# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:50:27 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4,4'-[(1s,5s)-bicyclo[3.3.1]non-9-ylidenemethanediyl]diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)[C](c2ccc(O)cc2)=[C]3C4C[CH2]CC3CCC4
#
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
 5HZ  5HZ  4,4'-[(1s,5s)-bicyclo[3.3.1]non-9-ylidenemethanediyl]diphenol  ligand  48  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5HZ
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
 5HZ  C01  C  CH2   0  -0.419   1.2940  -3.0803   1.2054
 5HZ  C02  C  CH2   0  -0.455   0.0240  -3.8617   1.5449
 5HZ  C03  C  CH2   0  -0.413  -1.2435  -3.0291   1.3607
 5HZ  C04  C  CH1   0  -0.320  -1.2833  -2.1987   0.0651
 5HZ  C05  C  CH2   0  -0.418  -1.4027  -3.0285  -1.2227
 5HZ  C06  C  CH2   0  -0.455  -0.1512  -3.8350  -1.5702
 5HZ  C07  C  CH2   0  -0.413   1.1324  -3.0304  -1.3761
 5HZ  C08  C  CH1   0  -0.322   1.1905  -2.2236  -0.0664
 5HZ  C09  C  C     0   0.171  -0.0372  -1.3539   0.0082
 5HZ  C10  C  C     0  -0.063  -0.0251  -0.0097   0.0223
 5HZ  C11  C  CR6   0   0.025   1.2253   0.7904   0.0769
 5HZ  C12  C  CR6   0   0.018  -1.2648   0.8085  -0.0165
 5HZ  C13  C  CR16  0  -0.281   1.4606   1.7919  -0.8654
 5HZ  C14  C  CR16  0  -0.370   2.6088   2.5664  -0.8340
 5HZ  C15  C  CR6   0   0.339   3.5566   2.3672   0.1677
 5HZ  C16  C  CR16  0  -0.329   3.3331   1.3852   1.1288
 5HZ  C17  C  CR16  0  -0.292   2.1810   0.6163   1.0780
 5HZ  C18  C  CR16  0  -0.287  -2.2017   0.6937  -1.0436
 5HZ  C19  C  CR16  0  -0.329  -3.3416   1.4811  -1.0826
 5HZ  C20  C  CR6   0   0.339  -3.5703   2.4215  -0.0817
 5HZ  C21  C  CR16  0  -0.370  -2.6424   2.5593   0.9483
 5HZ  C22  C  CR16  0  -0.281  -1.5057   1.7672   0.9672
 5HZ  O01  O  OH1   0  -0.634  -4.6888   3.1719  -0.1594
 5HZ  O02  O  OH1   0  -0.633   4.6880   3.0961   0.2559
 5HZ  H1   H  HCH2  0   0.221   1.5281  -2.4102   2.0389
 5HZ  H2   H  HCH2  0   0.226   2.1415  -3.7657   1.1154
 5HZ  H3   H  HCH2  0   0.223  -0.0304  -4.7700   0.9453
 5HZ  H4   H  HCH2  0   0.232   0.0806  -4.2039   2.5817
 5HZ  H5   H  HCH2  0   0.226  -2.1256  -3.6750   1.4048
 5HZ  H6   H  HCH2  0   0.220  -1.3332  -2.3290   2.1978
 5HZ  H7   H  HCH1  0   0.246  -2.1707  -1.5658   0.1267
 5HZ  H8   H  HCH2  0   0.226  -2.2692  -3.6922  -1.1523
 5HZ  H9   H  HCH2  0   0.221  -1.6114  -2.3352  -2.0440
 5HZ  H10  H  HCH2  0   0.223  -0.1160  -4.7493  -0.9787
 5HZ  H11  H  HCH2  0   0.232  -0.2144  -4.1651  -2.6105
 5HZ  H12  H  HCH2  0   0.226   2.0023  -3.6917  -1.4331
 5HZ  H13  H  HCH2  0   0.220   1.2336  -2.3181  -2.2015
 5HZ  H14  H  HCH1  0   0.246   2.0912  -1.6090  -0.1181
 5HZ  H17  H  HCR6  0   0.248   0.7331   1.9694  -1.6482
 5HZ  H18  H  HCR6  0   0.268   2.7646   3.3288  -1.5891
 5HZ  H19  H  HCR6  0   0.260   4.0571   1.2314   1.9197
 5HZ  H20  H  HCR6  0   0.254   2.0204  -0.1329   1.8431
 5HZ  H21  H  HCR6  0   0.253  -2.0352  -0.0237  -1.8376
 5HZ  H22  H  HCR6  0   0.260  -4.0516   1.3738  -1.8935
 5HZ  H23  H  HCR6  0   0.268  -2.8050   3.2882   1.7344
 5HZ  H24  H  HCR6  0   0.248  -0.7928   1.8958   1.7728
 5HZ  H25  H  HOH1  0   0.473  -4.7312   3.7855   0.5825
 5HZ  H26  H  HOH1  0   0.473   4.7280   3.7405  -0.4595

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
 5HZ  O01  C20  single    1.349  0.020  1.349
 5HZ  C19  C20  aromatic  1.392  0.020  1.392
 5HZ  C19  C18  aromatic  1.386  0.020  1.386
 5HZ  C20  C21  aromatic  1.393  0.020  1.393
 5HZ  C18  C12  aromatic  1.395  0.020  1.395
 5HZ  C21  C22  aromatic  1.386  0.020  1.386
 5HZ  C12  C22  aromatic  1.395  0.020  1.395
 5HZ  C12  C10  single    1.486  0.020  1.486
 5HZ  C17  C16  aromatic  1.386  0.020  1.386
 5HZ  C17  C11  aromatic  1.395  0.020  1.395
 5HZ  C16  C15  aromatic  1.392  0.020  1.392
 5HZ  C10  C11  single    1.485  0.020  1.485
 5HZ  C10  C09  double    1.344  0.020  1.344
 5HZ  C11  C13  aromatic  1.395  0.020  1.395
 5HZ  C15  O02  single    1.349  0.020  1.349
 5HZ  C15  C14  aromatic  1.393  0.020  1.393
 5HZ  C13  C14  aromatic  1.385  0.020  1.385
 5HZ  C05  C04  single    1.537  0.020  1.537
 5HZ  C05  C06  single    1.529  0.020  1.529
 5HZ  C09  C04  single    1.506  0.020  1.506
 5HZ  C09  C08  single    1.506  0.020  1.506
 5HZ  C04  C03  single    1.539  0.020  1.539
 5HZ  C06  C07  single    1.527  0.020  1.527
 5HZ  C03  C02  single    1.528  0.020  1.528
 5HZ  C08  C07  single    1.539  0.020  1.539
 5HZ  C08  C01  single    1.537  0.020  1.537
 5HZ  C01  C02  single    1.529  0.020  1.529
 5HZ  C01  H1   single    0.970  0.020  1.090
 5HZ  C01  H2   single    0.970  0.020  1.090
 5HZ  C02  H3   single    0.970  0.020  1.090
 5HZ  C02  H4   single    0.970  0.020  1.090
 5HZ  C03  H5   single    0.970  0.020  1.090
 5HZ  C03  H6   single    0.970  0.020  1.090
 5HZ  C04  H7   single    0.970  0.020  1.090
 5HZ  C05  H8   single    0.970  0.020  1.090
 5HZ  C05  H9   single    0.970  0.020  1.090
 5HZ  C06  H10  single    0.970  0.020  1.090
 5HZ  C06  H11  single    0.970  0.020  1.090
 5HZ  C07  H12  single    0.970  0.020  1.090
 5HZ  C07  H13  single    0.970  0.020  1.090
 5HZ  C08  H14  single    0.970  0.020  1.090
 5HZ  C13  H17  single    0.930  0.020  1.080
 5HZ  C14  H18  single    0.930  0.020  1.080
 5HZ  C16  H19  single    0.930  0.020  1.080
 5HZ  C17  H20  single    0.930  0.020  1.080
 5HZ  C18  H21  single    0.930  0.020  1.080
 5HZ  C19  H22  single    0.930  0.020  1.080
 5HZ  C21  H23  single    0.930  0.020  1.080
 5HZ  C22  H24  single    0.930  0.020  1.080
 5HZ  O01  H25  single    0.850  0.020  0.980
 5HZ  O02  H26  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
 5HZ  H2   C01  H1   106.29  3.000
 5HZ  H2   C01  C08  109.48  3.000
 5HZ  H1   C01  C08  107.65  3.000
 5HZ  H2   C01  C02  109.98  3.000
 5HZ  H1   C01  C02  108.74  3.000
 5HZ  C08  C01  C02  114.37  3.000
 5HZ  H4   C02  H3   105.28  3.000
 5HZ  H4   C02  C03  109.14  3.000
 5HZ  H3   C02  C03  110.28  3.000
 5HZ  H4   C02  C01  109.11  3.000
 5HZ  H3   C02  C01  110.19  3.000
 5HZ  C03  C02  C01  112.57  3.000
 5HZ  H6   C03  H5   106.29  3.000
 5HZ  H6   C03  C04  107.24  3.000
 5HZ  H5   C03  C04  109.36  3.000
 5HZ  H6   C03  C02  108.93  3.000
 5HZ  H5   C03  C02  110.02  3.000
 5HZ  C04  C03  C02  114.64  3.000
 5HZ  H7   C04  C09  110.45  3.000
 5HZ  H7   C04  C05  107.29  3.000
 5HZ  C09  C04  C05  109.60  3.000
 5HZ  H7   C04  C03  106.63  3.000
 5HZ  C09  C04  C03  108.23  3.000
 5HZ  C05  C04  C03  114.58  3.000
 5HZ  H9   C05  H8   106.36  3.000
 5HZ  H9   C05  C06  108.64  3.000
 5HZ  H8   C05  C06  110.06  3.000
 5HZ  H9   C05  C04  107.54  3.000
 5HZ  H8   C05  C04  109.59  3.000
 5HZ  C06  C05  C04  114.31  3.000
 5HZ  H11  C06  H10  105.37  3.000
 5HZ  H11  C06  C07  109.18  3.000
 5HZ  H10  C06  C07  110.24  3.000
 5HZ  H11  C06  C05  109.16  3.000
 5HZ  H10  C06  C05  110.23  3.000
 5HZ  C07  C06  C05  112.41  3.000
 5HZ  H13  C07  H12  106.29  3.000
 5HZ  H13  C07  C08  107.28  3.000
 5HZ  H12  C07  C08  109.33  3.000
 5HZ  H13  C07  C06  108.94  3.000
 5HZ  H12  C07  C06  110.06  3.000
 5HZ  C08  C07  C06  114.58  3.000
 5HZ  H14  C08  C09  110.47  3.000
 5HZ  H14  C08  C07  106.61  3.000
 5HZ  C09  C08  C07  108.30  3.000
 5HZ  H14  C08  C01  107.31  3.000
 5HZ  C07  C08  C01  114.49  3.000
 5HZ  C09  C08  C01  109.62  3.000
 5HZ  C10  C09  C08  124.78  3.000
 5HZ  C08  C09  C04  110.62  3.000
 5HZ  C10  C09  C04  124.60  3.000
 5HZ  C12  C10  C11  113.99  3.000
 5HZ  C11  C10  C09  123.13  3.000
 5HZ  C12  C10  C09  122.87  3.000
 5HZ  C17  C11  C13  117.31  3.000
 5HZ  C13  C11  C10  120.25  3.000
 5HZ  C17  C11  C10  122.40  3.000
 5HZ  C22  C12  C18  117.38  3.000
 5HZ  C22  C12  C10  120.28  3.000
 5HZ  C18  C12  C10  122.29  3.000
 5HZ  H17  C13  C14  118.77  3.000
 5HZ  H17  C13  C11  119.50  3.000
 5HZ  C14  C13  C11  121.72  3.000
 5HZ  H18  C14  C15  120.23  3.000
 5HZ  H18  C14  C13  119.76  3.000
 5HZ  C15  C14  C13  120.01  3.000
 5HZ  O02  C15  C16  118.08  3.000
 5HZ  O02  C15  C14  122.71  3.000
 5HZ  C16  C15  C14  119.21  3.000
 5HZ  H19  C16  C17  120.24  3.000
 5HZ  H19  C16  C15  119.80  3.000
 5HZ  C17  C16  C15  119.96  3.000
 5HZ  H20  C17  C16  118.76  3.000
 5HZ  H20  C17  C11  119.46  3.000
 5HZ  C16  C17  C11  121.78  3.000
 5HZ  H21  C18  C19  118.82  3.000
 5HZ  H21  C18  C12  119.41  3.000
 5HZ  C19  C18  C12  121.76  3.000
 5HZ  H22  C19  C20  119.83  3.000
 5HZ  H22  C19  C18  120.26  3.000
 5HZ  C20  C19  C18  119.91  3.000
 5HZ  O01  C20  C21  122.67  3.000
 5HZ  C21  C20  C19  119.27  3.000
 5HZ  O01  C20  C19  118.06  3.000
 5HZ  H23  C21  C22  119.83  3.000
 5HZ  H23  C21  C20  120.17  3.000
 5HZ  C22  C21  C20  120.00  3.000
 5HZ  H24  C22  C21  118.82  3.000
 5HZ  H24  C22  C12  119.50  3.000
 5HZ  C21  C22  C12  121.67  3.000
 5HZ  H25  O01  C20  110.26  3.000
 5HZ  H26  O02  C15  110.34  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
 5HZ  CONST_01  C15  C16  C17  C11    0.00   0.0  0
 5HZ  CONST_02  C15  C14  C13  C11    0.00   0.0  0
 5HZ  CONST_03  C20  C19  C18  C12    0.00   0.0  0
 5HZ  CONST_04  C20  C21  C22  C12    0.00   0.0  0
 5HZ  CONST_05  C16  C17  C11  C13    0.00   0.0  0
 5HZ  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 5HZ  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 5HZ  CONST_08  C17  C11  C13  C14    0.00   0.0  0
 5HZ  CONST_09  C21  C20  C19  C18    0.00   0.0  0
 5HZ  CONST_10  C21  C22  C12  C18    0.00   0.0  0
 5HZ  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 5HZ  CONST_12  C22  C12  C18  C19    0.00   0.0  0
 5HZ  CONST_13  C19  C18  C12  C10  180.00   0.0  0
 5HZ  CONST_14  C21  C22  C12  C10  180.00   0.0  0
 5HZ  CONST_15  C16  C17  C11  C10  180.00   0.0  0
 5HZ  CONST_16  C14  C13  C11  C10  180.00   0.0  0
 5HZ  CONST_17  O02  C15  C14  C13  180.00   0.0  0
 5HZ  CONST_18  O02  C15  C16  C17  180.00   0.0  0
 5HZ  CONST_19  O01  C20  C19  C18  180.00   0.0  0
 5HZ  CONST_20  O01  C20  C21  C22  180.00   0.0  0
 5HZ  CONST_21  H19  C16  C17  C11  180.00   0.0  0
 5HZ  CONST_22  H18  C14  C13  C11  180.00   0.0  0
 5HZ  CONST_23  H22  C19  C18  C12  180.00   0.0  0
 5HZ  CONST_24  H23  C21  C22  C12  180.00   0.0  0
 5HZ  CONST_25  H20  C17  C11  C13  180.00   0.0  0
 5HZ  CONST_26  H17  C13  C14  C15  180.00   0.0  0
 5HZ  CONST_27  H24  C22  C12  C18  180.00   0.0  0
 5HZ  CONST_28  H21  C18  C19  C20  180.00   0.0  0
 5HZ  Var_01    C04  C03  C02  C01   44.27  30.0  1
 5HZ  Var_02    C08  C01  C02  C03  -42.74  30.0  1
 5HZ  Var_03    C07  C06  C05  C04  -43.29  30.0  3
 5HZ  Var_04    C08  C07  C06  C05   44.71  30.0  3
 5HZ  Var_05    C12  C10  C09  C04   -5.21  30.0  2
 5HZ  Var_06    C18  C12  C10  C09  -57.05  30.0  2
 5HZ  Var_07    C17  C11  C10  C09  -55.15  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
 5HZ  chir_01  C04  C05  C09  C03  positiv
 5HZ  chir_02  C08  C09  C07  C01  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
 5HZ  plan-1  C10  0.020
 5HZ  plan-1  C11  0.020
 5HZ  plan-1  C13  0.020
 5HZ  plan-1  C14  0.020
 5HZ  plan-1  C15  0.020
 5HZ  plan-1  C16  0.020
 5HZ  plan-1  C17  0.020
 5HZ  plan-1  O02  0.020
 5HZ  plan-1  H17  0.020
 5HZ  plan-1  H18  0.020
 5HZ  plan-1  H19  0.020
 5HZ  plan-1  H20  0.020
 5HZ  plan-2  C10  0.020
 5HZ  plan-2  C12  0.020
 5HZ  plan-2  C18  0.020
 5HZ  plan-2  C19  0.020
 5HZ  plan-2  C20  0.020
 5HZ  plan-2  C21  0.020
 5HZ  plan-2  C22  0.020
 5HZ  plan-2  O01  0.020
 5HZ  plan-2  H21  0.020
 5HZ  plan-2  H22  0.020
 5HZ  plan-2  H23  0.020
 5HZ  plan-2  H24  0.020

