# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:33:22 2022
#   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  26  13  .  2022-03-22  2022-03-22
;
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   0.020  10.9576  42.8065  23.8518
 LUB  C4   C  CR5    0  -0.044  13.2168  42.4367  23.4982
 LUB  C5   C  CH2    0  -0.182  13.0175  42.9488  24.8930
 LUB  C6   C  CH2    0  -0.421  10.3329  44.1273  23.4113
 LUB  O11  O  OC    -1  -0.557  10.4612  41.6237  21.3126
 LUB  O10  O  O      0  -0.607  12.6101  41.4069  20.7911
 LUB  C3   C  CR5    0  -0.144  12.0258  42.3184  22.9053
 LUB  C12  C  CH2    0  -0.210  14.6081  42.1387  23.0240
 LUB  O13  O  OH1    0  -0.699  14.8316  42.3258  21.6612
 LUB  O1   O  O      0  -0.508  11.6252  42.9471  25.1021
 LUB  C7   C  CH2    0  -0.425   9.2636  44.6482  24.3634
 LUB  C8   C  CH3    0  -0.659   8.6194  45.9337  23.8636
 LUB  H1   H  HCR5   0   0.217  10.1589  42.0646  23.9781
 LUB  H2   H  HCH2   0   0.224  13.5095  42.3128  25.6399
 LUB  H3   H  HCH2   0   0.213  13.4503  43.9552  25.0039
 LUB  H4   H  HCH2   0   0.213  11.1242  44.8766  23.2916
 LUB  H5   H  HCH2   0   0.220   9.8943  43.9790  22.4217
 LUB  H7   H  HCH2   0   0.192  14.8495  41.1145  23.3580
 LUB  H8   H  HCH2   0   0.211  15.2964  42.7877  23.5784
 LUB  H9   H  HOH1   0   0.446  14.0246  41.9535  21.2082
 LUB  H10  H  HCH2   0   0.210   8.4930  43.8817  24.4950
 LUB  H11  H  HCH2   0   0.214   9.6971  44.8192  25.3517
 LUB  H12  H  HCH3   0   0.224   7.8545  46.2939  24.5527
 LUB  H13  H  HCH3   0   0.215   9.3598  46.7277  23.7494
 LUB  H14  H  HCH3   0   0.215   8.1454  45.7854  22.8915
 LUB  C9   C  C      0   0.422  11.6695  41.7481  21.5603

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   deloc   1.262  0.020  1.262
 LUB  O11  C9   deloc   1.240  0.020  1.240
 LUB  C9   C3   single  1.504  0.020  1.504
 LUB  O13  C12  single  1.394  0.020  1.394
 LUB  C3   C4   double  1.336  0.020  1.336
 LUB  C3   C2   single  1.508  0.020  1.508
 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  1.499  0.020  1.499
 LUB  C2   O1   single  1.424  0.020  1.424
 LUB  C8   C7   single  1.522  0.020  1.522
 LUB  C5   O1   single  1.408  0.020  1.408
 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  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   107.87  3.000
 LUB  H1   C2   C3   111.65  3.000
 LUB  O1   C2   C3   104.53  3.000
 LUB  H1   C2   C6   108.69  3.000
 LUB  O1   C2   C6   111.09  3.000
 LUB  C3   C2   C6   112.88  3.000
 LUB  C12  C4   C3   132.01  3.000
 LUB  C12  C4   C5   119.03  3.000
 LUB  C3   C4   C5   108.95  3.000
 LUB  H3   C5   H2   106.55  3.000
 LUB  H3   C5   O1   112.02  3.000
 LUB  H2   C5   O1   109.97  3.000
 LUB  H3   C5   C4   110.72  3.000
 LUB  H2   C5   C4   112.06  3.000
 LUB  O1   C5   C4   105.62  3.000
 LUB  H5   C6   H4   106.48  3.000
 LUB  H5   C6   C7   109.31  3.000
 LUB  H4   C6   C7   109.94  3.000
 LUB  H5   C6   C2   107.96  3.000
 LUB  H4   C6   C2   109.13  3.000
 LUB  C7   C6   C2   113.75  3.000
 LUB  C9   C3   C4   129.93  3.000
 LUB  C4   C3   C2   108.92  3.000
 LUB  C9   C3   C2   121.08  3.000
 LUB  H8   C12  H7   105.00  3.000
 LUB  H8   C12  O13  108.33  3.000
 LUB  H7   C12  O13  112.66  3.000
 LUB  H8   C12  C4   107.75  3.000
 LUB  H7   C12  C4   106.94  3.000
 LUB  O13  C12  C4   115.55  3.000
 LUB  H9   O13  C12  105.33  3.000
 LUB  C5   O1   C2   109.47  3.000
 LUB  H11  C7   H10  106.27  3.000
 LUB  H11  C7   C8   109.43  3.000
 LUB  H10  C7   C8   109.44  3.000
 LUB  H11  C7   C6   109.90  3.000
 LUB  H10  C7   C6   109.25  3.000
 LUB  C8   C7   C6   112.37  3.000
 LUB  H14  C8   H13  107.47  3.000
 LUB  H14  C8   H12  107.64  3.000
 LUB  H13  C8   H12  107.55  3.000
 LUB  H14  C8   C7   111.18  3.000
 LUB  H13  C8   C7   111.19  3.000
 LUB  H12  C8   C7   111.60  3.000
 LUB  C3   C9   O10  118.11  3.000
 LUB  C3   C9   O11  116.60  3.000
 LUB  O10  C9   O11  125.27  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  Var_01  C5   C4   C3  C2     2.56  30.0  1
 LUB  Var_02  C4   C5   O1  C2   -14.81  30.0  1
 LUB  Var_03  O1   C5   C4  C3     7.35  30.0  1
 LUB  Var_04  O10  C9   C3  C2   177.17  30.0  2
 LUB  Var_05  O13  C12  C4  C5  -148.97  30.0  1
 LUB  Var_06  C8   C7   C6  C2  -177.49  30.0  3
 LUB  Var_07  H12  C8   C7  C6   179.84  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  C9   0.020

