# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:34:26 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: (4S,4aR,6S)-4,4a-dimethyl-6-(1-methylethenyl)-1,2,3,4,4a,5,6,7-octahydronaphthalene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCCC2=CC[C@@H](C[C@]12C)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
 ION  ION  (4S,4aR,6S)-4,4a-dimethyl-6-(1-methylethenyl)-1,2,3,4,4a,5,6,7-octahydronaphthalene  ligand  39  15  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ION
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
 ION  C1    C  CH2   0  -0.414   0.7148  -0.1361  -0.7348
 ION  C2    C  CR6   0  -0.129   0.3376   0.3157   0.6860
 ION  C3    C  CR16  0  -0.204   1.1216  -0.5567   1.7087
 ION  C4    C  CH3   0  -0.673   2.6371  -0.4136   1.6016
 ION  C5    C  C     0  -0.423   0.6698  -0.3231   3.1491
 ION  C6    C  C     0  -0.427  -0.8228  -0.5614   3.3226
 ION  C7    C  C     0  -0.498  -1.6223   0.2953   2.3452
 ION  C8    C  CR6   0   0.218  -1.1483   0.1037   0.9312
 ION  C9    C  CH3   0  -0.668   0.6723   1.8064   0.8511
 ION  C10   C  C1    0  -0.342  -1.9973  -0.2445  -0.0367
 ION  C11   C  CH2   0  -0.443  -1.6362  -0.3991  -1.4816
 ION  C12   C  CH1   0  -0.339  -0.3069   0.2878  -1.7894
 ION  C13   C  C     0   0.209   0.1735   0.0239  -3.1948
 ION  C14   C  CH3   0  -0.734   0.5747  -1.3783  -3.5499
 ION  C15   C  C2    0  -0.607   0.2432   1.0099  -4.0880
 ION  H11   H  HCH2  0   0.225   0.8066  -1.2287  -0.7500
 ION  H12   H  HCH2  0   0.233   1.7006   0.2594  -0.9940
 ION  H3    H  HCR6  0   0.213   0.8728  -1.5981   1.4618
 ION  H41   H  HCH3  0   0.229   3.1261  -1.1314   2.2628
 ION  H42   H  HCH3  0   0.233   3.0044  -0.6021   0.5924
 ION  H43   H  HCH3  0   0.217   2.9743   0.5808   1.8998
 ION  H51   H  H     0   0.227   1.2324  -0.9885   3.8099
 ION  H52   H  H     0   0.210   0.9215   0.6963   3.4627
 ION  H61   H  H     0   0.212  -1.0460  -1.6181   3.1434
 ION  H62   H  H     0   0.227  -1.1293  -0.3453   4.3490
 ION  H71   H  H     0   0.235  -2.6885   0.0681   2.4181
 ION  H72   H  H     0   0.227  -1.5145   1.3480   2.6324
 ION  H91   H  HCH3  0   0.233   0.0970   2.4122   0.1497
 ION  H92   H  HCH3  0   0.231   0.4543   2.1805   1.8518
 ION  H93   H  HCH3  0   0.230   1.7286   1.9938   0.6529
 ION  H10   H  H     0   0.220  -3.0403  -0.4109   0.2200
 ION  H111  H  HCH2  0   0.227  -1.5889  -1.4635  -1.7404
 ION  H112  H  HCH2  0   0.237  -2.4304   0.0223  -2.1049
 ION  H121  H  HCH1  0   0.234  -0.4712   1.3668  -1.6980
 ION  H141  H  HCH3  0   0.242   0.8791  -1.4518  -4.5931
 ION  H142  H  HCH3  0   0.242   1.4085  -1.7229  -2.9342
 ION  H143  H  HCH3  0   0.236  -0.2415  -2.0864  -3.3916
 ION  H151  H  H     0   0.226   0.5840   0.8395  -5.1026
 ION  H152  H  H     0   0.227  -0.0369   2.0255  -3.8337

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
 ION  C1   C2    single  1.538  0.020  1.538
 ION  C1   C12   single  1.528  0.020  1.528
 ION  C1   H11   single  0.970  0.020  1.090
 ION  C1   H12   single  0.970  0.020  1.090
 ION  C2   C3    single  1.556  0.020  1.556
 ION  C2   C8    single  1.521  0.020  1.521
 ION  C2   C9    single  1.537  0.020  1.537
 ION  C3   C4    single  1.526  0.020  1.526
 ION  C3   C5    single  1.527  0.020  1.527
 ION  C3   H3    single  0.970  0.020  1.090
 ION  C4   H41   single  0.970  0.020  1.090
 ION  C4   H42   single  0.970  0.020  1.090
 ION  C4   H43   single  0.970  0.020  1.090
 ION  C5   C6    single  1.521  0.020  1.521
 ION  C5   H51   single  0.970  0.020  1.090
 ION  C5   H52   single  0.970  0.020  1.090
 ION  C6   C7    single  1.526  0.020  1.526
 ION  C6   H61   single  0.970  0.020  1.090
 ION  C6   H62   single  0.970  0.020  1.090
 ION  C7   C8    single  1.504  0.020  1.504
 ION  C7   H71   single  0.970  0.020  1.090
 ION  C7   H72   single  0.970  0.020  1.090
 ION  C8   C10   double  1.334  0.020  1.334
 ION  C9   H91   single  0.970  0.020  1.090
 ION  C9   H92   single  0.970  0.020  1.090
 ION  C9   H93   single  0.970  0.020  1.090
 ION  C10  C11   single  1.497  0.020  1.497
 ION  C10  H10   single  0.930  0.020  1.080
 ION  C11  C12   single  1.528  0.020  1.528
 ION  C11  H111  single  0.970  0.020  1.090
 ION  C11  H112  single  0.970  0.020  1.090
 ION  C12  C13   single  1.508  0.020  1.508
 ION  C12  H121  single  0.970  0.020  1.090
 ION  C13  C14   single  1.501  0.020  1.501
 ION  C13  C15   double  1.332  0.020  1.332
 ION  C14  H141  single  0.970  0.020  1.090
 ION  C14  H142  single  0.970  0.020  1.090
 ION  C14  H143  single  0.970  0.020  1.090
 ION  C15  H151  single  0.930  0.020  1.080
 ION  C15  H152  single  0.930  0.020  1.080

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
 ION  H12   C1   H11   106.36  3.000
 ION  H12   C1   C12   109.81  3.000
 ION  H11   C1   C12   108.83  3.000
 ION  H12   C1   C2    109.51  3.000
 ION  H11   C1   C2    109.03  3.000
 ION  C12   C1   C2    113.08  3.000
 ION  C9    C2   C8    109.31  3.000
 ION  C9    C2   C3    111.31  3.000
 ION  C8    C2   C3    107.94  3.000
 ION  C9    C2   C1    109.32  3.000
 ION  C8    C2   C1    110.34  3.000
 ION  C3    C2   C1    108.59  3.000
 ION  H3    C3   C5    106.85  3.000
 ION  H3    C3   C4    107.33  3.000
 ION  C5    C3   C4    110.22  3.000
 ION  H3    C3   C2    105.64  3.000
 ION  C5    C3   C2    112.64  3.000
 ION  C4    C3   C2    113.68  3.000
 ION  H43   C4   H42   107.84  3.000
 ION  H43   C4   H41   107.16  3.000
 ION  H42   C4   H41   107.22  3.000
 ION  H43   C4   C3    111.90  3.000
 ION  H42   C4   C3    112.54  3.000
 ION  H41   C4   C3    109.92  3.000
 ION  H52   C5   H51   105.96  3.000
 ION  H52   C5   C6    109.78  3.000
 ION  H51   C5   C6    109.90  3.000
 ION  H52   C5   C3    110.14  3.000
 ION  H51   C5   C3    108.94  3.000
 ION  C6    C5   C3    111.95  3.000
 ION  H62   C6   H61   106.71  3.000
 ION  H62   C6   C7    110.10  3.000
 ION  H61   C6   C7    109.28  3.000
 ION  H62   C6   C5    110.57  3.000
 ION  H61   C6   C5    109.42  3.000
 ION  C7    C6   C5    110.67  3.000
 ION  H72   C7   H71   106.15  3.000
 ION  H72   C7   C8    109.74  3.000
 ION  H71   C7   C8    110.12  3.000
 ION  H72   C7   C6    108.64  3.000
 ION  H71   C7   C6    110.60  3.000
 ION  C8    C7   C6    111.45  3.000
 ION  C10   C8   C7    121.00  3.000
 ION  C10   C8   C2    122.77  3.000
 ION  C7    C8   C2    116.22  3.000
 ION  H93   C9   H92   107.54  3.000
 ION  H93   C9   H91   107.37  3.000
 ION  H92   C9   H91   107.11  3.000
 ION  H93   C9   C2    110.98  3.000
 ION  H92   C9   C2    112.82  3.000
 ION  H91   C9   C2    110.78  3.000
 ION  H10   C10  C11   116.32  3.000
 ION  H10   C10  C8    118.65  3.000
 ION  C11   C10  C8    125.01  3.000
 ION  H112  C11  H111  105.71  3.000
 ION  H112  C11  C12   110.10  3.000
 ION  H111  C11  C12   110.57  3.000
 ION  H112  C11  C10   109.58  3.000
 ION  H111  C11  C10   109.78  3.000
 ION  C12   C11  C10   110.97  3.000
 ION  H121  C12  C13   107.33  3.000
 ION  H121  C12  C11   107.19  3.000
 ION  C13   C12  C11   112.72  3.000
 ION  H121  C12  C1    108.42  3.000
 ION  C13   C12  C1    112.42  3.000
 ION  C11   C12  C1    108.54  3.000
 ION  C15   C13  C14   121.25  3.000
 ION  C15   C13  C12   120.79  3.000
 ION  C14   C13  C12   117.97  3.000
 ION  H143  C14  H142  106.52  3.000
 ION  H143  C14  H141  107.69  3.000
 ION  H142  C14  H141  107.77  3.000
 ION  H143  C14  C13   111.82  3.000
 ION  H142  C14  C13   111.43  3.000
 ION  H141  C14  C13   111.37  3.000
 ION  H152  C15  H151  116.64  3.000
 ION  H152  C15  C13   121.51  3.000
 ION  H151  C15  C13   121.85  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
 ION  Var_01  C11   C10  C8   C2     -3.52   0.0  0
 ION  Var_02  C6    C7   C8   C2    -53.90  30.0  1
 ION  Var_03  C7    C6   C5   C3    -55.22  30.0  1
 ION  Var_04  C8    C7   C6   C5     52.87  30.0  1
 ION  Var_05  C12   C11  C10  C8    -17.24  30.0  1
 ION  Var_06  H151  C15  C13  C12  -179.89   0.0  2
 ION  Var_07  H141  C14  C13  C12   178.59  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
 ION  chir_01  C2   C3  C8   C1   positiv
 ION  chir_02  C3   C5  C4   C2   positiv
 ION  chir_03  C12  C1  C11  C13  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
 ION  plan-1  C2    0.020
 ION  plan-1  C7    0.020
 ION  plan-1  C8    0.020
 ION  plan-1  C10   0.020
 ION  plan-1  C11   0.020
 ION  plan-1  H10   0.020
 ION  plan-2  C12   0.020
 ION  plan-2  C13   0.020
 ION  plan-2  C14   0.020
 ION  plan-2  C15   0.020
 ION  plan-2  H151  0.020
 ION  plan-2  H152  0.020

