# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:55:49 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: L-serinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C(N)=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
 SET  SET  'L-serinamide             '  L-peptide  15  7  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SET
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
 SET  N     N  NH2   0  -0.787   1.5181   0.6000  -0.5849
 SET  CA    C  CH1   0  -0.247   0.1135   0.4717  -0.2553
 SET  CB    C  CH2   0  -0.137  -0.6699  -0.4958  -1.1480
 SET  OG    O  OH1   0  -0.669  -0.6138  -0.0100  -2.4688
 SET  C     C  C     0   0.511  -0.0178  -0.0055   1.1860
 SET  O     O  O     0  -0.489   0.7597  -0.8232   1.6568
 SET  H     H  HNH2  0   0.350   1.6097   0.8106  -1.5703
 SET  H2    H  HNH2  0   0.340   1.9808  -0.2891  -0.4389
 SET  HA    H  HCH1  0   0.253  -0.3499   1.4602  -0.3491
 SET  HB2   H  HCH2  0   0.203  -0.2233  -1.4949  -1.0643
 SET  HB3   H  HCH2  0   0.197  -1.7059  -0.5721  -0.7915
 SET  HG    H  HOH1  0   0.459  -0.9080  -0.7077  -3.0607
 SET  HNT1  H  HNH2  0   0.402  -1.2545   0.1908   2.8016
 SET  HNT2  H  HNH2  0   0.409  -1.6684   1.1890   1.4638
 SET  NT    N  NH2   0  -0.796  -1.0593   0.4950   1.8614

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
 SET  N   CA    single  1.458  0.019  1.458
 SET  N   H     single  0.860  0.020  0.860
 SET  N   H2    single  0.890  0.020  1.040
 SET  CA  CB    single  1.530  0.020  1.530
 SET  CA  C     single  1.525  0.021  1.525
 SET  CA  HA    single  0.970  0.020  0.970
 SET  CB  OG    single  1.408  0.020  1.408
 SET  CB  HB2   single  0.970  0.020  1.090
 SET  CB  HB3   single  0.970  0.020  1.090
 SET  OG  HG    single  0.850  0.020  0.980
 SET  NT  C     single  1.338  0.020  1.338
 SET  NT  HNT1  single  0.860  0.020  1.020
 SET  NT  HNT2  single  0.860  0.020  1.020
 SET  C   O     double  1.231  0.020  1.231

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
 SET  H2    N   H     106.36  3.000
 SET  H2    N   CA    109.42  3.000
 SET  H     N   CA    114.00  3.000
 SET  HA    CA  C     109.00  3.000
 SET  HA    CA  CB    109.00  3.000
 SET  C     CA  CB    110.10  1.900
 SET  HA    CA  N     110.00  3.000
 SET  C     CA  N     111.00  2.800
 SET  CB    CA  N     110.50  1.700
 SET  HB3   CB  HB2   107.21  3.000
 SET  HB3   CB  OG    111.47  3.000
 SET  HB2   CB  OG    111.67  3.000
 SET  HB3   CB  CA    109.70  3.000
 SET  HB2   CB  CA    108.81  3.000
 SET  OG    CB  CA    107.95  3.000
 SET  HG    OG  CB    108.36  3.000
 SET  O     C   NT    123.41  3.000
 SET  O     C   CA    120.80  1.700
 SET  NT    C   CA    115.29  3.000
 SET  HNT2  NT  HNT1  117.40  3.000
 SET  HNT2  NT  C     122.01  3.000
 SET  HNT1  NT  C     120.59  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
 SET  CONST_01  HNT1  NT  C  CA  180.00  0.0  0
 SET  CONST_02  HNT2  NT  C  CA    0.00  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
 SET  chir_01  CA  N  CB  C  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
 SET  plan-1  CA    0.020
 SET  plan-1  C     0.020
 SET  plan-1  O     0.020
 SET  plan-1  HNT1  0.020
 SET  plan-1  HNT2  0.020
 SET  plan-1  NT    0.020

