# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 11:36:52 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (but-3-en-1-yl)benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C=CCCc1ccccc1
#
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
 YGM  YGM  '(but-3-en-1-yl)benzene   '  ligand  22  10  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YGM
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
 YGM  C10  C  CR16  0  -0.320  -32.4526   5.8620   3.2365
 YGM  C01  C  C2    0  -0.532  -32.5466   8.4065   0.6527
 YGM  C02  C  C1    0  -0.164  -32.9079   9.3896   1.4696
 YGM  C03  C  CH2   0  -0.477  -32.6009   9.5187   2.9292
 YGM  C04  C  CH2   0  -0.528  -31.9520   8.3113   3.6025
 YGM  C05  C  CR6   0   0.147  -32.8469   7.1039   3.7283
 YGM  C06  C  CR16  0  -0.309  -34.0794   7.1935   4.3746
 YGM  C07  C  CR16  0  -0.237  -34.8945   6.0792   4.5169
 YGM  C08  C  CR16  0  -0.274  -34.4893   4.8469   4.0191
 YGM  C09  C  CR16  0  -0.239  -33.2627   4.7420   3.3783
 YGM  H1   H  HCR6  0   0.245  -31.4967   5.7700   2.7331
 YGM  H2   H  H     0   0.231  -31.9803   7.5446   0.9816
 YGM  H3   H  H     0   0.234  -32.8110   8.4315  -0.3965
 YGM  H4   H  H     0   0.236  -33.4750  10.2180   1.0539
 YGM  H5   H  HCH2  0   0.250  -31.9458  10.3867   3.0602
 YGM  H6   H  HCH2  0   0.240  -33.5210   9.7898   3.4564
 YGM  H7   H  HCH2  0   0.243  -31.0376   8.0352   3.0725
 YGM  H8   H  HCH2  0   0.257  -31.6364   8.6192   4.6033
 YGM  H9   H  HCR6  0   0.246  -34.4085   8.1440   4.7788
 YGM  H10  H  HCR6  0   0.249  -35.8479   6.1725   5.0216
 YGM  H11  H  HCR6  0   0.250  -35.1238   3.9771   4.1311
 YGM  H12  H  HCR6  0   0.250  -32.9338   3.7875   2.9870

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
 YGM  C01  C02  double    1.328  0.020  1.328
 YGM  C02  C03  single    1.497  0.020  1.497
 YGM  C03  C04  single    1.527  0.020  1.527
 YGM  C10  C09  aromatic  1.390  0.020  1.390
 YGM  C10  C05  aromatic  1.393  0.020  1.393
 YGM  C09  C08  aromatic  1.388  0.020  1.388
 YGM  C04  C05  single    1.508  0.020  1.508
 YGM  C05  C06  aromatic  1.395  0.020  1.395
 YGM  C08  C07  aromatic  1.389  0.020  1.389
 YGM  C06  C07  aromatic  1.388  0.020  1.388
 YGM  C10  H1   single    0.930  0.020  1.080
 YGM  C01  H2   single    0.930  0.020  1.080
 YGM  C01  H3   single    0.930  0.020  1.080
 YGM  C02  H4   single    0.930  0.020  1.080
 YGM  C03  H5   single    0.970  0.020  1.090
 YGM  C03  H6   single    0.970  0.020  1.090
 YGM  C04  H7   single    0.970  0.020  1.090
 YGM  C04  H8   single    0.970  0.020  1.090
 YGM  C06  H9   single    0.930  0.020  1.080
 YGM  C07  H10  single    0.930  0.020  1.080
 YGM  C08  H11  single    0.930  0.020  1.080
 YGM  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
 YGM  H1   C10  C09  119.54  3.000
 YGM  H1   C10  C05  119.28  3.000
 YGM  C09  C10  C05  121.18  3.000
 YGM  H3   C01  H2   116.15  3.000
 YGM  H3   C01  C02  120.84  3.000
 YGM  H2   C01  C02  123.01  3.000
 YGM  H4   C02  C03  114.48  3.000
 YGM  H4   C02  C01  118.10  3.000
 YGM  C03  C02  C01  127.42  3.000
 YGM  H6   C03  H5   104.41  3.000
 YGM  H6   C03  C04  109.91  3.000
 YGM  H5   C03  C04  108.64  3.000
 YGM  H6   C03  C02  108.58  3.000
 YGM  H5   C03  C02  107.92  3.000
 YGM  C04  C03  C02  116.67  3.000
 YGM  H8   C04  H7   105.88  3.000
 YGM  H8   C04  C05  108.68  3.000
 YGM  H7   C04  C05  109.56  3.000
 YGM  H8   C04  C03  107.67  3.000
 YGM  H7   C04  C03  109.97  3.000
 YGM  C05  C04  C03  114.69  3.000
 YGM  C06  C05  C04  120.77  3.000
 YGM  C06  C05  C10  118.10  3.000
 YGM  C04  C05  C10  121.10  3.000
 YGM  H9   C06  C07  119.17  3.000
 YGM  H9   C06  C05  119.83  3.000
 YGM  C07  C06  C05  121.00  3.000
 YGM  H10  C07  C08  120.01  3.000
 YGM  H10  C07  C06  119.71  3.000
 YGM  C08  C07  C06  120.27  3.000
 YGM  H11  C08  C09  120.34  3.000
 YGM  H11  C08  C07  120.31  3.000
 YGM  C09  C08  C07  119.35  3.000
 YGM  H12  C09  C08  120.13  3.000
 YGM  H12  C09  C10  119.77  3.000
 YGM  C08  C09  C10  120.10  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
 YGM  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 YGM  CONST_02  C07  C06  C05  C10    0.00   0.0  0
 YGM  CONST_03  C08  C09  C10  C05    0.00   0.0  0
 YGM  CONST_04  C08  C07  C06  C05    0.00   0.0  0
 YGM  CONST_05  C09  C10  C05  C06    0.00   0.0  0
 YGM  CONST_06  C09  C08  C07  C06    0.00   0.0  0
 YGM  CONST_07  C09  C10  C05  C04  180.00   0.0  0
 YGM  CONST_08  C07  C06  C05  C04  180.00   0.0  0
 YGM  CONST_09  H11  C08  C09  C10  180.00   0.0  0
 YGM  CONST_10  H9   C06  C05  C10  180.00   0.0  0
 YGM  CONST_11  H12  C09  C10  C05  180.00   0.0  0
 YGM  CONST_12  H10  C07  C06  C05  180.00   0.0  0
 YGM  CONST_13  H1   C10  C05  C06  180.00   0.0  0
 YGM  Var_01    C03  C04  C05  C10  125.69  30.0  2
 YGM  Var_02    C05  C04  C03  C02  -68.56  30.0  3
 YGM  Var_03    C04  C03  C02  C01   -8.31  30.0  3
 YGM  Var_04    H2   C01  C02  C03    1.29   0.0  2

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
 YGM  plan-1  C10  0.020
 YGM  plan-1  C04  0.020
 YGM  plan-1  C05  0.020
 YGM  plan-1  C06  0.020
 YGM  plan-1  C07  0.020
 YGM  plan-1  C08  0.020
 YGM  plan-1  C09  0.020
 YGM  plan-1  H1   0.020
 YGM  plan-1  H9   0.020
 YGM  plan-1  H10  0.020
 YGM  plan-1  H11  0.020
 YGM  plan-1  H12  0.020
 YGM  plan-2  C01  0.020
 YGM  plan-2  C02  0.020
 YGM  plan-2  C03  0.020
 YGM  plan-2  H2   0.020
 YGM  plan-2  H3   0.020
 YGM  plan-2  H4   0.020

