# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 01:01:47 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{S})-3-(4-aminocarbonylphenyl)-2-azanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)C(N)=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
 XA6  XA6  "(2S)-3-(4-aminocarbonylphenyl)-2-azanyl-propanoic acid"  L-peptide  26  15  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_XA6
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
 XA6  N    N  NH2    0  -0.780  -17.6715   -7.3372  21.8854
 XA6  CA   C  CH1    0  -0.207  -16.3705   -7.0699  21.2982
 XA6  CB   C  CH2    0  -0.523  -16.5460   -6.4590  19.8989
 XA6  CG   C  CR6    0   0.171  -17.2949   -7.3536  18.9573
 XA6  CD1  C  CR16   0  -0.307  -18.6403   -7.1487  18.6660
 XA6  CE1  C  CR16   0  -0.267  -19.3231   -7.9874  17.7980
 XA6  CD2  C  CR16   0  -0.296  -16.6555   -8.4404  18.3613
 XA6  CE2  C  CR16   0  -0.253  -17.3337   -9.2908  17.5060
 XA6  CZ1  C  CR6    0  -0.059  -18.6754   -9.0672  17.2012
 XA6  CH   C  C      0   0.477  -19.3605  -10.0148  16.2712
 XA6  OT   O  O      0  -0.475  -18.9479  -11.1553  16.1098
 XA6  NT   N  NH2    0  -0.813  -20.4486   -9.5429  15.6369
 XA6  C    C  C      0   0.382  -15.4260   -6.1580  22.1295
 XA6  O    O  O      0  -0.614  -14.2504   -6.0821  21.7169
 XA6  H1   H  HNH2   0   0.334  -17.5343   -7.8217  22.7643
 XA6  H2   H  HNH2   0   0.322  -18.0852   -6.4502  22.1509
 XA6  H4   H  HCH1   0   0.218  -15.8627   -8.0337  21.1717
 XA6  H5   H  HCH2   0   0.246  -15.5581   -6.2447  19.4887
 XA6  H6   H  HCH2   0   0.235  -17.0678   -5.5009  19.9909
 XA6  H7   H  HCR6   0   0.246  -19.1650   -6.3181  19.1225
 XA6  H8   H  HCR6   0   0.252  -20.3740   -7.7990  17.6157
 XA6  H9   H  HCR6   0   0.246  -15.6072   -8.6215  18.5701
 XA6  H10  H  HCR6   0   0.253  -16.8127  -10.1274  17.0593
 XA6  H11  H  HNH2   0   0.400  -20.9216  -10.1289  14.9683
 XA6  H12  H  HNH2   0   0.408  -20.6837   -8.5658  15.6250
 XA6  OXT  O  OC    -1  -0.596  -15.9146   -5.5741  23.1158

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
 XA6  NT   CH   single    1.345  0.020  1.345
 XA6  OT   CH   double    1.224  0.020  1.224
 XA6  CH   CZ1  single    1.494  0.020  1.494
 XA6  CZ1  CE2  aromatic  1.394  0.020  1.394
 XA6  CZ1  CE1  aromatic  1.393  0.020  1.393
 XA6  CE2  CD2  aromatic  1.384  0.020  1.384
 XA6  CE1  CD1  aromatic  1.387  0.020  1.387
 XA6  CD2  CG   aromatic  1.395  0.020  1.395
 XA6  CD1  CG   aromatic  1.392  0.020  1.392
 XA6  CG   CB   single    1.499  0.020  1.499
 XA6  CB   CA   single    1.530  0.020  1.530
 XA6  CA   N    single    1.458  0.019  1.458
 XA6  CA   C    single    1.525  0.021  1.525
 XA6  O    C    deloc     1.231  0.020  1.231
 XA6  N    H1   single    0.890  0.020  1.040
 XA6  N    H2   single    0.890  0.020  1.040
 XA6  CA   H4   single    0.970  0.020  1.090
 XA6  CB   H5   single    0.970  0.020  1.090
 XA6  CB   H6   single    0.970  0.020  1.090
 XA6  CD1  H7   single    0.930  0.020  1.080
 XA6  CE1  H8   single    0.930  0.020  1.080
 XA6  CD2  H9   single    0.930  0.020  1.080
 XA6  CE2  H10  single    0.930  0.020  1.080
 XA6  NT   H11  single    0.860  0.020  1.020
 XA6  NT   H12  single    0.860  0.020  1.020
 XA6  C    OXT  deloc     1.246  0.020  1.246

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
 XA6  H2   N    H1   104.27  3.000
 XA6  H2   N    CA   108.08  3.000
 XA6  H1   N    CA   108.51  3.000
 XA6  H4   CA   C    107.22  3.000
 XA6  H4   CA   CB   107.29  3.000
 XA6  C    CA   CB   110.10  1.900
 XA6  H4   CA   N    107.44  3.000
 XA6  C    CA   N    111.00  2.800
 XA6  CB   CA   N    110.50  1.700
 XA6  H6   CB   H5   106.94  3.000
 XA6  H6   CB   CG   109.69  3.000
 XA6  H5   CB   CG   109.48  3.000
 XA6  H6   CB   CA   109.01  3.000
 XA6  H5   CB   CA   108.48  3.000
 XA6  CG   CB   CA   113.06  3.000
 XA6  CD2  CG   CD1  117.93  3.000
 XA6  CD1  CG   CB   121.77  3.000
 XA6  CD2  CG   CB   120.29  3.000
 XA6  H7   CD1  CE1  119.27  3.000
 XA6  H7   CD1  CG   119.53  3.000
 XA6  CE1  CD1  CG   121.20  3.000
 XA6  H8   CE1  CZ1  120.91  3.000
 XA6  H8   CE1  CD1  118.54  3.000
 XA6  CZ1  CE1  CD1  120.53  3.000
 XA6  H9   CD2  CE2  119.36  3.000
 XA6  H9   CD2  CG   119.42  3.000
 XA6  CE2  CD2  CG   121.22  3.000
 XA6  H10  CE2  CZ1  119.81  3.000
 XA6  H10  CE2  CD2  119.63  3.000
 XA6  CZ1  CE2  CD2  120.56  3.000
 XA6  CH   CZ1  CE2  118.41  3.000
 XA6  CE2  CZ1  CE1  118.56  3.000
 XA6  CH   CZ1  CE1  123.02  3.000
 XA6  NT   CH   OT   122.52  3.000
 XA6  OT   CH   CZ1  121.25  3.000
 XA6  NT   CH   CZ1  116.23  3.000
 XA6  H12  NT   H11  116.61  3.000
 XA6  H12  NT   CH   122.41  3.000
 XA6  H11  NT   CH   119.28  3.000
 XA6  OXT  C    O    127.04  3.000
 XA6  OXT  C    CA   117.40  3.000
 XA6  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
 XA6  CONST_01  CZ1  CE2  CD2  CG      0.00   0.0  0
 XA6  CONST_02  CZ1  CE1  CD1  CG      0.00   0.0  0
 XA6  CONST_03  CE2  CZ1  CE1  CD1     0.00   0.0  0
 XA6  CONST_04  CE2  CD2  CG   CD1     0.00   0.0  0
 XA6  CONST_05  CD2  CE2  CZ1  CE1     0.00   0.0  0
 XA6  CONST_06  CD2  CG   CD1  CE1     0.00   0.0  0
 XA6  CONST_07  CE2  CD2  CG   CB    180.00   0.0  0
 XA6  CONST_08  CE1  CD1  CG   CB    180.00   0.0  0
 XA6  CONST_09  CH   CZ1  CE1  CD1   180.00   0.0  0
 XA6  CONST_10  CH   CZ1  CE2  CD2   180.00   0.0  0
 XA6  CONST_11  H10  CE2  CD2  CG    180.00   0.0  0
 XA6  CONST_12  H8   CE1  CD1  CG    180.00   0.0  0
 XA6  CONST_13  H9   CD2  CG   CD1   180.00   0.0  0
 XA6  CONST_14  H10  CE2  CZ1  CE1   180.00   0.0  0
 XA6  CONST_15  H7   CD1  CG   CD2   180.00   0.0  0
 XA6  CONST_16  H8   CE1  CZ1  CE2   180.00   0.0  0
 XA6  CONST_17  H9   CD2  CE2  CZ1   180.00   0.0  0
 XA6  CONST_18  H7   CD1  CE1  CZ1   180.00   0.0  0
 XA6  CONST_19  H11  NT   CH   CZ1   180.00   0.0  0
 XA6  CONST_20  H12  NT   CH   CZ1     0.00   0.0  0
 XA6  CONST_21  H11  NT   CH   OT      0.00   0.0  0
 XA6  CONST_22  H12  NT   CH   OT    180.00   0.0  0
 XA6  Var_01    CD2  CG   CB   CA    -77.60  30.0  2
 XA6  Var_02    CD1  CG   CB   CA    101.30  30.0  2
 XA6  Var_03    NT   CH   CZ1  CE1    24.06  30.0  2
 XA6  Var_04    OT   CH   CZ1  CE1  -155.61  30.0  2
 XA6  Var_05    NT   CH   CZ1  CE2  -157.29  30.0  2
 XA6  Var_06    OT   CH   CZ1  CE2    23.04  30.0  2
 XA6  Var_07    H5   CB   CG   CD1  -137.64  30.0  2
 XA6  Var_08    H6   CB   CG   CD1   -20.59  30.0  2
 XA6  Var_09    H5   CB   CG   CD2    43.46  30.0  2
 XA6  Var_10    H6   CB   CG   CD2   160.51  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
 XA6  chir_01  CA  CB  N  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
 XA6  plan-1  CB   0.020
 XA6  plan-1  CG   0.020
 XA6  plan-1  CD1  0.020
 XA6  plan-1  CE1  0.020
 XA6  plan-1  CD2  0.020
 XA6  plan-1  CE2  0.020
 XA6  plan-1  CZ1  0.020
 XA6  plan-1  CH   0.020
 XA6  plan-1  H7   0.020
 XA6  plan-1  H8   0.020
 XA6  plan-1  H9   0.020
 XA6  plan-1  H10  0.020
 XA6  plan-2  CZ1  0.020
 XA6  plan-2  CH   0.020
 XA6  plan-2  OT   0.020
 XA6  plan-2  NT   0.020
 XA6  plan-2  H11  0.020
 XA6  plan-2  H12  0.020
 XA6  plan-3  CA   0.020
 XA6  plan-3  C    0.020
 XA6  plan-3  O    0.020
 XA6  plan-3  OXT  0.020

