# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 17:42:03 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2S,3R,4R)-3,4-dihydroxy-2-methoxy-4-methyl-3-[(2S,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1C(=O)CC[C@@](C)(O)[C@@]1(O)[C@@]2(C)O[C@@H]2CC=C(C)C
#
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
 OVA  OVA  (2S,3R,4R)-3,4-dihydroxy-2-methoxy-4-methyl-3-[(2S,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexanone  ligand  47  21  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OVA
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
 OVA  C5    C  CH2   0  -0.542  -0.8793  -0.2701   3.8628
 OVA  C4    C  C     0   0.367   0.4522  -0.6149   3.2546
 OVA  C3    C  CH1   0  -0.020   0.7592   0.1310   1.9650
 OVA  C2    C  CT    0   0.152  -0.3665  -0.1693   0.9403
 OVA  C1    C  CT    0   0.197  -1.7273   0.3298   1.5210
 OVA  C6    C  CH2   0  -0.512  -2.0146  -0.3984   2.8441
 OVA  O11   O  OH1   0  -0.662  -1.5612   1.7085   1.7851
 OVA  C11   C  CH3   0  -0.679  -2.8889   0.1132   0.5559
 OVA  C21   C  CT    0   0.246  -0.0362   0.4718  -0.4235
 OVA  C22   C  CH1   0   0.014  -0.6097  -0.1437  -1.6283
 OVA  C23   C  CH2   0  -0.556  -0.9224   0.6054  -2.9010
 OVA  C24   C  C1    0  -0.257  -0.6884  -0.2645  -4.1018
 OVA  C25   C  C     0   0.093   0.3896  -0.2690  -4.8892
 OVA  C2A   C  CH3   0  -0.711   0.3336   1.9370  -0.4393
 OVA  O2A   O  O2    0  -0.481   0.7477  -0.3437  -1.2812
 OVA  C2B   C  CH3   0  -0.706   0.4903  -1.2100  -6.0545
 OVA  C2C   C  CH3   0  -0.715   1.5771   0.6281  -4.7087
 OVA  O31   O  O2    0  -0.480   1.9800  -0.2442   1.4152
 OVA  C31   C  CH3   0  -0.413   3.0851   0.4512   1.9443
 OVA  O41   O  O     0  -0.383   1.2213  -1.4132   3.7341
 OVA  O1    O  OH1   0  -0.666  -0.4058  -1.5583   0.7198
 OVA  H51   H  HCH2  0   0.273  -1.0686  -0.9005   4.7313
 OVA  H52   H  HCH2  0   0.273  -0.8250   0.7647   4.2148
 OVA  H3    H  HCH1  0   0.254   0.7446   1.2029   2.2107
 OVA  H61   H  HCH2  0   0.247  -2.2487  -1.4546   2.6765
 OVA  H62   H  HCH2  0   0.275  -2.9299   0.0155   3.2756
 OVA  H12   H  HOH1  0   0.455  -2.3883   2.0502   2.1424
 OVA  H111  H  HCH3  0   0.243  -3.8262   0.3947   1.0406
 OVA  H112  H  HCH3  0   0.248  -2.7842   0.7270  -0.3387
 OVA  H113  H  HCH3  0   0.235  -2.9849  -0.9268   0.2468
 OVA  H22   H  HCH1  0   0.242  -1.2311  -1.0283  -1.4966
 OVA  H231  H  HCH2  0   0.249  -1.9789   0.8884  -2.8615
 OVA  H232  H  HCH2  0   0.248  -0.3589   1.5353  -2.9656
 OVA  H24   H  H     0   0.226  -1.4777  -0.9794  -4.3206
 OVA  HA1   H  HCH3  0   0.238   0.8488   2.1809  -1.3664
 OVA  HA2   H  HCH3  0   0.244  -0.5456   2.5723  -0.3620
 OVA  HA3   H  HCH3  0   0.247   1.0087   2.2057   0.3716
 OVA  HB1   H  HCH3  0   0.231   1.3727  -1.8488  -5.9663
 OVA  HB2   H  HCH3  0   0.236  -0.3859  -1.8521  -6.1405
 OVA  HB3   H  HCH3  0   0.232   0.5998  -0.6602  -6.9931
 OVA  HC1   H  HCH3  0   0.238   1.5057   1.2731  -3.8365
 OVA  HC2   H  HCH3  0   0.235   2.4877   0.0331  -4.6038
 OVA  HC3   H  HCH3  0   0.232   1.7210   1.2601  -5.5889
 OVA  H11   H  HCH3  0   0.236   3.9762   0.0877   1.4341
 OVA  H12A  H  HCH3  0   0.207   3.0051   1.5302   1.7691
 OVA  H13   H  HCH3  0   0.214   3.2155   0.2899   3.0180
 OVA  HO1   H  HOH1  0   0.455  -0.9441  -1.9964   1.3857

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
 OVA  C5   C4    single  1.504  0.020  1.504
 OVA  C5   C6    single  1.531  0.020  1.531
 OVA  C5   H51   single  0.970  0.020  1.090
 OVA  C5   H52   single  0.970  0.020  1.090
 OVA  C4   C3    single  1.521  0.020  1.521
 OVA  C4   O41   double  1.208  0.020  1.208
 OVA  C3   C2    single  1.552  0.020  1.552
 OVA  C3   O31   single  1.390  0.020  1.390
 OVA  C3   H3    single  0.970  0.020  1.090
 OVA  C2   C1    single  1.561  0.020  1.561
 OVA  C2   C21   single  1.543  0.020  1.543
 OVA  C2   O1    single  1.407  0.020  1.407
 OVA  C1   C6    single  1.537  0.020  1.537
 OVA  C1   O11   single  1.414  0.020  1.414
 OVA  C1   C11   single  1.526  0.020  1.526
 OVA  C6   H61   single  0.970  0.020  1.090
 OVA  C6   H62   single  0.970  0.020  1.090
 OVA  O11  H12   single  0.850  0.020  0.980
 OVA  C11  H111  single  0.970  0.020  1.090
 OVA  C11  H112  single  0.970  0.020  1.090
 OVA  C11  H113  single  0.970  0.020  1.090
 OVA  C21  C22   single  1.469  0.020  1.469
 OVA  C21  C2A   single  1.511  0.020  1.511
 OVA  C21  O2A   single  1.420  0.020  1.420
 OVA  C22  C23   single  1.510  0.020  1.510
 OVA  C22  O2A   single  1.415  0.020  1.415
 OVA  C22  H22   single  0.970  0.020  1.090
 OVA  C23  C24   single  1.501  0.020  1.501
 OVA  C23  H231  single  0.970  0.020  1.090
 OVA  C23  H232  single  0.970  0.020  1.090
 OVA  C24  C25   double  1.335  0.020  1.335
 OVA  C24  H24   single  0.930  0.020  1.080
 OVA  C25  C2B   single  1.501  0.020  1.501
 OVA  C25  C2C   single  1.499  0.020  1.499
 OVA  C2A  HA1   single  0.970  0.020  1.090
 OVA  C2A  HA2   single  0.970  0.020  1.090
 OVA  C2A  HA3   single  0.970  0.020  1.090
 OVA  C2B  HB1   single  0.970  0.020  1.090
 OVA  C2B  HB2   single  0.970  0.020  1.090
 OVA  C2B  HB3   single  0.970  0.020  1.090
 OVA  C2C  HC1   single  0.970  0.020  1.090
 OVA  C2C  HC2   single  0.970  0.020  1.090
 OVA  C2C  HC3   single  0.970  0.020  1.090
 OVA  O31  C31   single  1.409  0.020  1.409
 OVA  C31  H11   single  0.970  0.020  1.090
 OVA  C31  H12A  single  0.970  0.020  1.090
 OVA  C31  H13   single  0.970  0.020  1.090
 OVA  O1   HO1   single  0.850  0.020  0.980

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
 OVA  H52   C5   H51   107.41  3.000
 OVA  H52   C5   C6    109.28  3.000
 OVA  H51   C5   C6    110.67  3.000
 OVA  H52   C5   C4    107.64  3.000
 OVA  H51   C5   C4    110.09  3.000
 OVA  C6    C5   C4    111.61  3.000
 OVA  O41   C4   C3    122.15  3.000
 OVA  O41   C4   C5    123.70  3.000
 OVA  C3    C4   C5    114.15  3.000
 OVA  H3    C3   O31   111.28  3.000
 OVA  H3    C3   C2    109.06  3.000
 OVA  O31   C3   C2    108.88  3.000
 OVA  H3    C3   C4    106.62  3.000
 OVA  O31   C3   C4    112.34  3.000
 OVA  C2    C3   C4    108.57  3.000
 OVA  O1    C2   C21   106.12  3.000
 OVA  O1    C2   C1    110.46  3.000
 OVA  C21   C2   C1    112.49  3.000
 OVA  O1    C2   C3    108.35  3.000
 OVA  C21   C2   C3    110.37  3.000
 OVA  C1    C2   C3    108.96  3.000
 OVA  C11   C1   O11   110.25  3.000
 OVA  C11   C1   C6    109.57  3.000
 OVA  O11   C1   C6    108.85  3.000
 OVA  C11   C1   C2    112.52  3.000
 OVA  O11   C1   C2    106.19  3.000
 OVA  C6    C1   C2    109.36  3.000
 OVA  H62   C6   H61   104.28  3.000
 OVA  H62   C6   C1    108.47  3.000
 OVA  H61   C6   C1    111.42  3.000
 OVA  H62   C6   C5    109.06  3.000
 OVA  H61   C6   C5    109.96  3.000
 OVA  C1    C6   C5    113.23  3.000
 OVA  H12   O11  C1    108.32  3.000
 OVA  H113  C11  H112  108.26  3.000
 OVA  H113  C11  H111  107.24  3.000
 OVA  H112  C11  H111  107.55  3.000
 OVA  H113  C11  C1    112.47  3.000
 OVA  H112  C11  C1    111.48  3.000
 OVA  H111  C11  C1    109.64  3.000
 OVA  O2A   C21  C2A   114.55  3.000
 OVA  O2A   C21  C22    58.64  3.000
 OVA  C2A   C21  C22   119.54  3.000
 OVA  O2A   C21  C2    114.43  3.000
 OVA  C2A   C21  C2    117.68  3.000
 OVA  C22   C21  C2    117.85  3.000
 OVA  H22   C22  O2A   113.76  3.000
 OVA  H22   C22  C23   112.75  3.000
 OVA  O2A   C22  C23   118.40  3.000
 OVA  H22   C22  C21   117.64  3.000
 OVA  O2A   C22  C21    58.92  3.000
 OVA  C23   C22  C21   124.35  3.000
 OVA  H232  C23  H231  106.31  3.000
 OVA  H232  C23  C24   111.50  3.000
 OVA  H231  C23  C24   109.22  3.000
 OVA  H232  C23  C22   111.50  3.000
 OVA  H231  C23  C22   107.33  3.000
 OVA  C24   C23  C22   110.77  3.000
 OVA  H24   C24  C25   117.73  3.000
 OVA  H24   C24  C23   115.39  3.000
 OVA  C25   C24  C23   126.85  3.000
 OVA  C2C   C25  C2B   114.54  3.000
 OVA  C2C   C25  C24   124.51  3.000
 OVA  C2B   C25  C24   120.95  3.000
 OVA  HA3   C2A  HA2   107.71  3.000
 OVA  HA3   C2A  HA1   106.59  3.000
 OVA  HA2   C2A  HA1   108.20  3.000
 OVA  HA3   C2A  C21   112.53  3.000
 OVA  HA2   C2A  C21   111.58  3.000
 OVA  HA1   C2A  C21   110.00  3.000
 OVA  C22   O2A  C21    62.44  3.000
 OVA  HB3   C2B  HB2   108.00  3.000
 OVA  HB3   C2B  HB1   106.40  3.000
 OVA  HB2   C2B  HB1   108.13  3.000
 OVA  HB3   C2B  C25   110.98  3.000
 OVA  HB2   C2B  C25   112.13  3.000
 OVA  HB1   C2B  C25   110.97  3.000
 OVA  HC3   C2C  HC2   106.41  3.000
 OVA  HC3   C2C  HC1   108.16  3.000
 OVA  HC2   C2C  HC1   107.50  3.000
 OVA  HC3   C2C  C25   110.69  3.000
 OVA  HC2   C2C  C25   110.23  3.000
 OVA  HC1   C2C  C25   113.55  3.000
 OVA  C31   O31  C3    114.02  3.000
 OVA  H13   C31  H12A  108.12  3.000
 OVA  H13   C31  H11   108.25  3.000
 OVA  H12A  C31  H11   108.26  3.000
 OVA  H13   C31  O31   112.92  3.000
 OVA  H12A  C31  O31   111.63  3.000
 OVA  H11   C31  O31   107.52  3.000
 OVA  HO1   O1   C2    110.90  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
 OVA  Var_01  C1   C6   C5   C4    -49.91  30.0  1
 OVA  Var_02  C6   C5   C4   C3     51.85  30.0  1
 OVA  Var_03  O2A  C22  C21  C2   -103.05  30.0  1
 OVA  Var_04  C2A  C21  O2A  C22  -110.88  30.0  1
 OVA  Var_05  C24  C23  C22  C21   145.69  30.0  3
 OVA  Var_06  HA1  C2A  C21  C2    161.39  30.0  3
 OVA  Var_07  C25  C24  C23  C22   -98.90  30.0  3
 OVA  Var_08  H11  C31  O31  C3   -179.23  30.0  3
 OVA  Var_09  C2B  C25  C24  C23   179.40   0.0  2
 OVA  Var_10  HB1  C2B  C25  C24  -121.82  30.0  3
 OVA  Var_11  HC1  C2C  C25  C24     2.41  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
 OVA  chir_01  C3   C4   C2   O31  positiv
 OVA  chir_02  C2   C21  C1   C3   positiv
 OVA  chir_03  C1   C2   C6   C11  positiv
 OVA  chir_04  C21  C22  C2A  O2A  both
 OVA  chir_05  C22  O2A  C21  C23  both

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
 OVA  plan-1  C5   0.020
 OVA  plan-1  C4   0.020
 OVA  plan-1  C3   0.020
 OVA  plan-1  O41  0.020
 OVA  plan-2  C23  0.020
 OVA  plan-2  C24  0.020
 OVA  plan-2  C25  0.020
 OVA  plan-2  C2B  0.020
 OVA  plan-2  C2C  0.020
 OVA  plan-2  H24  0.020

