# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:47:50 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N-(carboxycarbonyl)-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1ccccc1)NC(=O)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
 NDF  NDF  N-(carboxycarbonyl)-D-phenylalanine  D-peptide  26  17  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NDF
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
 NDF  CD1  C  CR16   0  -0.311  19.9373  26.2222  33.0046
 NDF  CE1  C  CR16   0  -0.241  21.0564  26.4098  33.8039
 NDF  CZ   C  CR16   0  -0.273  22.1581  25.5746  33.6677
 NDF  CE2  C  CR16   0  -0.243  22.1233  24.5462  32.7351
 NDF  CD2  C  CR16   0  -0.304  20.9985  24.3598  31.9426
 NDF  CG   C  CR6    0   0.154  19.8934  25.2004  32.0576
 NDF  CB   C  CH2    0  -0.512  18.7048  25.0429  31.1581
 NDF  CA   C  CH1    0  -0.194  18.8293  25.8448  29.8438
 NDF  C    C  C      0   0.413  17.5429  25.6231  29.0038
 NDF  O    O  O      0  -0.589  17.6580  24.9678  27.9519
 NDF  OXT  O  OC    -1  -0.602  16.5035  26.1048  29.4907
 NDF  N    N  NH1    0  -0.598  20.0035  25.4709  29.1050
 NDF  C2   C  C      0   0.346  21.1609  26.1393  29.0654
 NDF  O2'  O  O      0  -0.506  21.3908  27.1721  29.6828
 NDF  C1   C  C      0   0.326  22.2247  25.4704  28.1366
 NDF  O1   O  OC    -1  -0.588  21.8375  24.4772  27.4913
 NDF  O2   O  O      0  -0.577  23.3446  25.9970  28.1441
 NDF  HD1  H  HCR6   0   0.240  19.0839  26.8820  33.1157
 NDF  HE1  H  HCR6   0   0.247  21.0685  27.2089  34.5345
 NDF  HZ   H  HCR6   0   0.247  23.0332  25.7205  34.2878
 NDF  HE2  H  HCR6   0   0.246  22.9737  23.8850  32.6251
 NDF  HD2  H  HCR6   0   0.240  20.9814  23.5505  31.2222
 NDF  HB3  H  HCH2   0   0.242  17.8019  25.3762  31.6713
 NDF  HB2  H  HCH2   0   0.235  18.5635  23.9865  30.9103
 NDF  HA   H  HCH1   0   0.233  18.9051  26.9049  30.0977
 NDF  H    H  HNH1   0   0.370  19.9184  24.6955  28.4655

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
 NDF  CD1  CE1  aromatic  1.388  0.020  1.388
 NDF  CD1  CG   aromatic  1.394  0.020  1.394
 NDF  CD1  HD1  single    0.930  0.020  1.080
 NDF  CE1  CZ   aromatic  1.389  0.020  1.389
 NDF  CE1  HE1  single    0.930  0.020  1.080
 NDF  CZ   CE2  aromatic  1.389  0.020  1.389
 NDF  CZ   HZ   single    0.930  0.020  1.080
 NDF  CE2  CD2  aromatic  1.389  0.020  1.389
 NDF  CE2  HE2  single    0.930  0.020  1.080
 NDF  CD2  CG   aromatic  1.393  0.020  1.393
 NDF  CD2  HD2  single    0.930  0.020  1.080
 NDF  CG   CB   single    1.499  0.020  1.499
 NDF  CB   CA   single    1.521  0.033  1.521
 NDF  CB   HB3  single    0.970  0.020  1.090
 NDF  CB   HB2  single    0.970  0.020  1.090
 NDF  CA   C    single    1.525  0.021  1.525
 NDF  CA   N    single    1.458  0.019  1.458
 NDF  CA   HA   single    0.970  0.020  0.970
 NDF  C    O    deloc     1.231  0.020  1.231
 NDF  C    OXT  deloc     1.245  0.020  1.245
 NDF  N    C2   single    1.337  0.020  1.337
 NDF  N    H    single    0.860  0.020  0.860
 NDF  C2   O2'  double    1.225  0.020  1.225
 NDF  C2   C1   single    1.563  0.020  1.563
 NDF  C1   O1   deloc     1.246  0.020  1.246
 NDF  C1   O2   deloc     1.238  0.020  1.238

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
 NDF  HD1  CD1  CG   119.40  3.000
 NDF  HD1  CD1  CE1  119.56  3.000
 NDF  CG   CD1  CE1  121.05  3.000
 NDF  HE1  CE1  CZ   120.07  3.000
 NDF  HE1  CE1  CD1  119.82  3.000
 NDF  CZ   CE1  CD1  120.11  3.000
 NDF  HZ   CZ   CE2  120.32  3.000
 NDF  HZ   CZ   CE1  120.26  3.000
 NDF  CE2  CZ   CE1  119.42  3.000
 NDF  HE2  CE2  CD2  119.75  3.000
 NDF  HE2  CE2  CZ   120.05  3.000
 NDF  CD2  CE2  CZ   120.20  3.000
 NDF  HD2  CD2  CG   119.54  3.000
 NDF  HD2  CD2  CE2  119.51  3.000
 NDF  CG   CD2  CE2  120.95  3.000
 NDF  CB   CG   CD2  121.06  3.000
 NDF  CB   CG   CD1  120.65  3.000
 NDF  CD2  CG   CD1  118.26  3.000
 NDF  HB2  CB   HB3  107.14  3.000
 NDF  HB2  CB   CA   108.60  3.000
 NDF  HB3  CB   CA   107.96  3.000
 NDF  HB2  CB   CG   109.86  3.000
 NDF  HB3  CB   CG   109.99  3.000
 NDF  CA   CB   CG   113.09  3.000
 NDF  HA   CA   N    110.00  3.000
 NDF  HA   CA   C    110.00  3.000
 NDF  N    CA   C    111.00  2.800
 NDF  HA   CA   CB   109.00  3.000
 NDF  N    CA   CB   110.40  1.500
 NDF  C    CA   CB   110.50  1.500
 NDF  OXT  C    O    127.70  3.000
 NDF  OXT  C    CA   120.80  1.700
 NDF  O    C    CA   120.80  1.700
 NDF  H    N    C2   116.01  3.000
 NDF  H    N    CA   114.00  3.000
 NDF  C2   N    CA   126.33  3.000
 NDF  C1   C2   O2'  122.19  3.000
 NDF  C1   C2   N    113.13  3.000
 NDF  O2'  C2   N    124.68  3.000
 NDF  O2   C1   O1   128.57  3.000
 NDF  O2   C1   C2   115.49  3.000
 NDF  O1   C1   C2   115.94  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
 NDF  CONST_01  CE2  CZ   CE1  CD1    0.00   0.0  0
 NDF  CONST_02  CE2  CD2  CG   CD1    0.00   0.0  0
 NDF  CONST_03  CD2  CG   CD1  CE1    0.00   0.0  0
 NDF  CONST_04  CD2  CE2  CZ   CE1    0.00   0.0  0
 NDF  CONST_05  CG   CD1  CE1  CZ     0.00   0.0  0
 NDF  CONST_06  CG   CD2  CE2  CZ     0.00   0.0  0
 NDF  CONST_07  CB   CG   CD1  CE1  180.00   0.0  0
 NDF  CONST_08  CB   CG   CD2  CE2  180.00   0.0  0
 NDF  CONST_09  HZ   CZ   CE1  CD1  180.00   0.0  0
 NDF  CONST_10  HD2  CD2  CG   CD1  180.00   0.0  0
 NDF  CONST_11  HE2  CE2  CZ   CE1  180.00   0.0  0
 NDF  CONST_12  HD1  CD1  CE1  CZ   180.00   0.0  0
 NDF  CONST_13  HE1  CE1  CZ   CE2  180.00   0.0  0
 NDF  CONST_14  O2'  C2   N    CA     0.00   0.0  0
 NDF  CONST_15  C1   C2   N    CA   180.00   0.0  0
 NDF  CONST_16  H    N    C2   O2'  180.00   0.0  0
 NDF  Var_01    CA   CB   CG   CD1   89.64  30.0  2
 NDF  Var_02    O1   C1   C2   N      4.88  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
 NDF  chir_01  CA  CB  C  N  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
 NDF  plan-1  CD1  0.020
 NDF  plan-1  CE1  0.020
 NDF  plan-1  CZ   0.020
 NDF  plan-1  CE2  0.020
 NDF  plan-1  CD2  0.020
 NDF  plan-1  CG   0.020
 NDF  plan-1  CB   0.020
 NDF  plan-1  HD1  0.020
 NDF  plan-1  HE1  0.020
 NDF  plan-1  HZ   0.020
 NDF  plan-1  HE2  0.020
 NDF  plan-1  HD2  0.020
 NDF  plan-2  CA   0.020
 NDF  plan-2  N    0.020
 NDF  plan-2  C2   0.020
 NDF  plan-2  O2'  0.020
 NDF  plan-2  C1   0.020
 NDF  plan-2  H    0.020
 NDF  plan-3  CA   0.020
 NDF  plan-3  C    0.020
 NDF  plan-3  O    0.020
 NDF  plan-3  OXT  0.020
 NDF  plan-4  C2   0.020
 NDF  plan-4  C1   0.020
 NDF  plan-4  O1   0.020
 NDF  plan-4  O2   0.020

