# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 16:56:29 2022
#   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  22  10  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.660  6.1109  -5.9718  23.7189
 V1V  C02  C  CH2    0  -0.441  7.3746  -5.1377  23.9016
 V1V  C03  C  CH2    0  -0.433  8.1651  -4.8844  22.6099
 V1V  C04  C  CH1    0  -0.106  7.8024  -3.5905  21.8757
 V1V  N05  N  NH2    0  -0.822  6.3717  -3.5486  21.5953
 V1V  C23  C  CH1    0  -0.071  8.5707  -3.4619  20.5373
 V1V  O24  O  OH1    0  -0.669  9.9333  -3.7992  20.6682
 V1V  C26  C  C      0   0.390  8.4667  -2.0282  19.9575
 V1V  O27  O  O      0  -0.610  7.3059  -1.6406  19.6851
 V1V  O1   O  OC    -1  -0.583  9.5139  -1.3819  19.8085
 V1V  H1   H  HCH3   0   0.218  5.5997  -6.1270  24.6701
 V1V  H2   H  HCH3   0   0.220  5.4072  -5.5050  23.0320
 V1V  H3   H  HCH3   0   0.214  6.3565  -6.9554  23.3140
 V1V  H4   H  HCH2   0   0.223  8.0219  -5.6552  24.6138
 V1V  H5   H  HCH2   0   0.214  7.1278  -4.1825  24.3771
 V1V  H6   H  HCH2   0   0.207  8.0309  -5.7372  21.9325
 V1V  H7   H  HCH2   0   0.218  9.2268  -4.8478  22.8630
 V1V  H8   H  HCH1   0   0.182  8.1219  -2.7565  22.5260
 V1V  H9   H  HNH2   0   0.335  5.8668  -3.3648  22.4529
 V1V  H10  H  HNH2   0   0.347  6.2091  -2.7544  20.9850
 V1V  H12  H  HCH1   0   0.184  8.0702  -4.1459  19.8318
 V1V  H13  H  HOH1   0   0.442  9.9865  -4.7449  20.8332

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  deloc   1.254  0.020  1.254
 V1V  C26  C23  single  1.550  0.020  1.550
 V1V  C23  O24  single  1.410  0.020  1.410
 V1V  C23  C04  single  1.549  0.020  1.549
 V1V  C04  N05  single  1.458  0.020  1.458
 V1V  C04  C03  single  1.531  0.020  1.531
 V1V  C03  C02  single  1.535  0.020  1.535
 V1V  C01  C02  single  1.525  0.020  1.525
 V1V  C26  O1   deloc   1.240  0.020  1.240
 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

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   107.33  3.000
 V1V  H3   C01  H1   107.50  3.000
 V1V  H2   C01  H1   107.96  3.000
 V1V  H3   C01  C02  110.54  3.000
 V1V  H2   C01  C02  112.13  3.000
 V1V  H1   C01  C02  111.20  3.000
 V1V  H5   C02  H4   105.28  3.000
 V1V  H5   C02  C03  109.72  3.000
 V1V  H4   C02  C03  108.75  3.000
 V1V  H5   C02  C01  110.01  3.000
 V1V  H4   C02  C01  108.05  3.000
 V1V  C03  C02  C01  114.58  3.000
 V1V  H7   C03  H6   106.74  3.000
 V1V  H7   C03  C04  108.25  3.000
 V1V  H6   C03  C04  109.37  3.000
 V1V  H7   C03  C02  108.12  3.000
 V1V  H6   C03  C02  109.16  3.000
 V1V  C04  C03  C02  114.89  3.000
 V1V  H8   C04  C23  107.61  3.000
 V1V  H8   C04  N05  112.03  3.000
 V1V  C23  C04  N05  108.55  3.000
 V1V  H8   C04  C03  106.69  3.000
 V1V  N05  C04  C03  110.41  3.000
 V1V  C23  C04  C03  111.53  3.000
 V1V  H10  N05  H9   106.72  3.000
 V1V  H10  N05  C04  107.18  3.000
 V1V  H9   N05  C04  109.38  3.000
 V1V  H12  C23  C26  107.70  3.000
 V1V  H12  C23  O24  110.47  3.000
 V1V  C26  C23  O24  108.72  3.000
 V1V  H12  C23  C04  106.04  3.000
 V1V  O24  C23  C04  112.30  3.000
 V1V  C26  C23  C04  111.52  3.000
 V1V  H13  O24  C23  107.74  3.000
 V1V  O1   C26  O27  126.51  3.000
 V1V  O1   C26  C23  118.07  3.000
 V1V  O27  C26  C23  115.42  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  Var_01  C04  C03  C02  C01   92.32  30.0  1
 V1V  Var_02  H1   C01  C02  C03  179.37  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

