# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 16:07:21 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (3~{R},4~{R})-3-(hydroxymethyl)-4-(4-methoxy-3-oxidanyl-phenyl)-1-(3,4,5-trimethoxyphenyl)azetidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1O)[C@H]2[C@H](CO)C(=O)N2c3cc(OC)c(OC)c(OC)c3
#
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
 93X  93X  (3~{R},4~{R})-3-(hydroxymethyl)-4-(4-methoxy-3-oxidanyl-phenyl)-1-(3,4,5-trimethoxyphenyl)azetidin-2-one  ligand  51  28  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_93X
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
 93X  C29  C  CH2   0  -0.134  -1.7041  -4.0547   1.0205
 93X  O50  O  OH1   0  -0.665  -1.6971  -5.2823   0.3361
 93X  C3   C  C     0  -0.461  -1.3659  -2.9605   0.0324
 93X  C4   C  C     0   0.542   0.0807  -2.8825  -0.4308
 93X  O5   O  O     0  -0.439   0.8440  -3.6043  -1.0237
 93X  N1   N  N     0  -0.565   0.2354  -1.6375   0.1063
 93X  C6   C  CR6   0   0.421   1.2867  -0.7337   0.2021
 93X  C11  C  CR16  0  -0.512   2.4878  -0.9736  -0.4606
 93X  C10  C  CR6   0   0.361   3.5139  -0.0390  -0.3504
 93X  O23  O  O2    0  -0.464   4.7087  -0.1672  -0.9494
 93X  C24  C  CH3   0  -0.441   4.9597  -1.3260  -1.7198
 93X  C9   C  CR6   0   0.160   3.3483   1.1178   0.4169
 93X  O21  O  O2    0  -0.481   4.3667   2.0106   0.5365
 93X  C22  C  CH3   0  -0.409   4.3686   3.0307  -0.4531
 93X  C8   C  CR6   0   0.358   2.1329   1.3410   1.0666
 93X  O25  O  O2    0  -0.463   2.0466   2.4820   1.7690
 93X  C26  C  CH3   0  -0.441   0.8447   2.7597   2.4608
 93X  C7   C  CR16  0  -0.499   1.1013   0.4111   0.9698
 93X  C2   C  C     0  -0.163  -1.1228  -1.5578   0.6484
 93X  C12  C  CR6   0   0.172  -1.9567  -0.4168   0.1476
 93X  C17  C  CR16  0  -0.400  -2.7783   0.2688   1.0388
 93X  C16  C  CR6   0   0.296  -3.5681   1.3228   0.6133
 93X  O18  O  OH1   0  -0.631  -4.3482   1.9603   1.5084
 93X  C15  C  CR6   0   0.289  -3.5368   1.7104  -0.7360
 93X  O19  O  O2    0  -0.487  -4.3375   2.7514  -1.0468
 93X  C20  C  CH3   0  -0.432  -4.3706   3.2006  -2.3873
 93X  C14  C  CR16  0  -0.364  -2.7157   1.0306  -1.6229
 93X  C13  C  CR16  0  -0.325  -1.9286  -0.0273  -1.1822
 93X  H1   H  HCH2  0   0.219  -2.6857  -3.8321   1.4580
 93X  H2   H  HCH2  0   0.208  -0.9780  -4.0412   1.8440
 93X  H3   H  HOH1  0   0.459  -1.8828  -5.9810   0.9703
 93X  H4   H  H     0   0.303  -2.0790  -2.9463  -0.7958
 93X  H7   H  HCR6  0   0.293   2.6079  -1.8686  -1.0513
 93X  H8   H  HCH3  0   0.230   4.9164  -2.2350  -1.1145
 93X  H9   H  HCH3  0   0.230   4.2613  -1.4231  -2.5545
 93X  H10  H  HCH3  0   0.263   5.9658  -1.2183  -2.1172
 93X  H11  H  HCH3  0   0.236   5.2403   3.6566  -0.2687
 93X  H12  H  HCH3  0   0.220   4.4434   2.6174  -1.4618
 93X  H13  H  HCH3  0   0.221   3.4730   3.6536  -0.3953
 93X  H14  H  HCH3  0   0.265   0.9860   3.7199   2.9501
 93X  H15  H  HCH3  0   0.225  -0.0097   2.8344   1.7831
 93X  H16  H  HCH3  0   0.232   0.6290   2.0049   3.2211
 93X  H17  H  HCR6  0   0.291   0.1589   0.5740   1.4724
 93X  H18  H  H     0   0.280  -1.1241  -1.5742   1.7429
 93X  H19  H  HCR6  0   0.264  -2.8049  -0.0142   2.0854
 93X  H20  H  HOH1  0   0.473  -4.8311   2.6768   1.0790
 93X  H21  H  HCH3  0   0.231  -4.7208   2.4186  -3.0654
 93X  H22  H  HCH3  0   0.263  -5.0681   4.0331  -2.4186
 93X  H23  H  HCH3  0   0.232  -3.3900   3.5469  -2.7226
 93X  H24  H  HCR6  0   0.284  -2.6727   1.3168  -2.6652
 93X  H25  H  HCR6  0   0.254  -1.2888  -0.5326  -1.8949

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
 93X  C29  O50  single    1.405  0.020  1.405
 93X  C29  C3   single    1.513  0.020  1.513
 93X  C3   C4   single    1.521  0.020  1.521
 93X  C3   C2   single    1.551  0.020  1.551
 93X  C4   O5   double    1.206  0.020  1.206
 93X  N1   C6   single    1.390  0.020  1.390
 93X  N1   C2   single    1.465  0.020  1.465
 93X  C6   C11  aromatic  1.393  0.020  1.393
 93X  C6   C7   aromatic  1.391  0.020  1.391
 93X  C11  C10  aromatic  1.392  0.020  1.392
 93X  C10  O23  single    1.343  0.020  1.343
 93X  C10  C9   aromatic  1.398  0.020  1.398
 93X  O23  C24  single    1.414  0.020  1.414
 93X  C9   O21  single    1.360  0.020  1.360
 93X  C9   C8   aromatic  1.396  0.020  1.396
 93X  O21  C22  single    1.421  0.020  1.421
 93X  C8   O25  single    1.343  0.020  1.343
 93X  C8   C7   aromatic  1.392  0.020  1.392
 93X  O25  C26  single    1.414  0.020  1.414
 93X  C2   C12  single    1.499  0.020  1.499
 93X  C12  C17  aromatic  1.393  0.020  1.393
 93X  C12  C13  aromatic  1.386  0.020  1.386
 93X  C17  C16  aromatic  1.384  0.020  1.384
 93X  C16  O18  single    1.348  0.020  1.348
 93X  C16  C15  aromatic  1.404  0.020  1.404
 93X  C15  O19  single    1.350  0.020  1.350
 93X  C15  C14  aromatic  1.387  0.020  1.387
 93X  O19  C20  single    1.414  0.020  1.414
 93X  C14  C13  aromatic  1.390  0.020  1.390
 93X  C29  H1   single    0.970  0.020  1.090
 93X  C29  H2   single    0.970  0.020  1.090
 93X  O50  H3   single    0.850  0.020  0.980
 93X  C3   H4   single    0.970  0.020  1.090
 93X  C11  H7   single    0.930  0.020  1.080
 93X  C24  H8   single    0.970  0.020  1.090
 93X  C24  H9   single    0.970  0.020  1.090
 93X  C24  H10  single    0.970  0.020  1.090
 93X  C22  H11  single    0.970  0.020  1.090
 93X  C22  H12  single    0.970  0.020  1.090
 93X  C22  H13  single    0.970  0.020  1.090
 93X  C26  H14  single    0.970  0.020  1.090
 93X  C26  H15  single    0.970  0.020  1.090
 93X  C26  H16  single    0.970  0.020  1.090
 93X  C7   H17  single    0.930  0.020  1.080
 93X  C2   H18  single    0.970  0.020  1.090
 93X  C17  H19  single    0.930  0.020  1.080
 93X  O18  H20  single    0.850  0.020  0.980
 93X  C20  H21  single    0.970  0.020  1.090
 93X  C20  H22  single    0.970  0.020  1.090
 93X  C20  H23  single    0.970  0.020  1.090
 93X  C14  H24  single    0.930  0.020  1.080
 93X  C13  H25  single    0.930  0.020  1.080
 93X  N1   C4   single    1.365  0.020  1.365

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
 93X  H2   C29  H1   106.85  3.000
 93X  H2   C29  C3   109.46  3.000
 93X  H1   C29  C3   108.28  3.000
 93X  H2   C29  O50  111.88  3.000
 93X  H1   C29  O50  112.07  3.000
 93X  C3   C29  O50  108.22  3.000
 93X  H3   O50  C29  108.21  3.000
 93X  H4   C3   C2   113.04  3.000
 93X  H4   C3   C4   112.90  3.000
 93X  C2   C3   C4    85.73  3.000
 93X  H4   C3   C29  111.01  3.000
 93X  C2   C3   C29  115.45  3.000
 93X  C4   C3   C29  116.66  3.000
 93X  N1   C4   O5   131.88  3.000
 93X  N1   C4   C3    92.00  3.000
 93X  O5   C4   C3   136.12  3.000
 93X  C2   N1   C6   129.84  3.000
 93X  C2   N1   C4    95.17  3.000
 93X  C6   N1   C4   134.93  3.000
 93X  C7   C6   C11  121.29  3.000
 93X  C7   C6   N1   118.20  3.000
 93X  C11  C6   N1   120.51  3.000
 93X  H7   C11  C10  121.20  3.000
 93X  H7   C11  C6   119.96  3.000
 93X  C10  C11  C6   118.84  3.000
 93X  C9   C10  O23  115.42  3.000
 93X  C9   C10  C11  120.77  3.000
 93X  O23  C10  C11  123.81  3.000
 93X  C24  O23  C10  118.64  3.000
 93X  H10  C24  H9   108.73  3.000
 93X  H10  C24  H8   108.76  3.000
 93X  H9   C24  H8   108.90  3.000
 93X  H10  C24  O23  106.40  3.000
 93X  H9   C24  O23  112.06  3.000
 93X  H8   C24  O23  111.88  3.000
 93X  C8   C9   O21  120.40  3.000
 93X  C8   C9   C10  119.40  3.000
 93X  O21  C9   C10  120.19  3.000
 93X  C22  O21  C9   114.27  3.000
 93X  H13  C22  H12  108.70  3.000
 93X  H13  C22  H11  108.64  3.000
 93X  H12  C22  H11  108.60  3.000
 93X  H13  C22  O21  111.80  3.000
 93X  H12  C22  O21  111.81  3.000
 93X  H11  C22  O21  107.20  3.000
 93X  C7   C8   O25  123.81  3.000
 93X  C7   C8   C9   120.39  3.000
 93X  O25  C8   C9   115.81  3.000
 93X  C26  O25  C8   118.51  3.000
 93X  H16  C26  H15  108.92  3.000
 93X  H16  C26  H14  108.82  3.000
 93X  H15  C26  H14  108.68  3.000
 93X  H16  C26  O25  111.87  3.000
 93X  H15  C26  O25  111.99  3.000
 93X  H14  C26  O25  106.45  3.000
 93X  H17  C7   C8   120.88  3.000
 93X  H17  C7   C6   119.81  3.000
 93X  C8   C7   C6   119.31  3.000
 93X  H18  C2   C12  110.17  3.000
 93X  H18  C2   N1   111.73  3.000
 93X  C12  C2   N1   115.70  3.000
 93X  H18  C2   C3   112.54  3.000
 93X  C12  C2   C3   117.93  3.000
 93X  N1   C2   C3    87.09  3.000
 93X  C13  C12  C17  119.19  3.000
 93X  C13  C12  C2   121.54  3.000
 93X  C17  C12  C2   119.27  3.000
 93X  H19  C17  C16  118.78  3.000
 93X  H19  C17  C12  120.24  3.000
 93X  C16  C17  C12  120.98  3.000
 93X  C15  C16  O18  121.37  3.000
 93X  C15  C16  C17  119.53  3.000
 93X  O18  C16  C17  119.10  3.000
 93X  H20  O18  C16  110.20  3.000
 93X  C14  C15  O19  125.60  3.000
 93X  C14  C15  C16  119.51  3.000
 93X  O19  C15  C16  114.90  3.000
 93X  C20  O19  C15  118.51  3.000
 93X  H23  C20  H22  108.93  3.000
 93X  H23  C20  H21  108.91  3.000
 93X  H22  C20  H21  108.94  3.000
 93X  H23  C20  O19  111.75  3.000
 93X  H22  C20  O19  106.60  3.000
 93X  H21  C20  O19  111.62  3.000
 93X  H24  C14  C13  118.97  3.000
 93X  H24  C14  C15  120.67  3.000
 93X  C13  C14  C15  120.36  3.000
 93X  H25  C13  C14  118.74  3.000
 93X  H25  C13  C12  120.82  3.000
 93X  C14  C13  C12  120.43  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
 93X  CONST_01  C9   C10  C11  C6      0.00   0.0  0
 93X  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 93X  CONST_03  C8   C7   C6   C11     0.00   0.0  0
 93X  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 93X  CONST_05  C7   C6   C11  C10     0.00   0.0  0
 93X  CONST_06  C7   C8   C9   C10     0.00   0.0  0
 93X  CONST_07  C15  C16  C17  C12     0.00   0.0  0
 93X  CONST_08  C15  C14  C13  C12     0.00   0.0  0
 93X  CONST_09  C14  C13  C12  C17     0.00   0.0  0
 93X  CONST_10  C14  C15  C16  C17     0.00   0.0  0
 93X  CONST_11  C13  C12  C17  C16     0.00   0.0  0
 93X  CONST_12  C13  C14  C15  C16     0.00   0.0  0
 93X  CONST_13  C10  C11  C6   N1    180.00   0.0  0
 93X  CONST_14  C8   C7   C6   N1    180.00   0.0  0
 93X  CONST_15  C16  C17  C12  C2    180.00   0.0  0
 93X  CONST_16  C14  C13  C12  C2    180.00   0.0  0
 93X  CONST_17  C6   N1   C4   C3    180.00   0.0  0
 93X  CONST_18  C2   N1   C4   C3      0.00   0.0  0
 93X  CONST_19  O23  C10  C11  C6    180.00   0.0  0
 93X  CONST_20  O25  C8   C7   C6    180.00   0.0  0
 93X  CONST_21  O21  C9   C10  C11   180.00   0.0  0
 93X  CONST_22  O25  C8   C9   C10   180.00   0.0  0
 93X  CONST_23  C8   C9   C10  O23   180.00   0.0  0
 93X  CONST_24  C7   C8   C9   O21   180.00   0.0  0
 93X  CONST_25  O18  C16  C17  C12   180.00   0.0  0
 93X  CONST_26  O19  C15  C16  C17   180.00   0.0  0
 93X  CONST_27  C14  C15  C16  O18   180.00   0.0  0
 93X  CONST_28  C13  C14  C15  O19   180.00   0.0  0
 93X  CONST_29  C6   N1   C4   O5      0.00   0.0  0
 93X  CONST_30  C2   N1   C4   O5    180.00   0.0  0
 93X  CONST_31  H7   C11  C6   N1      0.00   0.0  0
 93X  CONST_32  H17  C7   C6   N1      0.00   0.0  0
 93X  CONST_33  H19  C17  C12  C2      0.00   0.0  0
 93X  CONST_34  H25  C13  C12  C2      0.00   0.0  0
 93X  CONST_35  H24  C14  C13  C12   180.00   0.0  0
 93X  Var_01    C11  C6   N1   C4      7.24  30.0  2
 93X  Var_02    C9   C10  O23  C24   178.69  30.0  2
 93X  Var_03    C8   C9   O21  C22   -90.17  30.0  2
 93X  Var_04    C7   C8   O25  C26     0.41  30.0  2
 93X  Var_05    C14  C15  O19  C20     0.61  30.0  2
 93X  Var_06    H8   C24  O23  C10   -62.06  30.0  3
 93X  Var_07    H11  C22  O21  C9   -178.30  30.0  3
 93X  Var_08    H14  C26  O25  C8   -179.67  30.0  3
 93X  Var_09    H21  C20  O19  C15    61.11  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
 93X  chir_01  C3  C29  C4  C2   positiv
 93X  chir_02  C2  N1   C3  C12  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
 93X  plan-1  N1   0.020
 93X  plan-1  C6   0.020
 93X  plan-1  C11  0.020
 93X  plan-1  C10  0.020
 93X  plan-1  O23  0.020
 93X  plan-1  C9   0.020
 93X  plan-1  O21  0.020
 93X  plan-1  C8   0.020
 93X  plan-1  O25  0.020
 93X  plan-1  C7   0.020
 93X  plan-1  H7   0.020
 93X  plan-1  H17  0.020
 93X  plan-2  C2   0.020
 93X  plan-2  C12  0.020
 93X  plan-2  C17  0.020
 93X  plan-2  C16  0.020
 93X  plan-2  O18  0.020
 93X  plan-2  C15  0.020
 93X  plan-2  O19  0.020
 93X  plan-2  C14  0.020
 93X  plan-2  C13  0.020
 93X  plan-2  H19  0.020
 93X  plan-2  H24  0.020
 93X  plan-2  H25  0.020
 93X  plan-3  C3   0.020
 93X  plan-3  C4   0.020
 93X  plan-3  O5   0.020
 93X  plan-3  N1   0.020
 93X  plan-3  C6   0.020
 93X  plan-3  C2   0.020

