# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 16:25:16 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: (1~{R},4~{R},4~{a}~{S},8~{a}~{R})-4,7-dimethyl-1-prop-1-en-2-yl-1,2,3,4,4~{a},5,6,8~{a}-octahydronaphthalene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC[C@H]([C@H]2C=C(C)CC[C@@H]12)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
 SJA  SJA  (1~{R},4~{R},4~{a}~{S},8~{a}~{R})-4,7-dimethyl-1-prop-1-en-2-yl-1,2,3,4,4~{a},5,6,8~{a}-octahydronaphthalene  ligand  39  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SJA
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
 SJA  C10  C  C     0   0.097  36.6951  -36.3973  20.8627
 SJA  C13  C  C     0   0.190  33.6790  -33.1047  20.4758
 SJA  C15  C  CH3   0  -0.735  32.3289  -32.5812  20.8808
 SJA  C01  C  CH3   0  -0.660  33.7901  -38.5021  18.1822
 SJA  C02  C  CH1   0  -0.213  33.9835  -37.3386  19.1491
 SJA  C03  C  CH2   0  -0.405  32.6381  -36.6995  19.4836
 SJA  C04  C  CH2   0  -0.433  32.7651  -35.4911  20.4018
 SJA  C05  C  CH1   0  -0.286  33.6813  -34.4426  19.7653
 SJA  C06  C  CH1   0  -0.254  35.0643  -35.0530  19.5026
 SJA  C07  C  CH1   0  -0.226  34.9619  -36.2912  18.5978
 SJA  C08  C  CH2   0  -0.438  36.3769  -36.8323  18.3922
 SJA  C09  C  CH2   0  -0.492  36.9988  -37.3036  19.7034
 SJA  C11  C  C1    0  -0.266  35.8183  -35.3967  20.7630
 SJA  C12  C  CH3   0  -0.713  37.4100  -36.7075  22.1426
 SJA  C14  C  C2    0  -0.607  34.7689  -32.3649  20.6804
 SJA  H2   H  HCH3  0   0.242  32.3815  -31.5353  21.1807
 SJA  H3   H  HCH3  0   0.233  31.6106  -32.6660  20.0619
 SJA  H4   H  HCH3  0   0.239  31.9140  -33.1457  21.7182
 SJA  H5   H  HCH3  0   0.223  33.0495  -39.2061  18.5664
 SJA  H6   H  HCH3  0   0.210  33.4362  -38.1472  17.2110
 SJA  H7   H  HCH3  0   0.227  34.7117  -39.0604  18.0156
 SJA  H8   H  HCH1  0   0.215  34.3859  -37.7426  20.0853
 SJA  H9   H  HCH2  0   0.202  32.1450  -36.3870  18.5546
 SJA  H10  H  HCH2  0   0.222  31.9844  -37.4487  19.9394
 SJA  H11  H  HCH2  0   0.237  31.7711  -35.0793  20.5848
 SJA  H12  H  HCH2  0   0.217  33.1595  -35.7944  21.3776
 SJA  H13  H  HCH1  0   0.234  33.2464  -34.2312  18.7756
 SJA  H14  H  HCH1  0   0.236  35.6443  -34.3068  18.9431
 SJA  H15  H  HCH1  0   0.212  34.5738  -35.9617  17.6247
 SJA  H16  H  HCH2  0   0.231  36.3927  -37.6424  17.6603
 SJA  H17  H  HCH2  0   0.224  36.9903  -36.0315  17.9686
 SJA  H18  H  HCH2  0   0.229  36.6526  -38.3143  19.9524
 SJA  H19  H  HCH2  0   0.237  38.0839  -37.3978  19.5887
 SJA  H20  H  H     0   0.225  35.6316  -34.7835  21.6394
 SJA  H22  H  HCH3  0   0.234  37.1296  -36.0234  22.9434
 SJA  H23  H  HCH3  0   0.228  37.1922  -37.7255  22.4777
 SJA  H24  H  HCH3  0   0.229  38.4940  -36.6505  22.0130
 SJA  H25  H  H     0   0.227  34.6972  -31.3847  21.1363
 SJA  H26  H  H     0   0.231  35.7641  -32.6883  20.4066

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
 SJA  C01  C02  single  1.525  0.020  1.525
 SJA  C08  C07  single  1.529  0.020  1.529
 SJA  C08  C09  single  1.526  0.020  1.526
 SJA  C07  C02  single  1.536  0.020  1.536
 SJA  C07  C06  single  1.537  0.020  1.537
 SJA  C02  C03  single  1.527  0.020  1.527
 SJA  C06  C05  single  1.534  0.020  1.534
 SJA  C06  C11  single  1.508  0.020  1.508
 SJA  C03  C04  single  1.523  0.020  1.523
 SJA  C05  C13  single  1.515  0.020  1.515
 SJA  C05  C04  single  1.531  0.020  1.531
 SJA  C09  C10  single  1.503  0.020  1.503
 SJA  C13  C15  single  1.504  0.020  1.504
 SJA  C13  C14  double  1.333  0.020  1.333
 SJA  C10  C11  double  1.334  0.020  1.334
 SJA  C10  C12  single  1.498  0.020  1.498
 SJA  C15  H2   single  0.970  0.020  1.090
 SJA  C15  H3   single  0.970  0.020  1.090
 SJA  C15  H4   single  0.970  0.020  1.090
 SJA  C01  H5   single  0.970  0.020  1.090
 SJA  C01  H6   single  0.970  0.020  1.090
 SJA  C01  H7   single  0.970  0.020  1.090
 SJA  C02  H8   single  0.970  0.020  1.090
 SJA  C03  H9   single  0.970  0.020  1.090
 SJA  C03  H10  single  0.970  0.020  1.090
 SJA  C04  H11  single  0.970  0.020  1.090
 SJA  C04  H12  single  0.970  0.020  1.090
 SJA  C05  H13  single  0.970  0.020  1.090
 SJA  C06  H14  single  0.970  0.020  1.090
 SJA  C07  H15  single  0.970  0.020  1.090
 SJA  C08  H16  single  0.970  0.020  1.090
 SJA  C08  H17  single  0.970  0.020  1.090
 SJA  C09  H18  single  0.970  0.020  1.090
 SJA  C09  H19  single  0.970  0.020  1.090
 SJA  C11  H20  single  0.930  0.020  1.080
 SJA  C12  H22  single  0.970  0.020  1.090
 SJA  C12  H23  single  0.970  0.020  1.090
 SJA  C12  H24  single  0.970  0.020  1.090
 SJA  C14  H25  single  0.930  0.020  1.080
 SJA  C14  H26  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
 SJA  C12  C10  C11  122.18  3.000
 SJA  C12  C10  C09  115.96  3.000
 SJA  C11  C10  C09  121.84  3.000
 SJA  C14  C13  C05  124.12  3.000
 SJA  C14  C13  C15  119.97  3.000
 SJA  C05  C13  C15  115.79  3.000
 SJA  H4   C15  H3   106.56  3.000
 SJA  H4   C15  H2   107.67  3.000
 SJA  H3   C15  H2   108.22  3.000
 SJA  H4   C15  C13  111.58  3.000
 SJA  H3   C15  C13  111.19  3.000
 SJA  H2   C15  C13  111.41  3.000
 SJA  H7   C01  H6   107.71  3.000
 SJA  H7   C01  H5   107.28  3.000
 SJA  H6   C01  H5   107.61  3.000
 SJA  H7   C01  C02  112.35  3.000
 SJA  H6   C01  C02  110.90  3.000
 SJA  H5   C01  C02  110.78  3.000
 SJA  H8   C02  C07  108.92  3.000
 SJA  H8   C02  C03  106.90  3.000
 SJA  C07  C02  C03  110.77  3.000
 SJA  H8   C02  C01  107.87  3.000
 SJA  C03  C02  C01  110.27  3.000
 SJA  C07  C02  C01  111.93  3.000
 SJA  H10  C03  H9   106.22  3.000
 SJA  H10  C03  C04  110.00  3.000
 SJA  H9   C03  C04  108.78  3.000
 SJA  H10  C03  C02  109.35  3.000
 SJA  H9   C03  C02  109.26  3.000
 SJA  C04  C03  C02  113.00  3.000
 SJA  H12  C04  H11  106.44  3.000
 SJA  H12  C04  C05  110.15  3.000
 SJA  H11  C04  C05  110.88  3.000
 SJA  H12  C04  C03  110.33  3.000
 SJA  H11  C04  C03  108.93  3.000
 SJA  C05  C04  C03  110.04  3.000
 SJA  H13  C05  C06  106.16  3.000
 SJA  H13  C05  C04  105.59  3.000
 SJA  C06  C05  C04  109.77  3.000
 SJA  H13  C05  C13  104.55  3.000
 SJA  C04  C05  C13  114.14  3.000
 SJA  C06  C05  C13  115.66  3.000
 SJA  H14  C06  C11  108.46  3.000
 SJA  H14  C06  C07  106.42  3.000
 SJA  C11  C06  C07  109.98  3.000
 SJA  H14  C06  C05  107.03  3.000
 SJA  C11  C06  C05  113.46  3.000
 SJA  C07  C06  C05  111.17  3.000
 SJA  H15  C07  C08  108.30  3.000
 SJA  H15  C07  C06  107.67  3.000
 SJA  C08  C07  C06  107.62  3.000
 SJA  H15  C07  C02  107.32  3.000
 SJA  C06  C07  C02  112.37  3.000
 SJA  C08  C07  C02  113.36  3.000
 SJA  H17  C08  H16  105.99  3.000
 SJA  H17  C08  C09  109.28  3.000
 SJA  H16  C08  C09  109.94  3.000
 SJA  H17  C08  C07  108.17  3.000
 SJA  H16  C08  C07  111.48  3.000
 SJA  C09  C08  C07  111.78  3.000
 SJA  H19  C09  H18  104.90  3.000
 SJA  H19  C09  C08  109.90  3.000
 SJA  H18  C09  C08  110.55  3.000
 SJA  H19  C09  C10  109.45  3.000
 SJA  H18  C09  C10  108.47  3.000
 SJA  C08  C09  C10  113.23  3.000
 SJA  H20  C11  C06  117.37  3.000
 SJA  H20  C11  C10  118.44  3.000
 SJA  C06  C11  C10  124.18  3.000
 SJA  H24  C12  H23  106.40  3.000
 SJA  H24  C12  H22  108.03  3.000
 SJA  H23  C12  H22  107.93  3.000
 SJA  H24  C12  C10  111.16  3.000
 SJA  H23  C12  C10  111.06  3.000
 SJA  H22  C12  C10  112.02  3.000
 SJA  H26  C14  H25  115.98  3.000
 SJA  H26  C14  C13  123.19  3.000
 SJA  H25  C14  C13  120.84  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
 SJA  Var_01  C07  C08  C09  C10   -40.32  30.0  1
 SJA  Var_02  C05  C04  C03  C02    57.42  30.0  1
 SJA  Var_03  C09  C10  C11  C06    -0.96  30.0  1
 SJA  Var_04  C11  C10  C09  C08     8.65  30.0  1
 SJA  Var_05  H22  C12  C10  C09  -178.98  30.0  3
 SJA  Var_06  H25  C14  C13  C05   175.87   0.0  2
 SJA  Var_07  H2   C15  C13  C05  -167.45  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
 SJA  chir_01  C02  C01  C07  C03  negativ
 SJA  chir_02  C05  C06  C13  C04  positiv
 SJA  chir_03  C06  C07  C05  C11  negativ
 SJA  chir_04  C07  C06  C02  C08  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
 SJA  plan-1  C13  0.020
 SJA  plan-1  C15  0.020
 SJA  plan-1  C05  0.020
 SJA  plan-1  C14  0.020
 SJA  plan-1  H25  0.020
 SJA  plan-1  H26  0.020

