# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 09:02:37 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 4,4'-{[(3S)-3-(4-methoxyphenyl)cyclohexylidene]methanediyl}diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@H]2CCCC(C2)=C(c3ccc(O)cc3)c4ccc(O)cc4
#
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
 5KD  5KD  4,4'-{[(3S)-3-(4-methoxyphenyl)cyclohexylidene]methanediyl}diphenol  ligand  55  29  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5KD
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
 5KD  O01  O  OH1   0  -0.633   7.1043   1.4057  -0.4661
 5KD  C02  C  CR6   0   0.339   5.7965   1.1157  -0.3106
 5KD  C03  C  CR16  0  -0.323   5.4429   0.2081   0.6867
 5KD  C04  C  CR16  0  -0.278   4.1133  -0.1248   0.8782
 5KD  C05  C  CR6   0   0.011   3.0966   0.4410   0.1064
 5KD  C06  C  C     0  -0.028   1.6795   0.0514   0.3208
 5KD  C07  C  CR6   0   0.021   1.4327  -1.4089   0.2251
 5KD  C08  C  CR16  0  -0.289   0.8048  -2.1214   1.2476
 5KD  C09  C  CR16  0  -0.328   0.6060  -3.4902   1.1657
 5KD  C10  C  CR6   0   0.340   1.0431  -4.1902   0.0442
 5KD  O11  O  OH1   0  -0.633   0.8321  -5.5216   0.0065
 5KD  C12  C  CR16  0  -0.371   1.6840  -3.5000  -0.9823
 5KD  C13  C  CR16  0  -0.280   1.8792  -2.1320  -0.8807
 5KD  C14  C  C     0   0.112   0.7111   0.9461   0.5891
 5KD  C15  C  CH2   0  -0.503   0.9616   2.4090   0.8323
 5KD  C16  C  CH2   0  -0.433   0.1773   3.2812  -0.1482
 5KD  C17  C  CH2   0  -0.414  -1.3097   2.9543  -0.1018
 5KD  C18  C  CH1   0  -0.329  -1.5567   1.4636  -0.3467
 5KD  C19  C  CR6   0   0.173  -3.0210   1.1074  -0.3165
 5KD  C20  C  CR16  0  -0.325  -3.6450   0.5539  -1.4338
 5KD  C21  C  CR16  0  -0.326  -4.9868   0.2145  -1.4258
 5KD  C22  C  CR6   0   0.361  -5.7546   0.4210  -0.2799
 5KD  O23  O  O2    0  -0.473  -7.0530   0.0612  -0.3513
 5KD  C24  C  CH3   0  -0.435  -7.8644   0.2469   0.7899
 5KD  C25  C  CR16  0  -0.367  -5.1514   0.9736   0.8476
 5KD  C26  C  CR16  0  -0.307  -3.8022   1.3067   0.8165
 5KD  C27  C  CH2   0  -0.482  -0.7524   0.6036   0.6492
 5KD  C28  C  CR16  0  -0.282   3.4717   1.3364  -0.8922
 5KD  C29  C  CR16  0  -0.373   4.8005   1.6759  -1.1041
 5KD  H1   H  HOH1  0   0.473   7.2240   2.0354  -1.1856
 5KD  H2   H  HCR6  0   0.261   6.2111  -0.2348   1.3086
 5KD  H3   H  HCR6  0   0.246   3.8627  -0.8389   1.6539
 5KD  H5   H  HCR6  0   0.255   0.4697  -1.5981   2.1347
 5KD  H6   H  HCR6  0   0.261   0.1201  -4.0193   1.9762
 5KD  H7   H  HOH1  0   0.473   1.1907  -5.8946  -0.8063
 5KD  H8   H  HCR6  0   0.268   2.0376  -4.0299  -1.8599
 5KD  H9   H  HCR6  0   0.249   2.3871  -1.6166  -1.6871
 5KD  H11  H  HCH2  0   0.235   0.6118   2.6406   1.8467
 5KD  H12  H  HCH2  0   0.249   2.0217   2.6563   0.8061
 5KD  H13  H  HCH2  0   0.234   0.3386   4.3361   0.0847
 5KD  H14  H  HCH2  0   0.218   0.5563   3.1212  -1.1628
 5KD  H15  H  HCH2  0   0.214  -1.7110   3.2370   0.8778
 5KD  H16  H  HCH2  0   0.236  -1.8524   3.5442  -0.8446
 5KD  H17  H  HCH1  0   0.239  -1.1809   1.2293  -1.3500
 5KD  H18  H  HCR6  0   0.247  -3.0665   0.3824  -2.3346
 5KD  H19  H  HCR6  0   0.257  -5.4476  -0.2128  -2.3079
 5KD  H20  H  HCH3  0   0.226  -7.5003  -0.3224   1.6493
 5KD  H21  H  HCH3  0   0.226  -7.9392   1.3001   1.0734
 5KD  H22  H  HCH3  0   0.258  -8.8557  -0.1149   0.5278
 5KD  H23  H  HCR6  0   0.275  -5.7118   1.1528   1.7557
 5KD  H24  H  HCR6  0   0.246  -3.3638   1.7324   1.7115
 5KD  H25  H  HCH2  0   0.254  -0.9347  -0.4483   0.4337
 5KD  H26  H  HCH2  0   0.233  -1.1275   0.7931   1.6622
 5KD  H27  H  HCR6  0   0.253   2.7145   1.7745  -1.5309
 5KD  H28  H  HCR6  0   0.268   5.0560   2.3714  -1.8960

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
 5KD  C09  C08  aromatic  1.386  0.020  1.386
 5KD  C09  C10  aromatic  1.392  0.020  1.392
 5KD  C03  C04  aromatic  1.384  0.020  1.384
 5KD  C03  C02  aromatic  1.394  0.020  1.394
 5KD  O11  C10  single    1.349  0.020  1.349
 5KD  C08  C07  aromatic  1.395  0.020  1.395
 5KD  O01  C02  single    1.349  0.020  1.349
 5KD  C04  C05  aromatic  1.396  0.020  1.396
 5KD  C10  C12  aromatic  1.393  0.020  1.393
 5KD  C02  C29  aromatic  1.391  0.020  1.391
 5KD  C07  C06  single    1.484  0.020  1.484
 5KD  C07  C13  aromatic  1.395  0.020  1.395
 5KD  C05  C28  aromatic  1.393  0.020  1.393
 5KD  C05  C06  single    1.485  0.020  1.485
 5KD  C29  C28  aromatic  1.388  0.020  1.388
 5KD  C12  C13  aromatic  1.386  0.020  1.386
 5KD  C06  C14  double    1.345  0.020  1.345
 5KD  C26  C25  aromatic  1.390  0.020  1.390
 5KD  C26  C19  aromatic  1.391  0.020  1.391
 5KD  C15  C14  single    1.504  0.020  1.504
 5KD  C15  C16  single    1.529  0.020  1.529
 5KD  C14  C27  single    1.504  0.020  1.504
 5KD  C17  C18  single    1.531  0.020  1.531
 5KD  C17  C16  single    1.523  0.020  1.523
 5KD  C25  C22  aromatic  1.393  0.020  1.393
 5KD  C18  C27  single    1.542  0.020  1.542
 5KD  C18  C19  single    1.507  0.020  1.507
 5KD  C19  C20  aromatic  1.394  0.020  1.394
 5KD  C24  O23  single    1.412  0.020  1.412
 5KD  C22  O23  single    1.349  0.020  1.349
 5KD  C22  C21  aromatic  1.395  0.020  1.395
 5KD  C20  C21  aromatic  1.384  0.020  1.384
 5KD  O01  H1   single    0.850  0.020  0.980
 5KD  C03  H2   single    0.930  0.020  1.080
 5KD  C04  H3   single    0.930  0.020  1.080
 5KD  C08  H5   single    0.930  0.020  1.080
 5KD  C09  H6   single    0.930  0.020  1.080
 5KD  O11  H7   single    0.850  0.020  0.980
 5KD  C12  H8   single    0.930  0.020  1.080
 5KD  C13  H9   single    0.930  0.020  1.080
 5KD  C15  H11  single    0.970  0.020  1.090
 5KD  C15  H12  single    0.970  0.020  1.090
 5KD  C16  H13  single    0.970  0.020  1.090
 5KD  C16  H14  single    0.970  0.020  1.090
 5KD  C17  H15  single    0.970  0.020  1.090
 5KD  C17  H16  single    0.970  0.020  1.090
 5KD  C18  H17  single    0.970  0.020  1.090
 5KD  C20  H18  single    0.930  0.020  1.080
 5KD  C21  H19  single    0.930  0.020  1.080
 5KD  C24  H20  single    0.970  0.020  1.090
 5KD  C24  H21  single    0.970  0.020  1.090
 5KD  C24  H22  single    0.970  0.020  1.090
 5KD  C25  H23  single    0.930  0.020  1.080
 5KD  C26  H24  single    0.930  0.020  1.080
 5KD  C27  H25  single    0.970  0.020  1.090
 5KD  C27  H26  single    0.970  0.020  1.090
 5KD  C28  H27  single    0.930  0.020  1.080
 5KD  C29  H28  single    0.930  0.020  1.080

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
 5KD  H1   O01  C02  110.31  3.000
 5KD  C29  C02  C03  119.25  3.000
 5KD  C29  C02  O01  122.81  3.000
 5KD  C03  C02  O01  117.94  3.000
 5KD  H2   C03  C04  120.24  3.000
 5KD  H2   C03  C02  119.81  3.000
 5KD  C04  C03  C02  119.96  3.000
 5KD  H3   C04  C05  119.62  3.000
 5KD  H3   C04  C03  118.67  3.000
 5KD  C05  C04  C03  121.70  3.000
 5KD  C28  C05  C06  121.95  3.000
 5KD  C06  C05  C04  120.57  3.000
 5KD  C28  C05  C04  117.44  3.000
 5KD  C14  C06  C07  123.19  3.000
 5KD  C14  C06  C05  122.76  3.000
 5KD  C07  C06  C05  114.05  3.000
 5KD  C13  C07  C08  117.41  3.000
 5KD  C13  C07  C06  120.53  3.000
 5KD  C08  C07  C06  122.01  3.000
 5KD  H5   C08  C09  118.77  3.000
 5KD  H5   C08  C07  119.51  3.000
 5KD  C09  C08  C07  121.72  3.000
 5KD  H6   C09  C10  119.86  3.000
 5KD  H6   C09  C08  120.19  3.000
 5KD  C10  C09  C08  119.95  3.000
 5KD  C12  C10  O11  122.72  3.000
 5KD  C12  C10  C09  119.26  3.000
 5KD  O11  C10  C09  118.02  3.000
 5KD  H7   O11  C10  110.34  3.000
 5KD  H8   C12  C13  119.72  3.000
 5KD  H8   C12  C10  120.28  3.000
 5KD  C13  C12  C10  120.00  3.000
 5KD  H9   C13  C12  118.76  3.000
 5KD  H9   C13  C07  119.58  3.000
 5KD  C12  C13  C07  121.66  3.000
 5KD  C27  C14  C15  112.16  3.000
 5KD  C27  C14  C06  123.84  3.000
 5KD  C15  C14  C06  123.99  3.000
 5KD  H12  C15  H11  106.53  3.000
 5KD  H12  C15  C16  110.76  3.000
 5KD  H11  C15  C16  107.98  3.000
 5KD  H12  C15  C14  112.29  3.000
 5KD  H11  C15  C14  107.55  3.000
 5KD  C16  C15  C14  111.46  3.000
 5KD  H14  C16  H13  106.71  3.000
 5KD  H14  C16  C17  109.56  3.000
 5KD  H13  C16  C17  110.18  3.000
 5KD  H14  C16  C15  109.47  3.000
 5KD  H13  C16  C15  109.79  3.000
 5KD  C17  C16  C15  111.03  3.000
 5KD  H16  C17  H15  106.65  3.000
 5KD  H16  C17  C18  109.68  3.000
 5KD  H15  C17  C18  109.59  3.000
 5KD  H16  C17  C16  110.38  3.000
 5KD  H15  C17  C16  109.23  3.000
 5KD  C18  C17  C16  111.20  3.000
 5KD  H17  C18  C27  107.03  3.000
 5KD  H17  C18  C19  107.50  3.000
 5KD  C27  C18  C19  111.22  3.000
 5KD  H17  C18  C17  107.41  3.000
 5KD  C19  C18  C17  112.56  3.000
 5KD  C27  C18  C17  110.83  3.000
 5KD  C26  C19  C20  117.29  3.000
 5KD  C20  C19  C18  120.83  3.000
 5KD  C26  C19  C18  121.88  3.000
 5KD  H18  C20  C21  118.90  3.000
 5KD  H18  C20  C19  119.33  3.000
 5KD  C21  C20  C19  121.77  3.000
 5KD  H19  C21  C22  119.57  3.000
 5KD  H19  C21  C20  120.29  3.000
 5KD  C22  C21  C20  120.14  3.000
 5KD  C25  C22  O23  124.42  3.000
 5KD  O23  C22  C21  116.54  3.000
 5KD  C25  C22  C21  119.04  3.000
 5KD  C24  O23  C22  118.36  3.000
 5KD  H22  C24  H21  108.70  3.000
 5KD  H22  C24  H20  108.66  3.000
 5KD  H21  C24  H20  108.69  3.000
 5KD  H22  C24  O23  106.58  3.000
 5KD  H21  C24  O23  112.05  3.000
 5KD  H20  C24  O23  112.04  3.000
 5KD  H23  C25  C26  118.80  3.000
 5KD  H23  C25  C22  121.38  3.000
 5KD  C26  C25  C22  119.82  3.000
 5KD  H24  C26  C25  117.92  3.000
 5KD  H24  C26  C19  120.13  3.000
 5KD  C25  C26  C19  121.95  3.000
 5KD  H26  C27  H25  107.00  3.000
 5KD  H26  C27  C18  108.77  3.000
 5KD  H25  C27  C18  108.88  3.000
 5KD  H26  C27  C14  109.29  3.000
 5KD  H25  C27  C14  112.02  3.000
 5KD  C18  C27  C14  110.77  3.000
 5KD  H27  C28  C29  118.71  3.000
 5KD  H27  C28  C05  119.64  3.000
 5KD  C29  C28  C05  121.64  3.000
 5KD  H28  C29  C28  119.60  3.000
 5KD  H28  C29  C02  120.41  3.000
 5KD  C28  C29  C02  119.99  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
 5KD  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 5KD  CONST_02  C05  C28  C29  C02    0.00   0.0  0
 5KD  CONST_03  C28  C05  C04  C03    0.00   0.0  0
 5KD  CONST_04  C28  C29  C02  C03    0.00   0.0  0
 5KD  CONST_05  C29  C02  C03  C04    0.00   0.0  0
 5KD  CONST_06  C29  C28  C05  C04    0.00   0.0  0
 5KD  CONST_07  C10  C09  C08  C07    0.00   0.0  0
 5KD  CONST_08  C10  C12  C13  C07    0.00   0.0  0
 5KD  CONST_09  C12  C10  C09  C08    0.00   0.0  0
 5KD  CONST_10  C12  C13  C07  C08    0.00   0.0  0
 5KD  CONST_11  C13  C07  C08  C09    0.00   0.0  0
 5KD  CONST_12  C13  C12  C10  C09    0.00   0.0  0
 5KD  CONST_13  C22  C25  C26  C19    0.00   0.0  0
 5KD  CONST_14  C22  C21  C20  C19    0.00   0.0  0
 5KD  CONST_15  C25  C26  C19  C20    0.00   0.0  0
 5KD  CONST_16  C25  C22  C21  C20    0.00   0.0  0
 5KD  CONST_17  C26  C25  C22  C21    0.00   0.0  0
 5KD  CONST_18  C26  C19  C20  C21    0.00   0.0  0
 5KD  CONST_19  C25  C26  C19  C18  180.00   0.0  0
 5KD  CONST_20  C21  C20  C19  C18  180.00   0.0  0
 5KD  CONST_21  C04  C03  C02  O01  180.00   0.0  0
 5KD  CONST_22  C28  C29  C02  O01  180.00   0.0  0
 5KD  CONST_23  C06  C05  C04  C03  180.00   0.0  0
 5KD  CONST_24  C09  C08  C07  C06  180.00   0.0  0
 5KD  CONST_25  C12  C13  C07  C06  180.00   0.0  0
 5KD  CONST_26  C29  C28  C05  C06  180.00   0.0  0
 5KD  CONST_27  O11  C10  C09  C08  180.00   0.0  0
 5KD  CONST_28  C13  C12  C10  O11  180.00   0.0  0
 5KD  CONST_29  O23  C22  C21  C20  180.00   0.0  0
 5KD  CONST_30  C26  C25  C22  O23  180.00   0.0  0
 5KD  CONST_31  H3   C04  C03  C02  180.00   0.0  0
 5KD  CONST_32  H27  C28  C29  C02  180.00   0.0  0
 5KD  CONST_33  H28  C29  C02  C03  180.00   0.0  0
 5KD  CONST_34  H2   C03  C04  C05  180.00   0.0  0
 5KD  CONST_35  H6   C09  C08  C07  180.00   0.0  0
 5KD  CONST_36  H8   C12  C13  C07  180.00   0.0  0
 5KD  CONST_37  H9   C13  C07  C08  180.00   0.0  0
 5KD  CONST_38  H5   C08  C09  C10  180.00   0.0  0
 5KD  CONST_39  H24  C26  C19  C18    0.00   0.0  0
 5KD  CONST_40  H18  C20  C19  C18    0.00   0.0  0
 5KD  CONST_41  H23  C25  C26  C19  180.00   0.0  0
 5KD  CONST_42  H19  C21  C20  C19  180.00   0.0  0
 5KD  Var_01    C17  C16  C15  C14   55.04  30.0  1
 5KD  Var_02    C18  C27  C14  C15   55.95  30.0  1
 5KD  Var_03    C18  C17  C16  C15  -54.93  30.0  1
 5KD  Var_04    C27  C14  C15  C16  -56.04  30.0  1
 5KD  Var_05    C07  C06  C05  C04  -55.16  30.0  2
 5KD  Var_06    C08  C07  C06  C05  125.80  30.0  2
 5KD  Var_07    C15  C14  C06  C05   -6.08  30.0  2
 5KD  Var_08    C25  C22  O23  C24   -0.30  30.0  3
 5KD  Var_09    H20  C24  O23  C22  -60.51  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
 5KD  chir_01  C18  C17  C27  C19  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
 5KD  plan-1  O01  0.020
 5KD  plan-1  C02  0.020
 5KD  plan-1  C03  0.020
 5KD  plan-1  C04  0.020
 5KD  plan-1  C05  0.020
 5KD  plan-1  C06  0.020
 5KD  plan-1  C28  0.020
 5KD  plan-1  C29  0.020
 5KD  plan-1  H2   0.020
 5KD  plan-1  H3   0.020
 5KD  plan-1  H27  0.020
 5KD  plan-1  H28  0.020
 5KD  plan-2  C06  0.020
 5KD  plan-2  C07  0.020
 5KD  plan-2  C08  0.020
 5KD  plan-2  C09  0.020
 5KD  plan-2  C10  0.020
 5KD  plan-2  O11  0.020
 5KD  plan-2  C12  0.020
 5KD  plan-2  C13  0.020
 5KD  plan-2  H5   0.020
 5KD  plan-2  H6   0.020
 5KD  plan-2  H8   0.020
 5KD  plan-2  H9   0.020
 5KD  plan-3  C18  0.020
 5KD  plan-3  C19  0.020
 5KD  plan-3  C20  0.020
 5KD  plan-3  C21  0.020
 5KD  plan-3  C22  0.020
 5KD  plan-3  O23  0.020
 5KD  plan-3  C25  0.020
 5KD  plan-3  C26  0.020
 5KD  plan-3  H18  0.020
 5KD  plan-3  H19  0.020
 5KD  plan-3  H23  0.020
 5KD  plan-3  H24  0.020

