# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 14 19:23:56 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CC[C@@H](CC1)[S](=O)(=O)N2[C@H]3CC[C@@H]2C[C@@H](C3)NC(=O)c4cc(on4)C5CC5
#
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
 8WD  8WD  N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide  ligand  59  29  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8WD
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
 8WD  N01  N  NH2   0  -0.793   7.6148   2.9639  -0.3307
 8WD  C04  C  CH1   0  -0.075   6.6801   1.9198   0.0618
 8WD  C06  C  CH2   0  -0.430   5.2872   2.5136   0.2414
 8WD  C09  C  CH2   0  -0.436   4.2749   1.4671   0.6983
 8WD  C12  C  CH1   0  -0.439   4.2419   0.2997  -0.2811
 8WD  C14  C  CH2   0  -0.434   5.6226  -0.3289  -0.4519
 8WD  C17  C  CH2   0  -0.446   6.6200   0.7345  -0.9030
 8WD  S20  S  S     0   1.401   3.0523  -0.9475   0.2386
 8WD  O21  O  OS    0  -0.667   3.0767  -2.0114  -0.7623
 8WD  O22  O  OS    0  -0.670   3.3220  -1.2923   1.6316
 8WD  N23  N  N     0  -0.589   1.6198  -0.1717   0.1786
 8WD  C24  C  CH1   0  -0.110   0.7739   0.1386   1.3319
 8WD  C26  C  CH2   0  -0.465   0.0037   1.3427   0.7737
 8WD  C29  C  CH2   0  -0.447  -0.0729   1.0925  -0.7494
 8WD  C32  C  CH1   0  -0.120   0.7079  -0.2133  -0.9679
 8WD  C34  C  CH2   0  -0.425  -0.1591  -1.4665  -0.8722
 8WD  C37  C  CH1   0  -0.096  -0.9277  -1.5765   0.4572
 8WD  C39  C  CH2   0  -0.456  -0.1042  -1.0701   1.6519
 8WD  N42  N  NH1   0  -0.657  -2.2140  -0.8925   0.4109
 8WD  C44  C  C     0   0.544  -3.2773  -1.3953  -0.2231
 8WD  O45  O  O     0  -0.476  -3.2884  -2.4503  -0.8385
 8WD  C46  C  CR5   0   0.138  -4.5165  -0.5718  -0.1416
 8WD  N47  N  N     0  -0.173  -4.5191   0.6143   0.3958
 8WD  O48  O  O     0  -0.337  -5.7934   1.0636   0.2988
 8WD  C49  C  CR5   0   0.508  -6.5618   0.1453  -0.3017
 8WD  C50  C  CR15  0  -0.499  -5.7971  -0.9328  -0.6134
 8WD  C52  C  CH1   0  -0.410  -7.9769   0.4369  -0.5036
 8WD  C54  C  CH2   0  -0.469  -8.4410   1.8320  -0.8413
 8WD  C57  C  CH2   0  -0.469  -8.7504   1.2589   0.4963
 8WD  H1   H  HNH2  0   0.343   8.5389   2.5634  -0.4428
 8WD  H2   H  HNH2  0   0.334   7.3607   3.3151  -1.2481
 8WD  H4   H  HCH1  0   0.215   7.0094   1.5422   1.0382
 8WD  H5   H  HCH2  0   0.242   5.3234   3.3274   0.9688
 8WD  H6   H  HCH2  0   0.218   4.9563   2.9513  -0.7079
 8WD  H7   H  HCH2  0   0.239   4.5534   1.1021   1.6903
 8WD  H8   H  HCH2  0   0.257   3.2862   1.9233   0.7843
 8WD  H9   H  HCH1  0   0.292   3.8740   0.6426  -1.2553
 8WD  H10  H  HCH2  0   0.237   5.9497  -0.7587   0.5000
 8WD  H11  H  HCH2  0   0.257   5.5880  -1.1410  -1.1787
 8WD  H12  H  HCH2  0   0.217   6.3392   1.1003  -1.8976
 8WD  H13  H  HCH2  0   0.239   7.6106   0.2825  -1.0005
 8WD  H14  H  HCH1  0   0.275   1.3721   0.4041   2.2020
 8WD  H15  H  HCH2  0   0.241  -0.9674   1.4743   1.2518
 8WD  H16  H  HCH2  0   0.264   0.5662   2.2536   0.9775
 8WD  H17  H  HCH2  0   0.245  -1.0925   1.0178  -1.1252
 8WD  H18  H  HCH2  0   0.259   0.4119   1.9060  -1.2883
 8WD  H19  H  HCH1  0   0.273   1.2588  -0.2069  -1.9088
 8WD  H20  H  HCH2  0   0.255  -0.8562  -1.5076  -1.7103
 8WD  H21  H  HCH2  0   0.249   0.4894  -2.3392  -0.9680
 8WD  H22  H  HCH1  0   0.272  -1.1439  -2.6329   0.6279
 8WD  H23  H  HCH2  0   0.260   0.5437  -1.8797   1.9930
 8WD  H24  H  HCH2  0   0.258  -0.7685  -0.8450   2.4903
 8WD  H25  H  HNH1  0   0.410  -2.3420  -0.0467   0.9436
 8WD  H26  H  HCR5  0   0.285  -6.1002  -1.8446  -1.0979
 8WD  H27  H  HCH1  0   0.293  -8.5069  -0.3787  -0.9786
 8WD  H28  H  HCH2  0   0.265  -7.6946   2.6129  -0.9074
 8WD  H29  H  HCH2  0   0.271  -9.2385   1.9113  -1.5677
 8WD  H30  H  HCH2  0   0.271  -9.7634   0.9416   0.7030
 8WD  H31  H  HCH2  0   0.265  -8.2170   1.6433   1.3559

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
 8WD  O45  C44  double    1.221  0.020  1.221
 8WD  N01  C04  single    1.455  0.020  1.455
 8WD  C39  C37  single    1.537  0.020  1.537
 8WD  C39  C24  single    1.528  0.020  1.528
 8WD  C17  C04  single    1.530  0.020  1.530
 8WD  C17  C14  single    1.526  0.020  1.526
 8WD  C06  C04  single    1.525  0.020  1.525
 8WD  C06  C09  single    1.526  0.020  1.526
 8WD  C37  N42  single    1.458  0.020  1.458
 8WD  C37  C34  single    1.540  0.020  1.540
 8WD  C44  N42  single    1.336  0.020  1.336
 8WD  C44  C46  single    1.490  0.020  1.490
 8WD  C12  C14  single    1.527  0.020  1.527
 8WD  C12  C09  single    1.524  0.020  1.524
 8WD  C12  S20  single    1.800  0.020  1.800
 8WD  C24  N23  single    1.463  0.020  1.463
 8WD  C24  C26  single    1.535  0.020  1.535
 8WD  C50  C46  aromatic  1.412  0.020  1.412
 8WD  C50  C49  aromatic  1.358  0.020  1.358
 8WD  C46  N47  aromatic  1.302  0.020  1.302
 8WD  O22  S20  double    1.460  0.020  1.460
 8WD  C54  C57  single    1.488  0.020  1.488
 8WD  C54  C52  single    1.509  0.020  1.509
 8WD  N23  S20  single    1.630  0.020  1.630
 8WD  N23  C32  single    1.466  0.020  1.466
 8WD  C34  C32  single    1.527  0.020  1.527
 8WD  S20  O21  double    1.461  0.020  1.461
 8WD  C26  C29  single    1.545  0.020  1.545
 8WD  C49  C52  single    1.459  0.020  1.459
 8WD  C49  O48  aromatic  1.340  0.020  1.340
 8WD  C57  C52  single    1.508  0.020  1.508
 8WD  N47  O48  aromatic  1.355  0.020  1.355
 8WD  C32  C29  single    1.537  0.020  1.537
 8WD  N01  H1   single    0.890  0.020  1.040
 8WD  N01  H2   single    0.890  0.020  1.040
 8WD  C04  H4   single    0.970  0.020  1.090
 8WD  C06  H5   single    0.970  0.020  1.090
 8WD  C06  H6   single    0.970  0.020  1.090
 8WD  C09  H7   single    0.970  0.020  1.090
 8WD  C09  H8   single    0.970  0.020  1.090
 8WD  C12  H9   single    0.970  0.020  1.090
 8WD  C14  H10  single    0.970  0.020  1.090
 8WD  C14  H11  single    0.970  0.020  1.090
 8WD  C17  H12  single    0.970  0.020  1.090
 8WD  C17  H13  single    0.970  0.020  1.090
 8WD  C24  H14  single    0.970  0.020  1.090
 8WD  C26  H15  single    0.970  0.020  1.090
 8WD  C26  H16  single    0.970  0.020  1.090
 8WD  C29  H17  single    0.970  0.020  1.090
 8WD  C29  H18  single    0.970  0.020  1.090
 8WD  C32  H19  single    0.970  0.020  1.090
 8WD  C34  H20  single    0.970  0.020  1.090
 8WD  C34  H21  single    0.970  0.020  1.090
 8WD  C37  H22  single    0.970  0.020  1.090
 8WD  C39  H23  single    0.970  0.020  1.090
 8WD  C39  H24  single    0.970  0.020  1.090
 8WD  N42  H25  single    0.860  0.020  1.020
 8WD  C50  H26  single    0.930  0.020  1.080
 8WD  C52  H27  single    0.970  0.020  1.090
 8WD  C54  H28  single    0.970  0.020  1.090
 8WD  C54  H29  single    0.970  0.020  1.090
 8WD  C57  H30  single    0.970  0.020  1.090
 8WD  C57  H31  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
 8WD  H2   N01  H1   105.37  3.000
 8WD  H2   N01  C04  109.35  3.000
 8WD  H1   N01  C04  109.39  3.000
 8WD  H4   C04  C17  107.84  3.000
 8WD  H4   C04  C06  107.65  3.000
 8WD  C17  C04  C06  109.89  3.000
 8WD  H4   C04  N01  107.11  3.000
 8WD  C06  C04  N01  109.82  3.000
 8WD  C17  C04  N01  114.27  3.000
 8WD  H6   C06  H5   106.81  3.000
 8WD  H6   C06  C09  109.44  3.000
 8WD  H5   C06  C09  109.49  3.000
 8WD  H6   C06  C04  109.22  3.000
 8WD  H5   C06  C04  109.77  3.000
 8WD  C09  C06  C04  111.97  3.000
 8WD  H8   C09  H7   107.37  3.000
 8WD  H8   C09  C12  110.54  3.000
 8WD  H7   C09  C12  109.44  3.000
 8WD  H8   C09  C06  109.73  3.000
 8WD  H7   C09  C06  109.37  3.000
 8WD  C12  C09  C06  110.32  3.000
 8WD  H9   C12  S20  104.56  3.000
 8WD  H9   C12  C14  109.44  3.000
 8WD  S20  C12  C14  110.16  3.000
 8WD  H9   C12  C09  109.80  3.000
 8WD  S20  C12  C09  111.07  3.000
 8WD  C14  C12  C09  111.57  3.000
 8WD  H11  C14  H10  107.27  3.000
 8WD  H11  C14  C17  110.04  3.000
 8WD  H10  C14  C17  109.60  3.000
 8WD  H11  C14  C12  110.64  3.000
 8WD  H10  C14  C12  109.55  3.000
 8WD  C17  C14  C12  109.71  3.000
 8WD  H13  C17  H12  106.80  3.000
 8WD  H13  C17  C14  109.30  3.000
 8WD  H12  C17  C14  109.47  3.000
 8WD  H13  C17  C04  109.94  3.000
 8WD  H12  C17  C04  108.89  3.000
 8WD  C14  C17  C04  112.29  3.000
 8WD  N23  S20  O22  108.05  3.000
 8WD  N23  S20  O21  109.64  3.000
 8WD  O22  S20  O21  118.59  3.000
 8WD  O21  S20  C12  107.20  3.000
 8WD  N23  S20  C12  103.91  3.000
 8WD  O22  S20  C12  108.48  3.000
 8WD  C32  N23  C24  105.24  3.000
 8WD  C32  N23  S20  124.20  3.000
 8WD  C24  N23  S20  125.43  3.000
 8WD  H14  C24  C39  109.96  3.000
 8WD  H14  C24  C26  112.03  3.000
 8WD  C39  C24  C26  114.11  3.000
 8WD  H14  C24  N23  111.34  3.000
 8WD  C26  C24  N23   99.78  3.000
 8WD  C39  C24  N23  109.24  3.000
 8WD  H16  C26  H15  106.07  3.000
 8WD  H16  C26  C29  110.20  3.000
 8WD  H15  C26  C29  114.05  3.000
 8WD  H16  C26  C24  109.19  3.000
 8WD  H15  C26  C24  112.47  3.000
 8WD  C29  C26  C24  104.85  3.000
 8WD  H18  C29  H17  107.28  3.000
 8WD  H18  C29  C32  109.75  3.000
 8WD  H17  C29  C32  111.60  3.000
 8WD  H18  C29  C26  110.15  3.000
 8WD  H17  C29  C26  113.43  3.000
 8WD  C32  C29  C26  104.63  3.000
 8WD  H19  C32  C34  110.23  3.000
 8WD  H19  C32  C29  111.99  3.000
 8WD  C34  C32  C29  113.57  3.000
 8WD  H19  C32  N23  111.13  3.000
 8WD  C29  C32  N23  100.41  3.000
 8WD  C34  C32  N23  109.12  3.000
 8WD  H21  C34  H20  106.38  3.000
 8WD  H21  C34  C37  108.38  3.000
 8WD  H20  C34  C37  109.98  3.000
 8WD  H21  C34  C32  108.26  3.000
 8WD  H20  C34  C32  110.22  3.000
 8WD  C37  C34  C32  113.35  3.000
 8WD  H22  C37  N42  106.51  3.000
 8WD  H22  C37  C39  107.67  3.000
 8WD  N42  C37  C39  110.06  3.000
 8WD  H22  C37  C34  107.64  3.000
 8WD  N42  C37  C34  112.31  3.000
 8WD  C39  C37  C34  112.35  3.000
 8WD  H24  C39  H23  105.89  3.000
 8WD  H24  C39  C37  109.78  3.000
 8WD  H23  C39  C37  108.46  3.000
 8WD  H24  C39  C24  110.30  3.000
 8WD  H23  C39  C24  108.12  3.000
 8WD  C37  C39  C24  113.94  3.000
 8WD  H25  N42  C44  117.75  3.000
 8WD  H25  N42  C37  119.29  3.000
 8WD  C44  N42  C37  122.74  3.000
 8WD  C46  C44  O45  119.82  3.000
 8WD  C46  C44  N42  115.33  3.000
 8WD  O45  C44  N42  124.84  3.000
 8WD  C50  C46  N47  111.66  3.000
 8WD  N47  C46  C44  121.84  3.000
 8WD  C50  C46  C44  126.50  3.000
 8WD  O48  N47  C46  105.93  3.000
 8WD  C49  O48  N47  110.14  3.000
 8WD  C52  C49  C50  132.31  3.000
 8WD  C52  C49  O48  118.78  3.000
 8WD  C50  C49  O48  108.91  3.000
 8WD  H26  C50  C49  128.12  3.000
 8WD  H26  C50  C46  128.51  3.000
 8WD  C49  C50  C46  103.36  3.000
 8WD  H27  C52  C57  116.78  3.000
 8WD  H27  C52  C54  116.61  3.000
 8WD  C57  C52  C54   59.10  3.000
 8WD  H27  C52  C49  112.65  3.000
 8WD  C57  C52  C49  120.98  3.000
 8WD  C54  C52  C49  120.95  3.000
 8WD  H29  C54  H28  114.49  3.000
 8WD  H29  C54  C57  118.61  3.000
 8WD  H28  C54  C57  118.44  3.000
 8WD  H29  C54  C52  116.42  3.000
 8WD  H28  C54  C52  117.95  3.000
 8WD  C57  C54  C52   60.43  3.000
 8WD  H31  C57  H30  114.46  3.000
 8WD  H31  C57  C54  118.35  3.000
 8WD  H30  C57  C54  118.66  3.000
 8WD  H31  C57  C52  117.87  3.000
 8WD  H30  C57  C52  116.57  3.000
 8WD  C54  C57  C52   60.47  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
 8WD  CONST_01  O48  C49  C50  C46     0.00   0.0  0
 8WD  CONST_02  C49  O48  N47  C46     0.00   0.0  0
 8WD  CONST_03  C49  C50  C46  N47     0.00   0.0  0
 8WD  CONST_04  C50  C49  O48  N47     0.00   0.0  0
 8WD  CONST_05  C50  C46  N47  O48     0.00   0.0  0
 8WD  CONST_06  C52  C49  C50  C46   180.00   0.0  0
 8WD  CONST_07  C52  C49  O48  N47   180.00   0.0  0
 8WD  CONST_08  C49  C50  C46  C44   180.00   0.0  0
 8WD  CONST_09  O48  N47  C46  C44   180.00   0.0  0
 8WD  CONST_10  H26  C50  C46  N47   180.00   0.0  0
 8WD  CONST_11  C46  C44  N42  C37   180.00   0.0  0
 8WD  CONST_12  O45  C44  N42  C37     0.00   0.0  0
 8WD  CONST_13  H25  N42  C44  C46     0.00   0.0  0
 8WD  Var_01    C12  C14  C17  C04    56.40  30.0  1
 8WD  Var_02    C12  C09  C06  C04   -56.17  30.0  1
 8WD  Var_03    C32  C29  C26  C24    -2.14  30.0  3
 8WD  Var_04    C54  C52  C49  O48    36.44  30.0  2
 8WD  Var_05    C57  C54  C52  C49  -109.92  30.0  1
 8WD  Var_06    C24  N23  S20  C12  -114.12  30.0  2
 8WD  Var_07    C50  C46  C44  N42  -173.70  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
 8WD  chir_01  C04  N01  C17  C06  positiv
 8WD  chir_02  C12  S20  C14  C09  positiv
 8WD  chir_03  C24  N23  C39  C26  positiv
 8WD  chir_04  C32  N23  C34  C29  negativ
 8WD  chir_05  C37  N42  C39  C34  positiv
 8WD  chir_06  C52  C54  C49  C57  both

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
 8WD  plan-1  C44  0.020
 8WD  plan-1  C46  0.020
 8WD  plan-1  N47  0.020
 8WD  plan-1  O48  0.020
 8WD  plan-1  C49  0.020
 8WD  plan-1  C50  0.020
 8WD  plan-1  C52  0.020
 8WD  plan-1  H26  0.020
 8WD  plan-2  C37  0.020
 8WD  plan-2  N42  0.020
 8WD  plan-2  C44  0.020
 8WD  plan-2  O45  0.020
 8WD  plan-2  C46  0.020
 8WD  plan-2  H25  0.020

