# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:32:50 2021
#   Inital geometry file: a 56 line input string
#   Ligand name: (2S,3S)-3-amino-2-hydroxyhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](N)[C@H](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
 V1V  V1V  '(2S,3S)-3-amino-2-hydroxyhexanoic acid'  L-peptide  23  10  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V1V
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
 V1V  C01  C  CH3   0  -0.663   6.1529  -5.9338  23.8213
 V1V  C02  C  CH2   0  -0.457   7.3983  -5.0567  23.8988
 V1V  C03  C  CH2   0  -0.438   8.1373  -4.8819  22.5639
 V1V  C04  C  CH1   0  -0.130   7.7621  -3.6239  21.7791
 V1V  N05  N  NH2   0  -0.807   6.3277  -3.5791  21.5387
 V1V  C23  C  CH1   0  -0.019   8.4920  -3.6262  20.4141
 V1V  O24  O  OH1   0  -0.667   9.8827  -3.7669  20.5390
 V1V  C26  C  C     0   0.505   8.2269  -2.3249  19.6825
 V1V  O27  O  O     0  -0.444   7.2984  -2.1568  18.9304
 V1V  O1   O  OH1   0  -0.581   9.0986  -1.3798  19.9931
 V1V  H1   H  HCH3  0   0.226   5.6831  -6.0350  24.8005
 V1V  H2   H  HCH3  0   0.218   5.4029  -5.5402  23.1356
 V1V  H3   H  HCH3  0   0.221   6.4112  -6.9361  23.4752
 V1V  H4   H  HCH2  0   0.236   8.0847  -5.5088  24.6176
 V1V  H5   H  HCH2  0   0.222   7.1467  -4.0771  24.3188
 V1V  H6   H  HCH2  0   0.223   7.9728  -5.7642  21.9340
 V1V  H7   H  HCH2  0   0.234   9.2087  -4.8400  22.7687
 V1V  H8   H  HCH1  0   0.216   8.1262  -2.7560  22.3524
 V1V  H9   H  HNH2  0   0.359   5.8417  -3.5698  22.4259
 V1V  H10  H  HNH2  0   0.350   6.0639  -2.7076  21.0965
 V1V  H12  H  HCH1  0   0.246   8.0482  -4.4280  19.8103
 V1V  H13  H  HOH1  0   0.465  10.0743  -4.6858  20.7497
 V1V  H14  H  HOH1  0   0.484   8.8750  -0.5605  19.5255

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
 V1V  O27  C26  double  1.207  0.020  1.207
 V1V  C26  C23  single  1.516  0.020  1.516
 V1V  C23  O24  single  1.403  0.020  1.403
 V1V  C23  C04  single  1.548  0.020  1.548
 V1V  C04  N05  single  1.455  0.020  1.455
 V1V  C04  C03  single  1.529  0.020  1.529
 V1V  C03  C02  single  1.536  0.020  1.536
 V1V  C01  C02  single  1.525  0.020  1.525
 V1V  C26  O1   single  1.323  0.020  1.323
 V1V  C01  H1   single  0.970  0.020  1.090
 V1V  C01  H2   single  0.970  0.020  1.090
 V1V  C01  H3   single  0.970  0.020  1.090
 V1V  C02  H4   single  0.970  0.020  1.090
 V1V  C02  H5   single  0.970  0.020  1.090
 V1V  C03  H6   single  0.970  0.020  1.090
 V1V  C03  H7   single  0.970  0.020  1.090
 V1V  C04  H8   single  0.970  0.020  1.090
 V1V  N05  H9   single  0.890  0.020  1.040
 V1V  N05  H10  single  0.890  0.020  1.040
 V1V  C23  H12  single  0.970  0.020  1.090
 V1V  O24  H13  single  0.850  0.020  0.980
 V1V  O1   H14  single  0.850  0.020  0.980

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
 V1V  H3   C01  H2   107.16  3.000
 V1V  H3   C01  H1   107.54  3.000
 V1V  H2   C01  H1   107.57  3.000
 V1V  H3   C01  C02  110.55  3.000
 V1V  H2   C01  C02  112.73  3.000
 V1V  H1   C01  C02  111.06  3.000
 V1V  H5   C02  H4   105.21  3.000
 V1V  H5   C02  C03  110.00  3.000
 V1V  H4   C02  C03  108.47  3.000
 V1V  H5   C02  C01  110.26  3.000
 V1V  H4   C02  C01  107.98  3.000
 V1V  C03  C02  C01  114.47  3.000
 V1V  H7   C03  H6   106.62  3.000
 V1V  H7   C03  C04  107.79  3.000
 V1V  H6   C03  C04  109.28  3.000
 V1V  H7   C03  C02  108.28  3.000
 V1V  H6   C03  C02  109.60  3.000
 V1V  C04  C03  C02  114.93  3.000
 V1V  H8   C04  C23  107.71  3.000
 V1V  H8   C04  N05  112.79  3.000
 V1V  C23  C04  N05  108.62  3.000
 V1V  H8   C04  C03  107.44  3.000
 V1V  N05  C04  C03  110.61  3.000
 V1V  C23  C04  C03  109.61  3.000
 V1V  H10  N05  H9   104.47  3.000
 V1V  H10  N05  C04  110.83  3.000
 V1V  H9   N05  C04  109.21  3.000
 V1V  H12  C23  C26  106.91  3.000
 V1V  H12  C23  O24  112.12  3.000
 V1V  C26  C23  O24  107.59  3.000
 V1V  H12  C23  C04  107.19  3.000
 V1V  O24  C23  C04  112.89  3.000
 V1V  C26  C23  C04  109.98  3.000
 V1V  H13  O24  C23  108.22  3.000
 V1V  O1   C26  O27  123.64  3.000
 V1V  O1   C26  C23  112.63  3.000
 V1V  O27  C26  C23  123.70  3.000
 V1V  H14  O1   C26  109.79  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
 V1V  CONST_01  H14  O1   C26  C23  180.00   0.0  0
 V1V  Var_01    C04  C03  C02  C01   95.00  30.0  1
 V1V  Var_02    H1   C01  C02  C03  178.97  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
 V1V  chir_01  C04  C23  N05  C03  negativ
 V1V  chir_02  C23  O24  C04  C26  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
 V1V  plan-1  C23  0.020
 V1V  plan-1  C26  0.020
 V1V  plan-1  O27  0.020
 V1V  plan-1  O1   0.020
 V1V  plan-1  H14  0.020

