# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 18:40:11 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 2-(3-bromophenoxy)-N-[(1S,2S,3R,5S)-2-hydroxybicyclo[3.1.0]hexan-3-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](C[C@@H]2C[C@H]12)NC(=O)COc3cccc(Br)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
 K5D  K5D  2-(3-bromophenoxy)-N-[(1S,2S,3R,5S)-2-hydroxybicyclo[3.1.0]hexan-3-yl]acetamide  ligand  35  19  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K5D
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
 K5D  C10  C   CR16  0  -0.236  -2.9990  -2.2971  -0.7862
 K5D  C17  C   CH1   0  -0.261   6.6233   0.9545  -0.7502
 K5D  C02  C   CH1   0   0.052   5.1873   0.0143   1.0102
 K5D  C03  C   CH1   0  -0.097   4.3336   0.6763  -0.0982
 K5D  C05  C   C     0   0.509   1.9160   0.3620   0.2398
 K5D  C06  C   CH2   0  -0.311   0.7419  -0.4955  -0.2077
 K5D  C08  C   CR6   0   0.398  -1.5925  -0.5820   0.1316
 K5D  C09  C   CR16  0  -0.373  -1.7362  -1.7403  -0.6268
 K5D  C11  C   CR16  0  -0.256  -4.1225  -1.7280  -0.2103
 K5D  C12  C   CR6   0  -0.093  -3.9529  -0.5712   0.5403
 K5D  C14  C   CR16  0  -0.323  -2.7125   0.0096   0.7211
 K5D  C16  C   CH2   0  -0.462   5.2363   0.7547  -1.3354
 K5D  C18  C   CH1   0  -0.304   6.5922   0.4825   0.6841
 K5D  C19  C   CH2   0  -0.467   7.3740  -0.2717  -0.3482
 K5D  N04  N   NH1   0  -0.655   3.0729   0.0237  -0.3543
 K5D  O07  O   O2    0  -0.461  -0.4227   0.0445   0.3562
 K5D  O15  O   O     0  -0.471   1.8021   1.2495   1.0638
 K5D  BR1  BR  BR    0  -0.045  -5.4619   0.2360   1.3411
 K5D  H1   H   HCR6  0   0.274  -3.1053  -3.1978  -1.3762
 K5D  H2   H   HCH1  0   0.256   7.1785   1.8437  -1.0209
 K5D  H3   H   HCH1  0   0.225   4.8804   0.4021   1.9891
 K5D  H4   H   HCH1  0   0.264   4.1283   1.6965   0.2317
 K5D  H5   H   HCH2  0   0.267   0.6884  -0.5113  -1.3026
 K5D  H6   H   HCH2  0   0.270   0.9102  -1.5268   0.1262
 K5D  H7   H   HCR6  0   0.290  -0.8896  -2.2205  -1.0970
 K5D  H8   H   HCR6  0   0.278  -5.0966  -2.1766  -0.3459
 K5D  H9   H   HCR6  0   0.287  -2.5882   0.9105   1.3082
 K5D  H10  H   HCH2  0   0.256   4.9429   1.5769  -1.9880
 K5D  H11  H   HCH2  0   0.239   5.1764  -0.1614  -1.9312
 K5D  H12  H   HCH1  0   0.261   7.1442   1.0127   1.4500
 K5D  H13  H   HCH2  0   0.246   7.0155  -1.2359  -0.6869
 K5D  H14  H   HCH2  0   0.255   8.4528  -0.2013  -0.2831
 K5D  H15  H   HNH1  0   0.406   3.0654  -0.7225  -1.0333
 K5D  O01  O   OH1   0  -0.664   5.1098  -1.3914   0.9913
 K5D  H16  H   HOH1  0   0.445   4.2042  -1.6452   1.1981

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
 K5D  C10  C11  aromatic  1.385  0.020  1.385
 K5D  C10  C09  aromatic  1.389  0.020  1.389
 K5D  C11  C12  aromatic  1.389  0.020  1.389
 K5D  C09  C08  aromatic  1.392  0.020  1.392
 K5D  C12  BR1  single    1.889  0.020  1.889
 K5D  C12  C14  aromatic  1.382  0.020  1.382
 K5D  C08  C14  aromatic  1.397  0.020  1.397
 K5D  C08  O07  single    1.346  0.020  1.346
 K5D  O07  C06  single    1.402  0.020  1.402
 K5D  C06  C05  single    1.521  0.020  1.521
 K5D  C05  O15  double    1.216  0.020  1.216
 K5D  C05  N04  single    1.344  0.020  1.344
 K5D  N04  C03  single    1.442  0.020  1.442
 K5D  C16  C03  single    1.533  0.020  1.533
 K5D  C16  C17  single    1.519  0.020  1.519
 K5D  C03  C02  single    1.548  0.020  1.548
 K5D  C17  C19  single    1.493  0.020  1.493
 K5D  C17  C18  single    1.510  0.020  1.510
 K5D  C02  C18  single    1.516  0.020  1.516
 K5D  C02  O01  single    1.408  0.020  1.408
 K5D  C19  C18  single    1.499  0.020  1.499
 K5D  C10  H1   single    0.930  0.020  1.080
 K5D  C17  H2   single    0.970  0.020  1.090
 K5D  C02  H3   single    0.970  0.020  1.090
 K5D  C03  H4   single    0.970  0.020  1.090
 K5D  C06  H5   single    0.970  0.020  1.090
 K5D  C06  H6   single    0.970  0.020  1.090
 K5D  C09  H7   single    0.930  0.020  1.080
 K5D  C11  H8   single    0.930  0.020  1.080
 K5D  C14  H9   single    0.930  0.020  1.080
 K5D  C16  H10  single    0.970  0.020  1.090
 K5D  C16  H11  single    0.970  0.020  1.090
 K5D  C18  H12  single    0.970  0.020  1.090
 K5D  C19  H13  single    0.970  0.020  1.090
 K5D  C19  H14  single    0.970  0.020  1.090
 K5D  N04  H15  single    0.860  0.020  1.020
 K5D  O01  H16  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
 K5D  H1   C10  C11  119.29  3.000
 K5D  H1   C10  C09  119.05  3.000
 K5D  C11  C10  C09  121.67  3.000
 K5D  H2   C17  C19  118.95  3.000
 K5D  H2   C17  C18  120.32  3.000
 K5D  C19  C17  C18   59.86  3.000
 K5D  H2   C17  C16  118.69  3.000
 K5D  C18  C17  C16  107.82  3.000
 K5D  C19  C17  C16  117.06  3.000
 K5D  H3   C02  O01  110.46  3.000
 K5D  H3   C02  C18  110.00  3.000
 K5D  O01  C02  C18  110.88  3.000
 K5D  H3   C02  C03  109.49  3.000
 K5D  O01  C02  C03  112.77  3.000
 K5D  C18  C02  C03  103.00  3.000
 K5D  H4   C03  N04  108.19  3.000
 K5D  H4   C03  C16  107.86  3.000
 K5D  N04  C03  C16  113.23  3.000
 K5D  H4   C03  C02  106.68  3.000
 K5D  C16  C03  C02  105.96  3.000
 K5D  N04  C03  C02  114.56  3.000
 K5D  O15  C05  N04  124.32  3.000
 K5D  N04  C05  C06  113.11  3.000
 K5D  O15  C05  C06  122.57  3.000
 K5D  H6   C06  H5   107.33  3.000
 K5D  H6   C06  O07  111.53  3.000
 K5D  H5   C06  O07  111.51  3.000
 K5D  H6   C06  C05  108.79  3.000
 K5D  H5   C06  C05  109.85  3.000
 K5D  O07  C06  C05  107.80  3.000
 K5D  O07  C08  C14  115.42  3.000
 K5D  O07  C08  C09  124.61  3.000
 K5D  C14  C08  C09  119.97  3.000
 K5D  H7   C09  C08  121.73  3.000
 K5D  H7   C09  C10  118.95  3.000
 K5D  C08  C09  C10  119.33  3.000
 K5D  H8   C11  C12  121.55  3.000
 K5D  H8   C11  C10  120.55  3.000
 K5D  C12  C11  C10  117.89  3.000
 K5D  BR1  C12  C14  118.82  3.000
 K5D  C14  C12  C11  122.03  3.000
 K5D  BR1  C12  C11  119.16  3.000
 K5D  H9   C14  C12  121.60  3.000
 K5D  H9   C14  C08  119.29  3.000
 K5D  C12  C14  C08  119.11  3.000
 K5D  H11  C16  H10  106.90  3.000
 K5D  H11  C16  C03  111.36  3.000
 K5D  H10  C16  C03  111.29  3.000
 K5D  H11  C16  C17  111.71  3.000
 K5D  H10  C16  C17  112.16  3.000
 K5D  C03  C16  C17  103.50  3.000
 K5D  H12  C18  C19  117.89  3.000
 K5D  H12  C18  C02  118.12  3.000
 K5D  C19  C18  C02  118.43  3.000
 K5D  H12  C18  C17  120.54  3.000
 K5D  C19  C18  C17   59.49  3.000
 K5D  C02  C18  C17  108.66  3.000
 K5D  H14  C19  H13  113.97  3.000
 K5D  H14  C19  C18  116.46  3.000
 K5D  H13  C19  C18  119.40  3.000
 K5D  H14  C19  C17  117.62  3.000
 K5D  H13  C19  C17  118.73  3.000
 K5D  C18  C19  C17   60.64  3.000
 K5D  H15  N04  C05  118.51  3.000
 K5D  H15  N04  C03  117.42  3.000
 K5D  C05  N04  C03  124.06  3.000
 K5D  C08  O07  C06  118.39  3.000
 K5D  H16  O01  C02  108.18  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
 K5D  CONST_01  C14  C12  C11  C10     0.00   0.0  0
 K5D  CONST_02  C14  C08  C09  C10     0.00   0.0  0
 K5D  CONST_03  C11  C10  C09  C08     0.00   0.0  0
 K5D  CONST_04  C11  C12  C14  C08     0.00   0.0  0
 K5D  CONST_05  C12  C11  C10  C09     0.00   0.0  0
 K5D  CONST_06  C12  C14  C08  C09     0.00   0.0  0
 K5D  CONST_07  BR1  C12  C11  C10   180.00   0.0  0
 K5D  CONST_08  O07  C08  C09  C10   180.00   0.0  0
 K5D  CONST_09  BR1  C12  C14  C08   180.00   0.0  0
 K5D  CONST_10  O07  C08  C14  C12   180.00   0.0  0
 K5D  CONST_11  H1   C10  C09  C08   180.00   0.0  0
 K5D  CONST_12  H8   C11  C10  C09   180.00   0.0  0
 K5D  CONST_13  H9   C14  C08  C09   180.00   0.0  0
 K5D  CONST_14  H7   C09  C10  C11   180.00   0.0  0
 K5D  CONST_15  C06  C05  N04  C03   180.00   0.0  0
 K5D  CONST_16  O15  C05  N04  C03     0.00   0.0  0
 K5D  CONST_17  H15  N04  C05  C06     0.00   0.0  0
 K5D  Var_01    C02  C18  C19  C17    95.92  30.0  1
 K5D  Var_02    C16  C17  C18  C02    -1.14  30.0  1
 K5D  Var_03    C18  C19  C17  C16   -95.79  30.0  1
 K5D  Var_04    C09  C08  O07  C06     0.04  30.0  2
 K5D  Var_05    H5   C06  O07  C08    61.53  30.0  3
 K5D  Var_06    O07  C06  C05  N04  -173.37  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
 K5D  chir_02  C02  C03  C18  O01  positiv
 K5D  chir_03  C03  N04  C02  C16  negativ
 K5D  chir_04  C17  C16  C19  C18  both
 K5D  chir_05  C18  C17  C02  C19  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
 K5D  plan-1  C10  0.020
 K5D  plan-1  C08  0.020
 K5D  plan-1  C09  0.020
 K5D  plan-1  C11  0.020
 K5D  plan-1  C12  0.020
 K5D  plan-1  C14  0.020
 K5D  plan-1  O07  0.020
 K5D  plan-1  BR1  0.020
 K5D  plan-1  H1   0.020
 K5D  plan-1  H7   0.020
 K5D  plan-1  H8   0.020
 K5D  plan-1  H9   0.020
 K5D  plan-2  C03  0.020
 K5D  plan-2  C05  0.020
 K5D  plan-2  C06  0.020
 K5D  plan-2  N04  0.020
 K5D  plan-2  O15  0.020
 K5D  plan-2  H15  0.020

