# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:11:25 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 4-(2-hydroxyethyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCc1ccc(O)cc1
#
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
 YRL  YRL  '4-(2-hydroxyethyl)phenol '  ligand  20  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_YRL
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
 YRL  C01   C  CR6   0   0.095  -0.4551   0.0352  -0.4753
 YRL  C02   C  CR16  0  -0.269   0.1844  -1.1833  -0.2516
 YRL  C03   C  CR16  0  -0.277   0.3225   1.1862  -0.4351
 YRL  C04   C  CR16  0  -0.302   1.5417  -1.2554   0.0082
 YRL  C05   C  CR16  0  -0.344   1.6862   1.1340  -0.1801
 YRL  C06   C  CR6   0   0.346   2.3034  -0.0904   0.0468
 YRL  O07   O  OH1   0  -0.619   3.6244  -0.2125   0.3025
 YRL  C08   C  CH2   0  -0.523  -1.9391   0.0942  -0.7064
 YRL  C09   C  CH2   0  -0.118  -2.7035  -0.0489   0.6011
 YRL  O10   O  OH1   0  -0.655  -4.0857   0.0036   0.3274
 YRL  H021  H  HCR6  0   0.231  -0.3888  -2.1028  -0.2820
 YRL  H031  H  HCR6  0   0.230  -0.1363   2.1516  -0.6114
 YRL  H041  H  HCR6  0   0.243   2.0156  -2.2129   0.1818
 YRL  H051  H  HCR6  0   0.235   2.2597   2.0540  -0.1622
 YRL  H071  H  HOH1  0   0.446   4.0400   0.6527   0.3403
 YRL  H082  H  HCH2  0   0.234  -2.2084   1.0414  -1.1795
 YRL  H081  H  HCH2  0   0.236  -2.2474  -0.7010  -1.3903
 YRL  H092  H  HCH2  0   0.188  -2.4249  -0.9970   1.0788
 YRL  H091  H  HCH2  0   0.189  -2.3969   0.7514   1.2874
 YRL  H101  H  HOH1  0   0.433  -4.5566  -0.1689   1.1451

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
 YRL  O10  C09   single    1.410  0.020  1.410
 YRL  C09  C08   single    1.521  0.020  1.521
 YRL  C08  C01   single    1.503  0.020  1.503
 YRL  C01  C02   aromatic  1.394  0.020  1.394
 YRL  C01  C03   aromatic  1.390  0.020  1.390
 YRL  C02  C04   aromatic  1.384  0.020  1.384
 YRL  C03  C05   aromatic  1.388  0.020  1.388
 YRL  C04  C06   aromatic  1.392  0.020  1.392
 YRL  C05  C06   aromatic  1.390  0.020  1.390
 YRL  C06  O07   single    1.351  0.020  1.351
 YRL  C02  H021  single    0.930  0.020  1.080
 YRL  C03  H031  single    0.930  0.020  1.080
 YRL  C04  H041  single    0.930  0.020  1.080
 YRL  C05  H051  single    0.930  0.020  1.080
 YRL  O07  H071  single    0.850  0.020  0.980
 YRL  C08  H082  single    0.970  0.020  1.090
 YRL  C08  H081  single    0.970  0.020  1.090
 YRL  C09  H092  single    0.970  0.020  1.090
 YRL  C09  H091  single    0.970  0.020  1.090
 YRL  O10  H101  single    0.850  0.020  0.980

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
 YRL  C08   C01  C03   121.63  3.000
 YRL  C03   C01  C02   117.56  3.000
 YRL  C08   C01  C02   120.79  3.000
 YRL  H021  C02  C04   118.67  3.000
 YRL  H021  C02  C01   119.63  3.000
 YRL  C04   C02  C01   121.71  3.000
 YRL  H031  C03  C05   118.65  3.000
 YRL  H031  C03  C01   119.77  3.000
 YRL  C05   C03  C01   121.59  3.000
 YRL  H041  C04  C06   119.75  3.000
 YRL  H041  C04  C02   120.38  3.000
 YRL  C06   C04  C02   119.87  3.000
 YRL  H051  C05  C06   120.66  3.000
 YRL  H051  C05  C03   119.39  3.000
 YRL  C06   C05  C03   119.95  3.000
 YRL  O07   C06  C05   123.00  3.000
 YRL  O07   C06  C04   117.68  3.000
 YRL  C05   C06  C04   119.32  3.000
 YRL  H071  O07  C06   110.44  3.000
 YRL  H081  C08  H082  106.87  3.000
 YRL  H081  C08  C09   109.12  3.000
 YRL  H082  C08  C09   109.26  3.000
 YRL  H081  C08  C01   110.25  3.000
 YRL  H082  C08  C01   110.12  3.000
 YRL  C09   C08  C01   111.12  3.000
 YRL  H091  C09  H092  106.66  3.000
 YRL  H091  C09  O10   111.59  3.000
 YRL  H092  C09  O10   111.43  3.000
 YRL  H091  C09  C08   109.17  3.000
 YRL  H092  C09  C08   109.13  3.000
 YRL  O10   C09  C08   108.80  3.000
 YRL  H101  O10  C09   108.00  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
 YRL  CONST_01  C06   C04  C02  C01     0.00   0.0  0
 YRL  CONST_02  C06   C05  C03  C01     0.00   0.0  0
 YRL  CONST_03  C05   C03  C01  C02     0.00   0.0  0
 YRL  CONST_04  C05   C06  C04  C02     0.00   0.0  0
 YRL  CONST_05  C04   C02  C01  C03     0.00   0.0  0
 YRL  CONST_06  C04   C06  C05  C03     0.00   0.0  0
 YRL  CONST_07  O07   C06  C04  C02   180.00   0.0  0
 YRL  CONST_08  O07   C06  C05  C03   180.00   0.0  0
 YRL  CONST_09  C08   C01  C02  C04   180.00   0.0  0
 YRL  CONST_10  C08   C01  C03  C05   180.00   0.0  0
 YRL  CONST_11  H041  C04  C02  C01   180.00   0.0  0
 YRL  CONST_12  H051  C05  C03  C01   180.00   0.0  0
 YRL  CONST_13  H031  C03  C01  C02   180.00   0.0  0
 YRL  CONST_14  H021  C02  C01  C03   180.00   0.0  0
 YRL  Var_01    C09   C08  C01  C02    77.46  30.0  2
 YRL  Var_02    O10   C09  C08  C01  -179.59  30.0  1

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
 YRL  plan-1  C01   0.020
 YRL  plan-1  C02   0.020
 YRL  plan-1  C03   0.020
 YRL  plan-1  C04   0.020
 YRL  plan-1  C05   0.020
 YRL  plan-1  C06   0.020
 YRL  plan-1  O07   0.020
 YRL  plan-1  C08   0.020
 YRL  plan-1  H021  0.020
 YRL  plan-1  H031  0.020
 YRL  plan-1  H041  0.020
 YRL  plan-1  H051  0.020

