# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:53:29 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (4R,5R)-5-amino-4-hydroxyhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)[C@H](O)CCC(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
 KAH  KAH  '(4R,5R)-5-amino-4-hydroxyhexanoic acid'  ligand  22  10  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KAH
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
 KAH  C4    C  CH1    0   0.045  -0.4795   0.2778   1.1645
 KAH  C5    C  CH1    0  -0.110   0.4740   0.3948   2.3697
 KAH  N5    N  NH2    0  -0.797   1.3550  -0.7500   2.5716
 KAH  C6    C  CH3    0  -0.655  -0.2972   0.6612   3.6553
 KAH  C3    C  CH2    0  -0.453   0.2618   0.1947  -0.1652
 KAH  C2    C  CH2    0  -0.578  -0.6612   0.1963  -1.3739
 KAH  C1    C  C      0   0.410   0.0362   0.1891  -2.7463
 KAH  O1    O  OC    -1  -0.634  -0.7178   0.1005  -3.7389
 KAH  OH1   O  O      0  -0.608   1.2794   0.2792  -2.7723
 KAH  OXT   O  OH1    0  -0.673  -1.3891  -0.7982   1.3297
 KAH  H4    H  HCH1   0   0.205  -1.1012   1.1818   1.1531
 KAH  H5    H  HCH1   0   0.215   1.1166   1.2611   2.1756
 KAH  HN51  H  HNH2   0   0.330   0.8083  -1.5893   2.7272
 KAH  HN52  H  HNH2   0   0.347   1.9140  -0.9233   1.7454
 KAH  HC1   H  HCH3   0   0.226   0.3856   0.8043   4.4930
 KAH  HC2   H  HCH3   0   0.220  -0.9131   1.5572   3.5658
 KAH  HC3   H  HCH3   0   0.217  -0.9590  -0.1723   3.8982
 KAH  HC31  H  HCH2   0   0.217   0.9522   1.0401  -0.2290
 KAH  HC32  H  HCH2   0   0.202   0.8883  -0.7052  -0.1835
 KAH  HC21  H  HCH2   0   0.220  -1.3395  -0.6610  -1.3317
 KAH  HC22  H  HCH2   0   0.219  -1.3144   1.0770  -1.3338
 KAH  HXT   H  HOH1   0   0.435  -0.9116  -1.6187   1.1681

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
 KAH  C4   C5    single  1.541  0.020  1.541
 KAH  C4   C3    single  1.525  0.020  1.525
 KAH  C4   OXT   single  1.419  0.020  1.419
 KAH  C4   H4    single  0.970  0.020  1.090
 KAH  C5   N5    single  1.459  0.020  1.459
 KAH  C5   C6    single  1.523  0.020  1.523
 KAH  C5   H5    single  0.970  0.020  1.090
 KAH  N5   HN51  single  0.890  0.020  1.040
 KAH  N5   HN52  single  0.890  0.020  1.040
 KAH  C6   HC1   single  0.970  0.020  1.090
 KAH  C6   HC2   single  0.970  0.020  1.090
 KAH  C6   HC3   single  0.970  0.020  1.090
 KAH  C3   C2    single  1.521  0.020  1.521
 KAH  C3   HC31  single  0.970  0.020  1.090
 KAH  C3   HC32  single  0.970  0.020  1.090
 KAH  C2   C1    single  1.539  0.020  1.539
 KAH  C2   HC21  single  0.970  0.020  1.090
 KAH  C2   HC22  single  0.970  0.020  1.090
 KAH  C1   O1    deloc   1.250  0.020  1.250
 KAH  C1   OH1   deloc   1.247  0.020  1.247
 KAH  OXT  HXT   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
 KAH  H4    C4   OXT   105.24  3.000
 KAH  H4    C4   C3    108.14  3.000
 KAH  OXT   C4   C3    111.84  3.000
 KAH  H4    C4   C5    107.23  3.000
 KAH  OXT   C4   C5    111.30  3.000
 KAH  C3    C4   C5    112.66  3.000
 KAH  H5    C5   C6    107.95  3.000
 KAH  H5    C5   N5    106.90  3.000
 KAH  C6    C5   N5    109.05  3.000
 KAH  H5    C5   C4    106.52  3.000
 KAH  C6    C5   C4    111.11  3.000
 KAH  N5    C5   C4    114.98  3.000
 KAH  HN52  N5   HN51  106.34  3.000
 KAH  HN52  N5   C5    110.79  3.000
 KAH  HN51  N5   C5    110.20  3.000
 KAH  HC3   C6   HC2   107.65  3.000
 KAH  HC3   C6   HC1   107.99  3.000
 KAH  HC2   C6   HC1   107.99  3.000
 KAH  HC3   C6   C5    111.18  3.000
 KAH  HC2   C6   C5    111.13  3.000
 KAH  HC1   C6   C5    110.76  3.000
 KAH  HC32  C3   HC31  105.83  3.000
 KAH  HC32  C3   C2    109.53  3.000
 KAH  HC31  C3   C2    109.63  3.000
 KAH  HC32  C3   C4    109.70  3.000
 KAH  HC31  C3   C4    108.41  3.000
 KAH  C2    C3   C4    113.45  3.000
 KAH  HC22  C2   HC21  104.98  3.000
 KAH  HC22  C2   C1    107.82  3.000
 KAH  HC21  C2   C1    108.16  3.000
 KAH  HC22  C2   C3    109.46  3.000
 KAH  HC21  C2   C3    110.17  3.000
 KAH  C1    C2   C3    115.69  3.000
 KAH  OH1   C1   O1    126.17  3.000
 KAH  OH1   C1   C2    118.03  3.000
 KAH  O1    C1   C2    115.79  3.000
 KAH  HXT   OXT  C4    107.98  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
 KAH  Var_01  C1  C2  C3  C4  176.89  30.0  3
 KAH  Var_02  O1  C1  C2  C3  175.42  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
 KAH  chir_01  C4  C5  C3  OXT  negativ
 KAH  chir_02  C5  N5  C4  C6   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
 KAH  plan-1  C2   0.020
 KAH  plan-1  C1   0.020
 KAH  plan-1  O1   0.020
 KAH  plan-1  OH1  0.020

