# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:32:32 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: (5~{S})-5-methyloxolan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCC(=O)O1
#
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
 YVR  YVR  (5~{S})-5-methyloxolan-2-one  ligand  15  7  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YVR
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
 YVR  O6  O  O     0  -0.441   2.2466   0.5673  -0.0417
 YVR  C5  C  C     0   0.548   1.1479   0.0871   0.0450
 YVR  O1  O  O2    0  -0.448   0.0609   0.8494   0.1539
 YVR  C4  C  CH2   0  -0.614   0.7563  -1.3686   0.0650
 YVR  C3  C  CH2   0  -0.484  -0.7340  -1.3256  -0.2327
 YVR  C2  C  CH1   0   0.043  -1.1359   0.0486   0.2967
 YVR  C7  C  CH3   0  -0.681  -2.2766   0.7109  -0.4340
 YVR  H1  H  HCH2  0   0.291   1.3492  -1.9450  -0.6430
 YVR  H2  H  HCH2  0   0.293   0.9633  -1.7620   1.0648
 YVR  H3  H  HCH2  0   0.254  -0.9126  -1.3853  -1.3088
 YVR  H4  H  HCH2  0   0.268  -1.2985  -2.1225   0.2471
 YVR  H5  H  HCH1  0   0.250  -1.3576  -0.0076   1.3668
 YVR  H6  H  HCH3  0   0.235  -2.0552   0.8148  -1.4968
 YVR  H7  H  HCH3  0   0.242  -3.1709   0.0954  -0.3342
 YVR  H8  H  HCH3  0   0.246  -2.5021   1.6947  -0.0231

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
 YVR  C7  C2  single  1.508  0.020  1.508
 YVR  C4  C3  single  1.520  0.020  1.520
 YVR  C4  C5  single  1.508  0.020  1.508
 YVR  C3  C2  single  1.526  0.020  1.526
 YVR  C5  O1  single  1.332  0.020  1.332
 YVR  C5  O6  double  1.202  0.020  1.202
 YVR  O1  C2  single  1.447  0.020  1.447
 YVR  C4  H1  single  0.970  0.020  1.090
 YVR  C4  H2  single  0.970  0.020  1.090
 YVR  C3  H3  single  0.970  0.020  1.090
 YVR  C3  H4  single  0.970  0.020  1.090
 YVR  C2  H5  single  0.970  0.020  1.090
 YVR  C7  H6  single  0.970  0.020  1.090
 YVR  C7  H7  single  0.970  0.020  1.090
 YVR  C7  H8  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
 YVR  C4  C5  O1  109.85  3.000
 YVR  O1  C5  O6  121.54  3.000
 YVR  C4  C5  O6  128.61  3.000
 YVR  C2  O1  C5  111.49  3.000
 YVR  H2  C4  H1  107.51  3.000
 YVR  H2  C4  C3  112.00  3.000
 YVR  H1  C4  C3  114.93  3.000
 YVR  H2  C4  C5  108.07  3.000
 YVR  H1  C4  C5  111.17  3.000
 YVR  C3  C4  C5  102.98  3.000
 YVR  H4  C3  H3  108.03  3.000
 YVR  H4  C3  C2  111.71  3.000
 YVR  H3  C3  C2  110.35  3.000
 YVR  H4  C3  C4  113.67  3.000
 YVR  H3  C3  C4  110.58  3.000
 YVR  C2  C3  C4  102.46  3.000
 YVR  H5  C2  C7  110.07  3.000
 YVR  H5  C2  C3  110.26  3.000
 YVR  C7  C2  C3  115.25  3.000
 YVR  H5  C2  O1  107.00  3.000
 YVR  C3  C2  O1  104.25  3.000
 YVR  C7  C2  O1  109.56  3.000
 YVR  H8  C7  H7  107.78  3.000
 YVR  H8  C7  H6  108.87  3.000
 YVR  H7  C7  H6  108.03  3.000
 YVR  H8  C7  C2  111.74  3.000
 YVR  H7  C7  C2  109.16  3.000
 YVR  H6  C7  C2  111.13  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
 YVR  Var_01  C2  C3  C4  C5  -27.41  30.0  1
 YVR  Var_02  C3  C4  C5  O1   17.04  30.0  1

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
 YVR  chir_01  C2  C7  C3  O1  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
 YVR  plan-1  O6  0.020
 YVR  plan-1  C5  0.020
 YVR  plan-1  O1  0.020
 YVR  plan-1  C4  0.020

