# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 06:38:40 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: (2s,4R)-2-{3-[(3-chloro-4-methylphenyl)methoxy]azetidine-1-carbonyl}-7-oxa-5-azaspiro[3.4]octan-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CO[C@H]2CN(C2)C(=O)[C@H]3C[C@]4(COC(=O)N4)C3)cc1Cl
#
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
 XOM  XOM  (2s,4R)-2-{3-[(3-chloro-4-methylphenyl)methoxy]azetidine-1-carbonyl}-7-oxa-5-azaspiro[3.4]octan-6-one  ligand  46  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XOM
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
 XOM  C4    C   CR6   0   0.021  92.4002  -35.0151  155.1792
 XOM  C5    C   CR6   0   0.157  92.0887  -33.6089  152.7463
 XOM  C6    C   CR6   0  -0.090  93.3147  -33.6819  153.4004
 XOM  C7    C   CR5   0   0.664  88.9662  -33.0599  165.8056
 XOM  C8    C   C     0   0.534  92.1691  -32.9148  161.0930
 XOM  C10   C   C     0  -0.443  90.1726  -33.9024  162.4361
 XOM  C13   C   CH2   0  -0.180  88.4429  -32.4552  163.6894
 XOM  C15   C   C     0  -0.024  91.7971  -34.0243  157.8850
 XOM  C17   C   CH3   0  -0.720  91.9086  -32.8585  151.4630
 XOM  C1    C   CR16  0  -0.252  91.1647  -34.9625  154.5410
 XOM  C2    C   CR16  0  -0.301  91.0195  -34.2703  153.3509
 XOM  C3    C   CR16  0  -0.238  93.4780  -34.3617  154.5986
 XOM  C9    C   C     0  -0.426  90.9817  -32.0863  163.2596
 XOM  C11   C   C     0  -0.272  90.8400  -33.6399  159.0250
 XOM  C12   C   C     0  -0.269  92.9819  -33.7532  158.8481
 XOM  C14   C   C     0  -0.415  90.8862  -32.6608  161.8409
 XOM  C16   C   C     0   0.137  89.8528  -33.0512  163.6709
 XOM  C18   C   CH2   0  -0.243  92.5578  -35.7503  156.4859
 XOM  N19   N   NR15  0  -0.685  89.8695  -33.6382  164.9804
 XOM  N20   N   N     0  -0.459  92.0082  -33.2974  159.8230
 XOM  O22   O   O     0  -0.485  93.2781  -32.8025  161.5998
 XOM  O23   O   O     0  -0.465  88.1434  -32.2867  165.0751
 XOM  O24   O   O2    0  -0.473  91.6199  -35.3382  157.4568
 XOM  CL25  CL  CL    0  -0.131  94.6974  -32.8886  152.7111
 XOM  H1    H   H     0   0.261  89.3344  -34.3270  161.8831
 XOM  H2    H   H     0   0.265  90.8827  -34.6960  162.6752
 XOM  H3    H   HCH2  0   0.260  88.3704  -31.4919  163.1870
 XOM  H4    H   HCH2  0   0.251  87.7161  -33.1434  163.2495
 XOM  H5    H   H     0   0.251  91.7700  -33.3175  157.0495
 XOM  H6    H   HCH3  0   0.251  92.5476  -33.2554  150.6728
 XOM  H7    H   HCH3  0   0.252  90.8766  -32.9214  151.1233
 XOM  H8    H   HCH3  0   0.251  92.1608  -31.8035  151.5788
 XOM  H9    H   HCR6  0   0.257  90.3071  -35.4607  154.9759
 XOM  H10   H   HCR6  0   0.257  90.0502  -34.2369  152.8685
 XOM  H11   H   HCR6  0   0.274  94.4470  -34.3775  155.0826
 XOM  H12   H   H     0   0.254  91.9239  -32.3658  163.7329
 XOM  H13   H   H     0   0.255  90.8143  -31.0178  163.3972
 XOM  H14   H   H     0   0.259  90.1642  -32.8077  158.8209
 XOM  H15   H   H     0   0.253  90.2656  -34.4824  159.4176
 XOM  H16   H   H     0   0.249  93.5273  -34.6483  159.1599
 XOM  H17   H   H     0   0.250  93.6943  -32.9907  158.5302
 XOM  H18   H   H     0   0.293  90.1908  -32.0866  161.2228
 XOM  H19   H   HCH2  0   0.257  92.3839  -36.8182  156.3399
 XOM  H20   H   HCH2  0   0.234  93.5866  -35.6389  156.8516
 XOM  H21   H   HNR5  0   0.405  90.6962  -34.0734  165.3603
 XOM  O21   O   O     0  -0.478  88.8498  -33.1785  166.9997

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
 XOM  C17   C5   single    1.497  0.020  1.497
 XOM  CL25  C6   single    1.737  0.020  1.737
 XOM  C5    C6   aromatic  1.391  0.020  1.391
 XOM  C5    C2   aromatic  1.395  0.020  1.395
 XOM  C6    C3   aromatic  1.387  0.020  1.387
 XOM  C2    C1   aromatic  1.384  0.020  1.384
 XOM  C3    C4   aromatic  1.388  0.020  1.388
 XOM  C1    C4   aromatic  1.392  0.020  1.392
 XOM  C4    C18  single    1.508  0.020  1.508
 XOM  C18   O24  single    1.411  0.020  1.411
 XOM  O24   C15  single    1.393  0.020  1.393
 XOM  C15   C12  single    1.551  0.020  1.551
 XOM  C15   C11  single    1.537  0.020  1.537
 XOM  C12   N20  single    1.451  0.020  1.451
 XOM  C11   N20  single    1.456  0.020  1.456
 XOM  N20   C8   single    1.336  0.020  1.336
 XOM  C8    O22  double    1.224  0.020  1.224
 XOM  C8    C14  single    1.507  0.020  1.507
 XOM  C14   C10  single    1.551  0.020  1.551
 XOM  C14   C9   single    1.534  0.020  1.534
 XOM  C10   C16  single    1.533  0.020  1.533
 XOM  C16   C9   single    1.541  0.020  1.541
 XOM  C16   C13  single    1.531  0.020  1.531
 XOM  C16   N19  single    1.435  0.020  1.435
 XOM  C13   O23  single    1.428  0.020  1.428
 XOM  N19   C7   single    1.353  0.020  1.353
 XOM  O23   C7   single    1.345  0.020  1.345
 XOM  C7    O21  double    1.206  0.020  1.206
 XOM  C10   H1   single    0.970  0.020  1.090
 XOM  C10   H2   single    0.970  0.020  1.090
 XOM  C13   H3   single    0.970  0.020  1.090
 XOM  C13   H4   single    0.970  0.020  1.090
 XOM  C15   H5   single    0.970  0.020  1.090
 XOM  C17   H6   single    0.970  0.020  1.090
 XOM  C17   H7   single    0.970  0.020  1.090
 XOM  C17   H8   single    0.970  0.020  1.090
 XOM  C1    H9   single    0.930  0.020  1.080
 XOM  C2    H10  single    0.930  0.020  1.080
 XOM  C3    H11  single    0.930  0.020  1.080
 XOM  C9    H12  single    0.970  0.020  1.090
 XOM  C9    H13  single    0.970  0.020  1.090
 XOM  C11   H14  single    0.970  0.020  1.090
 XOM  C11   H15  single    0.970  0.020  1.090
 XOM  C12   H16  single    0.970  0.020  1.090
 XOM  C12   H17  single    0.970  0.020  1.090
 XOM  C14   H18  single    0.970  0.020  1.090
 XOM  C18   H19  single    0.970  0.020  1.090
 XOM  C18   H20  single    0.970  0.020  1.090
 XOM  N19   H21  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
 XOM  C18   C4   C3   120.74  3.000
 XOM  C18   C4   C1   120.58  3.000
 XOM  C3    C4   C1   118.68  3.000
 XOM  C2    C5   C17  121.12  3.000
 XOM  C2    C5   C6   116.53  3.000
 XOM  C17   C5   C6   122.35  3.000
 XOM  CL25  C6   C3   118.22  3.000
 XOM  C3    C6   C5   122.38  3.000
 XOM  CL25  C6   C5   119.40  3.000
 XOM  O23   C7   O21  122.38  3.000
 XOM  O21   C7   N19  128.79  3.000
 XOM  O23   C7   N19  108.83  3.000
 XOM  O22   C8   N20  121.92  3.000
 XOM  O22   C8   C14  123.39  3.000
 XOM  N20   C8   C14  114.68  3.000
 XOM  H2    C10  H1   109.16  3.000
 XOM  H2    C10  C16  111.28  3.000
 XOM  H1    C10  C16  117.67  3.000
 XOM  H2    C10  C14  111.52  3.000
 XOM  H1    C10  C14  118.09  3.000
 XOM  C16   C10  C14   87.74  3.000
 XOM  H4    C13  H3   109.08  3.000
 XOM  H4    C13  O23  108.99  3.000
 XOM  H3    C13  O23  109.23  3.000
 XOM  H4    C13  C16  111.25  3.000
 XOM  H3    C13  C16  113.59  3.000
 XOM  O23   C13  C16  104.53  3.000
 XOM  H5    C15  O24  111.78  3.000
 XOM  H5    C15  C12  112.33  3.000
 XOM  O24   C15  C12  116.94  3.000
 XOM  H5    C15  C11  112.90  3.000
 XOM  C12   C15  C11   88.36  3.000
 XOM  O24   C15  C11  112.62  3.000
 XOM  H8    C17  H7   107.96  3.000
 XOM  H8    C17  H6   107.06  3.000
 XOM  H7    C17  H6   107.96  3.000
 XOM  H8    C17  C5   111.45  3.000
 XOM  H7    C17  C5   110.65  3.000
 XOM  H6    C17  C5   111.59  3.000
 XOM  H9    C1   C2   119.49  3.000
 XOM  H9    C1   C4   120.10  3.000
 XOM  C2    C1   C4   120.42  3.000
 XOM  H10   C2   C1   119.48  3.000
 XOM  H10   C2   C5   118.57  3.000
 XOM  C1    C2   C5   121.95  3.000
 XOM  H11   C3   C6   119.89  3.000
 XOM  H11   C3   C4   120.06  3.000
 XOM  C6    C3   C4   120.05  3.000
 XOM  H13   C9   H12  109.21  3.000
 XOM  H13   C9   C16  117.87  3.000
 XOM  H12   C9   C16  110.89  3.000
 XOM  H13   C9   C14  118.32  3.000
 XOM  H12   C9   C14  111.04  3.000
 XOM  C16   C9   C14   88.09  3.000
 XOM  H15   C11  H14  109.24  3.000
 XOM  H15   C11  N20  113.98  3.000
 XOM  H14   C11  N20  114.84  3.000
 XOM  H15   C11  C15  113.64  3.000
 XOM  H14   C11  C15  115.95  3.000
 XOM  N20   C11  C15   88.03  3.000
 XOM  H17   C12  H16  109.24  3.000
 XOM  H17   C12  N20  114.48  3.000
 XOM  H16   C12  N20  113.58  3.000
 XOM  H17   C12  C15  116.12  3.000
 XOM  H16   C12  C15  114.52  3.000
 XOM  N20   C12  C15   87.68  3.000
 XOM  H18   C14  C9   111.46  3.000
 XOM  H18   C14  C10  110.17  3.000
 XOM  C9    C14  C10   88.48  3.000
 XOM  H18   C14  C8   110.46  3.000
 XOM  C9    C14  C8   117.99  3.000
 XOM  C10   C14  C8   116.58  3.000
 XOM  N19   C16  C9   119.41  3.000
 XOM  N19   C16  C13   99.14  3.000
 XOM  C9    C16  C13  115.73  3.000
 XOM  N19   C16  C10  120.35  3.000
 XOM  C13   C16  C10  114.70  3.000
 XOM  C9    C16  C10   88.85  3.000
 XOM  H20   C18  H19  107.04  3.000
 XOM  H20   C18  O24  111.35  3.000
 XOM  H19   C18  O24  105.77  3.000
 XOM  H20   C18  C4   109.71  3.000
 XOM  H19   C18  C4   110.15  3.000
 XOM  O24   C18  C4   112.61  3.000
 XOM  H21   N19  C16  121.99  3.000
 XOM  H21   N19  C7   120.12  3.000
 XOM  C16   N19  C7   111.95  3.000
 XOM  C12   N20  C11   95.53  3.000
 XOM  C11   N20  C8   133.24  3.000
 XOM  C12   N20  C8   130.36  3.000
 XOM  C13   O23  C7   109.33  3.000
 XOM  C18   O24  C15  113.72  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
 XOM  CONST_01  C5    C6   C3   C4      0.00   0.0  0
 XOM  CONST_02  C5    C2   C1   C4      0.00   0.0  0
 XOM  CONST_03  C1    C2   C5   C6      0.00   0.0  0
 XOM  CONST_04  C1    C4   C3   C6      0.00   0.0  0
 XOM  CONST_05  C3    C6   C5   C2      0.00   0.0  0
 XOM  CONST_06  C3    C4   C1   C2      0.00   0.0  0
 XOM  CONST_07  CL25  C6   C3   C4    180.00   0.0  0
 XOM  CONST_08  C18   C4   C3   C6    180.00   0.0  0
 XOM  CONST_09  C3    C6   C5   C17   180.00   0.0  0
 XOM  CONST_10  C1    C2   C5   C17   180.00   0.0  0
 XOM  CONST_11  CL25  C6   C5   C2    180.00   0.0  0
 XOM  CONST_12  C18   C4   C1   C2    180.00   0.0  0
 XOM  CONST_13  C14   C8   N20  C11     0.00   0.0  0
 XOM  CONST_14  C14   C8   N20  C12   180.00   0.0  0
 XOM  CONST_15  H10   C2   C1   C4    180.00   0.0  0
 XOM  CONST_16  H11   C3   C6   C5    180.00   0.0  0
 XOM  CONST_17  H9    C1   C2   C5    180.00   0.0  0
 XOM  CONST_18  O22   C8   N20  C11   180.00   0.0  0
 XOM  CONST_19  O22   C8   N20  C12     0.00   0.0  0
 XOM  Var_01    C10   C16  N19  C7   -147.97  30.0  1
 XOM  Var_02    C16   C13  O23  C7    -18.97  30.0  1
 XOM  Var_03    C14   C9   C16  C10    19.74  30.0  3
 XOM  Var_04    O23   C13  C16  C10   153.35  30.0  1
 XOM  Var_05    C14   C10  C16  C13    98.44  30.0  3
 XOM  Var_06    N19   C7   O23  C13     5.36  30.0  1
 XOM  Var_07    C11   N20  C12  C15     4.91  30.0  1
 XOM  Var_08    O23   C7   N19  C16    12.00  30.0  1
 XOM  Var_09    O24   C18  C4   C1    -52.75  30.0  2
 XOM  Var_10    H6    C17  C5   C6     60.09  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
 XOM  chir_01  C15  O24  C12  C11  positiv
 XOM  chir_02  C14  C8   C10  C9   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
 XOM  plan-1  C8    0.020
 XOM  plan-1  C11   0.020
 XOM  plan-1  C12   0.020
 XOM  plan-1  C14   0.020
 XOM  plan-1  N20   0.020
 XOM  plan-1  O22   0.020
 XOM  plan-2  C7    0.020
 XOM  plan-2  C16   0.020
 XOM  plan-2  N19   0.020
 XOM  plan-2  H21   0.020
 XOM  plan-3  C4    0.020
 XOM  plan-3  C5    0.020
 XOM  plan-3  C6    0.020
 XOM  plan-3  C17   0.020
 XOM  plan-3  C1    0.020
 XOM  plan-3  C2    0.020
 XOM  plan-3  C3    0.020
 XOM  plan-3  C18   0.020
 XOM  plan-3  CL25  0.020
 XOM  plan-3  H9    0.020
 XOM  plan-3  H10   0.020
 XOM  plan-3  H11   0.020
 XOM  plan-4  C7    0.020
 XOM  plan-4  N19   0.020
 XOM  plan-4  O23   0.020
 XOM  plan-4  O21   0.020

