# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 22:05:05 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: N-methyl-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[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
 ZAE  ZAE  'N-methyl-D-phenylalanine '  D-peptide  25  13  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZAE
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
 ZAE  N    N  NH1    0  -0.581  34.4827  4.9748  11.8121
 ZAE  CA   C  CH1    0  -0.199  34.5589  5.7129  10.5726
 ZAE  C    C  C      0   0.410  33.9242  7.1191  10.7073
 ZAE  O    O  O      0  -0.596  33.7483  7.5656  11.8560
 ZAE  OXT  O  OC    -1  -0.614  33.6704  7.6988   9.6307
 ZAE  CB   C  CH2    0  -0.531  35.9817  5.8591   9.9680
 ZAE  CG   C  CR6    0   0.131  36.9084  6.6766  10.8187
 ZAE  CD1  C  CR16   0  -0.321  37.6488  6.0933  11.8464
 ZAE  CD2  C  CR16   0  -0.295  37.0259  8.0530  10.6246
 ZAE  CE1  C  CR16   0  -0.239  38.4797  6.8593  12.6548
 ZAE  CE2  C  CR16   0  -0.243  37.8561  8.8228  11.4271
 ZAE  CZ   C  CR16   0  -0.274  38.5858  8.2282  12.4492
 ZAE  C10  C  CH3    0  -0.520  34.9521  3.6110  11.7616
 ZAE  H    H  HNH1   0   0.332  34.9327  5.4913  12.5555
 ZAE  HA   H  HCH1   0   0.215  33.9775  5.1520   9.8301
 ZAE  HB2  H  HCH2   0   0.236  36.4106  4.8671   9.8039
 ZAE  HB3  H  HCH2   0   0.238  35.8822  6.3160   8.9821
 ZAE  HD1  H  HCR6   0   0.245  37.5909  5.0228  12.0069
 ZAE  HD2  H  HCR6   0   0.237  36.4518  8.5245   9.8360
 ZAE  HE1  H  HCR6   0   0.247  39.0485  6.3844  13.4445
 ZAE  HE2  H  HCR6   0   0.246  37.9345  9.8888  11.2536
 ZAE  HZ   H  HCR6   0   0.247  39.2356  8.8261  13.0753
 ZAE  H11  H  HCH3   0   0.189  36.0118  3.4741  11.5042
 ZAE  H12  H  HCH3   0   0.225  34.7930  3.1340  12.7300
 ZAE  H13  H  HCH3   0   0.215  34.3722  3.0492  11.0255

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
 ZAE  N    CA   single    1.458  0.019  1.458
 ZAE  N    C10  single    1.443  0.020  1.443
 ZAE  N    H    single    0.860  0.020  0.860
 ZAE  CA   C    single    1.525  0.021  1.525
 ZAE  CA   CB   single    1.521  0.033  1.521
 ZAE  CA   HA   single    0.970  0.020  0.970
 ZAE  C    O    deloc     1.231  0.020  1.231
 ZAE  C    OXT  deloc     1.249  0.020  1.249
 ZAE  CB   CG   single    1.500  0.020  1.500
 ZAE  CB   HB2  single    0.970  0.020  1.090
 ZAE  CB   HB3  single    0.970  0.020  1.090
 ZAE  CG   CD1  aromatic  1.394  0.020  1.394
 ZAE  CG   CD2  aromatic  1.395  0.020  1.395
 ZAE  CD1  CE1  aromatic  1.390  0.020  1.390
 ZAE  CD1  HD1  single    0.930  0.020  1.080
 ZAE  CD2  CE2  aromatic  1.388  0.020  1.388
 ZAE  CD2  HD2  single    0.930  0.020  1.080
 ZAE  CE1  CZ   aromatic  1.388  0.020  1.388
 ZAE  CE1  HE1  single    0.930  0.020  1.080
 ZAE  CE2  CZ   aromatic  1.389  0.020  1.389
 ZAE  CE2  HE2  single    0.930  0.020  1.080
 ZAE  CZ   HZ   single    0.930  0.020  1.080
 ZAE  C10  H11  single    0.970  0.020  1.090
 ZAE  C10  H12  single    0.970  0.020  1.090
 ZAE  C10  H13  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
 ZAE  H    N    C10  111.33  3.000
 ZAE  H    N    CA   114.00  3.000
 ZAE  C10  N    CA   115.82  3.000
 ZAE  HA   CA   CB   109.00  3.000
 ZAE  HA   CA   C    110.00  3.000
 ZAE  CB   CA   C    110.50  1.500
 ZAE  HA   CA   N    110.00  3.000
 ZAE  CB   CA   N    110.40  1.500
 ZAE  C    CA   N    111.00  2.800
 ZAE  OXT  C    O    126.89  3.000
 ZAE  OXT  C    CA   120.80  1.700
 ZAE  O    C    CA   120.80  1.700
 ZAE  HB3  CB   HB2  106.26  3.000
 ZAE  HB3  CB   CG   109.91  3.000
 ZAE  HB2  CB   CG   109.71  3.000
 ZAE  HB3  CB   CA   107.92  3.000
 ZAE  HB2  CB   CA   109.42  3.000
 ZAE  CG   CB   CA   113.36  3.000
 ZAE  CD2  CG   CD1  118.07  3.000
 ZAE  CD2  CG   CB   120.71  3.000
 ZAE  CD1  CG   CB   121.19  3.000
 ZAE  HD1  CD1  CE1  119.36  3.000
 ZAE  HD1  CD1  CG   119.59  3.000
 ZAE  CE1  CD1  CG   121.04  3.000
 ZAE  HD2  CD2  CE2  119.78  3.000
 ZAE  HD2  CD2  CG   119.08  3.000
 ZAE  CE2  CD2  CG   121.14  3.000
 ZAE  HE1  CE1  CZ   120.02  3.000
 ZAE  HE1  CE1  CD1  119.77  3.000
 ZAE  CZ   CE1  CD1  120.21  3.000
 ZAE  HE2  CE2  CZ   120.07  3.000
 ZAE  HE2  CE2  CD2  119.78  3.000
 ZAE  CZ   CE2  CD2  120.15  3.000
 ZAE  HZ   CZ   CE2  120.29  3.000
 ZAE  HZ   CZ   CE1  120.32  3.000
 ZAE  CE2  CZ   CE1  119.39  3.000
 ZAE  H13  C10  H12  107.20  3.000
 ZAE  H13  C10  H11  106.85  3.000
 ZAE  H12  C10  H11  107.10  3.000
 ZAE  H13  C10  N    109.68  3.000
 ZAE  H12  C10  N    109.54  3.000
 ZAE  H11  C10  N    116.07  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
 ZAE  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 ZAE  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 ZAE  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 ZAE  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 ZAE  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 ZAE  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 ZAE  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 ZAE  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 ZAE  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 ZAE  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 ZAE  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 ZAE  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 ZAE  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 ZAE  Var_01    CD1  CG   CB   CA    86.70  30.0  2
 ZAE  Var_02    H11  C10  N    CA    61.99  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
 ZAE  chir_01  CA  N  C  CB  negativ

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
 ZAE  plan-1  CB   0.020
 ZAE  plan-1  CG   0.020
 ZAE  plan-1  CD1  0.020
 ZAE  plan-1  CD2  0.020
 ZAE  plan-1  CE1  0.020
 ZAE  plan-1  CE2  0.020
 ZAE  plan-1  CZ   0.020
 ZAE  plan-1  HD1  0.020
 ZAE  plan-1  HD2  0.020
 ZAE  plan-1  HE1  0.020
 ZAE  plan-1  HE2  0.020
 ZAE  plan-1  HZ   0.020
 ZAE  plan-2  CA   0.020
 ZAE  plan-2  C    0.020
 ZAE  plan-2  O    0.020
 ZAE  plan-2  OXT  0.020

