# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:31:55 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: methyl (2~{R})-2-[(7~{R},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H]([C@@H]1N[C@H](c2ccc(Cl)cc2)c3c(C)c(C)sc3n4c(C)nnc14)C(=O)OC
#
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
 PMW  PMW  'methyl (2~{R})-2-[(7~{R},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]butanoate'  ligand  55  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PMW
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
 PMW  C13  C   CH3   0  -0.762   6.0508  -12.2790  -14.7895
 PMW  C17  C   CR5   0  -0.226   5.2361  -16.5442  -12.8448
 PMW  C20  C   CH3   0  -0.750   3.1503  -17.9510  -13.0095
 PMW  C21  C   CR5   0   0.166   3.8133  -16.0603  -14.6345
 PMW  C02  C   C     0   0.629   2.5203  -17.0177  -19.2067
 PMW  C04  C   CH3   0  -0.426   0.5895  -17.7956  -20.3056
 PMW  C05  C   CH1   0  -0.363   3.4524  -15.8372  -19.0423
 PMW  C06  C   CH2   0  -0.446   4.6782  -15.9957  -19.9626
 PMW  C07  C   CH3   0  -0.677   5.6939  -17.0477  -19.5389
 PMW  C08  C   CH1   0  -0.200   3.7776  -15.7273  -17.5552
 PMW  C09  C   CR5   0   0.459   4.5931  -14.5265  -17.2178
 PMW  C12  C   CR5   0   0.401   5.5099  -13.0174  -15.9547
 PMW  C18  C   CH3   0  -0.723   5.8371  -17.1491  -11.6181
 PMW  C19  C   CR5   0   0.146   4.0687  -16.8643  -13.4713
 PMW  C15  C   CR5   0  -0.060   4.8135  -15.1563  -14.8490
 PMW  C22  C   CH1   0  -0.163   2.5873  -16.3162  -15.4867
 PMW  C23  C   CR6   0   0.100   1.3045  -15.9729  -14.7617
 PMW  C24  C   CR16  0  -0.290   0.1459  -16.6859  -15.0520
 PMW  C25  C   CR16  0  -0.203  -1.0587  -16.3699  -14.4449
 PMW  C26  C   CR6   0  -0.052  -1.0999  -15.3179  -13.5416
 PMW  C28  C   CR16  0  -0.197   0.0373  -14.5864  -13.2424
 PMW  C29  C   CR16  0  -0.281   1.2357  -14.9198  -13.8586
 PMW  N10  N   N     0  -0.327   4.8849  -13.5057  -17.9610
 PMW  N11  N   N     0  -0.333   5.4682  -12.5653  -17.1733
 PMW  N14  N   NR5   0  -0.583   4.9659  -14.2738  -15.9260
 PMW  N30  N   NH1   0  -0.593   2.5404  -15.6736  -16.7865
 PMW  O01  O   O     0  -0.454   2.6920  -18.1022  -18.7070
 PMW  O03  O   O2    0  -0.450   1.5072  -16.7411  -20.0153
 PMW  S16  S   S2    0   0.230   6.0665  -15.2838  -13.6689
 PMW  CL1  CL  CL    0  -0.128  -2.5995  -14.9170  -12.7699
 PMW  H1   H   HCH3  0   0.283   6.2045  -11.2419  -15.0785
 PMW  H2   H   HCH3  0   0.267   5.3679  -12.3033  -13.9406
 PMW  H3   H   HCH3  0   0.270   7.0113  -12.6778  -14.4620
 PMW  H4   H   HCH3  0   0.251   3.0278  -18.7202  -13.7750
 PMW  H5   H   HCH3  0   0.259   3.5326  -18.4433  -12.1172
 PMW  H6   H   HCH3  0   0.253   2.1556  -17.5695  -12.7760
 PMW  H7   H   HCH3  0   0.252  -0.1631  -17.3655  -20.9598
 PMW  H8   H   HCH3  0   0.239   1.0816  -18.6226  -20.8171
 PMW  H9   H   HCH3  0   0.237   0.1107  -18.1677  -19.4001
 PMW  H10  H   HCH1  0   0.274   2.9242  -14.9321  -19.3519
 PMW  H11  H   HCH2  0   0.254   5.1699  -15.0252  -20.0238
 PMW  H12  H   HCH2  0   0.243   4.3217  -16.2141  -20.9725
 PMW  H13  H   HCH3  0   0.239   6.4922  -17.1097  -20.2784
 PMW  H14  H   HCH3  0   0.221   6.1630  -16.8009  -18.5854
 PMW  H15  H   HCH3  0   0.230   5.2543  -18.0400  -19.4468
 PMW  H16  H   HCH1  0   0.291   4.3136  -16.6292  -17.2433
 PMW  H17  H   HCH3  0   0.257   6.6017  -16.5060  -11.1850
 PMW  H18  H   HCH3  0   0.257   5.0796  -17.3169  -10.8532
 PMW  H19  H   HCH3  0   0.261   6.3045  -18.1098  -11.8398
 PMW  H20  H   HCH1  0   0.266   2.5797  -17.3974  -15.6741
 PMW  H21  H   HCR6  0   0.261   0.1818  -17.5053  -15.7596
 PMW  H22  H   HCR6  0   0.281  -1.9509  -16.9381  -14.6707
 PMW  H23  H   HCR6  0   0.281  -0.0031  -13.7689  -12.5357
 PMW  H24  H   HCR6  0   0.263   2.1247  -14.3511  -13.6131
 PMW  H25  H   HNH1  0   0.365   2.1905  -14.7253  -16.7202

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
 PMW  O03  C04  single    1.428  0.020  1.428
 PMW  O03  C02  single    1.325  0.020  1.325
 PMW  C06  C07  single    1.522  0.020  1.522
 PMW  C06  C05  single    1.541  0.020  1.541
 PMW  C02  C05  single    1.513  0.020  1.513
 PMW  C02  O01  double    1.206  0.020  1.206
 PMW  C05  C08  single    1.526  0.020  1.526
 PMW  N10  C09  aromatic  1.296  0.020  1.296
 PMW  N10  N11  aromatic  1.358  0.020  1.358
 PMW  C08  C09  single    1.490  0.020  1.490
 PMW  C08  N30  single    1.458  0.020  1.458
 PMW  C09  N14  aromatic  1.368  0.020  1.368
 PMW  N11  C12  aromatic  1.300  0.020  1.300
 PMW  N30  C22  single    1.451  0.020  1.451
 PMW  N14  C12  aromatic  1.369  0.020  1.369
 PMW  N14  C15  aromatic  1.401  0.020  1.401
 PMW  C12  C13  single    1.482  0.020  1.482
 PMW  C22  C23  single    1.513  0.020  1.513
 PMW  C22  C21  single    1.515  0.020  1.515
 PMW  C24  C23  aromatic  1.391  0.020  1.391
 PMW  C24  C25  aromatic  1.385  0.020  1.385
 PMW  C15  C21  aromatic  1.365  0.020  1.365
 PMW  C15  S16  aromatic  1.726  0.020  1.726
 PMW  C23  C29  aromatic  1.389  0.020  1.389
 PMW  C21  C19  aromatic  1.437  0.020  1.437
 PMW  C25  C26  aromatic  1.387  0.020  1.387
 PMW  S16  C17  aromatic  1.720  0.020  1.720
 PMW  C29  C28  aromatic  1.388  0.020  1.388
 PMW  C19  C20  single    1.496  0.020  1.496
 PMW  C19  C17  aromatic  1.363  0.020  1.363
 PMW  C26  C28  aromatic  1.385  0.020  1.385
 PMW  C26  CL1  single    1.733  0.020  1.733
 PMW  C17  C18  single    1.494  0.020  1.494
 PMW  C13  H1   single    0.970  0.020  1.090
 PMW  C13  H2   single    0.970  0.020  1.090
 PMW  C13  H3   single    0.970  0.020  1.090
 PMW  C20  H4   single    0.970  0.020  1.090
 PMW  C20  H5   single    0.970  0.020  1.090
 PMW  C20  H6   single    0.970  0.020  1.090
 PMW  C04  H7   single    0.970  0.020  1.090
 PMW  C04  H8   single    0.970  0.020  1.090
 PMW  C04  H9   single    0.970  0.020  1.090
 PMW  C05  H10  single    0.970  0.020  1.090
 PMW  C06  H11  single    0.970  0.020  1.090
 PMW  C06  H12  single    0.970  0.020  1.090
 PMW  C07  H13  single    0.970  0.020  1.090
 PMW  C07  H14  single    0.970  0.020  1.090
 PMW  C07  H15  single    0.970  0.020  1.090
 PMW  C08  H16  single    0.970  0.020  1.090
 PMW  C18  H17  single    0.970  0.020  1.090
 PMW  C18  H18  single    0.970  0.020  1.090
 PMW  C18  H19  single    0.970  0.020  1.090
 PMW  C22  H20  single    0.970  0.020  1.090
 PMW  C24  H21  single    0.930  0.020  1.080
 PMW  C25  H22  single    0.930  0.020  1.080
 PMW  C28  H23  single    0.930  0.020  1.080
 PMW  C29  H24  single    0.930  0.020  1.080
 PMW  N30  H25  single    0.890  0.020  1.040

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
 PMW  H3   C13  H2   108.06  3.000
 PMW  H3   C13  H1   107.70  3.000
 PMW  H2   C13  H1   108.47  3.000
 PMW  H3   C13  C12  112.06  3.000
 PMW  H2   C13  C12  111.88  3.000
 PMW  H1   C13  C12  108.53  3.000
 PMW  S16  C17  C19  111.43  3.000
 PMW  C19  C17  C18  128.82  3.000
 PMW  S16  C17  C18  119.73  3.000
 PMW  H6   C20  H5   107.64  3.000
 PMW  H6   C20  H4   107.10  3.000
 PMW  H5   C20  H4   107.19  3.000
 PMW  H6   C20  C19  111.84  3.000
 PMW  H5   C20  C19  111.47  3.000
 PMW  H4   C20  C19  111.35  3.000
 PMW  C22  C21  C15  128.06  3.000
 PMW  C15  C21  C19  111.56  3.000
 PMW  C22  C21  C19  120.32  3.000
 PMW  O03  C02  O01  123.31  3.000
 PMW  O01  C02  C05  124.66  3.000
 PMW  O03  C02  C05  111.98  3.000
 PMW  H9   C04  H8   109.23  3.000
 PMW  H9   C04  H7   109.35  3.000
 PMW  H8   C04  H7   109.31  3.000
 PMW  H9   C04  O03  111.45  3.000
 PMW  H8   C04  O03  111.45  3.000
 PMW  H7   C04  O03  105.98  3.000
 PMW  H10  C05  C08  108.63  3.000
 PMW  H10  C05  C06  107.49  3.000
 PMW  C08  C05  C06  114.82  3.000
 PMW  H10  C05  C02  108.53  3.000
 PMW  C08  C05  C02  107.06  3.000
 PMW  C06  C05  C02  110.17  3.000
 PMW  H12  C06  H11  105.86  3.000
 PMW  H12  C06  C07  109.68  3.000
 PMW  H11  C06  C07  109.27  3.000
 PMW  H12  C06  C05  108.23  3.000
 PMW  H11  C06  C05  107.51  3.000
 PMW  C07  C06  C05  115.82  3.000
 PMW  H15  C07  H14  107.80  3.000
 PMW  H15  C07  H13  107.53  3.000
 PMW  H14  C07  H13  106.91  3.000
 PMW  H15  C07  C06  112.57  3.000
 PMW  H14  C07  C06  111.95  3.000
 PMW  H13  C07  C06  109.82  3.000
 PMW  H16  C08  N30  107.20  3.000
 PMW  H16  C08  C09  109.36  3.000
 PMW  N30  C08  C09  108.39  3.000
 PMW  H16  C08  C05  108.83  3.000
 PMW  N30  C08  C05  109.61  3.000
 PMW  C09  C08  C05  113.28  3.000
 PMW  N14  C09  N10  109.55  3.000
 PMW  N14  C09  C08  120.78  3.000
 PMW  N10  C09  C08  128.91  3.000
 PMW  N14  C12  N11  109.02  3.000
 PMW  N14  C12  C13  125.85  3.000
 PMW  N11  C12  C13  125.13  3.000
 PMW  H19  C18  H18  107.75  3.000
 PMW  H19  C18  H17  107.46  3.000
 PMW  H18  C18  H17  107.45  3.000
 PMW  H19  C18  C17  111.22  3.000
 PMW  H18  C18  C17  111.05  3.000
 PMW  H17  C18  C17  111.72  3.000
 PMW  C21  C19  C20  123.18  3.000
 PMW  C20  C19  C17  123.68  3.000
 PMW  C21  C19  C17  113.14  3.000
 PMW  S16  C15  N14  119.56  3.000
 PMW  S16  C15  C21  112.06  3.000
 PMW  N14  C15  C21  128.15  3.000
 PMW  H20  C22  N30  106.45  3.000
 PMW  H20  C22  C23  107.43  3.000
 PMW  N30  C22  C23  107.54  3.000
 PMW  H20  C22  C21  105.56  3.000
 PMW  C23  C22  C21  112.22  3.000
 PMW  N30  C22  C21  117.09  3.000
 PMW  C29  C23  C24  118.88  3.000
 PMW  C29  C23  C22  121.71  3.000
 PMW  C24  C23  C22  119.33  3.000
 PMW  H21  C24  C25  119.18  3.000
 PMW  H21  C24  C23  119.76  3.000
 PMW  C25  C24  C23  121.05  3.000
 PMW  H22  C25  C26  120.65  3.000
 PMW  H22  C25  C24  120.39  3.000
 PMW  C26  C25  C24  118.96  3.000
 PMW  CL1  C26  C28  119.47  3.000
 PMW  CL1  C26  C25  119.40  3.000
 PMW  C28  C26  C25  121.12  3.000
 PMW  H23  C28  C29  120.26  3.000
 PMW  H23  C28  C26  120.66  3.000
 PMW  C29  C28  C26  119.09  3.000
 PMW  H24  C29  C28  118.80  3.000
 PMW  H24  C29  C23  120.31  3.000
 PMW  C28  C29  C23  120.89  3.000
 PMW  N11  N10  C09  108.02  3.000
 PMW  N10  N11  C12  108.45  3.000
 PMW  C15  N14  C12  129.60  3.000
 PMW  C15  N14  C09  125.45  3.000
 PMW  C12  N14  C09  104.95  3.000
 PMW  H25  N30  C22  111.54  3.000
 PMW  H25  N30  C08  111.24  3.000
 PMW  C22  N30  C08  115.39  3.000
 PMW  C04  O03  C02  117.46  3.000
 PMW  C15  S16  C17   91.79  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
 PMW  CONST_01  S16  C17  C19  C21     0.00   0.0  0
 PMW  CONST_02  C12  N11  N10  C09     0.00   0.0  0
 PMW  CONST_03  C15  S16  C17  C19     0.00   0.0  0
 PMW  CONST_04  C26  C25  C24  C23     0.00   0.0  0
 PMW  CONST_05  C26  C28  C29  C23     0.00   0.0  0
 PMW  CONST_06  C28  C29  C23  C24     0.00   0.0  0
 PMW  CONST_07  C28  C26  C25  C24     0.00   0.0  0
 PMW  CONST_08  C29  C23  C24  C25     0.00   0.0  0
 PMW  CONST_09  C29  C28  C26  C25     0.00   0.0  0
 PMW  CONST_10  N14  C12  N11  N10     0.00   0.0  0
 PMW  CONST_11  C25  C24  C23  C22   180.00   0.0  0
 PMW  CONST_12  C28  C29  C23  C22   180.00   0.0  0
 PMW  CONST_13  N10  N11  C12  C13   180.00   0.0  0
 PMW  CONST_14  S16  C17  C19  C20   180.00   0.0  0
 PMW  CONST_15  C18  C17  C19  C21   180.00   0.0  0
 PMW  CONST_16  C15  S16  C17  C18   180.00   0.0  0
 PMW  CONST_17  CL1  C26  C25  C24   180.00   0.0  0
 PMW  CONST_18  CL1  C26  C28  C29   180.00   0.0  0
 PMW  CONST_19  H21  C24  C23  C22     0.00   0.0  0
 PMW  CONST_20  H24  C29  C23  C22     0.00   0.0  0
 PMW  CONST_21  H22  C25  C24  C23   180.00   0.0  0
 PMW  CONST_22  H23  C28  C29  C23   180.00   0.0  0
 PMW  Var_01    H4   C20  C19  C17  -119.51  30.0  2
 PMW  Var_02    H17  C18  C17  C19  -162.67  30.0  2
 PMW  Var_03    H1   C13  C12  N11    11.88  30.0  2
 PMW  Var_04    C05  C02  O03  C04   177.00  30.0  3
 PMW  Var_05    H7   C04  O03  C02   179.03  30.0  3
 PMW  Var_06    H13  C07  C06  C05   177.40  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
 PMW  chir_01  C05  C06  C02  C08  negativ
 PMW  chir_02  C08  N30  C05  C09  negativ
 PMW  chir_03  C22  N30  C21  C23  negativ

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
 PMW  plan-1  C22  0.020
 PMW  plan-1  C23  0.020
 PMW  plan-1  C24  0.020
 PMW  plan-1  C25  0.020
 PMW  plan-1  C26  0.020
 PMW  plan-1  C28  0.020
 PMW  plan-1  C29  0.020
 PMW  plan-1  CL1  0.020
 PMW  plan-1  H21  0.020
 PMW  plan-1  H22  0.020
 PMW  plan-1  H23  0.020
 PMW  plan-1  H24  0.020
 PMW  plan-2  C17  0.020
 PMW  plan-2  C20  0.020
 PMW  plan-2  C21  0.020
 PMW  plan-2  C18  0.020
 PMW  plan-2  C19  0.020
 PMW  plan-2  C15  0.020
 PMW  plan-2  C22  0.020
 PMW  plan-2  N14  0.020
 PMW  plan-2  S16  0.020
 PMW  plan-3  C13  0.020
 PMW  plan-3  C08  0.020
 PMW  plan-3  C09  0.020
 PMW  plan-3  C12  0.020
 PMW  plan-3  C15  0.020
 PMW  plan-3  N10  0.020
 PMW  plan-3  N11  0.020
 PMW  plan-3  N14  0.020
 PMW  plan-4  C02  0.020
 PMW  plan-4  C05  0.020
 PMW  plan-4  O01  0.020
 PMW  plan-4  O03  0.020

