# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 17:07:38 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (1s,4s)-1,3,3-trimethyl-2-oxabicyclo[2.2.2]octane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC12CCC(CC1)C(C)(C)O2
#
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
 CNL  CNL  (1s,4s)-1,3,3-trimethyl-2-oxabicyclo[2.2.2]octane  ligand  29  11  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CNL
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
 CNL  C1    C  CT    0   0.191   1.2076  -0.3409  -0.0146
 CNL  C2    C  CH2   0  -0.430   1.2293   0.5686  -1.2462
 CNL  C3    C  CH2   0  -0.445   0.0032   1.5033  -1.2130
 CNL  C4    C  CH1   0  -0.295  -0.8403   1.1528   0.0138
 CNL  C5    C  CH2   0  -0.445   0.0084   1.4635   1.2475
 CNL  C6    C  CH2   0  -0.431   1.2284   0.5206   1.2512
 CNL  C7    C  CH3   0  -0.664   2.3545  -1.3339  -0.0327
 CNL  C8    C  CT    0   0.262  -1.2053  -0.3430  -0.0098
 CNL  C9    C  CH3   0  -0.663  -1.9987  -0.7536   1.2295
 CNL  C10   C  CH3   0  -0.663  -2.0148  -0.7110  -1.2519
 CNL  O     O  O2    0  -0.534   0.0069  -1.1097  -0.0313
 CNL  H21   H  HCH2  0   0.226   2.1614   1.1388  -1.2586
 CNL  H22   H  HCH2  0   0.228   1.2293  -0.0495  -2.1481
 CNL  H31   H  HCH2  0   0.237  -0.5790   1.4266  -2.1320
 CNL  H32   H  HCH2  0   0.234   0.3119   2.5483  -1.1409
 CNL  H4    H  HCH1  0   0.230  -1.7584   1.7464   0.0250
 CNL  H51   H  HCH2  0   0.237  -0.5714   1.3668   2.1661
 CNL  H52   H  HCH2  0   0.234   0.3243   2.5078   1.2023
 CNL  H61   H  HCH2  0   0.228   1.2198  -0.1324   2.1283
 CNL  H62   H  HCH2  0   0.227   2.1640   1.0836   1.2902
 CNL  H71   H  HCH3  0   0.228   2.3233  -1.9863   0.8416
 CNL  H72   H  HCH3  0   0.228   2.3236  -1.9557  -0.9290
 CNL  H73   H  HCH3  0   0.223   3.3098  -0.8080  -0.0238
 CNL  H91   H  HCH3  0   0.218  -2.9269  -0.1842   1.3024
 CNL  H92   H  HCH3  0   0.228  -2.2639  -1.8114   1.1788
 CNL  H93   H  HCH3  0   0.233  -1.4363  -0.5983   2.1501
 CNL  H101  H  HCH3  0   0.233  -1.4661  -0.5192  -2.1739
 CNL  H102  H  HCH3  0   0.228  -2.2760  -1.7708  -1.2361
 CNL  H103  H  HCH3  0   0.218  -2.9453  -0.1420  -1.2895

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
 CNL  C1   C2    single  1.531  0.020  1.531
 CNL  C1   C6    single  1.531  0.020  1.531
 CNL  C1   C7    single  1.517  0.020  1.517
 CNL  C1   O     single  1.426  0.020  1.426
 CNL  C2   C3    single  1.542  0.020  1.542
 CNL  C2   H21   single  0.970  0.020  1.090
 CNL  C2   H22   single  0.970  0.020  1.090
 CNL  C3   C4    single  1.530  0.020  1.530
 CNL  C3   H31   single  0.970  0.020  1.090
 CNL  C3   H32   single  0.970  0.020  1.090
 CNL  C4   C5    single  1.529  0.020  1.529
 CNL  C4   C8    single  1.540  0.020  1.540
 CNL  C4   H4    single  0.970  0.020  1.090
 CNL  C5   C6    single  1.542  0.020  1.542
 CNL  C5   H51   single  0.970  0.020  1.090
 CNL  C5   H52   single  0.970  0.020  1.090
 CNL  C6   H61   single  0.970  0.020  1.090
 CNL  C6   H62   single  0.970  0.020  1.090
 CNL  C7   H71   single  0.970  0.020  1.090
 CNL  C7   H72   single  0.970  0.020  1.090
 CNL  C7   H73   single  0.970  0.020  1.090
 CNL  C8   C9    single  1.528  0.020  1.528
 CNL  C8   C10   single  1.528  0.020  1.528
 CNL  C8   O     single  1.434  0.020  1.434
 CNL  C9   H91   single  0.970  0.020  1.090
 CNL  C9   H92   single  0.970  0.020  1.090
 CNL  C9   H93   single  0.970  0.020  1.090
 CNL  C10  H101  single  0.970  0.020  1.090
 CNL  C10  H102  single  0.970  0.020  1.090
 CNL  C10  H103  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
 CNL  O     C1   C7    106.47  3.000
 CNL  O     C1   C6    108.93  3.000
 CNL  C7    C1   C6    111.58  3.000
 CNL  O     C1   C2    108.83  3.000
 CNL  C7    C1   C2    111.62  3.000
 CNL  C6    C1   C2    109.30  3.000
 CNL  H22   C2   H21   106.60  3.000
 CNL  H22   C2   C3    111.12  3.000
 CNL  H21   C2   C3    111.24  3.000
 CNL  H22   C2   C1    109.13  3.000
 CNL  H21   C2   C1    109.34  3.000
 CNL  C3    C2   C1    109.36  3.000
 CNL  H32   C3   H31   105.89  3.000
 CNL  H32   C3   C4    108.80  3.000
 CNL  H31   C3   C4    111.43  3.000
 CNL  H32   C3   C2    110.89  3.000
 CNL  H31   C3   C2    111.33  3.000
 CNL  C4    C3   C2    108.47  3.000
 CNL  H4    C4   C8    109.18  3.000
 CNL  H4    C4   C5    110.33  3.000
 CNL  C8    C4   C5    109.96  3.000
 CNL  H4    C4   C3    110.29  3.000
 CNL  C8    C4   C3    109.94  3.000
 CNL  C5    C4   C3    107.12  3.000
 CNL  H52   C5   H51   105.87  3.000
 CNL  H52   C5   C6    110.86  3.000
 CNL  H51   C5   C6    111.37  3.000
 CNL  H52   C5   C4    108.75  3.000
 CNL  H51   C5   C4    111.49  3.000
 CNL  C6    C5   C4    108.47  3.000
 CNL  H62   C6   H61   106.61  3.000
 CNL  H62   C6   C5    111.25  3.000
 CNL  H61   C6   C5    111.16  3.000
 CNL  H62   C6   C1    109.33  3.000
 CNL  H61   C6   C1    109.08  3.000
 CNL  C5    C6   C1    109.35  3.000
 CNL  H73   C7   H72   107.83  3.000
 CNL  H73   C7   H71   107.87  3.000
 CNL  H72   C7   H71   108.46  3.000
 CNL  H73   C7   C1    110.27  3.000
 CNL  H72   C7   C1    111.18  3.000
 CNL  H71   C7   C1    111.10  3.000
 CNL  O     C8   C10   107.87  3.000
 CNL  O     C8   C9    107.90  3.000
 CNL  C10   C8   C9    108.65  3.000
 CNL  O     C8   C4    108.61  3.000
 CNL  C10   C8   C4    111.85  3.000
 CNL  C9    C8   C4    111.82  3.000
 CNL  H93   C9   H92   107.62  3.000
 CNL  H93   C9   H91   107.95  3.000
 CNL  H92   C9   H91   107.58  3.000
 CNL  H93   C9   C8    112.27  3.000
 CNL  H92   C9   C8    110.42  3.000
 CNL  H91   C9   C8    110.83  3.000
 CNL  H103  C10  H102  107.62  3.000
 CNL  H103  C10  H101  107.96  3.000
 CNL  H102  C10  H101  107.67  3.000
 CNL  H103  C10  C8    110.75  3.000
 CNL  H102  C10  C8    110.42  3.000
 CNL  H101  C10  C8    112.25  3.000
 CNL  C8    O    C1    115.04  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
 CNL  Var_01  C4    C3   C2  C1  -2.35  30.0  1
 CNL  Var_02  C4    C5   C6  C1   3.10  30.0  1
 CNL  Var_03  C4    C8   O   C1   0.50  30.0  3
 CNL  Var_04  H91   C9   C8  C4  59.65  30.0  3
 CNL  Var_05  H101  C10  C8  C4  60.87  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
 CNL  chir_01  C1  C6  C2  O   positiv
 CNL  chir_02  C4  C3  C5  C8  positiv

