  0.020  1.389
 GHX  N33  H1   single    0.860  0.020  1.020
 GHX  C32  H2   single    0.970  0.020  1.090
 GHX  C32  H3   single    0.970  0.020  1.090
 GHX  C31  H4   single    0.970  0.020  1.090
 GHX  C31  H5   single    0.970  0.020  1.090
 GHX  C30  H6   single    0.970  0.020  1.090
 GHX  C29  H7   single    0.970  0.020  1.090
 GHX  C29  H8   single    0.970  0.020  1.090
 GHX  C26  H9   single    0.970  0.020  1.090
 GHX  C27  H10  single    0.930  0.020  1.080
 GHX  N24  H13  single    0.860  0.020  1.020
 GHX  C15  H14  single    0.970  0.020  1.090
 GHX  C16  H15  single    0.970  0.020  1.090
 GHX  C16  H16  single    0.970  0.020  1.090
 GHX  C22  H17  single    0.930  0.020  1.080
 GHX  C21  H18  single    0.930  0.020  1.080
 GHX  C20  H19  single    0.930  0.020  1.080
 GHX  C19  H20  single    0.930  0.020  1.080
 GHX  C18  H21  single    0.930  0.020  1.080
 GHX  N13  H22  single    0.860  0.020  1.020
 GHX  C10  H23  single    0.970  0.020  1.090
 GHX  C10  H24  single    0.970  0.020  1.090
 GHX  C6   H25  single    0.930  0.020  1.080
 GHX  C5   H26  single    0.930  0.020  1.080
 GHX  C4   H27  single    0.930  0.020  1.080
 GHX  C3   H28  single    0.930  0.020  1.080
 GHX  C2   H29  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
 GHX  C30  C34  N33  107.39  3.000
 GHX  N33  C34  O1   126.45  3.000
 GHX  C30  C34  O1   126.16  3.000
 GHX  H1   N33  C32  122.59  3.000
 GHX  H1   N33  C34  122.14  3.000
 GHX  C32  N33  C34  114.63  3.000
 GHX  H3   C32  H2   108.01  3.000
 GHX  H3   C32  C31  112.62  3.000
 GHX  H2   C32  C31  111.64  3.000
 GHX  H3   C32  N33  111.12  3.000
 GHX  H2   C32  N33  111.18  3.000
 GHX  C31  C32  N33  102.25  3.000
 GHX  H5   C31  H4   107.80  3.000
 GHX  H5   C31  C30  110.03  3.000
 GHX  H4   C31  C30  113.42  3.000
 GHX  H5   C31  C32  109.72  3.000
 GHX  H4   C31  C32  112.14  3.000
 GHX  C30  C31  C32  103.69  3.000
 GHX  H6   C30  C29  109.18  3.000
 GHX  H6   C30  C31  109.41  3.000
 GHX  C29  C30  C31  115.68  3.000
 GHX  H6   C30  C34  106.07  3.000
 GHX  C31  C30  C34  103.36  3.000
 GHX  C29  C30  C34  112.61  3.000
 GHX  H8   C29  H7   106.85  3.000
 GHX  H8   C29  C26  109.84  3.000
 GHX  H7   C29  C26  108.29  3.000
 GHX  H8   C29  C30  109.94  3.000
 GHX  H7   C29  C30  109.64  3.000
 GHX  C26  C29  C30  112.12  3.000
 GHX  H9   C26  N24  109.13  3.000
 GHX  H9   C26  C27  105.80  3.000
 GHX  N24  C26  C27  111.79  3.000
 GHX  H9   C26  C29  108.33  3.000
 GHX  N24  C26  C29  111.44  3.000
 GHX  C27  C26  C29  110.13  3.000
 GHX  H10  C27  O28  121.70  3.000
 GHX  H10  C27  C26  114.04  3.000
 GHX  O28  C27  C26  124.26  3.000
 GHX  H13  N24  C23  118.49  3.000
 GHX  H13  N24  C26  117.45  3.000
 GHX  C23  N24  C26  122.72  3.000
 GHX  C15  C23  O25  121.62  3.000
 GHX  C15  C23  N24  114.65  3.000
 GHX  O25  C23  N24  123.71  3.000
 GHX  H14  C15  N13  108.04  3.000
 GHX  H14  C15  C16  108.81  3.000
 GHX  N13  C15  C16  111.71  3.000
 GHX  H14  C15  C23  110.07  3.000
 GHX  N13  C15  C23  109.49  3.000
 GHX  C16  C15  C23  108.70  3.000
 GHX  H16  C16  H15  107.07  3.000
 GHX  H16  C16  C17  110.82  3.000
 GHX  H15  C16  C17  110.42  3.000
 GHX  H16  C16  C15  108.73  3.000
 GHX  H15  C16  C15  108.73  3.000
 GHX  C17  C16  C15  110.97  3.000
 GHX  C18  C17  C22  118.66  3.000
 GHX  C22  C17  C16  120.63  3.000
 GHX  C18  C17  C16  120.63  3.000
 GHX  H17  C22  C21  119.66  3.000
 GHX  H17  C22  C17  119.60  3.000
 GHX  C21  C22  C17  120.75  3.000
 GHX  H18  C21  C20  119.96  3.000
 GHX  H18  C21  C22  119.90  3.000
 GHX  C20  C21  C22  120.14  3.000
 GHX  H19  C20  C19  120.23  3.000
 GHX  H19  C20  C21  120.16  3.000
 GHX  C19  C20  C21  119.61  3.000
 GHX  H20  C19  C18  119.82  3.000
 GHX  H20  C19  C20  120.13  3.000
 GHX  C18  C19  C20  120.05  3.000
 GHX  H21  C18  C19  119.71  3.000
 GHX  H21  C18  C17  119.50  3.000
 GHX  C19  C18  C17  120.79  3.000
 GHX  H22  N13  C12  118.42  3.000
 GHX  H22  N13  C15  117.41  3.000
 GHX  C12  N13  C15  122.22  3.000
 GHX  O11  C12  O14  123.99  3.000
 GHX  O11  C12  N13  110.45  3.000
 GHX  O14  C12  N13  125.55  3.000
 GHX  C10  O11  C12  116.78  3.000
 GHX  H24  C10  H23  108.13  3.000
 GHX  H24  C10  C1   110.88  3.000
 GHX  H23  C10  C1   110.69  3.000
 GHX  H24  C10  O11  110.23  3.000
 GHX  H23  C10  O11  110.06  3.000
 GHX  C1   C10  O11  106.86  3.000
 GHX  C2   C1   C6   119.12  3.000
 GHX  C2   C1   C10  120.24  3.000
 GHX  C6   C1   C10  120.63  3.000
 GHX  H25  C6   C5   119.81  3.000
 GHX  H25  C6   C1   119.66  3.000
 GHX  C5   C6   C1   120.53  3.000
 GHX  H26  C5   C4   120.11  3.000
 GHX  H26  C5   C6   119.91  3.000
 GHX  C4   C5   C6   119.97  3.000
 GHX  H27  C4   C3   120.05  3.000
 GHX  H27  C4   C5   120.09  3.000
 GHX  C3   C4   C5   119.86  3.000
 GHX  H28  C3   C2   119.96  3.000
 GHX  H28  C3   C4   120.06  3.000
 GHX  C2   C3   C4   119.98  3.000
 GHX  H29  C2   C3   119.78  3.000
 GHX  H29  C2   C1   119.69  3.000
 GHX  C3   C2   C1   120.53  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
 GHX  CONST_01  C20  C19  C18  C17     0.00   0.0  0
 GHX  CONST_02  C20  C21  C22  C17     0.00   0.0  0
 GHX  CONST_03  C19  C18  C17  C22     0.00   0.0  0
 GHX  CONST_04  C19  C20  C21  C22     0.00   0.0  0
 GHX  CONST_05  C18  C17  C22  C21     0.00   0.0  0
 GHX  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 GHX  CONST_07  C4   C5   C6   C1      0.00   0.0  0
 GHX  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 GHX  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 GHX  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 GHX  CONST_11  C2   C1   C6   C5      0.00   0.0  0
 GHX  CONST_12  C2   C3   C4   C5      0.00   0.0  0
 GHX  CONST_13  C30  C34  N33  C32     0.00   0.0  0
 GHX  CONST_14  C19  C18  C17  C16   180.00   0.0  0
 GHX  CONST_15  C21  C22  C17  C16   180.00   0.0  0
 GHX  CONST_16  C5   C6   C1   C10   180.00   0.0  0
 GHX  CONST_17  C3   C2   C1   C10   180.00   0.0  0
 GHX  CONST_18  C32  N33  C34  O1    180.00   0.0  0
 GHX  CONST_19  H20  C19  C18  C17   180.00   0.0  0
 GHX  CONST_20  H18  C21  C22  C17   180.00   0.0  0
 GHX  CONST_21  H21  C18  C17  C22   180.00   0.0  0
 GHX  CONST_22  H19  C20  C21  C22   180.00   0.0  0
 GHX  CONST_23  H17  C22  C21  C20   180.00   0.0  0
 GHX  CONST_24  H26  C5   C6   C1    180.00   0.0  0
 GHX  CONST_25  H28  C3   C2   C1    180.00   0.0  0
 GHX  CONST_26  H29  C2   C1   C6    180.00   0.0  0
 GHX  CONST_27  H27  C4   C5   C6    180.00   0.0  0
 GHX  CONST_28  H25  C6   C5   C4    180.00   0.0  0
 GHX  CONST_29  H1   N33  C34  C30   180.00   0.0  0
 GHX  CONST_30  O25  C23  N24  C26     0.00   0.0  0
 GHX  CONST_31  C15  C23  N24  C26   180.00   0.0  0
 GHX  CONST_32  H13  N24  C23  O25   180.00   0.0  0
 GHX  Var_01    C31  C32  N33  C34   -19.48  30.0  1
 GHX  Var_02    C30  C31  C32  N33    28.12  30.0  1
 GHX  Var_03    C18  C17  C16  C15    90.98  30.0  2
 GHX  Var_04    C6   C1   C10  O11   -92.70  30.0  2
 GHX  Var_05    C1   C10  O11  C12  -172.79  30.0  3
 GHX  Var_06    O14  C12  N13  C15    12.99  30.0  2

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
 GHX  chir_01  C30  C29  C34  C31  negativ
 GHX  chir_02  C26  N24  C27  C29  positiv
 GHX  chir_03  C15  N13  C23  C16  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
 GHX  plan-1  C16  0.020
 GHX  plan-1  C17  0.020
 GHX  plan-1  C22  0.020
 GHX  plan-1  C21  0.020
 GHX  plan-1  C20  0.020
 GHX  plan-1  C19  0.020
 GHX  plan-1  C18  0.020
 GHX  plan-1  H17  0.020
 GHX  plan-1  H18  0.020
 GHX  plan-1  H19  0.020
 GHX  plan-1  H20  0.020
 GHX  plan-1  H21  0.020
 GHX  plan-2  C10  0.020
 GHX  plan-2  C1   0.020
 GHX  plan-2  C6   0.020
 GHX  plan-2  C5   0.020
 GHX  plan-2  C4   0.020
 GHX  plan-2  C3   0.020
 GHX  plan-2  C2   0.020
 GHX  plan-2  H25  0.020
 GHX  plan-2  H26  0.020
 GHX  plan-2  H27  0.020
 GHX  plan-2  H28  0.020
 GHX  plan-2  H29  0.020
 GHX  plan-3  C26  0.020
 GHX  plan-3  N24  0.020
 GHX  plan-3  C23  0.020
 GHX  plan-3  O25  0.020
 GHX  plan-3  C15  0.020
 GHX  plan-3  H13  0.020
 GHX  plan-4  O1   0.020
 GHX  plan-4  C34  0.020
 GHX  plan-4  N33  0.020
 GHX  plan-4  C32  0.020
 GHX  plan-4  C30  0.020
 GHX  plan-4  H1   0.020
 GHX  plan-5  C26  0.020
 GHX  plan-5  C27  0.020
 GHX  plan-5  O28  0.020
 GHX  plan-5  H10  0.020
 GHX  plan-6  N13  0.020
 GHX  plan-6  C12  0.020
 GHX  plan-6  O14  0.020
 GHX  plan-6  O11  0.020

