# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 00:27:51 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 4-carboxy-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(cc1)C(O)=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
 99Y  99Y  4-carboxy-D-phenylalanine  peptide  24  15  .  2022-07-24  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_99Y
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
 99Y  C02  C  CH1    0  -0.202  -2.5085  -0.0885  -0.4633
 99Y  C03  C  CH2    0  -0.528  -1.6775   0.1627   0.8042
 99Y  C04  C  CR6    0   0.160  -0.1969   0.1292   0.5644
 99Y  C05  C  CR16   0  -0.305   0.4775   1.2766   0.1510
 99Y  C06  C  CR16   0  -0.278   1.8441   1.2604  -0.0866
 99Y  C07  C  CR6    0  -0.118   2.5862   0.0934   0.0792
 99Y  C08  C  C      0   0.390   4.0860   0.0751  -0.1745
 99Y  C11  C  CR16   0  -0.280   1.9129  -1.0545   0.4919
 99Y  C12  C  CR16   0  -0.300   0.5459  -1.0373   0.7284
 99Y  C13  C  C      0   0.380  -4.0032   0.1848  -0.1499
 99Y  N01  N  NH2    0  -0.775  -2.2050  -1.4032  -0.9996
 99Y  O09  O  OC    -1  -0.597   4.6672  -1.0181  -0.0276
 99Y  O10  O  O      0  -0.599   4.6118   1.1564  -0.5079
 99Y  O14  O  O      0  -0.604  -4.7932  -0.7768  -0.2100
 99Y  O1   O  OC    -1  -0.624  -4.2888   1.3635   0.1493
 99Y  H1   H  HCH1   0   0.218  -2.1970   0.6538  -1.2089
 99Y  H2   H  HCH2   0   0.242  -1.9598   1.1348   1.2106
 99Y  H3   H  HCH2   0   0.231  -1.9471  -0.5873   1.5559
 99Y  H4   H  HCR6   0   0.233  -0.0777   2.1995   0.0198
 99Y  H5   H  HCR6   0   0.235   2.3434   2.1678  -0.4004
 99Y  H6   H  HCR6   0   0.235   2.4689  -1.9727   0.6324
 99Y  H7   H  HCR6   0   0.229   0.0483  -1.9429   1.0550
 99Y  H8   H  HNH2   0   0.322  -2.5330  -2.0992  -0.3390
 99Y  H9   H  HNH2   0   0.333  -2.7759  -1.5543  -1.8227

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
 99Y  C13  O14  deloc     1.246  0.020  1.246
 99Y  C13  C02  single    1.551  0.020  1.551
 99Y  C03  C02  single    1.536  0.020  1.536
 99Y  C03  C04  single    1.500  0.020  1.500
 99Y  C12  C04  aromatic  1.393  0.020  1.393
 99Y  C12  C11  aromatic  1.387  0.020  1.387
 99Y  C02  N01  single    1.452  0.020  1.452
 99Y  C04  C05  aromatic  1.394  0.020  1.394
 99Y  C11  C07  aromatic  1.393  0.020  1.393
 99Y  C05  C06  aromatic  1.387  0.020  1.387
 99Y  C07  C06  aromatic  1.393  0.020  1.393
 99Y  C07  C08  single    1.521  0.020  1.521
 99Y  C08  O10  deloc     1.248  0.020  1.248
 99Y  C08  O09  deloc     1.247  0.020  1.247
 99Y  C13  O1   deloc     1.249  0.020  1.249
 99Y  C02  H1   single    0.970  0.020  1.090
 99Y  C03  H2   single    0.970  0.020  1.090
 99Y  C03  H3   single    0.970  0.020  1.090
 99Y  C05  H4   single    0.930  0.020  1.080
 99Y  C06  H5   single    0.930  0.020  1.080
 99Y  C11  H6   single    0.930  0.020  1.080
 99Y  C12  H7   single    0.930  0.020  1.080
 99Y  N01  H8   single    0.890  0.020  1.040
 99Y  N01  H9   single    0.890  0.020  1.040

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
 99Y  H1   C02  N01  107.59  3.000
 99Y  H1   C02  C13  106.95  3.000
 99Y  N01  C02  C13  115.82  3.000
 99Y  H1   C02  C03  107.24  3.000
 99Y  N01  C02  C03  109.86  3.000
 99Y  C13  C02  C03  109.01  3.000
 99Y  H3   C03  H2   106.90  3.000
 99Y  H3   C03  C04  109.71  3.000
 99Y  H2   C03  C04  109.57  3.000
 99Y  H3   C03  C02  108.72  3.000
 99Y  H2   C03  C02  108.25  3.000
 99Y  C04  C03  C02  113.48  3.000
 99Y  C12  C04  C05  117.81  3.000
 99Y  C05  C04  C03  120.44  3.000
 99Y  C12  C04  C03  121.75  3.000
 99Y  H4   C05  C06  119.56  3.000
 99Y  H4   C05  C04  119.25  3.000
 99Y  C06  C05  C04  121.19  3.000
 99Y  H5   C06  C07  119.42  3.000
 99Y  H5   C06  C05  119.63  3.000
 99Y  C07  C06  C05  120.95  3.000
 99Y  C11  C07  C08  121.06  3.000
 99Y  C08  C07  C06  121.03  3.000
 99Y  C11  C07  C06  117.91  3.000
 99Y  O10  C08  O09  126.51  3.000
 99Y  O09  C08  C07  116.77  3.000
 99Y  O10  C08  C07  116.72  3.000
 99Y  H6   C11  C12  119.63  3.000
 99Y  H6   C11  C07  119.28  3.000
 99Y  C12  C11  C07  121.09  3.000
 99Y  H7   C12  C11  119.57  3.000
 99Y  H7   C12  C04  119.38  3.000
 99Y  C11  C12  C04  121.05  3.000
 99Y  O1   C13  O14  126.50  3.000
 99Y  O1   C13  C02  115.78  3.000
 99Y  O14  C13  C02  117.72  3.000
 99Y  H9   N01  H8   104.16  3.000
 99Y  H9   N01  C02  108.50  3.000
 99Y  H8   N01  C02  108.25  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
 99Y  CONST_01  C07  C11  C12  C04    0.00   0.0  0
 99Y  CONST_02  C07  C06  C05  C04    0.00   0.0  0
 99Y  CONST_03  C11  C12  C04  C05    0.00   0.0  0
 99Y  CONST_04  C11  C07  C06  C05    0.00   0.0  0
 99Y  CONST_05  C12  C04  C05  C06    0.00   0.0  0
 99Y  CONST_06  C12  C11  C07  C06    0.00   0.0  0
 99Y  CONST_07  C11  C12  C04  C03  180.00   0.0  0
 99Y  CONST_08  C06  C05  C04  C03  180.00   0.0  0
 99Y  CONST_09  C08  C07  C06  C05  180.00   0.0  0
 99Y  CONST_10  C12  C11  C07  C08  180.00   0.0  0
 99Y  CONST_11  H6   C11  C12  C04  180.00   0.0  0
 99Y  CONST_12  H5   C06  C05  C04  180.00   0.0  0
 99Y  CONST_13  H7   C12  C04  C05  180.00   0.0  0
 99Y  CONST_14  H4   C05  C06  C07  180.00   0.0  0
 99Y  Var_01    C12  C04  C03  C02  -92.87  30.0  2
 99Y  Var_02    O10  C08  C07  C06    1.43  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
 99Y  chir_01  C02  C13  C03  N01  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
 99Y  plan-1  C03  0.020
 99Y  plan-1  C04  0.020
 99Y  plan-1  C05  0.020
 99Y  plan-1  C06  0.020
 99Y  plan-1  C07  0.020
 99Y  plan-1  C08  0.020
 99Y  plan-1  C11  0.020
 99Y  plan-1  C12  0.020
 99Y  plan-1  H4   0.020
 99Y  plan-1  H5   0.020
 99Y  plan-1  H6   0.020
 99Y  plan-1  H7   0.020
 99Y  plan-2  C07  0.020
 99Y  plan-2  C08  0.020
 99Y  plan-2  O09  0.020
 99Y  plan-2  O10  0.020
 99Y  plan-3  C02  0.020
 99Y  plan-3  C13  0.020
 99Y  plan-3  O14  0.020
 99Y  plan-3  O1   0.020

