# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 06:08:24 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2S)-hydroxy(phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](C(O)=O)c1ccccc1
#
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
 SMN  SMN  '(2S)-hydroxy(phenyl)ethanoic acid'  ligand  19  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SMN
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
 SMN  C1   C  CR6   0   0.083   0.1407   0.3764  -0.4194
 SMN  C2   C  CR16  0  -0.287   1.0394  -0.5276  -0.9773
 SMN  C3   C  CR16  0  -0.241   0.8812  -0.9491  -2.2903
 SMN  C4   C  CR16  0  -0.263  -0.1731  -0.4695  -3.0571
 SMN  C5   C  CR16  0  -0.241  -1.0692   0.4358  -2.5046
 SMN  C6   C  CR16  0  -0.296  -0.9114   0.8563  -1.1909
 SMN  C7   C  CH1   0  -0.118   0.2993   0.8216   1.0225
 SMN  C10  C  C     0   0.510  -0.3471  -0.2238   1.9200
 SMN  O8   O  OH1   0  -0.656   1.6331   1.0080   1.3826
 SMN  O11  O  O     0  -0.436   0.2922  -0.9260   2.6634
 SMN  O12  O  OH1   0  -0.573  -1.6541  -0.2791   1.7679
 SMN  H2   H  HCR6  0   0.254   1.8703  -0.9056  -0.3950
 SMN  H3   H  HCR6  0   0.258   1.5853  -1.6518  -2.7171
 SMN  H4   H  HCR6  0   0.258  -0.2927  -0.7963  -4.0817
 SMN  H5   H  HCR6  0   0.258  -1.8874   0.8222  -3.0983
 SMN  H6   H  HCR6  0   0.256  -1.6088   1.5690  -0.7667
 SMN  H7   H  HCH1  0   0.290  -0.2446   1.7641   1.1604
 SMN  HO8  H  HOH1  0   0.452   1.9035   0.2750   1.9504
 SMN  HO2  H  HOH1  0   0.492  -2.0331  -0.9805   2.3200

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
 SMN  C1   C2   aromatic  1.391  0.020  1.391
 SMN  C1   C6   aromatic  1.390  0.020  1.390
 SMN  C1   C7   single    1.517  0.020  1.517
 SMN  C2   C3   aromatic  1.388  0.020  1.388
 SMN  C2   H2   single    0.930  0.020  1.080
 SMN  C3   C4   aromatic  1.389  0.020  1.389
 SMN  C3   H3   single    0.930  0.020  1.080
 SMN  C4   C5   aromatic  1.388  0.020  1.388
 SMN  C4   H4   single    0.930  0.020  1.080
 SMN  C5   C6   aromatic  1.388  0.020  1.388
 SMN  C5   H5   single    0.930  0.020  1.080
 SMN  C6   H6   single    0.930  0.020  1.080
 SMN  C7   C10  single    1.522  0.020  1.522
 SMN  C7   O8   single    1.394  0.020  1.394
 SMN  C7   H7   single    0.970  0.020  1.090
 SMN  C10  O11  double    1.206  0.020  1.206
 SMN  C10  O12  single    1.317  0.020  1.317
 SMN  O8   HO8  single    0.850  0.020  0.980
 SMN  O12  HO2  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
 SMN  C7   C1   C6   120.34  3.000
 SMN  C7   C1   C2   120.28  3.000
 SMN  C6   C1   C2   119.38  3.000
 SMN  H2   C2   C3   119.35  3.000
 SMN  H2   C2   C1   120.45  3.000
 SMN  C3   C2   C1   120.20  3.000
 SMN  H3   C3   C4   120.01  3.000
 SMN  H3   C3   C2   119.74  3.000
 SMN  C4   C3   C2   120.25  3.000
 SMN  H4   C4   C5   120.15  3.000
 SMN  H4   C4   C3   120.15  3.000
 SMN  C5   C4   C3   119.69  3.000
 SMN  H5   C5   C6   119.79  3.000
 SMN  H5   C5   C4   120.16  3.000
 SMN  C6   C5   C4   120.04  3.000
 SMN  H6   C6   C5   119.76  3.000
 SMN  H6   C6   C1   119.80  3.000
 SMN  C5   C6   C1   120.44  3.000
 SMN  H7   C7   O8   109.08  3.000
 SMN  H7   C7   C10  107.79  3.000
 SMN  O8   C7   C10  110.24  3.000
 SMN  H7   C7   C1   108.65  3.000
 SMN  O8   C7   C1   112.62  3.000
 SMN  C10  C7   C1   108.33  3.000
 SMN  O12  C10  O11  124.95  3.000
 SMN  O12  C10  C7   112.47  3.000
 SMN  O11  C10  C7   122.57  3.000
 SMN  HO8  O8   C7   108.55  3.000
 SMN  HO2  O12  C10  110.64  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
 SMN  CONST_01  C4   C3   C2   C1    0.00  0.0  0
 SMN  CONST_02  C4   C5   C6   C1    0.00  0.0  0
 SMN  CONST_03  C5   C6   C1   C2    0.00  0.0  0
 SMN  CONST_04  C5   C4   C3   C2    0.00  0.0  0
 SMN  CONST_05  C6   C1   C2   C3    0.00  0.0  0
 SMN  CONST_06  C6   C5   C4   C3    0.00  0.0  0
 SMN  CONST_07  C7   C1   C2   C3  180.00  0.0  0
 SMN  CONST_08  C7   C1   C6   C5  180.00  0.0  0
 SMN  CONST_09  H3   C3   C2   C1  180.00  0.0  0
 SMN  CONST_10  H5   C5   C6   C1  180.00  0.0  0
 SMN  CONST_11  H6   C6   C1   C2  180.00  0.0  0
 SMN  CONST_12  H4   C4   C3   C2  180.00  0.0  0
 SMN  CONST_13  H2   C2   C3   C4  180.00  0.0  0
 SMN  CONST_14  HO2  O12  C10  C7  180.00  0.0  0

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
 SMN  chir_01  C7  C1  C10  O8  negativ

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
 SMN  plan-1  C1   0.020
 SMN  plan-1  C2   0.020
 SMN  plan-1  C3   0.020
 SMN  plan-1  C4   0.020
 SMN  plan-1  C5   0.020
 SMN  plan-1  C6   0.020
 SMN  plan-1  C7   0.020
 SMN  plan-1  H2   0.020
 SMN  plan-1  H3   0.020
 SMN  plan-1  H4   0.020
 SMN  plan-1  H5   0.020
 SMN  plan-1  H6   0.020
 SMN  plan-2  C7   0.020
 SMN  plan-2  C10  0.020
 SMN  plan-2  O11  0.020
 SMN  plan-2  O12  0.020
 SMN  plan-2  HO2  0.020

