# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:31:32 2021
#   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  54  24  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.287   -7.9132   -4.4833  20.9725
 3UM  C2   C  CT    0  -0.248   -8.2129   -3.1939  20.1012
 3UM  C3   C  CT    0  -0.058   -6.9161   -5.5253  20.3312
 3UM  O1   O  OH1   0  -0.680   -9.2008   -5.0777  21.0421
 3UM  O2   O  OH1   0  -0.662   -6.2379   -3.5115  22.4128
 3UM  O3   O  OH1   0  -0.588   -7.2942   -1.2338  21.1247
 3UM  C11  C  CH2   0  -0.487   -7.4795   -5.4107  23.2689
 3UM  C12  C  CH2   0  -0.437   -7.5069   -4.6357  18.0394
 3UM  C13  C  CH1   0  -0.206   -6.6151   -6.5320  22.6958
 3UM  C14  C  CH2   0  -0.477   -5.9696   -7.8948  20.6803
 3UM  C15  C  CH1   0  -0.313   -6.7256   -7.8038  23.5589
 3UM  C16  C  C1    0  -0.290   -5.6125   -8.9514  21.6700
 3UM  C17  C  C     0   0.162   -5.9066   -8.9247  22.9751
 3UM  C18  C  CH3   0  -0.673   -8.1612   -8.2932  23.7910
 3UM  C19  C  C1    0  -0.213   -5.4388  -10.0141  23.8314
 3UM  C20  C  C2    0  -0.567   -5.5620  -10.0994  25.1574
 3UM  C4   C  CH1   0   0.046   -7.4973   -4.1458  22.4169
 3UM  C5   C  CH2   0  -0.399   -8.4516   -3.6002  18.6271
 3UM  C6   C  C     0   0.601   -7.1213   -2.1226  20.1529
 3UM  C7   C  CH3   0  -0.645   -9.5225   -2.5185  20.5699
 3UM  C8   C  CH1   0  -0.264   -6.9182   -6.8158  21.2176
 3UM  C9   C  CH2   0  -0.416   -7.4280   -5.8702  18.9241
 3UM  C10  C  CH3   0  -0.712   -5.4647   -5.0307  20.1787
 3UM  O4   O  O     0  -0.450   -6.2353   -1.9932  19.3406
 3UM  H1   H  HOH1  0   0.449   -9.1327   -5.9748  21.3792
 3UM  H2   H  HOH1  0   0.454   -6.1743   -2.9701  23.2046
 3UM  H3   H  HOH1  0   0.473   -6.5820   -0.5789  21.0844
 3UM  H4   H  HCH2  0   0.243   -7.1280   -5.1577  24.2745
 3UM  H5   H  HCH2  0   0.225   -8.5081   -5.7511  23.4108
 3UM  H6   H  HCH2  0   0.228   -7.8772   -4.9175  17.0502
 3UM  H7   H  HCH2  0   0.225   -6.5126   -4.2161  17.8801
 3UM  H8   H  HCH1  0   0.232   -5.5696   -6.2097  22.7656
 3UM  H9   H  HCH2  0   0.249   -6.4019   -8.3721  19.7959
 3UM  H10  H  HCH2  0   0.250   -5.0287   -7.4584  20.3331
 3UM  H11  H  HCH1  0   0.235   -6.3082   -7.5461  24.5394
 3UM  H12  H  H     0   0.238   -5.0348   -9.7856  21.2805
 3UM  H13  H  HCH3  0   0.240   -8.1613   -9.2293  24.3500
 3UM  H14  H  HCH3  0   0.232   -8.7526   -7.5792  24.3639
 3UM  H15  H  HCH3  0   0.222   -8.6773   -8.4826  22.8486
 3UM  H16  H  H     0   0.237   -4.9327  -10.8231  23.3114
 3UM  H17  H  H     0   0.242   -5.1671  -10.9501  25.6962
 3UM  H18  H  H     0   0.238   -6.0483   -9.3377  25.7539
 3UM  H19  H  HCH1  0   0.226   -8.2549   -3.4744  22.8393
 3UM  H20  H  HCH2  0   0.232   -8.4620   -2.7017  18.0051
 3UM  H21  H  HCH2  0   0.229   -9.4639   -4.0070  18.5701
 3UM  H22  H  HCH3  0   0.239   -9.5396   -2.2687  21.6294
 3UM  H23  H  HCH3  0   0.230   -9.6823   -1.5929  20.0137
 3UM  H24  H  HCH3  0   0.242  -10.3731   -3.1614  20.3648
 3UM  H25  H  HCH1  0   0.214   -7.9175   -7.2713  21.1554
 3UM  H26  H  HCH2  0   0.216   -8.4128   -6.3440  18.9793
 3UM  H27  H  HCH2  0   0.232   -6.7615   -6.6070  18.4686
 3UM  H28  H  HCH3  0   0.239   -4.8951   -5.0697  21.1031
 3UM  H29  H  HCH3  0   0.216   -4.9448   -5.6579  19.4524
 3UM  H30  H  HCH3  0   0.261   -5.3977   -4.0192  19.8010

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  1.521  0.020  1.521
 3UM  C5   C2   single  1.548  0.020  1.548
 3UM  C9   C3   single  1.537  0.020  1.537
 3UM  O4   C6   double  1.209  0.020  1.209
 3UM  C6   C2   single  1.530  0.020  1.530
 3UM  C6   O3   single  1.328  0.020  1.328
 3UM  C2   C7   single  1.546  0.020  1.546
 3UM  C2   C1   single  1.585  0.020  1.585
 3UM  C10  C3   single  1.541  0.020  1.541
 3UM  C3   C1   single  1.578  0.020  1.578
 3UM  C3   C8   single  1.566  0.020  1.566
 3UM  C14  C8   single  1.534  0.020  1.534
 3UM  C14  C16  single  1.491  0.020  1.491
 3UM  C1   O1   single  1.420  0.020  1.420
 3UM  C1   C4   single  1.541  0.020  1.541
 3UM  C8   C13  single  1.535  0.020  1.535
 3UM  C16  C17  double  1.338  0.020  1.338
 3UM  C4   O2   single  1.410  0.020  1.410
 3UM  C4   C11  single  1.525  0.020  1.525
 3UM  C13  C11  single  1.527  0.020  1.527
 3UM  C13  C15  single  1.541  0.020  1.541
 3UM  C17  C15  single  1.506  0.020  1.506
 3UM  C17  C19  single  1.462  0.020  1.462
 3UM  C15  C18  single  1.534  0.020  1.534
 3UM  C19  C20  double  1.334  0.020  1.334
 3UM  O1   H1   single  0.850  0.020  0.980
 3UM  O2   H2   single  0.850  0.020  0.980
 3UM  O3   H3   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   106.90  3.000
 3UM  C4   C1   C3   110.79  3.000
 3UM  O1   C1   C3   108.44  3.000
 3UM  C4   C1   C2   112.85  3.000
 3UM  O1   C1   C2   101.31  3.000
 3UM  C3   C1   C2   115.67  3.000
 3UM  C7   C2   C6   106.75  3.000
 3UM  C7   C2   C5   105.83  3.000
 3UM  C6   C2   C5   109.02  3.000
 3UM  C7   C2   C1   110.42  3.000
 3UM  C6   C2   C1   114.59  3.000
 3UM  C5   C2   C1   109.83  3.000
 3UM  C10  C3   C9   107.17  3.000
 3UM  C10  C3   C8   108.78  3.000
 3UM  C9   C3   C8   109.45  3.000
 3UM  C8   C3   C1   108.25  3.000
 3UM  C10  C3   C1   115.04  3.000
 3UM  C9   C3   C1   108.05  3.000
 3UM  H1   O1   C1   110.11  3.000
 3UM  H2   O2   C4   108.06  3.000
 3UM  H3   O3   C6   109.05  3.000
 3UM  H5   C11  H4   104.76  3.000
 3UM  H5   C11  C4   108.66  3.000
 3UM  H4   C11  C4   108.98  3.000
 3UM  H5   C11  C13  110.66  3.000
 3UM  H4   C11  C13  109.43  3.000
 3UM  C4   C11  C13  113.94  3.000
 3UM  H7   C12  H6   106.01  3.000
 3UM  H7   C12  C9   110.48  3.000
 3UM  H6   C12  C9   109.55  3.000
 3UM  H7   C12  C5   111.16  3.000
 3UM  H6   C12  C5   108.36  3.000
 3UM  C9   C12  C5   111.12  3.000
 3UM  H8   C13  C8   107.69  3.000
 3UM  H8   C13  C15  105.98  3.000
 3UM  C8   C13  C15  111.87  3.000
 3UM  H8   C13  C11  107.46  3.000
 3UM  C15  C13  C11  110.80  3.000
 3UM  C8   C13  C11  112.66  3.000
 3UM  H10  C14  H9   104.91  3.000
 3UM  H10  C14  C8   111.25  3.000
 3UM  H9   C14  C8   110.23  3.000
 3UM  H10  C14  C16  106.70  3.000
 3UM  H9   C14  C16  108.79  3.000
 3UM  C8   C14  C16  114.46  3.000
 3UM  H11  C15  C18  107.21  3.000
 3UM  H11  C15  C17  108.33  3.000
 3UM  C18  C15  C17  109.27  3.000
 3UM  H11  C15  C13  106.24  3.000
 3UM  C18  C15  C13  114.52  3.000
 3UM  C17  C15  C13  110.99  3.000
 3UM  H12  C16  C17  118.79  3.000
 3UM  H12  C16  C14  115.67  3.000
 3UM  C17  C16  C14  125.49  3.000
 3UM  C19  C17  C16  119.08  3.000
 3UM  C19  C17  C15  120.09  3.000
 3UM  C16  C17  C15  120.83  3.000
 3UM  H15  C18  H14  108.13  3.000
 3UM  H15  C18  H13  107.09  3.000
 3UM  H14  C18  H13  107.04  3.000
 3UM  H15  C18  C15  111.54  3.000
 3UM  H14  C18  C15  112.23  3.000
 3UM  H13  C18  C15  110.58  3.000
 3UM  H16  C19  C20  118.09  3.000
 3UM  H16  C19  C17  115.04  3.000
 3UM  C20  C19  C17  126.87  3.000
 3UM  H18  C20  H17  116.28  3.000
 3UM  H18  C20  C19  122.95  3.000
 3UM  H17  C20  C19  120.77  3.000
 3UM  H19  C4   C11  107.49  3.000
 3UM  H19  C4   O2   110.04  3.000
 3UM  C11  C4   O2   111.36  3.000
 3UM  H19  C4   C1   107.98  3.000
 3UM  C11  C4   C1   110.20  3.000
 3UM  O2   C4   C1   109.69  3.000
 3UM  H21  C5   H20  105.52  3.000
 3UM  H21  C5   C12  107.58  3.000
 3UM  H20  C5   C12  110.24  3.000
 3UM  H21  C5   C2   106.88  3.000
 3UM  H20  C5   C2   109.14  3.000
 3UM  C12  C5   C2   116.83  3.000
 3UM  O4   C6   O3   121.02  3.000
 3UM  O3   C6   C2   113.60  3.000
 3UM  O4   C6   C2   125.10  3.000
 3UM  H24  C7   H23  106.93  3.000
 3UM  H24  C7   H22  107.91  3.000
 3UM  H23  C7   H22  107.40  3.000
 3UM  H24  C7   C2   110.34  3.000
 3UM  H23  C7   C2   109.87  3.000
 3UM  H22  C7   C2   114.11  3.000
 3UM  H25  C8   C14  104.52  3.000
 3UM  H25  C8   C13  108.08  3.000
 3UM  C14  C8   C13  110.19  3.000
 3UM  H25  C8   C3   108.10  3.000
 3UM  C13  C8   C3   113.11  3.000
 3UM  C14  C8   C3   112.37  3.000
 3UM  H27  C9   H26  106.14  3.000
 3UM  H27  C9   C12  109.66  3.000
 3UM  H26  C9   C12  109.52  3.000
 3UM  H27  C9   C3   109.26  3.000
 3UM  H26  C9   C3   110.54  3.000
 3UM  C12  C9   C3   111.58  3.000
 3UM  H30  C10  H29  105.99  3.000
 3UM  H30  C10  H28  107.34  3.000
 3UM  H29  C10  H28  107.21  3.000
 3UM  H30  C10  C3   113.14  3.000
 3UM  H29  C10  C3   109.27  3.000
 3UM  H28  C10  C3   113.46  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  CONST_01  H3   O3   C6   C2    180.00   0.0  0
 3UM  Var_01    C9   C12  C5   C2     52.08  30.0  1
 3UM  Var_02    C5   C12  C9   C3    -60.10  30.0  1
 3UM  Var_03    C15  C17  C16  C14     3.45  30.0  1
 3UM  Var_04    C8   C14  C16  C17    -8.98  30.0  1
 3UM  Var_05    C20  C19  C17  C15    -5.87  30.0  2
 3UM  Var_06    H17  C20  C19  C17  -179.29   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-1  H3   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

