# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:43:56 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(phenyl)methyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)[C](c2ccccc2)=[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
 5HX  5HX  4-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(phenyl)methyl]phenol  ligand  47  23  .  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_5HX
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
 5HX  C01  C  CH2   0  -0.420  -1.1568   2.8474  -1.1700
 5HX  C02  C  CH2   0  -0.456  -2.6083   2.5570  -1.5552
 5HX  C03  C  CH2   0  -0.413  -2.9689   1.0807  -1.4056
 5HX  C04  C  CH1   0  -0.319  -2.4773   0.4318  -0.0995
 5HX  C05  C  CH2   0  -0.420  -3.1691   0.9451   1.1732
 5HX  C06  C  CH2   0  -0.456  -2.8015   2.3790   1.5571
 5HX  C07  C  CH2   0  -0.413  -1.3074   2.6595   1.4092
 5HX  C08  C  CH1   0  -0.319  -0.6840   2.1311   0.1049
 5HX  C09  C  C     0   0.176  -0.9924   0.6605   0.0040
 5HX  C10  C  C     0  -0.067  -0.0680  -0.3141   0.0030
 5HX  C11  C  CR6   0   0.041  -0.4186  -1.7580   0.0180
 5HX  C12  C  CR6   0   0.021   1.3923  -0.0473  -0.0192
 5HX  C13  C  CR16  0  -0.300  -1.1919  -2.3132   1.0372
 5HX  C14  C  CR16  0  -0.245  -1.4924  -3.6693   1.0477
 5HX  C15  C  CR16  0  -0.271  -1.0192  -4.4969   0.0387
 5HX  C16  C  CR16  0  -0.242  -0.2363  -3.9590  -0.9762
 5HX  C17  C  CR16  0  -0.293   0.0667  -2.6055  -0.9798
 5HX  C18  C  CR16  0  -0.280   2.2230  -0.5846   0.9662
 5HX  C19  C  CR16  0  -0.324   3.5895  -0.3666   0.9639
 5HX  C20  C  CR6   0   0.340   4.1706   0.3937  -0.0497
 5HX  C21  C  CR16  0  -0.375   3.3632   0.9218  -1.0525
 5HX  C22  C  CR16  0  -0.287   1.9938   0.6974  -1.0308
 5HX  O01  O  OH1   0  -0.633   5.5064   0.5771  -0.0137
 5HX  H1   H  HCH2  0   0.221  -0.5040   2.5284  -1.9894
 5HX  H2   H  HCH2  0   0.227  -1.0055   3.9254  -1.0614
 5HX  H3   H  HCH2  0   0.223  -3.2874   3.1685  -0.9618
 5HX  H4   H  HCH2  0   0.233  -2.7726   2.8639  -2.5915
 5HX  H5   H  HCH2  0   0.227  -4.0516   0.9499  -1.4913
 5HX  H6   H  HCH2  0   0.220  -2.5252   0.5192  -2.2344
 5HX  H7   H  HCH1  0   0.246  -2.6933  -0.6348  -0.1834
 5HX  H8   H  HCH2  0   0.226  -4.2535   0.8518   1.0625
 5HX  H9   H  HCH2  0   0.222  -2.8887   0.2762   1.9938
 5HX  H10  H  HCH2  0   0.223  -3.3735   3.0894   0.9609
 5HX  H11  H  HCH2  0   0.233  -3.1009   2.5610   2.5925
 5HX  H12  H  HCH2  0   0.227  -1.1194   3.7339   1.4931
 5HX  H13  H  HCH2  0   0.220  -0.7719   2.1883   2.2400
 5HX  H14  H  HCH1  0   0.246   0.3931   2.2874   0.1892
 5HX  H17  H  HCR6  0   0.252  -1.5576  -1.6783   1.8353
 5HX  H18  H  HCR6  0   0.253  -2.0916  -4.0802   1.8502
 5HX  H19  H  HCR6  0   0.253  -1.2531  -5.5537   0.0451
 5HX  H20  H  HCR6  0   0.253   0.1414  -4.5960  -1.7659
 5HX  H21  H  HCR6  0   0.244   0.6841  -2.1975  -1.7716
 5HX  H22  H  HCR6  0   0.246   1.7911  -1.1834   1.7595
 5HX  H23  H  HCR6  0   0.260   4.2109  -0.7863   1.7454
 5HX  H24  H  HCR6  0   0.268   3.7999   1.5012  -1.8585
 5HX  H25  H  HCR6  0   0.256   1.3846   1.1067  -1.8276
 5HX  H26  H  HOH1  0   0.473   5.7909   1.1124  -0.7626

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
 5HX  C02  C01  single    1.530  0.020  1.530
 5HX  C02  C03  single    1.527  0.020  1.527
 5HX  C01  C08  single    1.537  0.020  1.537
 5HX  C03  C04  single    1.539  0.020  1.539
 5HX  C08  C07  single    1.539  0.020  1.539
 5HX  C08  C09  single    1.506  0.020  1.506
 5HX  C04  C09  single    1.506  0.020  1.506
 5HX  C04  C05  single    1.537  0.020  1.537
 5HX  C07  C06  single    1.527  0.020  1.527
 5HX  C06  C05  single    1.529  0.020  1.529
 5HX  C09  C10  double    1.343  0.020  1.343
 5HX  C22  C21  aromatic  1.388  0.020  1.388
 5HX  C22  C12  aromatic  1.393  0.020  1.393
 5HX  C21  C20  aromatic  1.392  0.020  1.392
 5HX  C10  C12  single    1.485  0.020  1.485
 5HX  C10  C11  single    1.486  0.020  1.486
 5HX  C13  C11  aromatic  1.395  0.020  1.395
 5HX  C13  C14  aromatic  1.389  0.020  1.389
 5HX  C12  C18  aromatic  1.396  0.020  1.396
 5HX  C11  C17  aromatic  1.396  0.020  1.396
 5HX  C14  C15  aromatic  1.388  0.020  1.388
 5HX  C20  O01  single    1.349  0.020  1.349
 5HX  C20  C19  aromatic  1.394  0.020  1.394
 5HX  C17  C16  aromatic  1.387  0.020  1.387
 5HX  C18  C19  aromatic  1.384  0.020  1.384
 5HX  C15  C16  aromatic  1.390  0.020  1.390
 5HX  C01  H1   single    0.970  0.020  1.090
 5HX  C01  H2   single    0.970  0.020  1.090
 5HX  C02  H3   single    0.970  0.020  1.090
 5HX  C02  H4   single    0.970  0.020  1.090
 5HX  C03  H5   single    0.970  0.020  1.090
 5HX  C03  H6   single    0.970  0.020  1.090
 5HX  C04  H7   single    0.970  0.020  1.090
 5HX  C05  H8   single    0.970  0.020  1.090
 5HX  C05  H9   single    0.970  0.020  1.090
 5HX  C06  H10  single    0.970  0.020  1.090
 5HX  C06  H11  single    0.970  0.020  1.090
 5HX  C07  H12  single    0.970  0.020  1.090
 5HX  C07  H13  single    0.970  0.020  1.090
 5HX  C08  H14  single    0.970  0.020  1.090
 5HX  C13  H17  single    0.930  0.020  1.080
 5HX  C14  H18  single    0.930  0.020  1.080
 5HX  C15  H19  single    0.930  0.020  1.080
 5HX  C16  H20  single    0.930  0.020  1.080
 5HX  C17  H21  single    0.930  0.020  1.080
 5HX  C18  H22  single    0.930  0.020  1.080
 5HX  C19  H23  single    0.930  0.020  1.080
 5HX  C21  H24  single    0.930  0.020  1.080
 5HX  C22  H25  single    0.930  0.020  1.080
 5HX  O01  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
 5HX  H2   C01  H1   106.19  3.000
 5HX  H2   C01  C08  109.53  3.000
 5HX  H1   C01  C08  107.54  3.000
 5HX  H2   C01  C02  110.09  3.000
 5HX  H1   C01  C02  108.78  3.000
 5HX  C08  C01  C02  114.35  3.000
 5HX  H4   C02  H3   105.37  3.000
 5HX  H4   C02  C03  109.20  3.000
 5HX  H3   C02  C03  110.00  3.000
 5HX  H4   C02  C01  109.15  3.000
 5HX  H3   C02  C01  110.35  3.000
 5HX  C03  C02  C01  112.52  3.000
 5HX  H6   C03  H5   106.29  3.000
 5HX  H6   C03  C04  107.26  3.000
 5HX  H5   C03  C04  109.41  3.000
 5HX  H6   C03  C02  109.02  3.000
 5HX  H5   C03  C02  109.97  3.000
 5HX  C04  C03  C02  114.54  3.000
 5HX  H7   C04  C09  110.42  3.000
 5HX  H7   C04  C05  107.51  3.000
 5HX  C09  C04  C05  109.65  3.000
 5HX  H7   C04  C03  106.48  3.000
 5HX  C05  C04  C03  114.72  3.000
 5HX  C09  C04  C03  108.02  3.000
 5HX  H9   C05  H8   106.12  3.000
 5HX  H9   C05  C06  108.85  3.000
 5HX  H8   C05  C06  110.09  3.000
 5HX  H9   C05  C04  107.54  3.000
 5HX  H8   C05  C04  109.51  3.000
 5HX  C06  C05  C04  114.38  3.000
 5HX  H11  C06  H10  105.42  3.000
 5HX  H11  C06  C07  109.21  3.000
 5HX  H10  C06  C07  109.93  3.000
 5HX  H11  C06  C05  109.15  3.000
 5HX  H10  C06  C05  110.35  3.000
 5HX  C07  C06  C05  112.52  3.000
 5HX  H13  C07  H12  106.29  3.000
 5HX  H13  C07  C08  107.28  3.000
 5HX  H12  C07  C08  109.42  3.000
 5HX  H13  C07  C06  109.02  3.000
 5HX  H12  C07  C06  109.94  3.000
 5HX  C08  C07  C06  114.53  3.000
 5HX  H14  C08  C09  110.30  3.000
 5HX  H14  C08  C07  106.57  3.000
 5HX  C09  C08  C07  108.01  3.000
 5HX  H14  C08  C01  107.51  3.000
 5HX  C09  C08  C01  109.66  3.000
 5HX  C07  C08  C01  114.73  3.000
 5HX  C10  C09  C08  124.58  3.000
 5HX  C10  C09  C04  124.63  3.000
 5HX  C08  C09  C04  110.78  3.000
 5HX  C12  C10  C11  114.01  3.000
 5HX  C11  C10  C09  122.86  3.000
 5HX  C12  C10  C09  123.13  3.000
 5HX  C17  C11  C13  118.25  3.000
 5HX  C17  C11  C10  120.04  3.000
 5HX  C13  C11  C10  121.68  3.000
 5HX  C22  C12  C18  117.48  3.000
 5HX  C18  C12  C10  120.36  3.000
 5HX  C22  C12  C10  122.13  3.000
 5HX  H17  C13  C14  119.57  3.000
 5HX  H17  C13  C11  119.48  3.000
 5HX  C14  C13  C11  120.94  3.000
 5HX  H18  C14  C15  120.09  3.000
 5HX  H18  C14  C13  119.73  3.000
 5HX  C15  C14  C13  120.18  3.000
 5HX  H19  C15  C16  120.25  3.000
 5HX  H19  C15  C14  120.27  3.000
 5HX  C16  C15  C14  119.47  3.000
 5HX  H20  C16  C17  119.74  3.000
 5HX  H20  C16  C15  120.09  3.000
 5HX  C17  C16  C15  120.17  3.000
 5HX  H21  C17  C16  119.59  3.000
 5HX  H21  C17  C11  119.45  3.000
 5HX  C16  C17  C11  120.97  3.000
 5HX  H22  C18  C19  118.80  3.000
 5HX  H22  C18  C12  119.48  3.000
 5HX  C19  C18  C12  121.71  3.000
 5HX  H23  C19  C20  119.80  3.000
 5HX  H23  C19  C18  120.29  3.000
 5HX  C20  C19  C18  119.92  3.000
 5HX  O01  C20  C21  122.84  3.000
 5HX  O01  C20  C19  117.87  3.000
 5HX  C21  C20  C19  119.29  3.000
 5HX  H24  C21  C22  119.69  3.000
 5HX  H24  C21  C20  120.32  3.000
 5HX  C22  C21  C20  119.99  3.000
 5HX  H25  C22  C21  118.83  3.000
 5HX  H25  C22  C12  119.56  3.000
 5HX  C21  C22  C12  121.60  3.000
 5HX  H26  O01  C20  110.31  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
 5HX  CONST_01  C15  C14  C13  C11    0.00   0.0  0
 5HX  CONST_02  C15  C16  C17  C11    0.00   0.0  0
 5HX  CONST_03  C20  C21  C22  C12    0.00   0.0  0
 5HX  CONST_04  C20  C19  C18  C12    0.00   0.0  0
 5HX  CONST_05  C16  C17  C11  C13    0.00   0.0  0
 5HX  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 5HX  CONST_07  C17  C11  C13  C14    0.00   0.0  0
 5HX  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 5HX  CONST_09  C21  C22  C12  C18    0.00   0.0  0
 5HX  CONST_10  C21  C20  C19  C18    0.00   0.0  0
 5HX  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 5HX  CONST_12  C22  C12  C18  C19    0.00   0.0  0
 5HX  CONST_13  C21  C22  C12  C10  180.00   0.0  0
 5HX  CONST_14  C19  C18  C12  C10  180.00   0.0  0
 5HX  CONST_15  C14  C13  C11  C10  180.00   0.0  0
 5HX  CONST_16  C16  C17  C11  C10  180.00   0.0  0
 5HX  CONST_17  O01  C20  C19  C18  180.00   0.0  0
 5HX  CONST_18  O01  C20  C21  C22  180.00   0.0  0
 5HX  CONST_19  H18  C14  C13  C11  180.00   0.0  0
 5HX  CONST_20  H20  C16  C17  C11  180.00   0.0  0
 5HX  CONST_21  H24  C21  C22  C12  180.00   0.0  0
 5HX  CONST_22  H23  C19  C18  C12  180.00   0.0  0
 5HX  CONST_23  H21  C17  C11  C13  180.00   0.0  0
 5HX  CONST_24  H19  C15  C14  C13  180.00   0.0  0
 5HX  CONST_25  H17  C13  C14  C15  180.00   0.0  0
 5HX  CONST_26  H25  C22  C12  C18  180.00   0.0  0
 5HX  CONST_27  H22  C18  C19  C20  180.00   0.0  0
 5HX  Var_01    C04  C03  C02  C01   44.84  30.0  1
 5HX  Var_02    C08  C01  C02  C03  -42.84  30.0  1
 5HX  Var_03    C07  C06  C05  C04  -42.80  30.0  3
 5HX  Var_04    C08  C07  C06  C05   44.80  30.0  3
 5HX  Var_05    C12  C10  C09  C04  174.18  30.0  2
 5HX  Var_06    C22  C12  C10  C09  -57.52  30.0  2
 5HX  Var_07    C13  C11  C10  C09  -58.06  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
 5HX  chir_01  C04  C03  C09  C05  negativ
 5HX  chir_02  C08  C01  C07  C09  negativ

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
 5HX  plan-1  C10  0.020
 5HX  plan-1  C11  0.020
 5HX  plan-1  C13  0.020
 5HX  plan-1  C14  0.020
 5HX  plan-1  C15  0.020
 5HX  plan-1  C16  0.020
 5HX  plan-1  C17  0.020
 5HX  plan-1  H17  0.020
 5HX  plan-1  H18  0.020
 5HX  plan-1  H19  0.020
 5HX  plan-1  H20  0.020
 5HX  plan-1  H21  0.020
 5HX  plan-2  C10  0.020
 5HX  plan-2  C12  0.020
 5HX  plan-2  C18  0.020
 5HX  plan-2  C19  0.020
 5HX  plan-2  C20  0.020
 5HX  plan-2  C21  0.020
 5HX  plan-2  C22  0.020
 5HX  plan-2  O01  0.020
 5HX  plan-2  H22  0.020
 5HX  plan-2  H23  0.020
 5HX  plan-2  H24  0.020
 5HX  plan-2  H25  0.020

