# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:19:27 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: N-carbamoyl-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(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
 NCB  NCB  'N-carbamoyl-D-alanine    '  L-peptide  16  9  .  2016-04-26  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NCB
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
 NCB  N    N  NH1    0  -0.592  26.1347   -9.8149  72.4874
 NCB  CA   C  CH1    0  -0.125  24.7467   -9.7975  72.0890
 NCB  C    C  C      0   0.395  23.8525   -9.9282  73.3511
 NCB  O    O  O      0  -0.652  22.6306  -10.0037  73.1350
 NCB  OXT  O  OC    -1  -0.614  24.4269   -9.9333  74.4589
 NCB  CB   C  CH3    0  -0.668  24.3891   -8.5318  71.3107
 NCB  O3   O  O      0  -0.575  27.0025  -10.3300  70.4533
 NCB  C3   C  C      0   0.538  27.1511  -10.1204  71.6555
 NCB  N2   N  NH2    0  -0.751  28.3954  -10.1266  72.2361
 NCB  H    H  HNH1   0   0.371  26.2714   -9.7735  73.4877
 NCB  HA   H  HCH1   0   0.190  24.5426  -10.6622  71.4480
 NCB  HB3  H  HCH3   0   0.234  23.3490   -8.5562  70.9896
 NCB  HB2  H  HCH3   0   0.228  24.5352   -7.6423  71.9268
 NCB  HB1  H  HCH3   0   0.211  25.0128   -8.4329  70.4231
 NCB  H22  H  HNH2   0   0.396  28.4726  -10.2478  73.2331
 NCB  H21  H  HNH2   0   0.413  29.1160  -10.5929  71.7107

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
 NCB  N   CA   single  1.458  0.019  1.458
 NCB  N   C3   single  1.348  0.020  1.348
 NCB  N   H    single  0.860  0.020  0.860
 NCB  CA  C    single  1.525  0.021  1.525
 NCB  CA  CB   single  1.521  0.033  1.521
 NCB  CA  HA   single  0.970  0.020  0.970
 NCB  C   O    deloc   1.231  0.020  1.231
 NCB  C   OXT  deloc   1.248  0.020  1.248
 NCB  CB  HB3  single  0.970  0.020  1.090
 NCB  CB  HB2  single  0.970  0.020  1.090
 NCB  CB  HB1  single  0.970  0.020  1.090
 NCB  O3  C3   double  1.229  0.020  1.229
 NCB  C3  N2   single  1.373  0.020  1.373
 NCB  N2  H22  single  0.890  0.020  1.040
 NCB  N2  H21  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
 NCB  H    N   C3   121.20  3.000
 NCB  H    N   CA   114.00  3.000
 NCB  C3   N   CA   123.85  3.000
 NCB  HA   CA  CB   109.00  3.000
 NCB  HA   CA  C    109.00  3.000
 NCB  CB   CA  C    110.50  1.500
 NCB  HA   CA  N    110.00  3.000
 NCB  CB   CA  N    110.40  1.500
 NCB  C    CA  N    111.00  2.800
 NCB  OXT  C   O    127.34  3.000
 NCB  OXT  C   CA   117.19  3.000
 NCB  O    C   CA   120.80  1.700
 NCB  HB1  CB  HB2  108.01  3.000
 NCB  HB1  CB  HB3  107.99  3.000
 NCB  HB2  CB  HB3  108.21  3.000
 NCB  HB1  CB  CA   110.86  3.000
 NCB  HB2  CB  CA   110.85  3.000
 NCB  HB3  CB  CA   110.80  3.000
 NCB  N2   C3  O3   121.48  3.000
 NCB  N2   C3  N    115.03  3.000
 NCB  O3   C3  N    123.43  3.000
 NCB  H21  N2  H22  113.96  3.000
 NCB  H21  N2  C3   115.48  3.000
 NCB  H22  N2  C3   119.24  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
 NCB  CONST_01  O3  C3  N   CA    0.00  0.0  0
 NCB  CONST_02  N2  C3  N   CA  180.00  0.0  0
 NCB  CONST_03  H   N   C3  O3  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
 NCB  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
 NCB  plan-1  N    0.020
 NCB  plan-1  CA   0.020
 NCB  plan-1  O3   0.020
 NCB  plan-1  C3   0.020
 NCB  plan-1  N2   0.020
 NCB  plan-1  H    0.020
 NCB  plan-1  H22  0.020
 NCB  plan-1  H21  0.020
 NCB  plan-2  CA   0.020
 NCB  plan-2  C    0.020
 NCB  plan-2  O    0.020
 NCB  plan-2  OXT  0.020

