# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 07:09:31 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: N-[(2S)-2-amino-3-hydroxypropyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC[C@H](N)CO
#
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
 1HD  1HD  N-[(2S)-2-amino-3-hydroxypropyl]acetamide  peptide  21  9  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1HD
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
 1HD  C    C  CH2   0  -0.130   2.5354  -0.6059  -0.0378
 1HD  CD   C  C     0   0.510  -2.1518   0.1338  -0.2507
 1HD  N    N  NH2   0  -0.780   1.1255   1.1716  -0.9437
 1HD  OE1  O  O     0  -0.508  -2.1545  -0.3928  -1.3562
 1HD  CA   C  CH1   0  -0.147   1.2880   0.2397   0.1559
 1HD  CB   C  CH2   0  -0.285   0.0910  -0.6978   0.3733
 1HD  C1   C  CH3   0  -0.778  -3.3229   0.9527   0.2348
 1HD  N1   N  NH1   0  -0.622  -1.1334   0.0235   0.6202
 1HD  O1   O  OH1   0  -0.668   3.6741   0.2198  -0.0654
 1HD  H1   H  HNH2  0   0.335   0.9298   0.6631  -1.7989
 1HD  H2   H  HNH2  0   0.346   0.3196   1.7617  -0.7785
 1HD  H4   H  HCH1  0   0.229   1.4181   0.8303   1.0708
 1HD  H5   H  HCH2  0   0.243  -0.0510  -1.3333  -0.5020
 1HD  H6   H  HCH2  0   0.242   0.2836  -1.3583   1.2228
 1HD  H7   H  HCH3  0   0.265  -4.2175   0.3300   0.2495
 1HD  H8   H  HCH3  0   0.247  -3.1820   1.3765   1.2274
 1HD  H9   H  HCH3  0   0.264  -3.5080   1.7685  -0.4637
 1HD  H10  H  HNH1  0   0.400  -1.2153   0.4897   1.5090
 1HD  H11  H  HOH1  0   0.452   4.4446  -0.3448  -0.1723
 1HD  H12  H  HCH2  0   0.197   2.5915  -1.3390   0.7780
 1HD  H13  H  HCH2  0   0.188   2.4312  -1.1827  -0.9691

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
 1HD  C    CA   single  1.525  0.021  1.525
 1HD  CA   CB   single  1.521  0.033  1.521
 1HD  CA   N    single  1.458  0.019  1.458
 1HD  CB   N1   single  1.442  0.020  1.442
 1HD  OE1  CD   double  1.224  0.020  1.224
 1HD  N1   CD   single  1.345  0.020  1.345
 1HD  CD   C1   single  1.509  0.020  1.509
 1HD  C    O1   single  1.407  0.020  1.407
 1HD  N    H1   single  0.890  0.020  1.040
 1HD  N    H2   single  0.890  0.020  1.040
 1HD  CA   H4   single  0.970  0.020  1.090
 1HD  CB   H5   single  0.970  0.020  1.090
 1HD  CB   H6   single  0.970  0.020  1.090
 1HD  C1   H7   single  0.970  0.020  1.090
 1HD  C1   H8   single  0.970  0.020  1.090
 1HD  C1   H9   single  0.970  0.020  1.090
 1HD  N1   H10  single  0.860  0.020  1.020
 1HD  O1   H11  single  0.850  0.020  0.980
 1HD  C    H12  single  0.970  0.020  1.090
 1HD  C    H13  single  0.970  0.020  1.090

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
 1HD  H13  C   H12  106.47  3.000
 1HD  H13  C   O1   111.57  3.000
 1HD  H12  C   O1   111.40  3.000
 1HD  H13  C   CA   108.78  3.000
 1HD  H12  C   CA   108.59  3.000
 1HD  O1   C   CA   109.90  3.000
 1HD  N1   CD  C1   115.08  3.000
 1HD  C1   CD  OE1  121.47  3.000
 1HD  N1   CD  OE1  123.45  3.000
 1HD  H2   N   H1   106.04  3.000
 1HD  H2   N   CA   109.88  3.000
 1HD  H1   N   CA   109.81  3.000
 1HD  H4   CA  CB   107.64  3.000
 1HD  H4   CA  N    107.44  3.000
 1HD  CB   CA  N    110.40  1.500
 1HD  H4   CA  C    107.98  3.000
 1HD  N    CA  C    111.00  2.800
 1HD  CB   CA  C    110.50  1.500
 1HD  H6   CB  H5   107.13  3.000
 1HD  H6   CB  N1   108.58  3.000
 1HD  H5   CB  N1   108.55  3.000
 1HD  H6   CB  CA   109.97  3.000
 1HD  H5   CB  CA   110.09  3.000
 1HD  N1   CB  CA   112.37  3.000
 1HD  H9   C1  H8   108.36  3.000
 1HD  H9   C1  H7   107.27  3.000
 1HD  H8   C1  H7   108.44  3.000
 1HD  H9   C1  CD   109.38  3.000
 1HD  H8   C1  CD   113.84  3.000
 1HD  H7   C1  CD   109.34  3.000
 1HD  H10  N1  CB   116.85  3.000
 1HD  H10  N1  CD   118.17  3.000
 1HD  CB   N1  CD   124.97  3.000
 1HD  H11  O1  C    107.83  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
 1HD  CONST_01  CB   N1  CD  OE1    0.00   0.0  0
 1HD  CONST_02  C1   CD  N1  CB   180.00   0.0  0
 1HD  CONST_03  H10  N1  CD  OE1  180.00   0.0  0
 1HD  Var_01    CA   CB  N1  CD   107.70  30.0  1
 1HD  Var_02    H7   C1  CD  OE1   59.53  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
 1HD  chir_01  CA  C  CB  N  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
 1HD  plan-1  CD   0.020
 1HD  plan-1  OE1  0.020
 1HD  plan-1  CB   0.020
 1HD  plan-1  C1   0.020
 1HD  plan-1  N1   0.020
 1HD  plan-1  H10  0.020

