# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 23:37:56 2020
#   Inital geometry file: a 168 line input string
#   Ligand name: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-3-cyclohexyl-L-alanyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC([C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CCCCC2)NC(=O)OCc3ccccc3)[S](O)(=O)=O
#
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
 M40  M40  '(1R,2S)-2-({N-[(benzyloxy)carbonyl]-3-cyclohexyl-L-alanyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid'  ligand  70  36  .  2021-08-14  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_M40
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
 M40  O01  O  O      0  -0.517   2.3949   0.3562   1.8534
 M40  C02  C  C      0   0.759   2.5711  -0.1861   0.7813
 M40  O03  O  O2     0  -0.482   3.6959  -0.8342   0.4518
 M40  C04  C  CH2    0  -0.237   4.7492  -0.8429   1.4210
 M40  C05  C  C      0   0.075   5.9080  -1.5567   0.7930
 M40  C06  C  C1     0  -0.285   6.7287  -0.8952  -0.1175
 M40  C07  C  C1     0  -0.242   7.7858  -1.5574  -0.7244
 M40  C08  C  C1     0  -0.262   8.0344  -2.8918  -0.4253
 M40  C09  C  C1     0  -0.242   7.2225  -3.5580   0.4823
 M40  C10  C  C1     0  -0.296   6.1629  -2.8923   1.0857
 M40  N11  N  NH1    0  -0.647   1.6939  -0.2200  -0.2366
 M40  C12  C  CH1    0  -0.251   0.3640   0.3206  -0.1547
 M40  C13  C  CH2    0  -0.420   0.2070   1.5925  -1.0033
 M40  C14  C  CH1    0  -0.228   0.9816   2.7982  -0.4753
 M40  C15  C  CH2    0  -0.414   0.9829   3.9215  -1.5136
 M40  C16  C  CH2    0  -0.433   1.7167   5.1632  -1.0169
 M40  C17  C  CH2    0  -0.429   1.1420   5.6562   0.3064
 M40  C18  C  CH2    0  -0.428   1.1472   4.5466   1.3514
 M40  C19  C  CH2    0  -0.425   0.4145   3.3054   0.8508
 M40  C20  C  C      0   0.593  -0.6448  -0.7309  -0.6137
 M40  N21  N  NH1    0  -0.626  -1.8957  -0.4750  -0.2130
 M40  C22  C  CH1    0  -0.135  -3.0517  -1.2528  -0.5853
 M40  C23  C  CH2    0  -0.432  -3.9917  -1.4295   0.6030
 M40  C24  C  CH1    0  -0.397  -3.5556  -2.4600   1.6524
 M40  C25  C  CH2    0  -0.473  -4.4691  -2.3749   2.8788
 M40  C26  C  CH2    0  -0.260  -3.7914  -1.3146   3.7522
 M40  N27  N  NH1    0  -0.620  -2.3989  -1.4745   3.3918
 M40  C28  C  C      0   0.548  -2.1860  -2.1723   2.2611
 M40  O29  O  O      0  -0.484  -1.1000  -2.5185   1.8284
 M40  O32  O  O      0  -0.495  -0.3220  -1.6815  -1.3095
 M40  H1   H  HCH2   0   0.246   5.0229   0.1802   1.6872
 M40  H3   H  H      0   0.255   6.5422   0.1465  -0.3512
 M40  H10  H  HCH2   0   0.237   0.5318   1.3622  -2.0238
 M40  H11  H  HCH2   0   0.233  -0.8536   1.8556  -1.0735
 M40  H12  H  HCH1   0   0.215   2.0252   2.4994  -0.3105
 M40  H13  H  HCH2   0   0.224   1.4350   3.5652  -2.4439
 M40  H14  H  HCH2   0   0.205  -0.0530   4.1883  -1.7555
 M40  H15  H  HCH2   0   0.207   2.7781   4.9265  -0.8845
 M40  H16  H  HCH2   0   0.225   1.6681   5.9529  -1.7706
 M40  H17  H  HCH2   0   0.224   1.7060   6.5208   0.6658
 M40  H18  H  HCH2   0   0.207   0.1136   6.0009   0.1487
 M40  H19  H  HCH2   0   0.208   2.1821   4.2802   1.5922
 M40  H20  H  HCH2   0   0.225   0.6938   4.8957   2.2824
 M40  H21  H  HCH2   0   0.203  -0.6477   3.5431   0.7139
 M40  H22  H  HCH2   0   0.232   0.4627   2.5239   1.6126
 M40  H23  H  HNH1   0   0.396  -2.0838   0.4025   0.2470
 M40  H24  H  HCH1   0   0.266  -2.6848  -2.2365  -0.8930
 M40  H25  H  HCH2   0   0.236  -4.1610  -0.4600   1.0805
 M40  H26  H  HCH2   0   0.260  -4.9635  -1.7554   0.2304
 M40  H27  H  HCH1   0   0.270  -3.5503  -3.4539   1.1996
 M40  H28  H  HCH2   0   0.252  -5.4975  -2.1138   2.6301
 M40  H29  H  HCH2   0   0.256  -4.4845  -3.3300   3.4069
 M40  H30  H  HCH2   0   0.233  -4.1521  -0.3065   3.5272
 M40  H31  H  HCH2   0   0.254  -3.9437  -1.4906   4.8166
 M40  H32  H  HNH1   0   0.393  -1.6428  -1.1214   3.9572
 M40  H35  H  HOH1   0   0.464  -4.2644  -2.1959  -2.8607
 M40  S1   S  S      0   1.401  -4.5554   0.9510  -1.5629
 M40  O2   O  OS     0  -0.757  -4.7164   1.5201  -2.9130
 M40  O3   O  OS    -1  -0.748  -3.6428   1.7419  -0.7088
 M40  O4   O  OS     0  -0.750  -5.8372   0.6396  -0.9069
 M40  C30  C  CH1    0  -0.148  -3.7203  -0.6541  -1.8352
 M40  H4   H  HCH2   0   0.247   4.4256  -1.3541   2.3300
 M40  H2   H  H      0   0.258   8.4181  -1.0315  -1.4279
 M40  H5   H  H      0   0.258   8.8603  -3.4092  -0.8958
 M40  H6   H  H      0   0.258   7.4129  -4.5961   0.7219
 M40  H7   H  H      0   0.255   5.5319  -3.4176   1.7928
 M40  H8   H  HNH1   0   0.394   1.9314  -0.7459  -1.0641
 M40  H9   H  HCH1   0   0.280   0.1632   0.5484   0.8932
 M40  H34  H  HCH1   0   0.261  -2.9273  -0.4445  -2.5650
 M40  O31  O  OH1    0  -0.652  -4.7024  -1.4987  -2.3616

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
 M40  O31  C30  single    1.398  0.020  1.398
 M40  C30  C22  single    1.539  0.020  1.539
 M40  C17  C16  single    1.525  0.020  1.525
 M40  C17  C18  single    1.524  0.020  1.524
 M40  C22  C23  single    1.525  0.020  1.525
 M40  C22  N21  single    1.442  0.020  1.442
 M40  C16  C15  single    1.525  0.020  1.525
 M40  C15  C14  single    1.530  0.020  1.530
 M40  C23  C24  single    1.534  0.020  1.534
 M40  N21  C20  single    1.338  0.020  1.338
 M40  C19  C18  single    1.526  0.020  1.526
 M40  C19  C14  single    1.529  0.020  1.529
 M40  C13  C14  single    1.527  0.020  1.527
 M40  C13  C12  single    1.537  0.020  1.537
 M40  C20  C12  single    1.528  0.020  1.528
 M40  C20  O32  double    1.222  0.020  1.222
 M40  C12  N11  single    1.438  0.020  1.438
 M40  O29  C28  double    1.219  0.020  1.219
 M40  C24  C28  single    1.526  0.020  1.526
 M40  C24  C25  single    1.532  0.020  1.532
 M40  C28  N27  single    1.346  0.020  1.346
 M40  C25  C26  single    1.532  0.020  1.532
 M40  N11  C02  single    1.344  0.020  1.344
 M40  N27  C26  single    1.447  0.020  1.447
 M40  O01  C02  double    1.214  0.020  1.214
 M40  C02  O03  single    1.339  0.020  1.339
 M40  O03  C04  single    1.431  0.020  1.431
 M40  C04  C05  single    1.499  0.020  1.499
 M40  C10  C05  aromatic  1.391  0.020  1.391
 M40  C10  C09  aromatic  1.389  0.020  1.389
 M40  C05  C06  aromatic  1.393  0.020  1.393
 M40  C09  C08  aromatic  1.388  0.020  1.388
 M40  C06  C07  aromatic  1.387  0.020  1.387
 M40  C08  C07  aromatic  1.390  0.020  1.390
 M40  C04  H1   single    0.970  0.020  1.090
 M40  C06  H3   single    0.930  0.020  1.080
 M40  C13  H10  single    0.970  0.020  1.090
 M40  C13  H11  single    0.970  0.020  1.090
 M40  C14  H12  single    0.970  0.020  1.090
 M40  C15  H13  single    0.970  0.020  1.090
 M40  C15  H14  single    0.970  0.020  1.090
 M40  C16  H15  single    0.970  0.020  1.090
 M40  C16  H16  single    0.970  0.020  1.090
 M40  C17  H17  single    0.970  0.020  1.090
 M40  C17  H18  single    0.970  0.020  1.090
 M40  C18  H19  single    0.970  0.020  1.090
 M40  C18  H20  single    0.970  0.020  1.090
 M40  C19  H21  single    0.970  0.020  1.090
 M40  C19  H22  single    0.970  0.020  1.090
 M40  N21  H23  single    0.860  0.020  1.020
 M40  C22  H24  single    0.970  0.020  1.090
 M40  C23  H25  single    0.970  0.020  1.090
 M40  C23  H26  single    0.970  0.020  1.090
 M40  C24  H27  single    0.970  0.020  1.090
 M40  C25  H28  single    0.970  0.020  1.090
 M40  C25  H29  single    0.970  0.020  1.090
 M40  C26  H30  single    0.970  0.020  1.090
 M40  C26  H31  single    0.970  0.020  1.090
 M40  N27  H32  single    0.860  0.020  1.020
 M40  O31  H35  single    0.850  0.020  0.980
 M40  S1   O2   deloc     1.474  0.020  1.474
 M40  S1   O3   deloc     1.479  0.020  1.479
 M40  S1   O4   deloc     1.473  0.020  1.473
 M40  S1   C30  single    1.830  0.020  1.830
 M40  C04  H4   single    0.970  0.020  1.090
 M40  C07  H2   single    0.930  0.020  1.080
 M40  C08  H5   single    0.930  0.020  1.080
 M40  C09  H6   single    0.930  0.020  1.080
 M40  C10  H7   single    0.930  0.020  1.080
 M40  N11  H8   single    0.860  0.020  1.020
 M40  C12  H9   single    0.970  0.020  1.090
 M40  C30  H34  single    0.970  0.020  1.090

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
 M40  N11  C02  O03  110.46  3.000
 M40  O03  C02  O01  123.72  3.000
 M40  N11  C02  O01  125.82  3.000
 M40  C04  O03  C02  117.02  3.000
 M40  H4   C04  H1   108.06  3.000
 M40  H4   C04  C05  110.79  3.000
 M40  H1   C04  C05  110.76  3.000
 M40  H4   C04  O03  110.40  3.000
 M40  H1   C04  O03  110.11  3.000
 M40  C05  C04  O03  106.74  3.000
 M40  C10  C05  C06  119.05  3.000
 M40  C06  C05  C04  120.21  3.000
 M40  C10  C05  C04  120.72  3.000
 M40  H3   C06  C07  119.71  3.000
 M40  H3   C06  C05  119.74  3.000
 M40  C07  C06  C05  120.55  3.000
 M40  H2   C07  C08  120.12  3.000
 M40  H2   C07  C06  119.85  3.000
 M40  C08  C07  C06  120.03  3.000
 M40  H5   C08  C09  120.08  3.000
 M40  H5   C08  C07  120.13  3.000
 M40  C09  C08  C07  119.80  3.000
 M40  H6   C09  C10  119.85  3.000
 M40  H6   C09  C08  120.15  3.000
 M40  C10  C09  C08  120.01  3.000
 M40  H7   C10  C09  119.69  3.000
 M40  H7   C10  C05  119.74  3.000
 M40  C09  C10  C05  120.57  3.000
 M40  H8   N11  C12  117.41  3.000
 M40  H8   N11  C02  118.74  3.000
 M40  C12  N11  C02  123.43  3.000
 M40  H9   C12  C20  108.10  3.000
 M40  H9   C12  C13  109.80  3.000
 M40  C20  C12  C13  109.65  3.000
 M40  H9   C12  N11  107.66  3.000
 M40  C20  C12  N11  109.57  3.000
 M40  C13  C12  N11  111.97  3.000
 M40  H11  C13  H10  106.14  3.000
 M40  H11  C13  C14  108.89  3.000
 M40  H10  C13  C14  109.74  3.000
 M40  H11  C13  C12  109.46  3.000
 M40  H10  C13  C12  108.06  3.000
 M40  C14  C13  C12  114.24  3.000
 M40  H12  C14  C19  108.22  3.000
 M40  H12  C14  C15  107.52  3.000
 M40  C19  C14  C15  110.21  3.000
 M40  H12  C14  C13  108.61  3.000
 M40  C19  C14  C13  111.94  3.000
 M40  C15  C14  C13  110.21  3.000
 M40  H14  C15  H13  106.38  3.000
 M40  H14  C15  C16  109.16  3.000
 M40  H13  C15  C16  110.08  3.000
 M40  H14  C15  C14  109.12  3.000
 M40  H13  C15  C14  109.78  3.000
 M40  C16  C15  C14  112.15  3.000
 M40  H16  C16  H15  106.41  3.000
 M40  H16  C16  C17  110.38  3.000
 M40  H15  C16  C17  109.28  3.000
 M40  H16  C16  C15  110.01  3.000
 M40  H15  C16  C15  109.24  3.000
 M40  C17  C16  C15  111.38  3.000
 M40  H18  C17  H17  106.42  3.000
 M40  H18  C17  C18  109.32  3.000
 M40  H17  C17  C18  110.40  3.000
 M40  H18  C17  C16  109.30  3.000
 M40  H17  C17  C16  110.29  3.000
 M40  C18  C17  C16  111.00  3.000
 M40  H20  C18  H19  106.40  3.000
 M40  H20  C18  C19  109.89  3.000
 M40  H19  C18  C19  109.15  3.000
 M40  H20  C18  C17  110.49  3.000
 M40  H19  C18  C17  109.32  3.000
 M40  C19  C18  C17  111.45  3.000
 M40  H22  C19  H21  106.54  3.000
 M40  H22  C19  C18  109.39  3.000
 M40  H21  C19  C18  109.25  3.000
 M40  H22  C19  C14  110.56  3.000
 M40  H21  C19  C14  108.83  3.000
 M40  C18  C19  C14  112.11  3.000
 M40  O32  C20  N21  124.50  3.000
 M40  O32  C20  C12  122.16  3.000
 M40  N21  C20  C12  113.31  3.000
 M40  H23  N21  C22  115.95  3.000
 M40  H23  N21  C20  118.51  3.000
 M40  C22  N21  C20  124.67  3.000
 M40  C30  C22  H24  105.49  3.000
 M40  H24  C22  C23  108.75  3.000
 M40  C30  C22  C23  114.21  3.000
 M40  H24  C22  N21  106.78  3.000
 M40  C23  C22  N21  110.81  3.000
 M40  C30  C22  N21  110.38  3.000
 M40  H26  C23  H25  106.02  3.000
 M40  H26  C23  C24  106.63  3.000
 M40  H25  C23  C24  109.92  3.000
 M40  H26  C23  C22  108.52  3.000
 M40  H25  C23  C22  109.43  3.000
 M40  C24  C23  C22  115.82  3.000
 M40  H27  C24  C28  109.42  3.000
 M40  H27  C24  C25  112.67  3.000
 M40  C28  C24  C25  101.85  3.000
 M40  H27  C24  C23  109.21  3.000
 M40  C25  C24  C23  109.93  3.000
 M40  C28  C24  C23  113.66  3.000
 M40  H29  C25  H28  107.86  3.000
 M40  H29  C25  C26  109.64  3.000
 M40  H28  C25  C26  112.44  3.000
 M40  H29  C25  C24  110.32  3.000
 M40  H28  C25  C24  113.17  3.000
 M40  C26  C25  C24  103.37  3.000
 M40  H31  C26  H30  107.68  3.000
 M40  H31  C26  N27  111.09  3.000
 M40  H30  C26  N27  111.58  3.000
 M40  H31  C26  C25  112.54  3.000
 M40  H30  C26  C25  112.01  3.000
 M40  N27  C26  C25  101.96  3.000
 M40  H32  N27  C28  122.30  3.000
 M40  H32  N27  C26  122.91  3.000
 M40  C28  N27  C26  114.76  3.000
 M40  O29  C28  N27  125.90  3.000
 M40  N27  C28  C24  106.91  3.000
 M40  O29  C28  C24  127.18  3.000
 M40  C30  S1   O4   106.14  3.000
 M40  C30  S1   O3   105.87  3.000
 M40  O4   S1   O3   113.12  3.000
 M40  C30  S1   O2   104.61  3.000
 M40  O4   S1   O2   113.23  3.000
 M40  O3   S1   O2   112.95  3.000
 M40  H34  C30  S1   105.13  3.000
 M40  H34  C30  O31  111.86  3.000
 M40  S1   C30  O31  105.39  3.000
 M40  H34  C30  C22  107.48  3.000
 M40  S1   C30  C22  114.75  3.000
 M40  O31  C30  C22  112.09  3.000
 M40  C30  O31  H35  108.24  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
 M40  CONST_01  C08  C09  C10  C05     0.00   0.0  0
 M40  CONST_02  C08  C07  C06  C05     0.00   0.0  0
 M40  CONST_03  C09  C10  C05  C06     0.00   0.0  0
 M40  CONST_04  C09  C08  C07  C06     0.00   0.0  0
 M40  CONST_05  C10  C05  C06  C07     0.00   0.0  0
 M40  CONST_06  C10  C09  C08  C07     0.00   0.0  0
 M40  CONST_07  C26  N27  C28  C24     0.00   0.0  0
 M40  CONST_08  C09  C10  C05  C04   180.00   0.0  0
 M40  CONST_09  C07  C06  C05  C04   180.00   0.0  0
 M40  CONST_10  O29  C28  N27  C26   180.00   0.0  0
 M40  CONST_11  H6   C09  C10  C05   180.00   0.0  0
 M40  CONST_12  H2   C07  C06  C05   180.00   0.0  0
 M40  CONST_13  H7   C10  C05  C06   180.00   0.0  0
 M40  CONST_14  H5   C08  C07  C06   180.00   0.0  0
 M40  CONST_15  H3   C06  C07  C08   180.00   0.0  0
 M40  CONST_16  H32  N27  C28  C24   180.00   0.0  0
 M40  CONST_17  C22  N21  C20  C12   180.00   0.0  0
 M40  CONST_18  O32  C20  N21  C22     0.00   0.0  0
 M40  CONST_19  H23  N21  C20  C12     0.00   0.0  0
 M40  Var_01    C17  C16  C15  C14   -55.42  30.0  1
 M40  Var_02    C17  C18  C19  C14    55.41  30.0  1
 M40  Var_03    C18  C17  C16  C15    55.03  30.0  1
 M40  Var_04    C19  C18  C17  C16   -55.04  30.0  1
 M40  Var_05    N27  C26  C25  C24   -29.64  30.0  1
 M40  Var_06    C28  N27  C26  C25    15.80  30.0  1
 M40  Var_07    C10  C05  C04  O03   -99.51  30.0  2
 M40  Var_08    C05  C04  O03  C02  -177.01  30.0  3
 M40  Var_09    C12  N11  C02  O01    -4.33  30.0  1
 M40  Var_10    N11  C02  O03  C04   177.80  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
 M40  chir_01  C12  C13  C20  N11  negativ
 M40  chir_02  C14  C13  C19  C15  positiv
 M40  chir_03  C22  N21  C30  C23  positiv
 M40  chir_04  C24  C25  C28  C23  positiv
 M40  chir_05  C30  S1   O31  C22  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
 M40  plan-1  C04  0.020
 M40  plan-1  C05  0.020
 M40  plan-1  C06  0.020
 M40  plan-1  C07  0.020
 M40  plan-1  C08  0.020
 M40  plan-1  C09  0.020
 M40  plan-1  C10  0.020
 M40  plan-1  H3   0.020
 M40  plan-1  H2   0.020
 M40  plan-1  H5   0.020
 M40  plan-1  H6   0.020
 M40  plan-1  H7   0.020
 M40  plan-2  C12  0.020
 M40  plan-2  C20  0.020
 M40  plan-2  N21  0.020
 M40  plan-2  C22  0.020
 M40  plan-2  O32  0.020
 M40  plan-2  H23  0.020
 M40  plan-3  C24  0.020
 M40  plan-3  C26  0.020
 M40  plan-3  N27  0.020
 M40  plan-3  C28  0.020
 M40  plan-3  O29  0.020
 M40  plan-3  H32  0.020
 M40  plan-4  O01  0.020
 M40  plan-4  C02  0.020
 M40  plan-4  O03  0.020
 M40  plan-4  N11  0.020

