# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 14:57:22 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2~{R})-2-methanoyl-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)C=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
 DUW  DUW  '(2~{R})-2-methanoyl-3-phenyl-propanoic acid'  ligand  23  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DUW
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
 DUW  O1   O  O     0  -0.422  -3.0986  -1.5305   0.4777
 DUW  C2   C  C     0   0.584  -2.7491  -0.4899  -0.0119
 DUW  O3   O  OH1   0  -0.587  -3.5829   0.4527  -0.4275
 DUW  C4   C  CH1   0  -0.509  -1.3080  -0.0881  -0.2611
 DUW  C5   C  CH2   0  -0.531  -0.3400  -0.8812   0.6274
 DUW  C6   C  CR6   0   0.124   1.0939  -0.5381   0.3259
 DUW  C7   C  CR16  0  -0.302   1.7367  -1.1004  -0.7753
 DUW  C8   C  CR16  0  -0.238   3.0488  -0.7665  -1.0784
 DUW  C9   C  CR16  0  -0.269   3.7393   0.1399  -0.2828
 DUW  C10  C  CR16  0  -0.239   3.1090   0.7058   0.8165
 DUW  C11  C  CR16  0  -0.307   1.7954   0.3675   1.1169
 DUW  C12  C  C1    0   0.207  -1.1327   1.3949  -0.0226
 DUW  O13  O  O     0  -0.355  -0.7990   2.1855  -0.8646
 DUW  H1   H  HOH1  0   0.490  -4.5037   0.1837  -0.2834
 DUW  H2   H  HCH1  0   0.325  -1.0978  -0.2924  -1.3173
 DUW  H3   H  HCH2  0   0.272  -0.5620  -0.6833   1.6785
 DUW  H4   H  HCH2  0   0.282  -0.5130  -1.9453   0.4628
 DUW  H5   H  HCR6  0   0.251   1.2070  -1.8123  -1.3987
 DUW  H6   H  HCR6  0   0.256   3.5348  -1.2171  -1.9342
 DUW  H7   H  HCR6  0   0.256   4.7635   0.3997  -0.5169
 DUW  H8   H  HCR6  0   0.256   3.6403   1.4095   1.4442
 DUW  H9   H  HCR6  0   0.252   1.3135   0.8103   1.9811
 DUW  H10  H  H     0   0.205  -1.3118   1.7100   1.0213

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
 DUW  C8   C9   aromatic  1.390  0.020  1.390
 DUW  C8   C7   aromatic  1.387  0.020  1.387
 DUW  C9   C10  aromatic  1.388  0.020  1.388
 DUW  C7   C6   aromatic  1.394  0.020  1.394
 DUW  C10  C11  aromatic  1.389  0.020  1.389
 DUW  O1   C2   double    1.202  0.020  1.202
 DUW  O3   C2   single    1.325  0.020  1.325
 DUW  C2   C4   single    1.517  0.020  1.517
 DUW  C6   C11  aromatic  1.392  0.020  1.392
 DUW  C6   C5   single    1.505  0.020  1.505
 DUW  C4   C5   single    1.535  0.020  1.535
 DUW  C4   C12  single    1.512  0.020  1.512
 DUW  C12  O13  double    1.202  0.020  1.202
 DUW  O3   H1   single    0.850  0.020  0.980
 DUW  C4   H2   single    0.970  0.020  1.090
 DUW  C5   H3   single    0.970  0.020  1.090
 DUW  C5   H4   single    0.970  0.020  1.090
 DUW  C7   H5   single    0.930  0.020  1.080
 DUW  C8   H6   single    0.930  0.020  1.080
 DUW  C9   H7   single    0.930  0.020  1.080
 DUW  C10  H8   single    0.930  0.020  1.080
 DUW  C11  H9   single    0.930  0.020  1.080
 DUW  C12  H10  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
 DUW  C4   C2   O3   110.97  3.000
 DUW  C4   C2   O1   124.93  3.000
 DUW  O3   C2   O1   124.09  3.000
 DUW  H1   O3   C2   110.70  3.000
 DUW  H2   C4   C12  108.21  3.000
 DUW  H2   C4   C5   109.91  3.000
 DUW  C12  C4   C5   110.02  3.000
 DUW  H2   C4   C2   106.93  3.000
 DUW  C12  C4   C2   110.12  3.000
 DUW  C5   C4   C2   111.55  3.000
 DUW  H4   C5   H3   106.84  3.000
 DUW  H4   C5   C6   110.08  3.000
 DUW  H3   C5   C6   110.18  3.000
 DUW  H4   C5   C4   108.48  3.000
 DUW  H3   C5   C4   109.59  3.000
 DUW  C6   C5   C4   111.54  3.000
 DUW  C11  C6   C7   118.63  3.000
 DUW  C11  C6   C5   120.97  3.000
 DUW  C7   C6   C5   120.38  3.000
 DUW  H5   C7   C8   119.62  3.000
 DUW  H5   C7   C6   119.60  3.000
 DUW  C8   C7   C6   120.78  3.000
 DUW  H6   C8   C9   120.07  3.000
 DUW  H6   C8   C7   119.82  3.000
 DUW  C9   C8   C7   120.11  3.000
 DUW  H7   C9   C10  120.22  3.000
 DUW  H7   C9   C8   120.19  3.000
 DUW  C10  C9   C8   119.59  3.000
 DUW  H8   C10  C11  119.80  3.000
 DUW  H8   C10  C9   120.10  3.000
 DUW  C11  C10  C9   120.09  3.000
 DUW  H9   C11  C10  119.55  3.000
 DUW  H9   C11  C6   119.65  3.000
 DUW  C10  C11  C6   120.79  3.000
 DUW  H10  C12  O13  121.27  3.000
 DUW  H10  C12  C4   114.19  3.000
 DUW  O13  C12  C4   124.52  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
 DUW  CONST_01  C9   C8   C7   C6    0.00   0.0  0
 DUW  CONST_02  C9   C10  C11  C6    0.00   0.0  0
 DUW  CONST_03  C10  C9   C8   C7    0.00   0.0  0
 DUW  CONST_04  C10  C11  C6   C7    0.00   0.0  0
 DUW  CONST_05  C11  C10  C9   C8    0.00   0.0  0
 DUW  CONST_06  C11  C6   C7   C8    0.00   0.0  0
 DUW  CONST_07  C8   C7   C6   C5  180.00   0.0  0
 DUW  CONST_08  C10  C11  C6   C5  180.00   0.0  0
 DUW  CONST_09  H6   C8   C7   C6  180.00   0.0  0
 DUW  CONST_10  H8   C10  C11  C6  180.00   0.0  0
 DUW  CONST_11  H7   C9   C8   C7  180.00   0.0  0
 DUW  CONST_12  H9   C11  C6   C7  180.00   0.0  0
 DUW  CONST_13  H5   C7   C8   C9  180.00   0.0  0
 DUW  CONST_14  H1   O3   C2   O1    0.00   0.0  0
 DUW  Var_01    C7   C6   C5   C4  -79.68  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
 DUW  chir_01  C4  C2  C5  C12  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
 DUW  plan-1  C5   0.020
 DUW  plan-1  C6   0.020
 DUW  plan-1  C7   0.020
 DUW  plan-1  C8   0.020
 DUW  plan-1  C9   0.020
 DUW  plan-1  C10  0.020
 DUW  plan-1  C11  0.020
 DUW  plan-1  H5   0.020
 DUW  plan-1  H6   0.020
 DUW  plan-1  H7   0.020
 DUW  plan-1  H8   0.020
 DUW  plan-1  H9   0.020
 DUW  plan-2  O1   0.020
 DUW  plan-2  C2   0.020
 DUW  plan-2  O3   0.020
 DUW  plan-2  C4   0.020
 DUW  plan-2  H1   0.020
 DUW  plan-3  C4   0.020
 DUW  plan-3  C12  0.020
 DUW  plan-3  O13  0.020
 DUW  plan-3  H10  0.020

