# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:00:15 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2R)-2-benzylbutanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H](Cc1ccccc1)C(O)=O
#
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
 BZS  BZS  '(2R)-2-benzylbutanedioic acid'  ligand  27  15  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BZS
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
 BZS  C1   C  C     0   0.557   0.4113   0.2302   3.3082
 BZS  C2   C  CH2   0  -0.582   0.8475  -0.6441   2.1662
 BZS  CA   C  CH1   0  -0.354   0.4538  -0.0834   0.8086
 BZS  C    C  C     0   0.564  -1.0438   0.0903   0.7094
 BZS  CB   C  CH2   0  -0.509   0.9242  -1.0419  -0.3033
 BZS  CG   C  CR6   0   0.131   0.5790  -0.5636  -1.6856
 BZS  CD1  C  CR16  0  -0.307   1.3342   0.4356  -2.2965
 BZS  CD2  C  CR16  0  -0.307  -0.5126  -1.0876  -2.3719
 BZS  CE1  C  CR16  0  -0.239   1.0059   0.9016  -3.5611
 BZS  CE2  C  CR16  0  -0.239  -0.8460  -0.6239  -3.6385
 BZS  CZ   C  CR16  0  -0.271  -0.0878   0.3730  -4.2365
 BZS  O1   O  O     0  -0.439  -0.2659   1.2216   3.1893
 BZS  O2   O  OH1   0  -0.592   0.8546  -0.2170   4.4751
 BZS  O3   O  O     0  -0.450  -1.8388  -0.7375   1.0847
 BZS  O4   O  OH1   0  -0.582  -1.3932   1.2194   0.1140
 BZS  H21  H  HCH2  0   0.301   1.9325  -0.7676   2.2126
 BZS  H22  H  HCH2  0   0.293   0.4281  -1.6435   2.3143
 BZS  HA   H  HCH1  0   0.282   0.9379   0.8838   0.6569
 BZS  HB1  H  HCH2  0   0.268   2.0073  -1.1485  -0.2060
 BZS  HB2  H  HCH2  0   0.258   0.4957  -2.0319  -0.1289
 BZS  HD1  H  HCR6  0   0.247   2.1914   0.8494  -1.7772
 BZS  HD2  H  HCR6  0   0.248  -1.1087  -1.8690  -1.9143
 BZS  HE1  H  HCR6  0   0.254   1.6067   1.6745  -4.0234
 BZS  HE2  H  HCR6  0   0.254  -1.6961  -1.0453  -4.1596
 BZS  HZ   H  HCR6  0   0.254  -0.3429   0.7334  -5.2247
 BZS  HO2  H  HOH1  0   0.482   0.5552   0.3638   5.1907
 BZS  HO4  H  HOH1  0   0.477  -2.3574   1.2609   0.0242

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
 BZS  C1   C2   single    1.503  0.020  1.503
 BZS  C1   O1   double    1.207  0.020  1.207
 BZS  C1   O2   single    1.326  0.020  1.326
 BZS  C2   CA   single    1.521  0.020  1.521
 BZS  C2   H21  single    0.970  0.020  1.090
 BZS  C2   H22  single    0.970  0.020  1.090
 BZS  CA   C    single    1.511  0.020  1.511
 BZS  CA   CB   single    1.542  0.020  1.542
 BZS  CA   HA   single    0.970  0.020  1.090
 BZS  C    O3   double    1.208  0.020  1.208
 BZS  C    O4   single    1.323  0.020  1.323
 BZS  CB   CG   single    1.503  0.020  1.503
 BZS  CB   HB1  single    0.970  0.020  1.090
 BZS  CB   HB2  single    0.970  0.020  1.090
 BZS  CG   CD1  aromatic  1.393  0.020  1.393
 BZS  CG   CD2  aromatic  1.392  0.020  1.392
 BZS  CD1  CE1  aromatic  1.387  0.020  1.387
 BZS  CD1  HD1  single    0.930  0.020  1.080
 BZS  CD2  CE2  aromatic  1.389  0.020  1.389
 BZS  CD2  HD2  single    0.930  0.020  1.080
 BZS  CE1  CZ   aromatic  1.390  0.020  1.390
 BZS  CE1  HE1  single    0.930  0.020  1.080
 BZS  CE2  CZ   aromatic  1.388  0.020  1.388
 BZS  CE2  HE2  single    0.930  0.020  1.080
 BZS  CZ   HZ   single    0.930  0.020  1.080
 BZS  O2   HO2  single    0.850  0.020  0.980
 BZS  O4   HO4  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
 BZS  O2   C1   O1   123.47  3.000
 BZS  O2   C1   C2   112.06  3.000
 BZS  O1   C1   C2   124.47  3.000
 BZS  H22  C2   H21  105.76  3.000
 BZS  H22  C2   CA   111.00  3.000
 BZS  H21  C2   CA   109.67  3.000
 BZS  H22  C2   C1   108.50  3.000
 BZS  H21  C2   C1   108.76  3.000
 BZS  CA   C2   C1   112.88  3.000
 BZS  HA   CA   CB   108.38  3.000
 BZS  HA   CA   C    109.17  3.000
 BZS  CB   CA   C    109.06  3.000
 BZS  HA   CA   C2   109.62  3.000
 BZS  CB   CA   C2   109.61  3.000
 BZS  C    CA   C2   110.95  3.000
 BZS  O4   C    O3   123.43  3.000
 BZS  O4   C    CA   112.91  3.000
 BZS  O3   C    CA   123.60  3.000
 BZS  HB2  CB   HB1  106.62  3.000
 BZS  HB2  CB   CG   110.19  3.000
 BZS  HB1  CB   CG   109.91  3.000
 BZS  HB2  CB   CA   109.18  3.000
 BZS  HB1  CB   CA   107.40  3.000
 BZS  CG   CB   CA   113.29  3.000
 BZS  CD2  CG   CD1  118.61  3.000
 BZS  CD2  CG   CB   120.92  3.000
 BZS  CD1  CG   CB   120.46  3.000
 BZS  HD1  CD1  CE1  119.70  3.000
 BZS  HD1  CD1  CG   119.49  3.000
 BZS  CE1  CD1  CG   120.82  3.000
 BZS  HD2  CD2  CE2  119.57  3.000
 BZS  HD2  CD2  CG   119.63  3.000
 BZS  CE2  CD2  CG   120.80  3.000
 BZS  HE1  CE1  CZ   120.04  3.000
 BZS  HE1  CE1  CD1  119.86  3.000
 BZS  CZ   CE1  CD1  120.10  3.000
 BZS  HE2  CE2  CZ   120.08  3.000
 BZS  HE2  CE2  CD2  119.82  3.000
 BZS  CZ   CE2  CD2  120.10  3.000
 BZS  HZ   CZ   CE2  120.25  3.000
 BZS  HZ   CZ   CE1  120.17  3.000
 BZS  CE2  CZ   CE1  119.58  3.000
 BZS  HO2  O2   C1   110.15  3.000
 BZS  HO4  O4   C    109.93  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
 BZS  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 BZS  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 BZS  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 BZS  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 BZS  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 BZS  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 BZS  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 BZS  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 BZS  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 BZS  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 BZS  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 BZS  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 BZS  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 BZS  CONST_14  HO2  O2   C1   C2   180.00   0.0  0
 BZS  CONST_15  HO4  O4   C    CA   180.00   0.0  0
 BZS  Var_01    CD1  CG   CB   CA    77.99  30.0  2
 BZS  Var_02    O1   C1   C2   CA     5.28  30.0  2

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
 BZS  chir_01  CA  C2  C  CB  positiv

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
 BZS  plan-1  CB   0.020
 BZS  plan-1  CG   0.020
 BZS  plan-1  CD1  0.020
 BZS  plan-1  CD2  0.020
 BZS  plan-1  CE1  0.020
 BZS  plan-1  CE2  0.020
 BZS  plan-1  CZ   0.020
 BZS  plan-1  HD1  0.020
 BZS  plan-1  HD2  0.020
 BZS  plan-1  HE1  0.020
 BZS  plan-1  HE2  0.020
 BZS  plan-1  HZ   0.020
 BZS  plan-2  C1   0.020
 BZS  plan-2  C2   0.020
 BZS  plan-2  O1   0.020
 BZS  plan-2  O2   0.020
 BZS  plan-2  HO2  0.020
 BZS  plan-3  CA   0.020
 BZS  plan-3  C    0.020
 BZS  plan-3  O3   0.020
 BZS  plan-3  O4   0.020
 BZS  plan-3  HO4  0.020

