# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 02:40:32 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: [(1~{R},5~{S})-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2~{S})-3-oxidanyl-2-phenyl-propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H]2CC[C@H]1C[C@H](C2)OC(=O)[C@H](CO)c3ccccc3
#
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
 HYO  HYO  '[(1~{R},5~{S})-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2~{S})-3-oxidanyl-2-phenyl-propanoate'  ligand  44  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HYO
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
 HYO  C10  C  CH2   0  -0.431   3.0591  -0.9124  -0.8314
 HYO  C13  C  C     0   0.630  -0.4431  -0.7816  -1.6904
 HYO  C15  C  CR6   0   0.127  -2.2360  -0.5697  -0.0384
 HYO  C17  C  CR16  0  -0.295  -2.9168   0.5662  -0.4729
 HYO  C20  C  CR16  0  -0.240  -2.7093   0.0600   2.2466
 HYO  C21  C  CR16  0  -0.265  -3.3840   1.1899   1.8059
 HYO  C05  C  CH1   0  -0.129   2.2483   1.4801   0.4681
 HYO  C06  C  CH1   0  -0.131   3.3979  -0.4682   0.5900
 HYO  C07  C  CH2   0  -0.469   1.4466   0.6513   1.4979
 HYO  C08  C  CH2   0  -0.462   2.2336  -0.6716   1.5869
 HYO  C09  C  CH2   0  -0.442   1.7787   1.2699  -0.9696
 HYO  C11  C  CH1   0  -0.010   1.8520  -0.1894  -1.4205
 HYO  C12  C  CH3   0  -0.526   4.3295   1.4660   1.7234
 HYO  C14  C  CH1   0  -0.492  -1.5886  -1.5188  -1.0234
 HYO  C16  C  CH2   0  -0.117  -2.5746  -2.0611  -2.0455
 HYO  C18  C  CR16  0  -0.303  -2.1395  -0.8119   1.3286
 HYO  C19  C  CR16  0  -0.239  -3.4883   1.4380   0.4433
 HYO  N04  N  NT    0  -0.400   3.6198   0.9780   0.5575
 HYO  O01  O  O2    0  -0.455   0.6756  -0.9179  -1.0023
 HYO  O02  O  O     0  -0.452  -0.5572  -0.1113  -2.6868
 HYO  O03  O  OH1   0  -0.669  -1.8642  -2.9073  -2.9177
 HYO  H1   H  HCH2  0   0.241   3.9195  -0.6997  -1.4701
 HYO  H2   H  HCH2  0   0.243   2.9012  -1.9926  -0.8784
 HYO  H4   H  HCR6  0   0.257  -2.6238  -0.1454   3.3059
 HYO  H5   H  HCR6  0   0.257  -3.8267   1.8733   2.5189
 HYO  H6   H  HCH1  0   0.237   2.2230   2.5492   0.6918
 HYO  H7   H  HCH1  0   0.237   4.3086  -0.9818   0.9070
 HYO  H8   H  HCH2  0   0.234   1.4320   1.1612   2.4628
 HYO  H9   H  HCH2  0   0.251   0.4067   0.5107   1.2045
 HYO  H10  H  HCH2  0   0.238   1.6258  -1.5441   1.3513
 HYO  H11  H  HCH2  0   0.235   2.6222  -0.8254   2.5953
 HYO  H12  H  HCH2  0   0.245   0.7709   1.6657  -1.1127
 HYO  H13  H  HCH2  0   0.240   2.4310   1.8500  -1.6272
 HYO  H14  H  HCH1  0   0.257   1.9044  -0.2321  -2.5103
 HYO  H15  H  HCH3  0   0.199   3.8880   1.1793   2.6875
 HYO  H16  H  HCH3  0   0.231   5.3553   1.0943   1.7107
 HYO  H17  H  HCH3  0   0.231   4.3754   2.5555   1.6935
 HYO  H18  H  HCH1  0   0.286  -1.1829  -2.3637  -0.4615
 HYO  H19  H  HCH2  0   0.223  -3.3585  -2.6029  -1.5039
 HYO  H20  H  HCH2  0   0.202  -3.0626  -1.2390  -2.5812
 HYO  H21  H  HCR6  0   0.255  -1.6131  -1.6911   1.6804
 HYO  H22  H  HCR6  0   0.257  -4.0155   2.3149   0.0903
 HYO  H24  H  HOH1  0   0.459  -2.4954  -3.3706  -3.4758
 HYO  H3   H  HCR6  0   0.254  -3.0023   0.7809  -1.5307

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
 HYO  C09  C11  single    1.529  0.020  1.529
 HYO  C09  C05  single    1.527  0.020  1.527
 HYO  C10  C11  single    1.525  0.020  1.525
 HYO  C10  C06  single    1.527  0.020  1.527
 HYO  C11  O01  single    1.446  0.020  1.446
 HYO  N04  C12  single    1.450  0.020  1.450
 HYO  N04  C05  single    1.463  0.020  1.463
 HYO  N04  C06  single    1.463  0.020  1.463
 HYO  C05  C07  single    1.546  0.020  1.546
 HYO  C06  C08  single    1.546  0.020  1.546
 HYO  O02  C13  double    1.206  0.020  1.206
 HYO  O01  C13  single    1.320  0.020  1.320
 HYO  C19  C17  aromatic  1.388  0.020  1.388
 HYO  C19  C21  aromatic  1.389  0.020  1.389
 HYO  C13  C14  single    1.517  0.020  1.517
 HYO  C17  C15  aromatic  1.394  0.020  1.394
 HYO  C07  C08  single    1.542  0.020  1.542
 HYO  C21  C20  aromatic  1.388  0.020  1.388
 HYO  C15  C14  single    1.513  0.020  1.513
 HYO  C15  C18  aromatic  1.392  0.020  1.392
 HYO  C14  C16  single    1.520  0.020  1.520
 HYO  C16  O03  single    1.408  0.020  1.408
 HYO  C20  C18  aromatic  1.388  0.020  1.388
 HYO  C10  H1   single    0.970  0.020  1.090
 HYO  C10  H2   single    0.970  0.020  1.090
 HYO  C17  H3   single    0.930  0.020  1.080
 HYO  C20  H4   single    0.930  0.020  1.080
 HYO  C21  H5   single    0.930  0.020  1.080
 HYO  C05  H6   single    0.970  0.020  1.090
 HYO  C06  H7   single    0.970  0.020  1.090
 HYO  C07  H8   single    0.970  0.020  1.090
 HYO  C07  H9   single    0.970  0.020  1.090
 HYO  C08  H10  single    0.970  0.020  1.090
 HYO  C08  H11  single    0.970  0.020  1.090
 HYO  C09  H12  single    0.970  0.020  1.090
 HYO  C09  H13  single    0.970  0.020  1.090
 HYO  C11  H14  single    0.970  0.020  1.090
 HYO  C12  H15  single    0.970  0.020  1.090
 HYO  C12  H16  single    0.970  0.020  1.090
 HYO  C12  H17  single    0.970  0.020  1.090
 HYO  C14  H18  single    0.970  0.020  1.090
 HYO  C16  H19  single    0.970  0.020  1.090
 HYO  C16  H20  single    0.970  0.020  1.090
 HYO  C18  H21  single    0.930  0.020  1.080
 HYO  C19  H22  single    0.930  0.020  1.080
 HYO  O03  H24  single    0.850  0.020  0.980

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
 HYO  H2   C10  H1   106.32  3.000
 HYO  H2   C10  C11  109.73  3.000
 HYO  H1   C10  C11  107.77  3.000
 HYO  H2   C10  C06  111.08  3.000
 HYO  H1   C10  C06  108.23  3.000
 HYO  C11  C10  C06  113.40  3.000
 HYO  O02  C13  O01  124.61  3.000
 HYO  O01  C13  C14  111.13  3.000
 HYO  O02  C13  C14  124.19  3.000
 HYO  C18  C15  C14  120.04  3.000
 HYO  C18  C15  C17  118.81  3.000
 HYO  C14  C15  C17  121.15  3.000
 HYO  H3   C17  C19  119.20  3.000
 HYO  H3   C17  C15  120.31  3.000
 HYO  C19  C17  C15  120.49  3.000
 HYO  H4   C20  C18  119.71  3.000
 HYO  H4   C20  C21  120.24  3.000
 HYO  C18  C20  C21  120.06  3.000
 HYO  H5   C21  C19  120.18  3.000
 HYO  H5   C21  C20  120.25  3.000
 HYO  C19  C21  C20  119.57  3.000
 HYO  H6   C05  N04  110.18  3.000
 HYO  H6   C05  C09  108.69  3.000
 HYO  N04  C05  C09  107.37  3.000
 HYO  H6   C05  C07  112.09  3.000
 HYO  N04  C05  C07  105.15  3.000
 HYO  C09  C05  C07  113.20  3.000
 HYO  H7   C06  N04  110.16  3.000
 HYO  H7   C06  C08  112.25  3.000
 HYO  N04  C06  C08  104.98  3.000
 HYO  H7   C06  C10  108.56  3.000
 HYO  C08  C06  C10  113.25  3.000
 HYO  N04  C06  C10  107.48  3.000
 HYO  H9   C07  H8   106.60  3.000
 HYO  H9   C07  C08  113.07  3.000
 HYO  H8   C07  C08  110.89  3.000
 HYO  H9   C07  C05  112.62  3.000
 HYO  H8   C07  C05  110.21  3.000
 HYO  C08  C07  C05  103.52  3.000
 HYO  H11  C08  H10  106.59  3.000
 HYO  H11  C08  C07  110.85  3.000
 HYO  H10  C08  C07  112.95  3.000
 HYO  H11  C08  C06  110.25  3.000
 HYO  H10  C08  C06  112.72  3.000
 HYO  C07  C08  C06  103.55  3.000
 HYO  H13  C09  H12  106.24  3.000
 HYO  H13  C09  C11  107.49  3.000
 HYO  H12  C09  C11  110.58  3.000
 HYO  H13  C09  C05  108.05  3.000
 HYO  H12  C09  C05  110.93  3.000
 HYO  C11  C09  C05  113.22  3.000
 HYO  H14  C11  O01  107.94  3.000
 HYO  H14  C11  C09  109.51  3.000
 HYO  O01  C11  C09  110.89  3.000
 HYO  H14  C11  C10  109.21  3.000
 HYO  O01  C11  C10  107.06  3.000
 HYO  C09  C11  C10  112.11  3.000
 HYO  H17  C12  H16  107.48  3.000
 HYO  H17  C12  H15  107.56  3.000
 HYO  H16  C12  H15  107.40  3.000
 HYO  H17  C12  N04  109.56  3.000
 HYO  H16  C12  N04  109.64  3.000
 HYO  H15  C12  N04  114.92  3.000
 HYO  H18  C14  C16  108.10  3.000
 HYO  H18  C14  C15  108.00  3.000
 HYO  C16  C14  C15  112.57  3.000
 HYO  H18  C14  C13  108.76  3.000
 HYO  C16  C14  C13  111.56  3.000
 HYO  C15  C14  C13  107.73  3.000
 HYO  H20  C16  H19  107.09  3.000
 HYO  H20  C16  O03  111.89  3.000
 HYO  H19  C16  O03  111.71  3.000
 HYO  H20  C16  C14  110.48  3.000
 HYO  H19  C16  C14  107.94  3.000
 HYO  O03  C16  C14  107.68  3.000
 HYO  H21  C18  C20  119.62  3.000
 HYO  H21  C18  C15  119.60  3.000
 HYO  C20  C18  C15  120.78  3.000
 HYO  H22  C19  C21  120.08  3.000
 HYO  H22  C19  C17  119.62  3.000
 HYO  C21  C19  C17  120.30  3.000
 HYO  C12  N04  C06  112.90  3.000
 HYO  C06  N04  C05  101.44  3.000
 HYO  C12  N04  C05  113.11  3.000
 HYO  C11  O01  C13  119.12  3.000
 HYO  H24  O03  C16  108.54  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
 HYO  CONST_01  C21  C19  C17  C15    0.00   0.0  0
 HYO  CONST_02  C21  C20  C18  C15    0.00   0.0  0
 HYO  CONST_03  C20  C21  C19  C17    0.00   0.0  0
 HYO  CONST_04  C20  C18  C15  C17    0.00   0.0  0
 HYO  CONST_05  C19  C17  C15  C18    0.00   0.0  0
 HYO  CONST_06  C19  C21  C20  C18    0.00   0.0  0
 HYO  CONST_07  C14  C15  C18  C20  180.00   0.0  0
 HYO  CONST_08  C19  C17  C15  C14  180.00   0.0  0
 HYO  CONST_09  H22  C19  C17  C15  180.00   0.0  0
 HYO  CONST_10  H4   C20  C18  C15  180.00   0.0  0
 HYO  CONST_11  H5   C21  C19  C17  180.00   0.0  0
 HYO  CONST_12  H21  C18  C15  C17  180.00   0.0  0
 HYO  CONST_13  H3   C17  C19  C21  180.00   0.0  0
 HYO  Var_01    C06  C08  C07  C05   -0.46  30.0  3
 HYO  Var_02    H15  C12  N04  C05   61.44  30.0  3
 HYO  Var_03    O02  C13  O01  C11    2.25  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
 HYO  chir_01  C05  C09  N04  C07  positiv
 HYO  chir_02  C06  N04  C10  C08  positiv
 HYO  chir_03  C11  O01  C10  C09  positiv
 HYO  chir_04  C14  C16  C15  C13  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
 HYO  plan-1  C15  0.020
 HYO  plan-1  C17  0.020
 HYO  plan-1  C20  0.020
 HYO  plan-1  C21  0.020
 HYO  plan-1  C14  0.020
 HYO  plan-1  C18  0.020
 HYO  plan-1  C19  0.020
 HYO  plan-1  H4   0.020
 HYO  plan-1  H5   0.020
 HYO  plan-1  H21  0.020
 HYO  plan-1  H22  0.020
 HYO  plan-1  H3   0.020
 HYO  plan-2  C13  0.020
 HYO  plan-2  C14  0.020
 HYO  plan-2  O01  0.020
 HYO  plan-2  O02  0.020

