# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 05:30:11 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)[C](c2cccc(O)c2)=[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
 5J0  5J0  3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol  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_5J0
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
 5J0  C01  C  CH2   0  -0.419  -2.7246  -1.6432  -1.5007
 5J0  C02  C  CH2   0  -0.457  -2.0468  -2.8990  -2.0504
 5J0  C03  C  CH2   0  -0.413  -0.5376  -2.9061  -1.8095
 5J0  C04  C  CH1   0  -0.319  -0.1092  -2.4632  -0.3998
 5J0  C05  C  CH2   0  -0.420  -0.4905  -3.4411   0.7223
 5J0  C06  C  CH2   0  -0.455  -1.9893  -3.5105   1.0153
 5J0  C07  C  CH2   0  -0.412  -2.6390  -2.1286   1.0430
 5J0  C08  C  CH1   0  -0.317  -2.2256  -1.2045  -0.1158
 5J0  C09  C  C     0   0.181  -0.7223  -1.1154  -0.1274
 5J0  C10  C  C     0  -0.075  -0.0262   0.0132   0.0798
 5J0  C11  C  CR6   0   0.055  -0.6752   1.3424   0.2354
 5J0  C12  C  CR6   0   0.024   1.4543   0.0534   0.1871
 5J0  C13  C  CR16  0  -0.286   2.1474  -0.6863   1.1425
 5J0  C14  C  CR16  0  -0.375   3.5289  -0.6174   1.2544
 5J0  C15  C  CR6   0   0.339   4.2547   0.2111   0.4043
 5J0  C16  C  CR16  0  -0.323   3.5788   0.9682  -0.5513
 5J0  C17  C  CR16  0  -0.281   2.2002   0.8901  -0.6456
 5J0  C18  C  CR16  0  -0.382  -1.4511   1.8821  -0.7852
 5J0  C19  C  CR6   0   0.365  -2.0442   3.1350  -0.6429
 5J0  C20  C  CR16  0  -0.398  -1.8520   3.8624   0.5274
 5J0  C21  C  CR16  0  -0.230  -1.0661   3.3287   1.5404
 5J0  C22  C  CR16  0  -0.320  -0.4730   2.0847   1.4009
 5J0  O01  O  OH1   0  -0.633   5.5974   0.3253   0.4650
 5J0  O02  O  OH1   0  -0.636  -2.7883   3.5944  -1.6709
 5J0  H1   H  HCH2  0   0.221  -2.5456  -0.8137  -2.1933
 5J0  H2   H  HCH2  0   0.226  -3.8087  -1.7861  -1.4730
 5J0  H3   H  HCH2  0   0.224  -2.5022  -3.7933  -1.6243
 5J0  H4   H  HCH2  0   0.233  -2.2351  -2.9648  -3.1253
 5J0  H5   H  HCH2  0   0.227  -0.1311  -3.9006  -2.0150
 5J0  H6   H  HCH2  0   0.221  -0.0593  -2.2272  -2.5227
 5J0  H7   H  HCH1  0   0.245   0.9794  -2.3906  -0.4116
 5J0  H8   H  HCH2  0   0.227  -0.1063  -4.4377   0.4861
 5J0  H9   H  HCH2  0   0.221   0.0303  -3.1197   1.6308
 5J0  H10  H  HCH2  0   0.223  -2.4896  -4.1473   0.2864
 5J0  H11  H  HCH2  0   0.232  -2.1448  -3.9984   1.9810
 5J0  H12  H  HCH2  0   0.227  -3.7283  -2.2242   1.0629
 5J0  H13  H  HCH2  0   0.220  -2.3564  -1.6260   1.9737
 5J0  H14  H  HCH1  0   0.246  -2.6633  -0.2271   0.0934
 5J0  H15  H  HCR6  0   0.254   1.5989  -1.3232   1.8261
 5J0  H16  H  HCR6  0   0.268   4.0365  -1.2025   2.0135
 5J0  H17  H  HCR6  0   0.260   4.1369   1.6187  -1.2135
 5J0  H18  H  HCR6  0   0.247   1.6933   1.4931  -1.3899
 5J0  H19  H  HCR6  0   0.255  -1.5956   1.3264  -1.7042
 5J0  H20  H  HCR6  0   0.267  -2.3061   4.8393   0.6494
 5J0  H21  H  HCR6  0   0.256  -0.9190   3.8984   2.4491
 5J0  H22  H  HCR6  0   0.241   0.1411   1.6828   2.1971
 5J0  H23  H  HOH1  0   0.473   5.9481  -0.2181   1.1792
 5J0  H24  H  HOH1  0   0.473  -3.1452   4.4648  -1.4620

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
 5J0  O01  C15  single    1.349  0.020  1.349
 5J0  C14  C15  aromatic  1.391  0.020  1.391
 5J0  C14  C13  aromatic  1.388  0.020  1.388
 5J0  C15  C16  aromatic  1.394  0.020  1.394
 5J0  C13  C12  aromatic  1.393  0.020  1.393
 5J0  C16  C17  aromatic  1.384  0.020  1.384
 5J0  C12  C17  aromatic  1.396  0.020  1.396
 5J0  C12  C10  single    1.485  0.020  1.485
 5J0  O02  C19  single    1.350  0.020  1.350
 5J0  C18  C19  aromatic  1.393  0.020  1.393
 5J0  C18  C11  aromatic  1.391  0.020  1.391
 5J0  C19  C20  aromatic  1.391  0.020  1.391
 5J0  C10  C11  single    1.487  0.020  1.487
 5J0  C10  C09  double    1.342  0.020  1.342
 5J0  C11  C22  aromatic  1.397  0.020  1.397
 5J0  C20  C21  aromatic  1.389  0.020  1.389
 5J0  C22  C21  aromatic  1.385  0.020  1.385
 5J0  C09  C04  single    1.506  0.020  1.506
 5J0  C09  C08  single    1.506  0.020  1.506
 5J0  C04  C05  single    1.536  0.020  1.536
 5J0  C04  C03  single    1.538  0.020  1.538
 5J0  C05  C06  single    1.529  0.020  1.529
 5J0  C06  C07  single    1.527  0.020  1.527
 5J0  C08  C07  single    1.539  0.020  1.539
 5J0  C08  C01  single    1.536  0.020  1.536
 5J0  C03  C02  single    1.528  0.020  1.528
 5J0  C01  C02  single    1.529  0.020  1.529
 5J0  C01  H1   single    0.970  0.020  1.090
 5J0  C01  H2   single    0.970  0.020  1.090
 5J0  C02  H3   single    0.970  0.020  1.090
 5J0  C02  H4   single    0.970  0.020  1.090
 5J0  C03  H5   single    0.970  0.020  1.090
 5J0  C03  H6   single    0.970  0.020  1.090
 5J0  C04  H7   single    0.970  0.020  1.090
 5J0  C05  H8   single    0.970  0.020  1.090
 5J0  C05  H9   single    0.970  0.020  1.090
 5J0  C06  H10  single    0.970  0.020  1.090
 5J0  C06  H11  single    0.970  0.020  1.090
 5J0  C07  H12  single    0.970  0.020  1.090
 5J0  C07  H13  single    0.970  0.020  1.090
 5J0  C08  H14  single    0.970  0.020  1.090
 5J0  C13  H15  single    0.930  0.020  1.080
 5J0  C14  H16  single    0.930  0.020  1.080
 5J0  C16  H17  single    0.930  0.020  1.080
 5J0  C17  H18  single    0.930  0.020  1.080
 5J0  C18  H19  single    0.930  0.020  1.080
 5J0  C20  H20  single    0.930  0.020  1.080
 5J0  C21  H21  single    0.930  0.020  1.080
 5J0  C22  H22  single    0.930  0.020  1.080
 5J0  O01  H23  single    0.850  0.020  0.980
 5J0  O02  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
 5J0  H2   C01  H1   106.07  3.000
 5J0  H2   C01  C08  109.66  3.000
 5J0  H1   C01  C08  107.51  3.000
 5J0  H2   C01  C02  109.94  3.000
 5J0  H1   C01  C02  108.79  3.000
 5J0  C08  C01  C02  114.50  3.000
 5J0  H4   C02  H3   105.25  3.000
 5J0  H4   C02  C03  108.96  3.000
 5J0  H3   C02  C03  110.31  3.000
 5J0  H4   C02  C01  109.06  3.000
 5J0  H3   C02  C01  110.36  3.000
 5J0  C03  C02  C01  112.63  3.000
 5J0  H6   C03  H5   106.20  3.000
 5J0  H6   C03  C04  107.27  3.000
 5J0  H5   C03  C04  109.30  3.000
 5J0  H6   C03  C02  109.01  3.000
 5J0  H5   C03  C02  109.97  3.000
 5J0  C04  C03  C02  114.71  3.000
 5J0  H7   C04  C09  110.41  3.000
 5J0  H7   C04  C05  107.33  3.000
 5J0  C09  C04  C05  109.67  3.000
 5J0  H7   C04  C03  106.68  3.000
 5J0  C05  C04  C03  114.64  3.000
 5J0  C09  C04  C03  108.06  3.000
 5J0  H9   C05  H8   106.22  3.000
 5J0  H9   C05  C06  108.69  3.000
 5J0  H8   C05  C06  110.15  3.000
 5J0  H9   C05  C04  107.51  3.000
 5J0  H8   C05  C04  109.57  3.000
 5J0  C06  C05  C04  114.34  3.000
 5J0  H11  C06  H10  105.36  3.000
 5J0  H11  C06  C07  109.11  3.000
 5J0  H10  C06  C07  110.22  3.000
 5J0  H11  C06  C05  109.21  3.000
 5J0  H10  C06  C05  110.39  3.000
 5J0  C07  C06  C05  112.30  3.000
 5J0  H13  C07  H12  106.36  3.000
 5J0  H13  C07  C08  107.17  3.000
 5J0  H12  C07  C08  109.50  3.000
 5J0  H13  C07  C06  108.72  3.000
 5J0  H12  C07  C06  110.17  3.000
 5J0  C08  C07  C06  114.55  3.000
 5J0  H14  C08  C09  110.42  3.000
 5J0  H14  C08  C07  106.60  3.000
 5J0  C09  C08  C07  108.03  3.000
 5J0  H14  C08  C01  107.36  3.000
 5J0  C07  C08  C01  114.85  3.000
 5J0  C09  C08  C01  109.53  3.000
 5J0  C10  C09  C08  124.50  3.000
 5J0  C08  C09  C04  110.79  3.000
 5J0  C10  C09  C04  124.72  3.000
 5J0  C12  C10  C11  113.79  3.000
 5J0  C11  C10  C09  122.77  3.000
 5J0  C12  C10  C09  123.44  3.000
 5J0  C22  C11  C18  119.14  3.000
 5J0  C22  C11  C10  119.94  3.000
 5J0  C18  C11  C10  120.89  3.000
 5J0  C17  C12  C13  117.48  3.000
 5J0  C17  C12  C10  120.38  3.000
 5J0  C13  C12  C10  122.09  3.000
 5J0  H15  C13  C14  118.83  3.000
 5J0  H15  C13  C12  119.54  3.000
 5J0  C14  C13  C12  121.62  3.000
 5J0  H16  C14  C15  120.32  3.000
 5J0  H16  C14  C13  119.71  3.000
 5J0  C15  C14  C13  119.97  3.000
 5J0  O01  C15  C16  117.87  3.000
 5J0  C16  C15  C14  119.30  3.000
 5J0  O01  C15  C14  122.83  3.000
 5J0  H17  C16  C17  120.36  3.000
 5J0  H17  C16  C15  119.70  3.000
 5J0  C17  C16  C15  119.94  3.000
 5J0  H18  C17  C16  118.77  3.000
 5J0  H18  C17  C12  119.55  3.000
 5J0  C16  C17  C12  121.69  3.000
 5J0  H19  C18  C19  119.40  3.000
 5J0  H19  C18  C11  119.84  3.000
 5J0  C19  C18  C11  120.75  3.000
 5J0  O02  C19  C20  122.61  3.000
 5J0  C20  C19  C18  119.81  3.000
 5J0  O02  C19  C18  117.58  3.000
 5J0  H20  C20  C21  120.08  3.000
 5J0  H20  C20  C19  120.53  3.000
 5J0  C21  C20  C19  119.39  3.000
 5J0  H21  C21  C22  119.93  3.000
 5J0  H21  C21  C20  119.14  3.000
 5J0  C22  C21  C20  120.93  3.000
 5J0  H22  C22  C21  120.14  3.000
 5J0  H22  C22  C11  119.90  3.000
 5J0  C21  C22  C11  119.96  3.000
 5J0  H23  O01  C15  110.36  3.000
 5J0  H24  O02  C19  110.28  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
 5J0  CONST_01  C20  C19  C18  C11    0.00   0.0  0
 5J0  CONST_02  C20  C21  C22  C11    0.00   0.0  0
 5J0  CONST_03  C15  C14  C13  C12    0.00   0.0  0
 5J0  CONST_04  C15  C16  C17  C12    0.00   0.0  0
 5J0  CONST_05  C16  C15  C14  C13    0.00   0.0  0
 5J0  CONST_06  C16  C17  C12  C13    0.00   0.0  0
 5J0  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 5J0  CONST_08  C17  C12  C13  C14    0.00   0.0  0
 5J0  CONST_09  C21  C20  C19  C18    0.00   0.0  0
 5J0  CONST_10  C21  C22  C11  C18    0.00   0.0  0
 5J0  CONST_11  C22  C11  C18  C19    0.00   0.0  0
 5J0  CONST_12  C22  C21  C20  C19    0.00   0.0  0
 5J0  CONST_13  C14  C13  C12  C10  180.00   0.0  0
 5J0  CONST_14  C16  C17  C12  C10  180.00   0.0  0
 5J0  CONST_15  C19  C18  C11  C10  180.00   0.0  0
 5J0  CONST_16  C21  C22  C11  C10  180.00   0.0  0
 5J0  CONST_17  O02  C19  C18  C11  180.00   0.0  0
 5J0  CONST_18  O01  C15  C14  C13  180.00   0.0  0
 5J0  CONST_19  O01  C15  C16  C17  180.00   0.0  0
 5J0  CONST_20  O02  C19  C20  C21  180.00   0.0  0
 5J0  CONST_21  H21  C21  C22  C11  180.00   0.0  0
 5J0  CONST_22  H16  C14  C13  C12  180.00   0.0  0
 5J0  CONST_23  H17  C16  C17  C12  180.00   0.0  0
 5J0  CONST_24  H18  C17  C12  C13  180.00   0.0  0
 5J0  CONST_25  H15  C13  C14  C15  180.00   0.0  0
 5J0  CONST_26  H20  C20  C19  C18  180.00   0.0  0
 5J0  CONST_27  H22  C22  C11  C18  180.00   0.0  0
 5J0  CONST_28  H19  C18  C19  C20  180.00   0.0  0
 5J0  Var_01    C04  C03  C02  C01   43.99  30.0  1
 5J0  Var_02    C08  C01  C02  C03  -42.31  30.0  1
 5J0  Var_03    C07  C06  C05  C04  -43.30  30.0  3
 5J0  Var_04    C08  C07  C06  C05   45.23  30.0  3
 5J0  Var_05    C12  C10  C09  C04   -5.69  30.0  2
 5J0  Var_06    C13  C12  C10  C09  -57.93  30.0  3
 5J0  Var_07    C18  C11  C10  C09  -60.60  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
 5J0  chir_01  C04  C09  C05  C03  negativ
 5J0  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
 5J0  plan-1  C10  0.020
 5J0  plan-1  C12  0.020
 5J0  plan-1  C13  0.020
 5J0  plan-1  C14  0.020
 5J0  plan-1  C15  0.020
 5J0  plan-1  C16  0.020
 5J0  plan-1  C17  0.020
 5J0  plan-1  O01  0.020
 5J0  plan-1  H15  0.020
 5J0  plan-1  H16  0.020
 5J0  plan-1  H17  0.020
 5J0  plan-1  H18  0.020
 5J0  plan-2  C10  0.020
 5J0  plan-2  C11  0.020
 5J0  plan-2  C18  0.020
 5J0  plan-2  C19  0.020
 5J0  plan-2  C20  0.020
 5J0  plan-2  C21  0.020
 5J0  plan-2  C22  0.020
 5J0  plan-2  O02  0.020
 5J0  plan-2  H19  0.020
 5J0  plan-2  H20  0.020
 5J0  plan-2  H21  0.020
 5J0  plan-2  H22  0.020

