# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:03:12 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: (2~{S})-4-(hydroxymethyl)-2-propyl-2,5-dihydrofuran-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H]1OCC(=C1C(O)=O)CO
#
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
 LUB  LUB  '(2~{S})-4-(hydroxymethyl)-2-propyl-2,5-dihydrofuran-3-carboxylic acid'  ligand  27  13  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LUB
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
 LUB  C2   C  CR15  0   0.018  10.8753  42.8077  23.7868
 LUB  C4   C  CR5   0   0.030  13.1521  42.4201  23.4652
 LUB  C5   C  CH2   0  -0.193  12.9222  42.8833  24.8669
 LUB  C6   C  CH2   0  -0.426  10.2963  44.1626  23.3900
 LUB  O11  O  OH1   0  -0.583  10.4426  41.7062  21.2269
 LUB  O10  O  O     0  -0.468  12.5996  41.5047  20.7143
 LUB  C3   C  CR5   0  -0.096  11.9664  42.3394  22.8521
 LUB  C12  C  CH2   0  -0.246  14.5410  42.1195  22.9838
 LUB  O13  O  OH1   0  -0.672  14.8654  42.6659  21.7363
 LUB  O1   O  O     0  -0.502  11.5267  42.8711  25.0487
 LUB  C7   C  CH2   0  -0.428   9.2170  44.6598  24.3441
 LUB  C8   C  CH3   0  -0.663   8.6466  46.0044  23.9155
 LUB  H1   H  HCR5  0   0.244  10.0607  42.0777  23.8661
 LUB  H2   H  HCH2  0   0.251  13.4031  42.2217  25.5965
 LUB  H3   H  HCH2  0   0.240  13.3562  43.8841  25.0105
 LUB  H4   H  HCH2  0   0.226  11.1081  44.8960  23.3261
 LUB  H5   H  HCH2  0   0.228   9.8759  44.0818  22.3835
 LUB  H6   H  HOH1  0   0.491  10.3204  41.3469  20.3348
 LUB  H7   H  HCH2  0   0.231  14.6704  41.0278  23.0135
 LUB  H8   H  HCH2  0   0.245  15.2510  42.5250  23.7080
 LUB  H9   H  HOH1  0   0.456  14.2381  42.2877  21.1015
 LUB  H10  H  HCH2  0   0.216   8.4124  43.9198  24.3975
 LUB  H11  H  HCH2  0   0.221   9.6263  44.7418  25.3538
 LUB  H12  H  HCH3  0   0.228   7.8647  46.3427  24.5963
 LUB  H13  H  HCH3  0   0.218   9.4214  46.7728  23.8953
 LUB  H14  H  HCH3  0   0.217   8.2127  45.9492  22.9153
 LUB  C9   C  C     0   0.518  11.7306  41.8249  21.5029

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
 LUB  O10  C9   double  1.216  0.020  1.216
 LUB  O11  C9   single  1.323  0.020  1.323
 LUB  C9   C3   single  1.463  0.020  1.463
 LUB  O13  C12  single  1.400  0.020  1.400
 LUB  C3   C4   double  1.337  0.020  1.337
 LUB  C3   C2   single  1.511  0.020  1.511
 LUB  C12  C4   single  1.500  0.020  1.500
 LUB  C6   C2   single  1.526  0.020  1.526
 LUB  C6   C7   single  1.524  0.020  1.524
 LUB  C4   C5   single  1.494  0.020  1.494
 LUB  C2   O1   single  1.421  0.020  1.421
 LUB  C8   C7   single  1.522  0.020  1.522
 LUB  C5   O1   single  1.407  0.020  1.407
 LUB  C2   H1   single  0.970  0.020  1.090
 LUB  C5   H2   single  0.970  0.020  1.090
 LUB  C5   H3   single  0.970  0.020  1.090
 LUB  C6   H4   single  0.970  0.020  1.090
 LUB  C6   H5   single  0.970  0.020  1.090
 LUB  O11  H6   single  0.850  0.020  0.980
 LUB  C12  H7   single  0.970  0.020  1.090
 LUB  C12  H8   single  0.970  0.020  1.090
 LUB  O13  H9   single  0.850  0.020  0.980
 LUB  C7   H10  single  0.970  0.020  1.090
 LUB  C7   H11  single  0.970  0.020  1.090
 LUB  C8   H12  single  0.970  0.020  1.090
 LUB  C8   H13  single  0.970  0.020  1.090
 LUB  C8   H14  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
 LUB  H1   C2   O1   107.82  3.000
 LUB  H1   C2   C3   112.01  3.000
 LUB  O1   C2   C3   103.42  3.000
 LUB  H1   C2   C6   109.15  3.000
 LUB  O1   C2   C6   111.41  3.000
 LUB  C3   C2   C6   112.85  3.000
 LUB  C12  C4   C3   131.43  3.000
 LUB  C12  C4   C5   120.37  3.000
 LUB  C3   C4   C5   108.20  3.000
 LUB  H3   C5   H2   106.81  3.000
 LUB  H3   C5   O1   112.46  3.000
 LUB  H2   C5   O1   110.11  3.000
 LUB  H3   C5   C4   110.10  3.000
 LUB  H2   C5   C4   111.71  3.000
 LUB  O1   C5   C4   105.73  3.000
 LUB  H5   C6   H4   106.29  3.000
 LUB  H5   C6   C7   109.14  3.000
 LUB  H4   C6   C7   110.05  3.000
 LUB  H5   C6   C2   108.64  3.000
 LUB  H4   C6   C2   109.17  3.000
 LUB  C7   C6   C2   113.30  3.000
 LUB  H6   O11  C9   110.37  3.000
 LUB  C9   C3   C4   125.94  3.000
 LUB  C4   C3   C2   109.75  3.000
 LUB  C9   C3   C2   124.26  3.000
 LUB  H8   C12  H7   105.91  3.000
 LUB  H8   C12  O13  107.18  3.000
 LUB  H7   C12  O13  112.60  3.000
 LUB  H8   C12  C4   108.34  3.000
 LUB  H7   C12  C4   107.40  3.000
 LUB  O13  C12  C4   114.97  3.000
 LUB  H9   O13  C12  106.34  3.000
 LUB  C5   O1   C2   109.88  3.000
 LUB  H11  C7   H10  106.32  3.000
 LUB  H11  C7   C8   109.53  3.000
 LUB  H10  C7   C8   109.60  3.000
 LUB  H11  C7   C6   109.74  3.000
 LUB  H10  C7   C6   109.31  3.000
 LUB  C8   C7   C6   112.17  3.000
 LUB  H14  C8   H13  107.51  3.000
 LUB  H14  C8   H12  107.62  3.000
 LUB  H13  C8   H12  107.59  3.000
 LUB  H14  C8   C7   111.24  3.000
 LUB  H13  C8   C7   111.17  3.000
 LUB  H12  C8   C7   111.53  3.000
 LUB  C3   C9   O10  125.12  3.000
 LUB  C3   C9   O11  112.39  3.000
 LUB  O10  C9   O11  122.47  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
 LUB  CONST_01  H6   O11  C9  C3   180.00   0.0  0
 LUB  Var_01    C5   C4   C3  C2     2.70  30.0  1
 LUB  Var_02    C4   C5   O1  C2   -16.39  30.0  1
 LUB  Var_03    O1   C5   C4  C3     8.13  30.0  1
 LUB  Var_04    O10  C9   C3  C2   176.25  30.0  2
 LUB  Var_05    O13  C12  C4  C5  -133.38  30.0  2
 LUB  Var_06    C8   C7   C6  C2  -179.34  30.0  3
 LUB  Var_07    H12  C8   C7  C6   179.10  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
 LUB  chir_01  C2  C3  C6  O1  positiv

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
 LUB  plan-1  O11  0.020
 LUB  plan-1  O10  0.020
 LUB  plan-1  C3   0.020
 LUB  plan-1  H6   0.020
 LUB  plan-1  C9   0.020

