# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:24:38 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (2R)-amino(4-hydroxyphenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C(O)=O)c1ccc(O)cc1
#
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
 NTY  NTY  '(2R)-amino(4-hydroxyphenyl)ethanoic acid'  L-peptide  20  12  .  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_NTY
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
 NTY  N    N  NH2    0  -0.801   3.1321  -0.3583  -2.2699
 NTY  CA   C  CH1    0  -0.262   1.9258  -0.9122  -1.6840
 NTY  CG   C  CR6    0   0.099   1.9017  -0.9423  -0.1694
 NTY  CD1  C  CR16   0  -0.308   0.7608  -0.5842   0.5391
 NTY  CD2  C  CR16   0  -0.292   3.0103  -1.3641   0.5632
 NTY  CE1  C  CR16   0  -0.372   0.7182  -0.6342   1.9263
 NTY  CE2  C  CR16   0  -0.325   2.9865  -1.4224   1.9473
 NTY  CZ   C  CR6    0   0.332   1.8350  -1.0552   2.6406
 NTY  OH   O  OH1    0  -0.638   1.8586  -1.1203   3.9906
 NTY  C    C  C      0   0.406   1.6988  -2.3702  -2.1670
 NTY  O    O  O      0  -0.600   2.7163  -3.0234  -2.4688
 NTY  OXT  O  OC    -1  -0.605   0.5212  -2.7712  -2.1611
 NTY  H    H  HNH2   0   0.337   3.8463  -1.0753  -2.2790
 NTY  HN2  H  HNH2   0   0.334   3.4812   0.4091  -1.7102
 NTY  HA   H  HCH1   0   0.219   1.0662  -0.3181  -2.0127
 NTY  HD1  H  HCR6   0   0.245  -0.1170  -0.2447   0.0019
 NTY  HD2  H  HCR6   0   0.240   3.9183  -1.6555   0.0492
 NTY  HE1  H  HCR6   0   0.263  -0.1844  -0.3360   2.4486
 NTY  HE2  H  HCR6   0   0.255   3.8612  -1.7520   2.4948
 NTY  HOH  H  HOH1   0   0.471   1.0155  -0.8253   4.3517

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
 NTY  N    CA   single    1.458  0.019  1.458
 NTY  N    H    single    0.860  0.020  0.860
 NTY  N    HN2  single    0.890  0.020  1.040
 NTY  CA   CG   single    1.515  0.020  1.515
 NTY  CA   C    single    1.525  0.021  1.525
 NTY  CA   HA   single    0.970  0.020  0.970
 NTY  CG   CD1  aromatic  1.390  0.020  1.390
 NTY  CG   CD2  aromatic  1.394  0.020  1.394
 NTY  CD1  CE1  aromatic  1.389  0.020  1.389
 NTY  CD1  HD1  single    0.930  0.020  1.080
 NTY  CD2  CE2  aromatic  1.386  0.020  1.386
 NTY  CD2  HD2  single    0.930  0.020  1.080
 NTY  CE1  CZ   aromatic  1.391  0.020  1.391
 NTY  CE1  HE1  single    0.930  0.020  1.080
 NTY  CE2  CZ   aromatic  1.393  0.020  1.393
 NTY  CE2  HE2  single    0.930  0.020  1.080
 NTY  CZ   OH   single    1.352  0.020  1.352
 NTY  OH   HOH  single    0.850  0.020  0.980
 NTY  C    O    deloc     1.231  0.020  1.231
 NTY  C    OXT  deloc     1.244  0.020  1.244

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
 NTY  HN2  N    H    107.39  3.000
 NTY  HN2  N    CA   110.67  3.000
 NTY  H    N    CA   114.00  3.000
 NTY  HA   CA   C    109.00  3.000
 NTY  HA   CA   CG   107.35  3.000
 NTY  C    CA   CG   106.86  3.000
 NTY  HA   CA   N    110.00  3.000
 NTY  C    CA   N    111.00  2.800
 NTY  CG   CA   N    115.12  3.000
 NTY  CD2  CG   CD1  117.57  3.000
 NTY  CD2  CG   CA   121.24  3.000
 NTY  CD1  CG   CA   121.17  3.000
 NTY  HD1  CD1  CE1  118.78  3.000
 NTY  HD1  CD1  CG   119.54  3.000
 NTY  CE1  CD1  CG   121.68  3.000
 NTY  HD2  CD2  CE2  118.50  3.000
 NTY  HD2  CD2  CG   119.91  3.000
 NTY  CE2  CD2  CG   121.60  3.000
 NTY  HE1  CE1  CZ   120.27  3.000
 NTY  HE1  CE1  CD1  119.78  3.000
 NTY  CZ   CE1  CD1  119.94  3.000
 NTY  HE2  CE2  CZ   119.74  3.000
 NTY  HE2  CE2  CD2  120.25  3.000
 NTY  CZ   CE2  CD2  120.01  3.000
 NTY  OH   CZ   CE2  118.02  3.000
 NTY  OH   CZ   CE1  122.78  3.000
 NTY  CE2  CZ   CE1  119.20  3.000
 NTY  HOH  OH   CZ   110.14  3.000
 NTY  OXT  C    O    127.23  3.000
 NTY  OXT  C    CA   116.08  3.000
 NTY  O    C    CA   120.80  1.700

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
 NTY  CONST_01  CZ   CE1  CD1  CG     0.00  0.0  0
 NTY  CONST_02  CZ   CE2  CD2  CG     0.00  0.0  0
 NTY  CONST_03  CE2  CD2  CG   CD1    0.00  0.0  0
 NTY  CONST_04  CE2  CZ   CE1  CD1    0.00  0.0  0
 NTY  CONST_05  CE1  CD1  CG   CD2    0.00  0.0  0
 NTY  CONST_06  CE1  CZ   CE2  CD2    0.00  0.0  0
 NTY  CONST_07  CE1  CD1  CG   CA   180.00  0.0  0
 NTY  CONST_08  CE2  CD2  CG   CA   180.00  0.0  0
 NTY  CONST_09  OH   CZ   CE1  CD1  180.00  0.0  0
 NTY  CONST_10  OH   CZ   CE2  CD2  180.00  0.0  0
 NTY  CONST_11  HE1  CE1  CD1  CG   180.00  0.0  0
 NTY  CONST_12  HE2  CE2  CD2  CG   180.00  0.0  0
 NTY  CONST_13  HD2  CD2  CG   CD1  180.00  0.0  0
 NTY  CONST_14  HD1  CD1  CG   CD2  180.00  0.0  0

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
 NTY  chir_01  CA  N  CG  C  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
 NTY  plan-1  CA   0.020
 NTY  plan-1  CG   0.020
 NTY  plan-1  CD1  0.020
 NTY  plan-1  CD2  0.020
 NTY  plan-1  CE1  0.020
 NTY  plan-1  CE2  0.020
 NTY  plan-1  CZ   0.020
 NTY  plan-1  OH   0.020
 NTY  plan-1  HD1  0.020
 NTY  plan-1  HD2  0.020
 NTY  plan-1  HE1  0.020
 NTY  plan-1  HE2  0.020
 NTY  plan-2  CA   0.020
 NTY  plan-2  C    0.020
 NTY  plan-2  O    0.020
 NTY  plan-2  OXT  0.020

