# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 21:49:57 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (2R)-2-(acetylamino)-4-phenylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H](CCc1ccccc1)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
 RDM  RDM  '(2R)-2-(acetylamino)-4-phenylbutanoic acid'  ligand  30  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RDM
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
 RDM  C4   C  CH2    0  -0.529  50.4927   8.3625  48.1526
 RDM  C5   C  CR6    0   0.142  51.5548   7.4984  48.7727
 RDM  C6   C  CR16   0  -0.308  52.3550   7.9831  49.8059
 RDM  C7   C  CR16   0  -0.238  53.3698   7.2059  50.3481
 RDM  C8   C  CR16   0  -0.272  53.6016   5.9247  49.8632
 RDM  C9   C  CR16   0  -0.238  52.8108   5.4300  48.8345
 RDM  C10  C  CR16   0  -0.311  51.7969   6.2118  48.2963
 RDM  C11  C  C      0   0.415  49.3089  11.0929  47.3029
 RDM  O2   O  O      0  -0.588  48.0692  11.1259  47.2255
 RDM  O1   O  OC    -1  -0.602  50.0437  11.7558  48.0605
 RDM  C2   C  CH1    0  -0.226  50.0669  10.1408  46.3307
 RDM  N    N  NH1    0  -0.596  49.1890   9.3193  45.5233
 RDM  C1   C  C      0   0.485  48.4312   9.7491  44.4954
 RDM  O    O  O      0  -0.505  47.5211   9.0667  44.0380
 RDM  C    C  CH3    0  -0.803  48.7881  11.0899  43.9010
 RDM  C3   C  CH2    0  -0.414  51.0825   9.2623  47.0613
 RDM  H1   H  HCH2   0   0.245  50.0253   8.9825  48.9214
 RDM  H2   H  HCH2   0   0.238  49.7071   7.7213  47.7446
 RDM  H3   H  HCR6   0   0.243  52.1796   8.9809  50.1924
 RDM  H4   H  HCR6   0   0.249  53.9779   7.5997  51.1528
 RDM  H5   H  HCR6   0   0.250  54.3907   5.3159  50.2856
 RDM  H6   H  HCR6   0   0.249  52.9808   4.4315  48.4516
 RDM  H7   H  HCR6   0   0.243  51.1831   5.8164  47.4948
 RDM  H9   H  HCH1   0   0.254  50.6448  10.7773  45.6533
 RDM  H10  H  HNH1   0   0.375  48.8516   8.4690  45.9512
 RDM  H11  H  HCH3   0   0.257  48.1915  11.2662  43.0095
 RDM  H12  H  HCH3   0   0.262  48.5938  11.8908  44.6144
 RDM  H13  H  HCH3   0   0.256  49.8431  11.1449  43.6295
 RDM  H14  H  HCH2   0   0.231  51.6072   8.6425  46.3285
 RDM  H15  H  HCH2   0   0.236  51.8328   9.9122  47.5125

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
 RDM  O    C1   double    1.226  0.020  1.226
 RDM  C    C1   single    1.509  0.020  1.509
 RDM  C1   N    single    1.347  0.020  1.347
 RDM  N    C2   single    1.448  0.020  1.448
 RDM  C2   C3   single    1.529  0.020  1.529
 RDM  C2   C11  single    1.558  0.020  1.558
 RDM  C3   C4   single    1.532  0.020  1.532
 RDM  C11  O2   deloc     1.243  0.020  1.243
 RDM  C11  O1   deloc     1.246  0.020  1.246
 RDM  C4   C5   single    1.503  0.020  1.503
 RDM  C10  C5   aromatic  1.393  0.020  1.393
 RDM  C10  C9   aromatic  1.389  0.020  1.389
 RDM  C5   C6   aromatic  1.394  0.020  1.394
 RDM  C9   C8   aromatic  1.389  0.020  1.389
 RDM  C6   C7   aromatic  1.388  0.020  1.388
 RDM  C8   C7   aromatic  1.389  0.020  1.389
 RDM  C4   H1   single    0.970  0.020  1.090
 RDM  C4   H2   single    0.970  0.020  1.090
 RDM  C6   H3   single    0.930  0.020  1.080
 RDM  C7   H4   single    0.930  0.020  1.080
 RDM  C8   H5   single    0.930  0.020  1.080
 RDM  C9   H6   single    0.930  0.020  1.080
 RDM  C10  H7   single    0.930  0.020  1.080
 RDM  C2   H9   single    0.970  0.020  1.090
 RDM  N    H10  single    0.890  0.020  1.040
 RDM  C    H11  single    0.970  0.020  1.090
 RDM  C    H12  single    0.970  0.020  1.090
 RDM  C    H13  single    0.970  0.020  1.090
 RDM  C3   H14  single    0.970  0.020  1.090
 RDM  C3   H15  single    0.970  0.020  1.090

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
 RDM  H2   C4   H1   106.74  3.000
 RDM  H2   C4   C3   110.81  3.000
 RDM  H1   C4   C3   109.42  3.000
 RDM  H2   C4   C5   108.94  3.000
 RDM  H1   C4   C5   109.76  3.000
 RDM  C3   C4   C5   111.06  3.000
 RDM  C10  C5   C6   118.35  3.000
 RDM  C6   C5   C4   120.77  3.000
 RDM  C10  C5   C4   120.84  3.000
 RDM  H3   C6   C7   119.61  3.000
 RDM  H3   C6   C5   119.43  3.000
 RDM  C7   C6   C5   120.96  3.000
 RDM  H4   C7   C8   120.07  3.000
 RDM  H4   C7   C6   119.81  3.000
 RDM  C8   C7   C6   120.12  3.000
 RDM  H5   C8   C9   120.26  3.000
 RDM  H5   C8   C7   120.27  3.000
 RDM  C9   C8   C7   119.48  3.000
 RDM  H6   C9   C10  119.78  3.000
 RDM  H6   C9   C8   120.07  3.000
 RDM  C10  C9   C8   120.15  3.000
 RDM  H7   C10  C9   119.64  3.000
 RDM  H7   C10  C5   119.42  3.000
 RDM  C9   C10  C5   120.94  3.000
 RDM  C2   C11  O1   114.68  3.000
 RDM  O1   C11  O2   127.74  3.000
 RDM  C2   C11  O2   117.57  3.000
 RDM  H9   C2   C3   106.21  3.000
 RDM  H9   C2   N    107.75  3.000
 RDM  C3   C2   N    110.07  3.000
 RDM  H9   C2   C11  106.73  3.000
 RDM  C3   C2   C11  112.10  3.000
 RDM  N    C2   C11  113.56  3.000
 RDM  H10  N    C1   113.82  3.000
 RDM  H10  N    C2   116.35  3.000
 RDM  C1   N    C2   125.83  3.000
 RDM  C    C1   O    121.53  3.000
 RDM  C    C1   N    116.79  3.000
 RDM  O    C1   N    121.64  3.000
 RDM  H13  C    H12  107.35  3.000
 RDM  H13  C    H11  108.57  3.000
 RDM  H12  C    H11  108.65  3.000
 RDM  H13  C    C1   111.81  3.000
 RDM  H12  C    C1   110.66  3.000
 RDM  H11  C    C1   109.71  3.000
 RDM  H15  C3   H14  106.55  3.000
 RDM  H15  C3   C2   108.20  3.000
 RDM  H14  C3   C2   108.91  3.000
 RDM  H15  C3   C4   108.67  3.000
 RDM  H14  C3   C4   109.21  3.000
 RDM  C2   C3   C4   114.97  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
 RDM  CONST_01  C8   C9   C10  C5    0.00   0.0  0
 RDM  CONST_02  C8   C7   C6   C5    0.00   0.0  0
 RDM  CONST_03  C9   C10  C5   C6    0.00   0.0  0
 RDM  CONST_04  C9   C8   C7   C6    0.00   0.0  0
 RDM  CONST_05  C10  C5   C6   C7    0.00   0.0  0
 RDM  CONST_06  C10  C9   C8   C7    0.00   0.0  0
 RDM  CONST_07  C9   C10  C5   C4  180.00   0.0  0
 RDM  CONST_08  C7   C6   C5   C4  180.00   0.0  0
 RDM  CONST_09  H6   C9   C10  C5  180.00   0.0  0
 RDM  CONST_10  H4   C7   C6   C5  180.00   0.0  0
 RDM  CONST_11  H7   C10  C5   C6  180.00   0.0  0
 RDM  CONST_12  H5   C8   C7   C6  180.00   0.0  0
 RDM  CONST_13  H3   C6   C7   C8  180.00   0.0  0
 RDM  CONST_16  H10  N    C1   O     0.00   0.0  0
 RDM  Var_01    C3   C4   C5   C6   84.19  30.0  3
 RDM  Var_02    C2   C3   C4   C5  177.66  30.0  1
 RDM  Var_03    H11  C    C1   N   172.93  30.0  3

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
 RDM  chir_01  C2  N  C3  C11  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
 RDM  plan-1  C4   0.020
 RDM  plan-1  C5   0.020
 RDM  plan-1  C6   0.020
 RDM  plan-1  C7   0.020
 RDM  plan-1  C8   0.020
 RDM  plan-1  C9   0.020
 RDM  plan-1  C10  0.020
 RDM  plan-1  H3   0.020
 RDM  plan-1  H4   0.020
 RDM  plan-1  H5   0.020
 RDM  plan-1  H6   0.020
 RDM  plan-1  H7   0.020
 RDM  plan-2  C2   0.020
 RDM  plan-2  N    0.020
 RDM  plan-2  C1   0.020
 RDM  plan-2  O    0.020
 RDM  plan-2  C    0.020
 RDM  plan-2  H10  0.020
 RDM  plan-3  C11  0.020
 RDM  plan-3  O2   0.020
 RDM  plan-3  O1   0.020
 RDM  plan-3  C2   0.020

