# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:42:38 2021
#   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  31  16  .  2022-03-23  2022-11-17
;
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  -0.544  50.4597   8.3039  48.0559
 RDM  C5   C  CR6   0   0.145  51.5144   7.4650  48.7225
 RDM  C6   C  CR16  0  -0.304  52.3367   8.0152  49.7042
 RDM  C7   C  CR16  0  -0.240  53.3352   7.2593  50.3021
 RDM  C8   C  CR16  0  -0.272  53.5265   5.9353  49.9266
 RDM  C9   C  CR16  0  -0.239  52.7136   5.3768  48.9500
 RDM  C10  C  CR16  0  -0.315  51.7162   6.1382  48.3531
 RDM  C11  C  C     0   0.542  49.3116  11.0036  47.2332
 RDM  O2   O  O     0  -0.427  48.1152  11.0260  47.3568
 RDM  O1   O  OH1   0  -0.586  50.1445  11.7643  47.9275
 RDM  C2   C  CH1   0  -0.222  50.0634  10.1078  46.2541
 RDM  N    N  NH1   0  -0.607  49.1519   9.3243  45.4656
 RDM  C1   C  C     0   0.501  48.4204   9.7556  44.4116
 RDM  O    O  O     0  -0.491  47.5651   9.0443  43.9068
 RDM  C    C  CH3   0  -0.811  48.7372  11.1291  43.8769
 RDM  C3   C  CH2   0  -0.438  51.0713   9.2069  46.9800
 RDM  H1   H  HCH2  0   0.258  49.9491   8.9094  48.8102
 RDM  H2   H  HCH2  0   0.252  49.7021   7.6468  47.6218
 RDM  H3   H  HCR6  0   0.247  52.1910   9.0456  50.0091
 RDM  H4   H  HCR6  0   0.254  53.9610   7.7030  51.0660
 RDM  H5   H  HCR6  0   0.254  54.3014   5.3424  50.3948
 RDM  H6   H  HCR6  0   0.254  52.8515   4.3449  48.6535
 RDM  H7   H  HCR6  0   0.248  51.0833   5.6914  47.5948
 RDM  H8   H  HOH1  0   0.487  49.6524  12.3263  48.5455
 RDM  H9   H  HCH1  0   0.315  50.6419  10.7621  45.5956
 RDM  H10  H  HNH1  0   0.396  48.8787   8.4247  45.8351
 RDM  H11  H  HCH3  0   0.274  48.1191  11.3310  43.0064
 RDM  H12  H  HCH3  0   0.265  48.5445  11.9055  44.6183
 RDM  H13  H  HCH3  0   0.270  49.7850  11.2116  43.5845
 RDM  H14  H  HCH2  0   0.269  51.5690   8.5945  46.2249
 RDM  H15  H  HCH2  0   0.266  51.8439   9.8343  47.4255

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    1.222  0.020  1.222
 RDM  C    C1   single    1.507  0.020  1.507
 RDM  C1   N    single    1.354  0.020  1.354
 RDM  N    C2   single    1.437  0.020  1.437
 RDM  C2   C3   single    1.534  0.020  1.534
 RDM  C2   C11  single    1.525  0.020  1.525
 RDM  C3   C4   single    1.532  0.020  1.532
 RDM  C11  O2   double    1.203  0.020  1.203
 RDM  C11  O1   single    1.325  0.020  1.325
 RDM  C4   C5   single    1.503  0.020  1.503
 RDM  C10  C5   aromatic  1.392  0.020  1.392
 RDM  C10  C9   aromatic  1.390  0.020  1.390
 RDM  C5   C6   aromatic  1.394  0.020  1.394
 RDM  C9   C8   aromatic  1.388  0.020  1.388
 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  O1   H8   single    0.850  0.020  0.980
 RDM  C2   H9   single    0.970  0.020  1.090
 RDM  N    H10  single    0.860  0.020  1.020
 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   106.45  3.000
 RDM  H2   C4   C3   110.62  3.000
 RDM  H1   C4   C3   110.15  3.000
 RDM  H2   C4   C5   109.08  3.000
 RDM  H1   C4   C5   109.31  3.000
 RDM  C3   C4   C5   111.11  3.000
 RDM  C10  C5   C6   118.53  3.000
 RDM  C6   C5   C4   120.39  3.000
 RDM  C10  C5   C4   121.06  3.000
 RDM  H3   C6   C7   119.55  3.000
 RDM  H3   C6   C5   119.60  3.000
 RDM  C7   C6   C5   120.86  3.000
 RDM  H4   C7   C8   120.11  3.000
 RDM  H4   C7   C6   119.78  3.000
 RDM  C8   C7   C6   120.11  3.000
 RDM  H5   C8   C9   120.22  3.000
 RDM  H5   C8   C7   120.25  3.000
 RDM  C9   C8   C7   119.53  3.000
 RDM  H6   C9   C10  119.74  3.000
 RDM  H6   C9   C8   120.11  3.000
 RDM  C10  C9   C8   120.14  3.000
 RDM  H7   C10  C9   119.58  3.000
 RDM  H7   C10  C5   119.59  3.000
 RDM  C9   C10  C5   120.82  3.000
 RDM  C2   C11  O1   111.34  3.000
 RDM  O1   C11  O2   124.11  3.000
 RDM  C2   C11  O2   124.55  3.000
 RDM  H8   O1   C11  110.37  3.000
 RDM  H9   C2   C3   106.78  3.000
 RDM  H9   C2   N    109.34  3.000
 RDM  C3   C2   N    110.86  3.000
 RDM  H9   C2   C11  107.20  3.000
 RDM  C3   C2   C11  111.40  3.000
 RDM  N    C2   C11  111.08  3.000
 RDM  H10  N    C1   114.99  3.000
 RDM  H10  N    C2   117.14  3.000
 RDM  C1   N    C2   126.59  3.000
 RDM  C    C1   O    122.08  3.000
 RDM  C    C1   N    116.93  3.000
 RDM  O    C1   N    120.97  3.000
 RDM  H13  C    H12  107.34  3.000
 RDM  H13  C    H11  108.51  3.000
 RDM  H12  C    H11  108.17  3.000
 RDM  H13  C    C1   111.46  3.000
 RDM  H12  C    C1   111.74  3.000
 RDM  H11  C    C1   109.51  3.000
 RDM  H15  C3   H14  106.39  3.000
 RDM  H15  C3   C2   108.72  3.000
 RDM  H14  C3   C2   107.54  3.000
 RDM  H15  C3   C4   109.58  3.000
 RDM  H14  C3   C4   109.69  3.000
 RDM  C2   C3   C4   114.59  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_14  O    C1   N    C2   180.00   0.0  0
 RDM  CONST_15  C    C1   N    C2     0.00   0.0  0
 RDM  CONST_16  H10  N    C1   O      0.00   0.0  0
 RDM  CONST_17  H8   O1   C11  O2     0.00   0.0  0
 RDM  Var_01    C3   C4   C5   C6    78.84  30.0  3
 RDM  Var_02    C2   C3   C4   C5  -179.57  30.0  1
 RDM  Var_03    H11  C    C1   N    177.07  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
 RDM  plan-3  H8   0.020

