# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:49:43 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 1-[(4~{S})-9-propan-2-ylsulfonyl-1-oxa-9-azaspiro[5.5]undecan-4-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[S](=O)(=O)N1CCC2(CC1)C[C@H](CCO2)NC(=O)NCc3ccc(OC(F)(F)F)cc3
#
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
 E3N  E3N  1-[(4~{S})-9-propan-2-ylsulfonyl-1-oxa-9-azaspiro[5.5]undecan-4-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea  ligand  63  33  .  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_E3N
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
 E3N  C10  C  CH2   0  -0.303   5.2756   0.2518  -1.3705
 E3N  C13  C  CH1   0  -0.430   8.0875   1.0300   0.1823
 E3N  C15  C  CH3   0  -0.656   9.2576   1.9972   0.3021
 E3N  C20  C  CH2   0  -0.446   1.5597  -0.8227  -1.1609
 E3N  C22  C  CH2   0  -0.384  -4.0445  -2.7767  -0.0201
 E3N  C24  C  CR16  0  -0.308  -6.1143  -1.3989  -0.4293
 E3N  C26  C  CR6   0   0.300  -6.4424   0.7152   0.6241
 E3N  C28  C  CT    0   1.072  -7.0731   2.9050   0.1037
 E3N  C02  C  C     0   0.756  -1.6350  -2.2661  -0.0195
 E3N  C04  C  CH1   0  -0.070   0.7598  -1.8005  -0.3071
 E3N  C05  C  CH2   0  -0.450   1.4734  -3.1493  -0.2968
 E3N  C06  C  CH2   0  -0.197   2.9204  -2.9783   0.1320
 E3N  C08  C  CT    0   0.197   3.0281  -0.7438  -0.7316
 E3N  C09  C  CH2   0  -0.429   3.8319   0.0148  -1.7852
 E3N  C14  C  CH3   0  -0.664   8.0997  -0.0391   1.2615
 E3N  C18  C  CH2   0  -0.287   4.6254   0.2088   0.9996
 E3N  C19  C  CH2   0  -0.456   3.1730  -0.0073   0.6076
 E3N  C23  C  CR6   0   0.128  -4.8926  -1.5495   0.2162
 E3N  C25  C  CR16  0  -0.284  -6.8980  -0.2690  -0.2321
 E3N  C32  C  CR16  0  -0.283  -5.2326   0.5915   1.2888
 E3N  C33  C  CR16  0  -0.294  -4.4650  -0.5427   1.0807
 E3N  F29  F  F     0  -0.300  -5.8384   3.4061   0.1821
 E3N  F30  F  F     0  -0.277  -7.9255   3.8313   0.5126
 E3N  F31  F  F     0  -0.300  -7.3061   2.6620  -1.1881
 E3N  N03  N  NH1   0  -0.689  -0.5946  -1.8838  -0.8088
 E3N  N11  N  N     0  -0.583   5.3084   0.9240  -0.0743
 E3N  N21  N  NH1   0  -0.671  -2.7979  -2.4932  -0.6888
 E3N  O01  O  O     0  -0.549  -1.5353  -2.3883   1.1983
 E3N  O07  O  O2    0  -0.504   3.6036  -2.0411  -0.6738
 E3N  O16  O  OS    0  -0.672   6.3523   2.4810   1.5842
 E3N  O17  O  OS    0  -0.673   6.5825   2.9229  -0.8695
 E3N  S12  S  S     0   1.374   6.5414   1.9671   0.2320
 E3N  H1   H  HCH2  0   0.240   5.8267  -0.6939  -1.3258
 E3N  H2   H  HCH2  0   0.270   5.7627   0.8742  -2.1195
 E3N  H3   H  HCH1  0   0.297   8.0970   0.5617  -0.8064
 E3N  H4   H  HCH3  0   0.242   9.2415   2.5251   1.2560
 E3N  H5   H  HCH3  0   0.257  10.1871   1.4302   0.2544
 E3N  H6   H  HCH3  0   0.254   9.2713   2.7281  -0.5038
 E3N  H7   H  HCH2  0   0.237   1.5157  -1.1463  -2.2078
 E3N  H8   H  HCH2  0   0.249   1.1151   0.1742  -1.1167
 E3N  H9   H  HCH2  0   0.266  -3.8247  -3.2682   0.9269
 E3N  H10  H  HCH2  0   0.267  -4.6030  -3.4924  -0.6249
 E3N  H11  H  HCR6  0   0.264  -6.4681  -2.1733  -1.0989
 E3N  H12  H  HCH1  0   0.247   0.6984  -1.4213   0.7153
 E3N  H13  H  HCH2  0   0.243   0.9735  -3.8456   0.3800
 E3N  H14  H  HCH2  0   0.223   1.4348  -3.5829  -1.3013
 E3N  H15  H  HCH2  0   0.204   2.9659  -2.7021   1.1937
 E3N  H16  H  HCH2  0   0.243   3.4627  -3.9197   0.0310
 E3N  H17  H  HCH2  0   0.242   3.3503   0.9778  -1.9725
 E3N  H18  H  HCH2  0   0.251   3.8226  -0.5397  -2.7268
 E3N  H19  H  HCH3  0   0.250   7.2769  -0.7448   1.1598
 E3N  H20  H  HCH3  0   0.263   9.0250  -0.6092   1.1820
 E3N  H21  H  HCH3  0   0.245   8.0618   0.3987   2.2583
 E3N  H22  H  HCH2  0   0.273   4.6671   0.7962   1.9131
 E3N  H23  H  HCH2  0   0.233   5.1101  -0.7518   1.2034
 E3N  H24  H  HCH2  0   0.247   2.6764   0.9628   0.5240
 E3N  H25  H  HCH2  0   0.254   2.6753  -0.5387   1.4213
 E3N  H26  H  HCR6  0   0.279  -7.8530  -0.1702  -0.7311
 E3N  H27  H  HCR6  0   0.278  -4.8992   1.3594   1.9744
 E3N  H28  H  HCR6  0   0.263  -3.5241  -0.6440   1.6062
 E3N  H29  H  HNH1  0   0.384  -0.6944  -1.9887  -1.8074
 E3N  H30  H  HNH1  0   0.392  -2.8544  -2.2499  -1.6649
 E3N  O27  O  O2    0  -0.523  -7.2450   1.8253   0.8737

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
 E3N  C33  C32  aromatic  1.385  0.020  1.385
 E3N  C33  C23  aromatic  1.394  0.020  1.394
 E3N  C32  C26  aromatic  1.386  0.020  1.386
 E3N  C22  C23  single    1.510  0.020  1.510
 E3N  C22  N21  single    1.443  0.020  1.443
 E3N  C23  C24  aromatic  1.390  0.020  1.390
 E3N  C26  O27  single    1.392  0.020  1.392
 E3N  C26  C25  aromatic  1.382  0.020  1.382
 E3N  O01  C02  double    1.228  0.020  1.228
 E3N  O27  C28  single    1.337  0.020  1.337
 E3N  F29  C28  single    1.335  0.020  1.335
 E3N  N21  C02  single    1.361  0.020  1.361
 E3N  C24  C25  aromatic  1.389  0.020  1.389
 E3N  F30  C28  single    1.324  0.020  1.324
 E3N  C02  N03  single    1.361  0.020  1.361
 E3N  C28  F31  single    1.335  0.020  1.335
 E3N  C14  C13  single    1.519  0.020  1.519
 E3N  N03  C04  single    1.447  0.020  1.447
 E3N  C19  C18  single    1.520  0.020  1.520
 E3N  C19  C08  single    1.535  0.020  1.535
 E3N  C04  C20  single    1.525  0.020  1.525
 E3N  C04  C05  single    1.526  0.020  1.526
 E3N  O16  S12  double    1.459  0.020  1.459
 E3N  C18  N11  single    1.460  0.020  1.460
 E3N  C20  C08  single    1.532  0.020  1.532
 E3N  C13  S12  single    1.809  0.020  1.809
 E3N  C13  C15  single    1.523  0.020  1.523
 E3N  C08  C09  single    1.527  0.020  1.527
 E3N  C08  O07  single    1.420  0.020  1.420
 E3N  S12  N11  single    1.644  0.020  1.644
 E3N  S12  O17  double    1.459  0.020  1.459
 E3N  C05  C06  single    1.519  0.020  1.519
 E3N  N11  C10  single    1.460  0.020  1.460
 E3N  C06  O07  single    1.412  0.020  1.412
 E3N  C09  C10  single    1.521  0.020  1.521
 E3N  C10  H1   single    0.970  0.020  1.090
 E3N  C10  H2   single    0.970  0.020  1.090
 E3N  C13  H3   single    0.970  0.020  1.090
 E3N  C15  H4   single    0.970  0.020  1.090
 E3N  C15  H5   single    0.970  0.020  1.090
 E3N  C15  H6   single    0.970  0.020  1.090
 E3N  C20  H7   single    0.970  0.020  1.090
 E3N  C20  H8   single    0.970  0.020  1.090
 E3N  C22  H9   single    0.970  0.020  1.090
 E3N  C22  H10  single    0.970  0.020  1.090
 E3N  C24  H11  single    0.930  0.020  1.080
 E3N  C04  H12  single    0.970  0.020  1.090
 E3N  C05  H13  single    0.970  0.020  1.090
 E3N  C05  H14  single    0.970  0.020  1.090
 E3N  C06  H15  single    0.970  0.020  1.090
 E3N  C06  H16  single    0.970  0.020  1.090
 E3N  C09  H17  single    0.970  0.020  1.090
 E3N  C09  H18  single    0.970  0.020  1.090
 E3N  C14  H19  single    0.970  0.020  1.090
 E3N  C14  H20  single    0.970  0.020  1.090
 E3N  C14  H21  single    0.970  0.020  1.090
 E3N  C18  H22  single    0.970  0.020  1.090
 E3N  C18  H23  single    0.970  0.020  1.090
 E3N  C19  H24  single    0.970  0.020  1.090
 E3N  C19  H25  single    0.970  0.020  1.090
 E3N  C25  H26  single    0.930  0.020  1.080
 E3N  C32  H27  single    0.930  0.020  1.080
 E3N  C33  H28  single    0.930  0.020  1.080
 E3N  N03  H29  single    0.890  0.020  1.040
 E3N  N21  H30  single    0.860  0.020  1.020

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
 E3N  H2   C10  H1   107.24  3.000
 E3N  H2   C10  N11  109.72  3.000
 E3N  H1   C10  N11  110.47  3.000
 E3N  H2   C10  C09  109.04  3.000
 E3N  H1   C10  C09  110.74  3.000
 E3N  N11  C10  C09  109.58  3.000
 E3N  H3   C13  S12  104.71  3.000
 E3N  H3   C13  C14  109.92  3.000
 E3N  S12  C13  C14  110.61  3.000
 E3N  H3   C13  C15  109.66  3.000
 E3N  S12  C13  C15  109.00  3.000
 E3N  C14  C13  C15  112.64  3.000
 E3N  H6   C15  H5   107.84  3.000
 E3N  H6   C15  H4   108.85  3.000
 E3N  H5   C15  H4   107.62  3.000
 E3N  H6   C15  C13  112.21  3.000
 E3N  H5   C15  C13  108.75  3.000
 E3N  H4   C15  C13  111.41  3.000
 E3N  H8   C20  H7   106.96  3.000
 E3N  H8   C20  C08  109.37  3.000
 E3N  H7   C20  C08  108.73  3.000
 E3N  H8   C20  C04  110.43  3.000
 E3N  H7   C20  C04  108.92  3.000
 E3N  C08  C20  C04  112.27  3.000
 E3N  H10  C22  H9   106.81  3.000
 E3N  H10  C22  N21  108.32  3.000
 E3N  H9   C22  N21  108.50  3.000
 E3N  H10  C22  C23  109.41  3.000
 E3N  H9   C22  C23  110.12  3.000
 E3N  N21  C22  C23  113.46  3.000
 E3N  H11  C24  C25  119.01  3.000
 E3N  H11  C24  C23  119.79  3.000
 E3N  C25  C24  C23  121.21  3.000
 E3N  O27  C26  C32  119.24  3.000
 E3N  O27  C26  C25  119.27  3.000
 E3N  C32  C26  C25  121.42  3.000
 E3N  O27  C28  F31  112.81  3.000
 E3N  F31  C28  F30  108.30  3.000
 E3N  O27  C28  F30  107.72  3.000
 E3N  F31  C28  F29  106.66  3.000
 E3N  F30  C28  F29  108.36  3.000
 E3N  O27  C28  F29  112.84  3.000
 E3N  O01  C02  N21  122.72  3.000
 E3N  N21  C02  N03  114.52  3.000
 E3N  O01  C02  N03  122.76  3.000
 E3N  H12  C04  N03  106.98  3.000
 E3N  H12  C04  C05  109.08  3.000
 E3N  N03  C04  C05  112.91  3.000
 E3N  H12  C04  C20  109.33  3.000
 E3N  C05  C04  C20  108.98  3.000
 E3N  N03  C04  C20  109.50  3.000
 E3N  H14  C05  H13  107.46  3.000
 E3N  H14  C05  C06  109.71  3.000
 E3N  H13  C05  C06  109.45  3.000
 E3N  H14  C05  C04  109.11  3.000
 E3N  H13  C05  C04  110.71  3.000
 E3N  C06  C05  C04  110.36  3.000
 E3N  H16  C06  H15  106.62  3.000
 E3N  H16  C06  O07  106.22  3.000
 E3N  H15  C06  O07  111.39  3.000
 E3N  H16  C06  C05  110.50  3.000
 E3N  H15  C06  C05  109.93  3.000
 E3N  O07  C06  C05  111.99  3.000
 E3N  O07  C08  C19  111.37  3.000
 E3N  O07  C08  C09  105.58  3.000
 E3N  C19  C08  C09  108.29  3.000
 E3N  O07  C08  C20  110.65  3.000
 E3N  C09  C08  C20  109.68  3.000
 E3N  C19  C08  C20  111.07  3.000
 E3N  H18  C09  H17  107.20  3.000
 E3N  H18  C09  C08  109.75  3.000
 E3N  H17  C09  C08  108.91  3.000
 E3N  H18  C09  C10  108.79  3.000
 E3N  H17  C09  C10  109.13  3.000
 E3N  C08  C09  C10  112.89  3.000
 E3N  H21  C14  H20  107.85  3.000
 E3N  H21  C14  H19  108.64  3.000
 E3N  H20  C14  H19  107.21  3.000
 E3N  H21  C14  C13  111.53  3.000
 E3N  H20  C14  C13  108.85  3.000
 E3N  H19  C14  C13  112.57  3.000
 E3N  H23  C18  H22  107.49  3.000
 E3N  H23  C18  N11  111.08  3.000
 E3N  H22  C18  N11  109.61  3.000
 E3N  H23  C18  C19  110.27  3.000
 E3N  H22  C18  C19  109.29  3.000
 E3N  N11  C18  C19  109.09  3.000
 E3N  H25  C19  H24  106.37  3.000
 E3N  H25  C19  C18  108.21  3.000
 E3N  H24  C19  C18  109.13  3.000
 E3N  H25  C19  C08  111.94  3.000
 E3N  H24  C19  C08  108.44  3.000
 E3N  C18  C19  C08  112.54  3.000
 E3N  C33  C23  C24  118.64  3.000
 E3N  C24  C23  C22  120.60  3.000
 E3N  C33  C23  C22  120.76  3.000
 E3N  H26  C25  C26  120.78  3.000
 E3N  H26  C25  C24  120.45  3.000
 E3N  C26  C25  C24  118.77  3.000
 E3N  H27  C32  C33  120.37  3.000
 E3N  H27  C32  C26  120.63  3.000
 E3N  C33  C32  C26  119.00  3.000
 E3N  H28  C33  C32  119.03  3.000
 E3N  H28  C33  C23  120.01  3.000
 E3N  C32  C33  C23  120.96  3.000
 E3N  H29  N03  C04  116.22  3.000
 E3N  H29  N03  C02  117.98  3.000
 E3N  C04  N03  C02  122.06  3.000
 E3N  S12  N11  C18  121.65  3.000
 E3N  S12  N11  C10  118.31  3.000
 E3N  C18  N11  C10  114.64  3.000
 E3N  H30  N21  C02  118.96  3.000
 E3N  H30  N21  C22  116.61  3.000
 E3N  C02  N21  C22  122.90  3.000
 E3N  C08  O07  C06  115.68  3.000
 E3N  O17  S12  O16  118.21  3.000
 E3N  O17  S12  N11  107.23  3.000
 E3N  O16  S12  N11  107.40  3.000
 E3N  O17  S12  C13  107.13  3.000
 E3N  N11  S12  C13  107.90  3.000
 E3N  O16  S12  C13  108.59  3.000
 E3N  C28  O27  C26  117.80  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
 E3N  CONST_01  C32  C33  C23  C24     0.00   0.0  0
 E3N  CONST_02  C32  C26  C25  C24     0.00   0.0  0
 E3N  CONST_03  C23  C33  C32  C26     0.00   0.0  0
 E3N  CONST_04  C23  C24  C25  C26     0.00   0.0  0
 E3N  CONST_05  C33  C32  C26  C25     0.00   0.0  0
 E3N  CONST_06  C33  C23  C24  C25     0.00   0.0  0
 E3N  CONST_07  C32  C33  C23  C22   180.00   0.0  0
 E3N  CONST_08  C25  C24  C23  C22   180.00   0.0  0
 E3N  CONST_09  O27  C26  C25  C24   180.00   0.0  0
 E3N  CONST_10  O27  C26  C32  C33   180.00   0.0  0
 E3N  CONST_11  H28  C33  C23  C24   180.00   0.0  0
 E3N  CONST_12  H11  C24  C25  C26   180.00   0.0  0
 E3N  CONST_13  H27  C32  C33  C23   180.00   0.0  0
 E3N  CONST_14  H26  C25  C24  C23   180.00   0.0  0
 E3N  CONST_15  O01  C02  N03  C04     0.00   0.0  0
 E3N  CONST_16  N21  C02  N03  C04   180.00   0.0  0
 E3N  CONST_17  O01  C02  N21  C22     0.00   0.0  0
 E3N  CONST_18  N03  C02  N21  C22   180.00   0.0  0
 E3N  CONST_19  H30  N21  C02  O01   180.00   0.0  0
 E3N  CONST_20  H29  N03  C02  O01   180.00   0.0  0
 E3N  Var_01    C19  C18  N11  C10   -58.24  30.0  1
 E3N  Var_02    C19  C08  C09  C10    53.17  30.0  1
 E3N  Var_03    C18  C19  C08  C20  -174.46  30.0  1
 E3N  Var_04    O07  C06  C05  C04   -55.33  30.0  1
 E3N  Var_05    N11  C18  C19  C08    56.02  30.0  1
 E3N  Var_06    N11  C10  C09  C08   -54.64  30.0  1
 E3N  Var_07    C18  N11  C10  C09    57.54  30.0  1
 E3N  Var_08    O16  S12  N11  C10  -179.19  30.0  1
 E3N  Var_09    N21  C22  C23  C24   113.93  30.0  3
 E3N  Var_10    C32  C26  O27  C28    90.61  30.0  1
 E3N  Var_11    N11  S12  C13  C15   173.51  30.0  3
 E3N  Var_12    F29  C28  O27  C26   -60.25  30.0  3
 E3N  Var_13    C23  C22  N21  C02    93.80  30.0  1
 E3N  Var_14    H19  C14  C13  C15  -178.55  30.0  3
 E3N  Var_15    H4   C15  C13  C14   -60.65  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
 E3N  chir_01  C04  N03  C20  C05  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
 E3N  plan-1  C22  0.020
 E3N  plan-1  C02  0.020
 E3N  plan-1  C04  0.020
 E3N  plan-1  N03  0.020
 E3N  plan-1  N21  0.020
 E3N  plan-1  O01  0.020
 E3N  plan-1  H29  0.020
 E3N  plan-1  H30  0.020
 E3N  plan-2  C22  0.020
 E3N  plan-2  C24  0.020
 E3N  plan-2  C26  0.020
 E3N  plan-2  C23  0.020
 E3N  plan-2  C25  0.020
 E3N  plan-2  C32  0.020
 E3N  plan-2  C33  0.020
 E3N  plan-2  H11  0.020
 E3N  plan-2  H26  0.020
 E3N  plan-2  H27  0.020
 E3N  plan-2  H28  0.020
 E3N  plan-2  O27  0.020

