# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 11:55:03 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (2-methylprop-2-en-1-yl)benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C)Cc1ccccc1
#
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
 YGS  YGS  "(2-methylprop-2-en-1-yl)benzene"
  ligand  22  10  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YGS
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
 YGS  C10  C  CR16  0  -0.285  40.2201  -19.4713  11.5380
 YGS  C01  C  C2    0  -0.592  37.3792  -19.1573  13.9903
 YGS  C02  C  C     0   0.169  38.6507  -19.4698  14.2312
 YGS  C03  C  CH3   0  -0.708  39.5105  -18.6792  15.1690
 YGS  C04  C  CH2   0  -0.573  39.3114  -20.6502  13.5668
 YGS  C05  C  CR6   0   0.127  40.4586  -20.2424  12.6747
 YGS  C06  C  CR16  0  -0.319  41.7681  -20.6138  12.9629
 YGS  C07  C  CR16  0  -0.238  42.8166  -20.2283  12.1353
 YGS  C08  C  CR16  0  -0.270  42.5674  -19.4614  11.0063
 YGS  C09  C  CR16  0  -0.239  41.2628  -19.0835  10.7096
 YGS  H1   H  HCR6  0   0.245  39.2057  -19.1712  11.3007
 YGS  H2   H  H     0   0.229  36.9030  -18.3102  14.4688
 YGS  H3   H  H     0   0.230  36.7703  -19.7394  13.3093
 YGS  H4   H  HCH3  0   0.241  38.9579  -17.8667  15.6387
 YGS  H5   H  HCH3  0   0.235  39.9151  -19.3201  15.9563
 YGS  H6   H  HCH3  0   0.239  40.3687  -18.2491  14.6479
 YGS  H7   H  HCH2  0   0.258  38.5710  -21.2022  12.9828
 YGS  H8   H  HCH2  0   0.254  39.6829  -21.3333  14.3371
 YGS  H9   H  HCR6  0   0.246  41.9712  -21.2132  13.8428
 YGS  H10  H  HCR6  0   0.251  43.8290  -20.5280  12.3749
 YGS  H11  H  HCR6  0   0.251  43.3821  -19.1595  10.3607
 YGS  H12  H  HCR6  0   0.251  41.0582  -18.4854   9.8305

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
 YGS  C09  C08  aromatic  1.390  0.020  1.390
 YGS  C09  C10  aromatic  1.387  0.020  1.387
 YGS  C08  C07  aromatic  1.387  0.020  1.387
 YGS  C10  C05  aromatic  1.394  0.020  1.394
 YGS  C07  C06  aromatic  1.390  0.020  1.390
 YGS  C05  C06  aromatic  1.391  0.020  1.391
 YGS  C05  C04  single    1.509  0.020  1.509
 YGS  C04  C02  single    1.507  0.020  1.507
 YGS  C01  C02  double    1.331  0.020  1.331
 YGS  C02  C03  single    1.498  0.020  1.498
 YGS  C10  H1   single    0.930  0.020  1.080
 YGS  C01  H2   single    0.930  0.020  1.080
 YGS  C01  H3   single    0.930  0.020  1.080
 YGS  C03  H4   single    0.970  0.020  1.090
 YGS  C03  H5   single    0.970  0.020  1.090
 YGS  C03  H6   single    0.970  0.020  1.090
 YGS  C04  H7   single    0.970  0.020  1.090
 YGS  C04  H8   single    0.970  0.020  1.090
 YGS  C06  H9   single    0.930  0.020  1.080
 YGS  C07  H10  single    0.930  0.020  1.080
 YGS  C08  H11  single    0.930  0.020  1.080
 YGS  C09  H12  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
 YGS  H1   C10  C09  119.69  3.000
 YGS  H1   C10  C05  119.45  3.000
 YGS  C09  C10  C05  120.86  3.000
 YGS  H3   C01  H2   116.80  3.000
 YGS  H3   C01  C02  121.63  3.000
 YGS  H2   C01  C02  121.57  3.000
 YGS  C04  C02  C03  115.96  3.000
 YGS  C03  C02  C01  122.52  3.000
 YGS  C04  C02  C01  121.52  3.000
 YGS  H6   C03  H5   106.49  3.000
 YGS  H6   C03  H4   108.10  3.000
 YGS  H5   C03  H4   108.34  3.000
 YGS  H6   C03  C02  111.11  3.000
 YGS  H5   C03  C02  110.73  3.000
 YGS  H4   C03  C02  111.87  3.000
 YGS  H8   C04  H7   106.90  3.000
 YGS  H8   C04  C05  109.06  3.000
 YGS  H7   C04  C05  109.61  3.000
 YGS  H8   C04  C02  109.11  3.000
 YGS  H7   C04  C02  109.53  3.000
 YGS  C05  C04  C02  112.46  3.000
 YGS  C06  C05  C04  121.39  3.000
 YGS  C04  C05  C10  120.08  3.000
 YGS  C06  C05  C10  118.53  3.000
 YGS  H9   C06  C07  119.69  3.000
 YGS  H9   C06  C05  119.48  3.000
 YGS  C07  C06  C05  120.83  3.000
 YGS  H10  C07  C08  120.07  3.000
 YGS  H10  C07  C06  119.78  3.000
 YGS  C08  C07  C06  120.15  3.000
 YGS  H11  C08  C09  120.22  3.000
 YGS  H11  C08  C07  120.28  3.000
 YGS  C09  C08  C07  119.50  3.000
 YGS  H12  C09  C08  120.05  3.000
 YGS  H12  C09  C10  119.82  3.000
 YGS  C08  C09  C10  120.13  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
 YGS  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 YGS  CONST_02  C07  C06  C05  C10     0.00   0.0  0
 YGS  CONST_03  C08  C09  C10  C05     0.00   0.0  0
 YGS  CONST_04  C08  C07  C06  C05     0.00   0.0  0
 YGS  CONST_05  C09  C08  C07  C06     0.00   0.0  0
 YGS  CONST_06  C09  C10  C05  C06     0.00   0.0  0
 YGS  CONST_07  C09  C10  C05  C04   180.00   0.0  0
 YGS  CONST_08  C07  C06  C05  C04   180.00   0.0  0
 YGS  CONST_09  H11  C08  C09  C10   180.00   0.0  0
 YGS  CONST_10  H9   C06  C05  C10   180.00   0.0  0
 YGS  CONST_11  H12  C09  C10  C05   180.00   0.0  0
 YGS  CONST_12  H10  C07  C06  C05   180.00   0.0  0
 YGS  CONST_13  H11  C08  C07  C06   180.00   0.0  0
 YGS  CONST_14  H1   C10  C05  C06   180.00   0.0  0
 YGS  CONST_15  H12  C09  C08  C07   180.00   0.0  0
 YGS  CONST_16  H1   C10  C09  C08   180.00   0.0  0
 YGS  CONST_17  H9   C06  C07  C08   180.00   0.0  0
 YGS  CONST_18  H10  C07  C08  C09   180.00   0.0  0
 YGS  Var_01    C02  C04  C05  C10   -64.81  30.0  2
 YGS  Var_02    C06  C05  C04  C02   114.84  30.0  3
 YGS  Var_03    H7   C04  C05  C10    57.29  30.0  2
 YGS  Var_04    H8   C04  C05  C10   174.01  30.0  2
 YGS  Var_05    H7   C04  C05  C06  -123.07  30.0  2
 YGS  Var_06    H8   C04  C05  C06    -6.34  30.0  2
 YGS  Var_07    C05  C04  C02  C01   116.86  30.0  1
 YGS  Var_08    C05  C04  C02  C03   -63.08  30.0  1
 YGS  Var_09    H2   C01  C02  C03    -0.18   0.0  2
 YGS  Var_10    H3   C01  C02  C03  -179.99   0.0  2
 YGS  Var_11    H2   C01  C02  C04   179.88   0.0  2
 YGS  Var_12    H3   C01  C02  C04     0.08   0.0  2
 YGS  Var_13    H7   C04  C02  C01    -5.29  30.0  1
 YGS  Var_14    H8   C04  C02  C01  -121.99  30.0  1
 YGS  Var_15    H4   C03  C02  C01     2.19  30.0  3
 YGS  Var_16    H5   C03  C02  C01   123.15  30.0  3
 YGS  Var_17    H6   C03  C02  C01  -118.73  30.0  3
 YGS  Var_18    H7   C04  C02  C03   174.77  30.0  1
 YGS  Var_19    H8   C04  C02  C03    58.07  30.0  1
 YGS  Var_20    H4   C03  C02  C04  -177.87  30.0  3
 YGS  Var_21    H5   C03  C02  C04   -56.91  30.0  3
 YGS  Var_22    H6   C03  C02  C04    61.21  30.0  3

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
 YGS  plan-1  C10  0.020
 YGS  plan-1  C04  0.020
 YGS  plan-1  C05  0.020
 YGS  plan-1  C06  0.020
 YGS  plan-1  C07  0.020
 YGS  plan-1  C08  0.020
 YGS  plan-1  C09  0.020
 YGS  plan-1  H1   0.020
 YGS  plan-1  H9   0.020
 YGS  plan-1  H10  0.020
 YGS  plan-1  H11  0.020
 YGS  plan-1  H12  0.020
 YGS  plan-2  C01  0.020
 YGS  plan-2  C02  0.020
 YGS  plan-2  C03  0.020
 YGS  plan-2  C04  0.020
 YGS  plan-2  H2   0.020
 YGS  plan-2  H3   0.020

