# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 22:58:21 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-hydroxy-5-(2-phenylethyl)pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=CC(=CNC1=O)CCc2ccccc2
#
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
 2LD  2LD  3-hydroxy-5-(2-phenylethyl)pyridin-2(1H)-one  ligand  29  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2LD
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
 2LD  C4   C  CR16  0  -0.309  -3.2628   1.2628   0.0561
 2LD  C5   C  CR16  0  -0.310  -3.4777  -1.0958   0.4061
 2LD  C6   C  CR6   0   0.133  -2.6730   0.0411   0.3742
 2LD  C7   C  CR16  0  -0.275   1.7727   0.8881  -0.2095
 2LD  C8   C  CR16  0  -0.038   1.7834  -1.4795  -0.4245
 2LD  C10  C  CR6   0   0.195   3.1109   0.8928   0.0234
 2LD  C13  C  CH2   0  -0.507  -0.4124  -0.3151  -0.6677
 2LD  C1   C  CR16  0  -0.273  -5.4127   0.2087  -0.1852
 2LD  C2   C  CR16  0  -0.241  -4.6207   1.3493  -0.2207
 2LD  C3   C  CR16  0  -0.241  -4.8363  -1.0152   0.1293
 2LD  C9   C  CR6   0   0.004   1.0705  -0.3285  -0.4438
 2LD  C11  C  CR6   0   0.447   3.8696  -0.3446   0.0440
 2LD  C12  C  CH2   0  -0.512  -1.1947  -0.0529   0.6274
 2LD  N14  N  NR16  0  -0.652   3.1275  -1.4603  -0.1874
 2LD  O15  O  O     0  -0.525   5.0861  -0.3721   0.2507
 2LD  H1   H  HCR6  0   0.244  -2.6519   2.1584   0.0306
 2LD  H2   H  HCR6  0   0.246  -3.0381  -2.0545   0.6565
 2LD  H3   H  HCR6  0   0.267   1.2306   1.8276  -0.2260
 2LD  H4   H  HCR6  0   0.295   1.3516  -2.4550  -0.5925
 2LD  H5   H  HCH2  0   0.251  -0.6647   0.4542  -1.4033
 2LD  H6   H  HCH2  0   0.252  -0.7330  -1.2687  -1.0936
 2LD  H7   H  HCR6  0   0.253  -6.4722   0.2739  -0.3965
 2LD  H8   H  HCR6  0   0.253  -5.0609   2.3084  -0.4618
 2LD  H9   H  HCR6  0   0.253  -5.4469  -1.9086   0.1619
 2LD  H11  H  HCH2  0   0.248  -0.8391   0.8739   1.0858
 2LD  H12  H  HCH2  0   0.260  -0.9837  -0.8569   1.3362
 2LD  H13  H  HOH1  0   0.471   4.7281   1.8057   0.3614
 2LD  H10  H  HNR6  0   0.429   3.6232  -2.3417  -0.1811
 2LD  O16  O  OH1   0  -0.617   3.7924   2.0242   0.2394

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
 2LD  C8   N14  single    1.365  0.020  1.365
 2LD  C8   C9   double    1.354  0.020  1.354
 2LD  N14  C11  single    1.360  0.020  1.360
 2LD  C13  C9   single    1.500  0.020  1.500
 2LD  C13  C12  single    1.536  0.020  1.536
 2LD  C9   C7   single    1.424  0.020  1.424
 2LD  C5   C3   aromatic  1.389  0.020  1.389
 2LD  C5   C6   aromatic  1.393  0.020  1.393
 2LD  C11  O15  double    1.234  0.020  1.234
 2LD  C11  C10  single    1.452  0.020  1.452
 2LD  C3   C1   aromatic  1.389  0.020  1.389
 2LD  C12  C6   single    1.503  0.020  1.503
 2LD  C7   C10  double    1.358  0.020  1.358
 2LD  C6   C4   aromatic  1.393  0.020  1.393
 2LD  C10  O16  single    1.338  0.020  1.338
 2LD  C1   C2   aromatic  1.389  0.020  1.389
 2LD  C4   C2   aromatic  1.388  0.020  1.388
 2LD  C4   H1   single    0.930  0.020  1.080
 2LD  C5   H2   single    0.930  0.020  1.080
 2LD  C7   H3   single    0.930  0.020  1.080
 2LD  C8   H4   single    0.930  0.020  1.080
 2LD  C13  H5   single    0.970  0.020  1.090
 2LD  C13  H6   single    0.970  0.020  1.090
 2LD  C1   H7   single    0.930  0.020  1.080
 2LD  C2   H8   single    0.930  0.020  1.080
 2LD  C3   H9   single    0.930  0.020  1.080
 2LD  C12  H11  single    0.970  0.020  1.090
 2LD  C12  H12  single    0.970  0.020  1.090
 2LD  O16  H13  single    0.850  0.020  0.980
 2LD  N14  H10  single    0.860  0.020  1.020

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
 2LD  H1   C4   C2   119.66  3.000
 2LD  H1   C4   C6   119.41  3.000
 2LD  C2   C4   C6   120.93  3.000
 2LD  H2   C5   C3   119.60  3.000
 2LD  H2   C5   C6   119.52  3.000
 2LD  C3   C5   C6   120.87  3.000
 2LD  C12  C6   C5   120.89  3.000
 2LD  C12  C6   C4   120.64  3.000
 2LD  C5   C6   C4   118.44  3.000
 2LD  H3   C7   C9   119.41  3.000
 2LD  H3   C7   C10  119.46  3.000
 2LD  C9   C7   C10  121.13  3.000
 2LD  H4   C8   N14  115.69  3.000
 2LD  H4   C8   C9   123.72  3.000
 2LD  N14  C8   C9   120.60  3.000
 2LD  O16  C10  C11  116.88  3.000
 2LD  O16  C10  C7   122.16  3.000
 2LD  C11  C10  C7   120.96  3.000
 2LD  H6   C13  H5   106.50  3.000
 2LD  H6   C13  C12  109.17  3.000
 2LD  H5   C13  C12  109.24  3.000
 2LD  H6   C13  C9   109.91  3.000
 2LD  H5   C13  C9   109.56  3.000
 2LD  C12  C13  C9   112.29  3.000
 2LD  H7   C1   C3   120.23  3.000
 2LD  H7   C1   C2   120.25  3.000
 2LD  C3   C1   C2   119.52  3.000
 2LD  H8   C2   C1   120.09  3.000
 2LD  H8   C2   C4   119.82  3.000
 2LD  C1   C2   C4   120.09  3.000
 2LD  H9   C3   C1   119.99  3.000
 2LD  H9   C3   C5   119.86  3.000
 2LD  C1   C3   C5   120.14  3.000
 2LD  C13  C9   C8   122.03  3.000
 2LD  C13  C9   C7   120.29  3.000
 2LD  C8   C9   C7   117.66  3.000
 2LD  O15  C11  N14  123.23  3.000
 2LD  O15  C11  C10  122.45  3.000
 2LD  N14  C11  C10  114.32  3.000
 2LD  H12  C12  H11  106.80  3.000
 2LD  H12  C12  C13  108.85  3.000
 2LD  H11  C12  C13  109.43  3.000
 2LD  H12  C12  C6   110.21  3.000
 2LD  H11  C12  C6   109.73  3.000
 2LD  C13  C12  C6   111.70  3.000
 2LD  H10  N14  C11  116.53  3.000
 2LD  H10  N14  C8   118.12  3.000
 2LD  C11  N14  C8   125.35  3.000
 2LD  H13  O16  C10  108.75  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
 2LD  CONST_01  C3   C5   C6   C4     0.00   0.0  0
 2LD  CONST_02  C3   C1   C2   C4     0.00   0.0  0
 2LD  CONST_03  C2   C1   C3   C5     0.00   0.0  0
 2LD  CONST_04  C2   C4   C6   C5     0.00   0.0  0
 2LD  CONST_05  C1   C3   C5   C6     0.00   0.0  0
 2LD  CONST_06  C1   C2   C4   C6     0.00   0.0  0
 2LD  CONST_07  C10  C11  N14  C8     0.00   0.0  0
 2LD  CONST_08  C12  C6   C4   C2   180.00   0.0  0
 2LD  CONST_09  C12  C6   C5   C3   180.00   0.0  0
 2LD  CONST_10  O15  C11  N14  C8   180.00   0.0  0
 2LD  CONST_11  H2   C5   C6   C4   180.00   0.0  0
 2LD  CONST_12  H7   C1   C2   C4   180.00   0.0  0
 2LD  CONST_13  H1   C4   C6   C5   180.00   0.0  0
 2LD  CONST_14  H9   C3   C5   C6   180.00   0.0  0
 2LD  CONST_15  H8   C2   C4   C6   180.00   0.0  0
 2LD  CONST_16  H10  N14  C11  C10  180.00   0.0  0
 2LD  Var_01    C13  C12  C6   C4   -88.88  30.0  2
 2LD  Var_02    C9   C13  C12  C6   176.53  30.0  1
 2LD  Var_03    C12  C13  C9   C7   -73.66  30.0  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
 2LD  plan-1  C4   0.020
 2LD  plan-1  C5   0.020
 2LD  plan-1  C6   0.020
 2LD  plan-1  C1   0.020
 2LD  plan-1  C2   0.020
 2LD  plan-1  C3   0.020
 2LD  plan-1  C12  0.020
 2LD  plan-1  H1   0.020
 2LD  plan-1  H2   0.020
 2LD  plan-1  H7   0.020
 2LD  plan-1  H8   0.020
 2LD  plan-1  H9   0.020
 2LD  plan-2  C7   0.020
 2LD  plan-2  C8   0.020
 2LD  plan-2  C10  0.020
 2LD  plan-2  C13  0.020
 2LD  plan-2  C9   0.020
 2LD  plan-2  C11  0.020
 2LD  plan-2  N14  0.020
 2LD  plan-2  O15  0.020
 2LD  plan-2  H3   0.020
 2LD  plan-2  H4   0.020
 2LD  plan-2  H10  0.020
 2LD  plan-2  O16  0.020

