# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:17:37 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: (2S)-2-amino-4-(4-amino-2-oxopyrimidin-1(2H)-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCN1C=CC(=NC1=O)N)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
 LHC  LHC  '(2S)-2-amino-4-(4-amino-2-oxopyrimidin-1(2H)-yl)butanoic acid'  L-peptide  26  15  .  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 (side chain)
;

data_comp_LHC
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
 LHC  N     N  NH2    0  -0.790   -9.7916  -18.2163  11.1638
 LHC  CA    C  CH1    0  -0.201  -10.7727  -17.7395  12.1322
 LHC  CB    C  CH2    0  -0.429  -10.0594  -17.5292  13.4721
 LHC  CG    C  CH2    0  -0.311  -10.9952  -17.2290  14.6351
 LHC  N1    N  NR6    0  -0.506  -10.2886  -17.2318  15.9142
 LHC  C6    C  CR16   0   0.098  -10.1622  -18.3860  16.6016
 LHC  C5    C  CR16   0  -0.474   -9.4847  -18.4546  17.7674
 LHC  C4    C  CR6    0   0.506   -8.9095  -17.2336  18.2307
 LHC  N4    N  NH2    0  -0.813   -8.2371  -17.2165  19.3846
 LHC  N3    N  N      0  -0.539   -9.0153  -16.1068  17.5546
 LHC  C2    C  CR6    0   0.582   -9.6800  -16.0572  16.3787
 LHC  O2    O  O      0  -0.516   -9.7734  -15.0320  15.7161
 LHC  C     C  C      0   0.387  -11.5159  -16.4434  11.7212
 LHC  O     O  O      0  -0.601  -10.8909  -15.6495  10.9895
 LHC  OXT   O  OC    -1  -0.610  -12.6631  -16.2866  12.1893
 LHC  HN    H  HNH2   0   0.333  -10.2816  -18.5100  10.3267
 LHC  HA    H  HCH1   0   0.206  -11.5144  -18.5334  12.2733
 LHC  HB    H  HCH2   0   0.222   -9.3259  -16.7227  13.3708
 LHC  HBA   H  HCH2   0   0.227   -9.4971  -18.4397  13.6994
 LHC  HG    H  HCH2   0   0.261  -11.4875  -16.2687  14.5203
 LHC  HGA   H  HCH2   0   0.247  -11.7785  -17.9861  14.6934
 LHC  H6    H  HCR6   0   0.307  -10.6413  -19.2543  16.1684
 LHC  H5    H  HCR6   0   0.281   -9.3967  -19.3812  18.3142
 LHC  HN4   H  HNH2   0   0.410   -8.1510  -18.0389  19.9554
 LHC  HN4A  H  HNH2   0   0.398   -7.8491  -16.3552  19.7294
 LHC  HNA   H  HNH2   0   0.323   -9.2498  -17.4113  10.8671

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
 LHC  N    HN    single  0.890  0.020  1.040
 LHC  N    CA    single  1.458  0.019  1.458
 LHC  N    HNA   single  0.890  0.020  1.040
 LHC  C    CA    single  1.525  0.021  1.525
 LHC  CA   HA    single  0.970  0.020  0.970
 LHC  CA   CB    single  1.521  0.033  1.521
 LHC  HBA  CB    single  0.970  0.020  1.090
 LHC  CB   HB    single  0.970  0.020  1.090
 LHC  CB   CG    single  1.523  0.020  1.523
 LHC  HG   CG    single  0.970  0.020  1.090
 LHC  CG   HGA   single  0.970  0.020  1.090
 LHC  CG   N1    single  1.461  0.020  1.461
 LHC  N1   C2    single  1.402  0.020  1.402
 LHC  N1   C6    single  1.349  0.020  1.349
 LHC  H6   C6    single  0.930  0.020  1.080
 LHC  C6   C5    double  1.350  0.020  1.350
 LHC  C5   C4    single  1.427  0.020  1.427
 LHC  C5   H5    single  0.930  0.020  1.080
 LHC  N3   C4    double  1.318  0.020  1.318
 LHC  C4   N4    single  1.336  0.020  1.336
 LHC  N4   HN4   single  0.860  0.020  1.020
 LHC  N4   HN4A  single  0.860  0.020  1.020
 LHC  C2   N3    single  1.352  0.020  1.352
 LHC  O2   C2    double  1.224  0.020  1.224
 LHC  O    C     deloc   1.231  0.020  1.231
 LHC  C    OXT   deloc   1.249  0.020  1.249

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
 LHC  HNA   N   HN   104.28  3.000
 LHC  HNA   N   CA   107.09  3.000
 LHC  HN    N   CA   108.53  3.000
 LHC  HA    CA  C    110.00  3.000
 LHC  HA    CA  CB   109.00  3.000
 LHC  C     CA  CB   110.50  1.500
 LHC  CB    CA  N    110.40  1.500
 LHC  HA    CA  N    110.00  3.000
 LHC  C     CA  N    111.00  2.800
 LHC  HBA   CB  HB   106.73  3.000
 LHC  HB    CB  CG   109.71  3.000
 LHC  HBA   CB  CG   108.74  3.000
 LHC  CG    CB  CA   114.13  3.000
 LHC  HB    CB  CA   109.39  3.000
 LHC  HBA   CB  CA   107.86  3.000
 LHC  HGA   CG  HG   107.10  3.000
 LHC  HGA   CG  N1   107.40  3.000
 LHC  HG    CG  N1   108.28  3.000
 LHC  N1    CG  CB   111.78  3.000
 LHC  HGA   CG  CB   110.20  3.000
 LHC  HG    CG  CB   111.87  3.000
 LHC  C2    N1  C6   120.48  3.000
 LHC  C6    N1  CG   119.53  3.000
 LHC  C2    N1  CG   119.89  3.000
 LHC  H6    C6  C5   121.80  3.000
 LHC  C5    C6  N1   122.03  3.000
 LHC  H6    C6  N1   116.16  3.000
 LHC  H5    C5  C4   122.49  3.000
 LHC  H5    C5  C6   121.46  3.000
 LHC  C4    C5  C6   116.05  3.000
 LHC  N3    C4  N4   118.20  3.000
 LHC  N4    C4  C5   119.63  3.000
 LHC  N3    C4  C5   122.17  3.000
 LHC  HN4A  N4  HN4  118.24  3.000
 LHC  HN4A  N4  C4   120.09  3.000
 LHC  HN4   N4  C4   121.57  3.000
 LHC  C2    N3  C4   121.13  3.000
 LHC  O2    C2  N3   122.63  3.000
 LHC  O2    C2  N1   119.28  3.000
 LHC  N3    C2  N1   118.09  3.000
 LHC  OXT   C   O    126.88  3.000
 LHC  OXT   C   CA   120.80  1.700
 LHC  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
 LHC  CONST_01  C4    N3  C2  N1    0.00   0.0  0
 LHC  CONST_02  N3    C2  N1  C6    0.00   0.0  0
 LHC  CONST_03  C2    N3  C4  C5    0.00   0.0  0
 LHC  CONST_04  N3    C2  N1  CG  180.00   0.0  0
 LHC  CONST_05  O2    C2  N1  C6  180.00   0.0  0
 LHC  CONST_06  O2    C2  N3  C4  180.00   0.0  0
 LHC  CONST_07  C2    N3  C4  N4  180.00   0.0  0
 LHC  CONST_08  O2    C2  N1  CG    0.00   0.0  0
 LHC  CONST_09  HN4   N4  C4  C5    0.00   0.0  0
 LHC  CONST_10  HN4A  N4  C4  C5  180.00   0.0  0
 LHC  Var_01    C2    N1  CG  CB   87.62  30.0  3
 LHC  Var_02    N1    CG  CB  CA  171.64  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
 LHC  chir_01  CA  N  C  CB  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
 LHC  plan-1  CG    0.020
 LHC  plan-1  N1    0.020
 LHC  plan-1  C6    0.020
 LHC  plan-1  C5    0.020
 LHC  plan-1  C4    0.020
 LHC  plan-1  N4    0.020
 LHC  plan-1  N3    0.020
 LHC  plan-1  C2    0.020
 LHC  plan-1  O2    0.020
 LHC  plan-1  H6    0.020
 LHC  plan-1  H5    0.020
 LHC  plan-1  HN4   0.020
 LHC  plan-1  HN4A  0.020
 LHC  plan-2  CA    0.020
 LHC  plan-2  C     0.020
 LHC  plan-2  O     0.020
 LHC  plan-2  OXT   0.020

