# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:46:22 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (3~{S})-3-oxidanyldecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC[C@H](O)CC(O)=O
#
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
 5UF  5UF  '(3~{S})-3-oxidanyldecanoic acid'  ligand  33  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5UF
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
 5UF  C1   C  C     0   0.549  -4.4629   0.2253   0.2418
 5UF  C2   C  CH2   0  -0.594  -3.1354   0.8534  -0.0844
 5UF  C3   C  CH1   0   0.039  -1.9675  -0.0987   0.1594
 5UF  C4   C  CH2   0  -0.452  -0.6397   0.6021  -0.1036
 5UF  C5   C  CH2   0  -0.410   0.5822  -0.2766   0.1317
 5UF  C6   C  CH2   0  -0.412   1.8898   0.4811  -0.0628
 5UF  O14  O  OH1   0  -0.666  -2.1217  -1.2811  -0.5984
 5UF  O13  O  OH1   0  -0.592  -5.4166   0.5808  -0.6119
 5UF  O12  O  O     0  -0.450  -4.6644  -0.4966   1.1871
 5UF  C7   C  CH2   0  -0.411   3.1248  -0.3867   0.1424
 5UF  C8   C  CH2   0  -0.406   4.4306   0.3727  -0.0548
 5UF  C9   C  CH2   0  -0.418   5.6693  -0.4926   0.1407
 5UF  C10  C  CH3   0  -0.662   6.9673   0.2739  -0.0723
 5UF  H1   H  HCH2  0   0.264  -3.1256   1.2170  -1.1148
 5UF  H2   H  HCH2  0   0.287  -3.0318   1.7355   0.5563
 5UF  H3   H  HCH1  0   0.230  -1.9886  -0.4186   1.2051
 5UF  H4   H  HCH2  0   0.219  -0.6262   0.9866  -1.1309
 5UF  H5   H  HCH2  0   0.226  -0.5868   1.4798   0.5481
 5UF  H6   H  HCH2  0   0.210   0.5482  -0.6862   1.1473
 5UF  H7   H  HCH2  0   0.213   0.5597  -1.1347  -0.5459
 5UF  H8   H  HCH2  0   0.208   1.9124   0.9114  -1.0703
 5UF  H9   H  HCH2  0   0.208   1.9232   1.3301   0.6291
 5UF  H10  H  HOH1  0   0.443  -2.0019  -1.0632  -1.5294
 5UF  H11  H  HOH1  0   0.478  -6.2625   0.1910  -0.3432
 5UF  H12  H  HCH2  0   0.206   3.1038  -0.8177   1.1496
 5UF  H13  H  HCH2  0   0.206   3.0919  -1.2348  -0.5506
 5UF  H14  H  HCH2  0   0.205   4.4479   0.8076  -1.0606
 5UF  H15  H  HCH2  0   0.205   4.4665   1.2188   0.6406
 5UF  H16  H  HCH2  0   0.210   5.6564  -0.9209   1.1480
 5UF  H17  H  HCH2  0   0.209   5.6305  -1.3417  -0.5490
 5UF  H18  H  HCH3  0   0.225   7.8393  -0.3675   0.0626
 5UF  H19  H  HCH3  0   0.215   7.0167   0.6902  -1.0803
 5UF  H20  H  HCH3  0   0.215   7.0565   1.1046   0.6302

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
 5UF  O12  C1   double  1.206  0.020  1.206
 5UF  C1   O13  single  1.328  0.020  1.328
 5UF  C1   C2   single  1.504  0.020  1.504
 5UF  C2   C3   single  1.526  0.020  1.526
 5UF  C3   C4   single  1.524  0.020  1.524
 5UF  C3   O14  single  1.413  0.020  1.413
 5UF  C4   C5   single  1.523  0.020  1.523
 5UF  C5   C6   single  1.524  0.020  1.524
 5UF  C6   C7   single  1.523  0.020  1.523
 5UF  C7   C8   single  1.523  0.020  1.523
 5UF  C8   C9   single  1.524  0.020  1.524
 5UF  C9   C10  single  1.522  0.020  1.522
 5UF  C2   H1   single  0.970  0.020  1.090
 5UF  C2   H2   single  0.970  0.020  1.090
 5UF  C3   H3   single  0.970  0.020  1.090
 5UF  C4   H4   single  0.970  0.020  1.090
 5UF  C4   H5   single  0.970  0.020  1.090
 5UF  C5   H6   single  0.970  0.020  1.090
 5UF  C5   H7   single  0.970  0.020  1.090
 5UF  C6   H8   single  0.970  0.020  1.090
 5UF  C6   H9   single  0.970  0.020  1.090
 5UF  O14  H10  single  0.850  0.020  0.980
 5UF  O13  H11  single  0.850  0.020  0.980
 5UF  C7   H12  single  0.970  0.020  1.090
 5UF  C7   H13  single  0.970  0.020  1.090
 5UF  C8   H14  single  0.970  0.020  1.090
 5UF  C8   H15  single  0.970  0.020  1.090
 5UF  C9   H16  single  0.970  0.020  1.090
 5UF  C9   H17  single  0.970  0.020  1.090
 5UF  C10  H18  single  0.970  0.020  1.090
 5UF  C10  H19  single  0.970  0.020  1.090
 5UF  C10  H20  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
 5UF  O12  C1   O13  122.94  3.000
 5UF  O13  C1   C2   112.49  3.000
 5UF  O12  C1   C2   124.55  3.000
 5UF  H2   C2   H1   106.42  3.000
 5UF  H2   C2   C3   109.67  3.000
 5UF  H1   C2   C3   110.57  3.000
 5UF  H2   C2   C1   107.03  3.000
 5UF  H1   C2   C1   110.57  3.000
 5UF  C3   C2   C1   112.34  3.000
 5UF  H3   C3   O14  105.42  3.000
 5UF  H3   C3   C4   108.44  3.000
 5UF  O14  C3   C4   112.79  3.000
 5UF  H3   C3   C2   108.69  3.000
 5UF  O14  C3   C2   110.65  3.000
 5UF  C4   C3   C2   110.62  3.000
 5UF  H5   C4   H4   106.01  3.000
 5UF  H5   C4   C5   109.38  3.000
 5UF  H4   C4   C5   109.69  3.000
 5UF  H5   C4   C3   107.94  3.000
 5UF  H4   C4   C3   109.48  3.000
 5UF  C5   C4   C3   114.01  3.000
 5UF  H7   C5   H6   106.28  3.000
 5UF  H7   C5   C6   109.19  3.000
 5UF  H6   C5   C6   109.32  3.000
 5UF  H7   C5   C4   109.90  3.000
 5UF  H6   C5   C4   109.50  3.000
 5UF  C6   C5   C4   112.45  3.000
 5UF  H9   C6   H8   106.00  3.000
 5UF  H9   C6   C7   109.37  3.000
 5UF  H8   C6   C7   109.32  3.000
 5UF  H9   C6   C5   109.32  3.000
 5UF  H8   C6   C5   109.29  3.000
 5UF  C7   C6   C5   113.28  3.000
 5UF  H10  O14  C3   108.39  3.000
 5UF  H11  O13  C1   109.93  3.000
 5UF  H13  C7   H12  106.04  3.000
 5UF  H13  C7   C8   109.25  3.000
 5UF  H12  C7   C8   109.36  3.000
 5UF  H13  C7   C6   109.36  3.000
 5UF  H12  C7   C6   109.41  3.000
 5UF  C8   C7   C6   113.18  3.000
 5UF  H15  C8   H14  105.98  3.000
 5UF  H15  C8   C9   109.29  3.000
 5UF  H14  C8   C9   109.29  3.000
 5UF  H15  C8   C7   109.32  3.000
 5UF  H14  C8   C7   109.28  3.000
 5UF  C9   C8   C7   113.40  3.000
 5UF  H17  C9   H16  106.02  3.000
 5UF  H17  C9   C10  109.43  3.000
 5UF  H16  C9   C10  109.62  3.000
 5UF  H17  C9   C8   109.32  3.000
 5UF  H16  C9   C8   109.31  3.000
 5UF  C10  C9   C8   112.91  3.000
 5UF  H20  C10  H19  107.48  3.000
 5UF  H20  C10  H18  107.61  3.000
 5UF  H19  C10  H18  107.59  3.000
 5UF  H20  C10  C9   111.27  3.000
 5UF  H19  C10  C9   111.09  3.000
 5UF  H18  C10  C9   111.60  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
 5UF  CONST_01  H11  O13  C1  C2   180.00   0.0  0
 5UF  Var_01    O12  C1   C2  C3    39.68  30.0  2
 5UF  Var_02    C6   C5   C4  C3  -176.67  30.0  3
 5UF  Var_03    C7   C6   C5  C4  -178.92  30.0  3
 5UF  Var_04    C8   C7   C6  C5   179.91  30.0  3
 5UF  Var_05    C9   C8   C7  C6  -179.64  30.0  3
 5UF  Var_06    C10  C9   C8  C7   179.44  30.0  3
 5UF  Var_07    H18  C10  C9  C8  -179.41  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
 5UF  chir_01  C3  C2  C4  O14  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
 5UF  plan-1  C1   0.020
 5UF  plan-1  C2   0.020
 5UF  plan-1  O13  0.020
 5UF  plan-1  O12  0.020
 5UF  plan-1  H11  0.020

