# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:59:16 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: (5S)-5-[(6R)-6-hydroxy-6-methyl-5-oxooctyl]furan-2(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@](C)(O)C(=O)CCCC[C@@H]1OC(=O)C=C1
#
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
 XVR  XVR  (5S)-5-[(6R)-6-hydroxy-6-methyl-5-oxooctyl]furan-2(5H)-one  ligand  37  17  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XVR
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
 XVR  O15  O  O     0  -0.407   -9.7788  34.3495  -29.5438
 XVR  C11  C  C     0   0.379  -10.3318  34.4958  -28.4743
 XVR  C12  C  CT    0   0.145  -10.1053  33.4586  -27.3728
 XVR  O16  O  OH1   0  -0.685   -9.1805  32.5046  -27.8303
 XVR  C13  C  CH2   0  -0.439  -11.4396  32.7623  -27.0497
 XVR  C14  C  CH3   0  -0.679  -12.1332  32.1516  -28.2595
 XVR  C10  C  CH2   0  -0.580  -11.2315  35.6659  -28.1941
 XVR  C9   C  CH2   0  -0.416  -11.7815  36.3466  -29.4398
 XVR  C8   C  CH2   0  -0.427  -12.6954  37.5107  -29.0796
 XVR  C7   C  CH2   0  -0.442  -13.2840  38.1772  -30.3166
 XVR  C4   C  CR15  0  -0.024  -14.1472  39.3875  -29.9960
 XVR  C3   C  CR15  0  -0.168  -14.7679  40.0138  -31.1987
 XVR  C2   C  CR15  0  -0.394  -16.0911  39.9658  -31.0937
 XVR  O5   O  O     0  -0.455  -15.2690  39.0138  -29.1916
 XVR  C1   C  CR5   0   0.539  -16.4189  39.3275  -29.8115
 XVR  O6   O  O     0  -0.442  -17.4911  39.0916  -29.3195
 XVR  C5   C  CH3   0  -0.672   -9.5445  34.1410  -26.1238
 XVR  H1   H  HOH1  0   0.442   -8.9663  32.7277  -28.7473
 XVR  H2   H  HCH2  0   0.229  -12.1100  33.4645  -26.5487
 XVR  H3   H  HCH2  0   0.246  -11.2213  31.9835  -26.3140
 XVR  H4   H  HCH3  0   0.240  -12.9957  31.5624  -27.9486
 XVR  H5   H  HCH3  0   0.220  -12.5001  32.9133  -28.9514
 XVR  H6   H  HCH3  0   0.229  -11.4639  31.4918  -28.8117
 XVR  H7   H  HCH2  0   0.288  -10.6474  36.3815  -27.6026
 XVR  H8   H  HCH2  0   0.267  -12.0483  35.3576  -27.5368
 XVR  H9   H  HCH2  0   0.230  -12.3375  35.6201  -30.0402
 XVR  H10  H  HCH2  0   0.233  -10.9604  36.7039  -30.0653
 XVR  H11  H  HCH2  0   0.227  -12.1362  38.2495  -28.4964
 XVR  H12  H  HCH2  0   0.231  -13.5014  37.1516  -28.4341
 XVR  H13  H  HCH2  0   0.242  -13.8706  37.4570  -30.8945
 XVR  H14  H  HCH2  0   0.247  -12.4763  38.5195  -30.9698
 XVR  H15  H  HCR5  0   0.281  -13.5593  40.1215  -29.4336
 XVR  H16  H  HCR5  0   0.297  -14.1837  40.4189  -32.0121
 XVR  H17  H  HCR5  0   0.288  -16.8358  40.3159  -31.7915
 XVR  H18  H  HCH3  0   0.247   -9.3495  33.3897  -25.3571
 XVR  H19  H  HCH3  0   0.243   -8.6075  34.6565  -26.3402
 XVR  H20  H  HCH3  0   0.235  -10.2432  34.8639  -25.7037

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
 XVR  C3   C2   double  1.328  0.020  1.328
 XVR  C3   C4   single  1.491  0.020  1.491
 XVR  C2   C1   single  1.469  0.020  1.469
 XVR  C7   C4   single  1.521  0.020  1.521
 XVR  C7   C8   single  1.523  0.020  1.523
 XVR  C4   O5   single  1.430  0.020  1.430
 XVR  C1   O6   double  1.203  0.020  1.203
 XVR  C1   O5   single  1.343  0.020  1.343
 XVR  O15  C11  double  1.213  0.020  1.213
 XVR  C9   C8   single  1.523  0.020  1.523
 XVR  C9   C10  single  1.522  0.020  1.522
 XVR  C11  C10  single  1.502  0.020  1.502
 XVR  C11  C12  single  1.530  0.020  1.530
 XVR  C14  C13  single  1.522  0.020  1.522
 XVR  O16  C12  single  1.405  0.020  1.405
 XVR  C12  C13  single  1.539  0.020  1.539
 XVR  C12  C5   single  1.530  0.020  1.530
 XVR  O16  H1   single  0.850  0.020  0.980
 XVR  C13  H2   single  0.970  0.020  1.090
 XVR  C13  H3   single  0.970  0.020  1.090
 XVR  C14  H4   single  0.970  0.020  1.090
 XVR  C14  H5   single  0.970  0.020  1.090
 XVR  C14  H6   single  0.970  0.020  1.090
 XVR  C10  H7   single  0.970  0.020  1.090
 XVR  C10  H8   single  0.970  0.020  1.090
 XVR  C9   H9   single  0.970  0.020  1.090
 XVR  C9   H10  single  0.970  0.020  1.090
 XVR  C8   H11  single  0.970  0.020  1.090
 XVR  C8   H12  single  0.970  0.020  1.090
 XVR  C7   H13  single  0.970  0.020  1.090
 XVR  C7   H14  single  0.970  0.020  1.090
 XVR  C4   H15  single  0.970  0.020  1.090
 XVR  C3   H16  single  0.930  0.020  1.080
 XVR  C2   H17  single  0.930  0.020  1.080
 XVR  C5   H18  single  0.970  0.020  1.090
 XVR  C5   H19  single  0.970  0.020  1.090
 XVR  C5   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
 XVR  C10  C11  C12  118.84  3.000
 XVR  C12  C11  O15  119.05  3.000
 XVR  C10  C11  O15  122.10  3.000
 XVR  C5   C12  C13  110.38  3.000
 XVR  C5   C12  O16  109.11  3.000
 XVR  C13  C12  O16  109.37  3.000
 XVR  C5   C12  C11  109.86  3.000
 XVR  C13  C12  C11  109.24  3.000
 XVR  O16  C12  C11  108.87  3.000
 XVR  H1   O16  C12  107.31  3.000
 XVR  H3   C13  H2   105.77  3.000
 XVR  H3   C13  C14  109.87  3.000
 XVR  H2   C13  C14  110.04  3.000
 XVR  H3   C13  C12  106.88  3.000
 XVR  H2   C13  C12  109.72  3.000
 XVR  C14  C13  C12  114.18  3.000
 XVR  H6   C14  H5   107.91  3.000
 XVR  H6   C14  H4   107.65  3.000
 XVR  H5   C14  H4   106.97  3.000
 XVR  H6   C14  C13  111.44  3.000
 XVR  H5   C14  C13  112.12  3.000
 XVR  H4   C14  C13  110.53  3.000
 XVR  H8   C10  H7   104.94  3.000
 XVR  H8   C10  C9   110.38  3.000
 XVR  H7   C10  C9   110.00  3.000
 XVR  H8   C10  C11  109.88  3.000
 XVR  H7   C10  C11  106.85  3.000
 XVR  C9   C10  C11  114.33  3.000
 XVR  H10  C9   H9   106.56  3.000
 XVR  H10  C9   C8   109.67  3.000
 XVR  H9   C9   C8   109.41  3.000
 XVR  H10  C9   C10  110.07  3.000
 XVR  H9   C9   C10  109.61  3.000
 XVR  C8   C9   C10  111.40  3.000
 XVR  H12  C8   H11  106.48  3.000
 XVR  H12  C8   C7   109.78  3.000
 XVR  H11  C8   C7   109.54  3.000
 XVR  H12  C8   C9   109.33  3.000
 XVR  H11  C8   C9   109.59  3.000
 XVR  C7   C8   C9   111.97  3.000
 XVR  H14  C7   H13  106.66  3.000
 XVR  H14  C7   C4   107.22  3.000
 XVR  H13  C7   C4   109.33  3.000
 XVR  H14  C7   C8   109.67  3.000
 XVR  H13  C7   C8   110.36  3.000
 XVR  C4   C7   C8   113.35  3.000
 XVR  H15  C4   O5   107.89  3.000
 XVR  H15  C4   C3   110.85  3.000
 XVR  O5   C4   C3   103.70  3.000
 XVR  H15  C4   C7   109.68  3.000
 XVR  O5   C4   C7   110.85  3.000
 XVR  C3   C4   C7   113.61  3.000
 XVR  H16  C3   C2   127.72  3.000
 XVR  H16  C3   C4   122.66  3.000
 XVR  C2   C3   C4   109.62  3.000
 XVR  H17  C2   C1   123.46  3.000
 XVR  H17  C2   C3   128.67  3.000
 XVR  C1   C2   C3   107.87  3.000
 XVR  C1   O5   C4   110.54  3.000
 XVR  O6   C1   O5   121.89  3.000
 XVR  O5   C1   C2   108.25  3.000
 XVR  O6   C1   C2   129.86  3.000
 XVR  H20  C5   H19  108.29  3.000
 XVR  H20  C5   H18  107.49  3.000
 XVR  H19  C5   H18  108.13  3.000
 XVR  H20  C5   C12  112.07  3.000
 XVR  H19  C5   C12  111.32  3.000
 XVR  H18  C5   C12  109.39  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
 XVR  Var_01  C1  C2   C3   C4      0.89  30.0  1
 XVR  Var_02  O5  C1   C2   C3     -0.03  30.0  1
 XVR  Var_03  C4  C7   C8   C9   -177.13  30.0  2
 XVR  Var_04  C9  C10  C11  O15    20.74  30.0  3
 XVR  Var_05  C8  C9   C10  C11   179.35  30.0  1
 XVR  Var_06  C7  C8   C9   C10  -178.41  30.0  3
 XVR  Var_07  H4  C14  C13  C12   172.37  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
 XVR  chir_01  C12  O16  C13  C5  negativ
 XVR  chir_02  C4   O5   C3   C7  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
 XVR  plan-1  O15  0.020
 XVR  plan-1  C11  0.020
 XVR  plan-1  C12  0.020
 XVR  plan-1  C10  0.020
 XVR  plan-2  C2   0.020
 XVR  plan-2  O5   0.020
 XVR  plan-2  C1   0.020
 XVR  plan-2  O6   0.020

