# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:34:49 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (5beta,6alpha,8alpha,14alpha)-13-ethenyl-5,6-dihydroxy-14-methylpodocarp-12-en-15-oic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1[C@@H]2C[C@@H](O)[C@]3(O)[C@](C)(CCC[C@]3(C)C(O)=O)[C@H]2CC=C1C=C
#
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
 3UM  3UM  '(5beta,6alpha,8alpha,14alpha)-13-ethenyl-5,6-dihydroxy-14-methylpodocarp-12-en-15-oic acid'  ligand  53  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 OK
;

data_comp_3UM
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
 3UM  C1   C  CT     0   0.237   1.2545   0.4761  -0.4955
 3UM  C2   C  CT     0  -0.230   2.8350   0.3499  -0.3929
 3UM  C3   C  CT     0  -0.059   0.5036  -0.8198  -0.0376
 3UM  O1   O  OH1    0  -0.677   0.9654   0.5747  -1.8888
 3UM  O2   O  OH1    0  -0.720   0.7941   1.8991   1.5143
 3UM  O3   O  OC    -1  -0.559   4.3607  -0.5383   1.2512
 3UM  C11  C  CH2    0  -0.424  -0.8508   1.8392  -0.1807
 3UM  C12  C  CH2    0  -0.441   2.5542  -2.1634  -0.7776
 3UM  C13  C  CH1    0  -0.220  -1.6331   0.6029   0.2423
 3UM  C14  C  CH2    0  -0.485  -1.8271  -1.9112   0.0594
 3UM  C15  C  CH1    0  -0.312  -3.1227   0.7554  -0.1189
 3UM  C16  C  C1     0  -0.287  -3.2844  -1.6776   0.2705
 3UM  C17  C  C      0   0.156  -3.8945  -0.4872   0.2339
 3UM  C18  C  CH3    0  -0.670  -3.3804   1.1103  -1.5903
 3UM  C19  C  C1     0  -0.214  -5.3267  -0.4091   0.5159
 3UM  C20  C  C2     0  -0.568  -6.0726   0.6965   0.5692
 3UM  C4   C  CH1    0   0.029   0.6360   1.7603   0.1364
 3UM  C5   C  CH2    0  -0.370   3.2560  -0.8849  -1.2056
 3UM  C6   C  C      0   0.492   3.4896   0.3098   1.0219
 3UM  C7   C  CH3    0  -0.690   3.5108   1.5756  -1.0451
 3UM  C8   C  CH1    0  -0.188  -1.0203  -0.6695  -0.3499
 3UM  C9   C  CH2    0  -0.410   1.0409  -2.0161  -0.8490
 3UM  C10  C  CH3    0  -0.700   0.7170  -1.1300   1.4523
 3UM  O4   O  O      0  -0.628   3.1768   1.2221   1.8398
 3UM  H1   H  HOH1   0   0.439   1.1746   1.4654  -2.1879
 3UM  H2   H  HOH1   0   0.453   1.7540   1.6858   1.7094
 3UM  H4   H  HCH2   0   0.217  -0.9791   2.0122  -1.2491
 3UM  H5   H  HCH2   0   0.216  -1.2618   2.7255   0.3157
 3UM  H6   H  HCH2   0   0.214   2.8672  -2.9893  -1.4235
 3UM  H7   H  HCH2   0   0.212   2.8650  -2.4353   0.2326
 3UM  H8   H  HCH1   0   0.218  -1.5898   0.5276   1.3350
 3UM  H9   H  HCH2   0   0.237  -1.4504  -2.3507   0.9884
 3UM  H10  H  HCH2   0   0.243  -1.7022  -2.7017  -0.6874
 3UM  H11  H  HCH1   0   0.228  -3.5048   1.5865   0.4866
 3UM  H12  H  H      0   0.233  -3.8728  -2.5607   0.5075
 3UM  H13  H  HCH3   0   0.222  -2.8950   0.4017  -2.2636
 3UM  H14  H  HCH3   0   0.234  -4.4478   1.0899  -1.8112
 3UM  H15  H  HCH3   0   0.228  -3.0206   2.1082  -1.8388
 3UM  H16  H  H      0   0.235  -5.8122  -1.3628   0.7072
 3UM  H17  H  H      0   0.240  -7.1289   0.6409   0.7960
 3UM  H18  H  H      0   0.237  -5.6720   1.6871   0.3936
 3UM  H19  H  HCH1   0   0.170   1.1138   2.6123  -0.3864
 3UM  H20  H  HCH2   0   0.203   3.0401  -0.7037  -2.2617
 3UM  H21  H  HCH2   0   0.211   4.3373  -1.0064  -1.1320
 3UM  H22  H  HCH3   0   0.237   3.2361   2.5185  -0.5734
 3UM  H23  H  HCH3   0   0.236   4.5962   1.4827  -0.9668
 3UM  H24  H  HCH3   0   0.220   3.2900   1.6474  -2.1115
 3UM  H25  H  HCH1   0   0.222  -1.1044  -0.5871  -1.4370
 3UM  H26  H  HCH2   0   0.221   0.5691  -2.9335  -0.4851
 3UM  H27  H  HCH2   0   0.212   0.7367  -1.9159  -1.8950
 3UM  H28  H  HCH3   0   0.238   0.2169  -0.4272   2.1136
 3UM  H29  H  HCH3   0   0.218   0.3399  -2.1266   1.6823
 3UM  H30  H  HCH3   0   0.245   1.7654  -1.1508   1.7331

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
 3UM  C12  C5   single  1.520  0.020  1.520
 3UM  C12  C9   single  1.522  0.020  1.522
 3UM  C5   C2   single  1.537  0.020  1.537
 3UM  C9   C3   single  1.542  0.020  1.542
 3UM  O4   C6   deloc   1.265  0.020  1.265
 3UM  C6   C2   single  1.559  0.020  1.559
 3UM  C6   O3   deloc   1.237  0.020  1.237
 3UM  C2   C7   single  1.544  0.020  1.544
 3UM  C2   C1   single  1.589  0.020  1.589
 3UM  C10  C3   single  1.537  0.020  1.537
 3UM  C3   C1   single  1.566  0.020  1.566
 3UM  C3   C8   single  1.563  0.020  1.563
 3UM  C14  C8   single  1.536  0.020  1.536
 3UM  C14  C16  single  1.491  0.020  1.491
 3UM  C1   O1   single  1.426  0.020  1.426
 3UM  C1   C4   single  1.559  0.020  1.559
 3UM  C8   C13  single  1.531  0.020  1.531
 3UM  C16  C17  double  1.338  0.020  1.338
 3UM  C4   O2   single  1.394  0.020  1.394
 3UM  C4   C11  single  1.522  0.020  1.522
 3UM  C13  C11  single  1.523  0.020  1.523
 3UM  C13  C15  single  1.540  0.020  1.540
 3UM  C17  C15  single  1.505  0.020  1.505
 3UM  C17  C19  single  1.462  0.020  1.462
 3UM  C15  C18  single  1.535  0.020  1.535
 3UM  C19  C20  double  1.335  0.020  1.335
 3UM  O1   H1   single  0.850  0.020  0.980
 3UM  O2   H2   single  0.850  0.020  0.980
 3UM  C11  H4   single  0.970  0.020  1.090
 3UM  C11  H5   single  0.970  0.020  1.090
 3UM  C12  H6   single  0.970  0.020  1.090
 3UM  C12  H7   single  0.970  0.020  1.090
 3UM  C13  H8   single  0.970  0.020  1.090
 3UM  C14  H9   single  0.970  0.020  1.090
 3UM  C14  H10  single  0.970  0.020  1.090
 3UM  C15  H11  single  0.970  0.020  1.090
 3UM  C16  H12  single  0.930  0.020  1.080
 3UM  C18  H13  single  0.970  0.020  1.090
 3UM  C18  H14  single  0.970  0.020  1.090
 3UM  C18  H15  single  0.970  0.020  1.090
 3UM  C19  H16  single  0.930  0.020  1.080
 3UM  C20  H17  single  0.930  0.020  1.080
 3UM  C20  H18  single  0.930  0.020  1.080
 3UM  C4   H19  single  0.970  0.020  1.090
 3UM  C5   H20  single  0.970  0.020  1.090
 3UM  C5   H21  single  0.970  0.020  1.090
 3UM  C7   H22  single  0.970  0.020  1.090
 3UM  C7   H23  single  0.970  0.020  1.090
 3UM  C7   H24  single  0.970  0.020  1.090
 3UM  C8   H25  single  0.970  0.020  1.090
 3UM  C9   H26  single  0.970  0.020  1.090
 3UM  C9   H27  single  0.970  0.020  1.090
 3UM  C10  H28  single  0.970  0.020  1.090
 3UM  C10  H29  single  0.970  0.020  1.090
 3UM  C10  H30  single  0.970  0.020  1.090

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
 3UM  C4   C1   O1   104.98  3.000
 3UM  C4   C1   C3   111.89  3.000
 3UM  O1   C1   C3   104.22  3.000
 3UM  C4   C1   C2   115.72  3.000
 3UM  O1   C1   C2   105.68  3.000
 3UM  C3   C1   C2   113.10  3.000
 3UM  C7   C2   C6   102.70  3.000
 3UM  C7   C2   C5   107.12  3.000
 3UM  C6   C2   C5   110.12  3.000
 3UM  C7   C2   C1   110.19  3.000
 3UM  C6   C2   C1   118.57  3.000
 3UM  C5   C2   C1   107.59  3.000
 3UM  C10  C3   C9   107.77  3.000
 3UM  C10  C3   C8   110.40  3.000
 3UM  C9   C3   C8   108.01  3.000
 3UM  C8   C3   C1   109.23  3.000
 3UM  C10  C3   C1   112.57  3.000
 3UM  C9   C3   C1   108.72  3.000
 3UM  H1   O1   C1   108.87  3.000
 3UM  H2   O2   C4   106.24  3.000
 3UM  H5   C11  H4   105.75  3.000
 3UM  H5   C11  C4   108.29  3.000
 3UM  H4   C11  C4   109.11  3.000
 3UM  H5   C11  C13  109.76  3.000
 3UM  H4   C11  C13  109.92  3.000
 3UM  C4   C11  C13  113.69  3.000
 3UM  H7   C12  H6   106.07  3.000
 3UM  H7   C12  C9   110.53  3.000
 3UM  H6   C12  C9   109.26  3.000
 3UM  H7   C12  C5   109.80  3.000
 3UM  H6   C12  C5   109.67  3.000
 3UM  C9   C12  C5   111.37  3.000
 3UM  H8   C13  C8   108.22  3.000
 3UM  H8   C13  C15  106.18  3.000
 3UM  C8   C13  C15  112.25  3.000
 3UM  H8   C13  C11  108.20  3.000
 3UM  C15  C13  C11  110.57  3.000
 3UM  C8   C13  C11  111.19  3.000
 3UM  H10  C14  H9   104.47  3.000
 3UM  H10  C14  C8   110.00  3.000
 3UM  H9   C14  C8   111.71  3.000
 3UM  H10  C14  C16  108.74  3.000
 3UM  H9   C14  C16  106.21  3.000
 3UM  C8   C14  C16  115.11  3.000
 3UM  H11  C15  C18  107.18  3.000
 3UM  H11  C15  C17  108.52  3.000
 3UM  C18  C15  C17  109.24  3.000
 3UM  H11  C15  C13  106.41  3.000
 3UM  C18  C15  C13  114.20  3.000
 3UM  C17  C15  C13  111.06  3.000
 3UM  H12  C16  C17  118.80  3.000
 3UM  H12  C16  C14  115.62  3.000
 3UM  C17  C16  C14  125.54  3.000
 3UM  C19  C17  C16  119.27  3.000
 3UM  C19  C17  C15  120.24  3.000
 3UM  C16  C17  C15  120.48  3.000
 3UM  H15  C18  H14  107.11  3.000
 3UM  H15  C18  H13  107.88  3.000
 3UM  H14  C18  H13  107.36  3.000
 3UM  H15  C18  C15  112.02  3.000
 3UM  H14  C18  C15  110.75  3.000
 3UM  H13  C18  C15  111.50  3.000
 3UM  H16  C19  C20  118.03  3.000
 3UM  H16  C19  C17  115.13  3.000
 3UM  C20  C19  C17  126.83  3.000
 3UM  H18  C20  H17  116.25  3.000
 3UM  H18  C20  C19  122.99  3.000
 3UM  H17  C20  C19  120.76  3.000
 3UM  H19  C4   C11  106.44  3.000
 3UM  H19  C4   O2   109.94  3.000
 3UM  C11  C4   O2   108.15  3.000
 3UM  H19  C4   C1   105.73  3.000
 3UM  C11  C4   C1   110.23  3.000
 3UM  O2   C4   C1   115.95  3.000
 3UM  H21  C5   H20  106.23  3.000
 3UM  H21  C5   C12  110.18  3.000
 3UM  H20  C5   C12  108.68  3.000
 3UM  H21  C5   C2   108.99  3.000
 3UM  H20  C5   C2   108.88  3.000
 3UM  C12  C5   C2   113.60  3.000
 3UM  O4   C6   O3   123.29  3.000
 3UM  O3   C6   C2   118.78  3.000
 3UM  O4   C6   C2   117.67  3.000
 3UM  H24  C7   H23  106.07  3.000
 3UM  H24  C7   H22  108.36  3.000
 3UM  H23  C7   H22  107.04  3.000
 3UM  H24  C7   C2   112.11  3.000
 3UM  H23  C7   C2   109.71  3.000
 3UM  H22  C7   C2   113.19  3.000
 3UM  H25  C8   C14  106.58  3.000
 3UM  H25  C8   C13  106.92  3.000
 3UM  C14  C8   C13  111.00  3.000
 3UM  H25  C8   C3   106.32  3.000
 3UM  C13  C8   C3   113.13  3.000
 3UM  C14  C8   C3   112.40  3.000
 3UM  H27  C9   H26  105.95  3.000
 3UM  H27  C9   C12  109.28  3.000
 3UM  H26  C9   C12  109.39  3.000
 3UM  H27  C9   C3   109.59  3.000
 3UM  H26  C9   C3   108.98  3.000
 3UM  C12  C9   C3   113.38  3.000
 3UM  H30  C10  H29  105.19  3.000
 3UM  H30  C10  H28  107.42  3.000
 3UM  H29  C10  H28  107.68  3.000
 3UM  H30  C10  C3   112.87  3.000
 3UM  H29  C10  C3   109.94  3.000
 3UM  H28  C10  C3   113.30  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
 3UM  Var_01  C9   C12  C5   C2     56.48  30.0  1
 3UM  Var_02  C5   C12  C9   C3    -55.18  30.0  1
 3UM  Var_03  C15  C17  C16  C14     3.67  30.0  1
 3UM  Var_04  C8   C14  C16  C17    -5.48  30.0  1
 3UM  Var_05  C20  C19  C17  C15    -3.79  30.0  2
 3UM  Var_06  H17  C20  C19  C17  -179.46   0.0  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
 3UM  chir_01  C1   C3   C2   C4   positiv
 3UM  chir_02  C2   C5   C7   C1   negativ
 3UM  chir_03  C3   C1   C8   C9   negativ
 3UM  chir_04  C13  C8   C11  C15  negativ
 3UM  chir_05  C15  C13  C17  C18  positiv
 3UM  chir_06  C4   O2   C1   C11  negativ
 3UM  chir_07  C8   C3   C14  C13  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
 3UM  plan-1  C2   0.020
 3UM  plan-1  O3   0.020
 3UM  plan-1  C6   0.020
 3UM  plan-1  O4   0.020
 3UM  plan-2  C17  0.020
 3UM  plan-2  C19  0.020
 3UM  plan-2  C20  0.020
 3UM  plan-2  H16  0.020
 3UM  plan-2  H17  0.020
 3UM  plan-2  H18  0.020

