# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 15:28:40 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (4R)-4-amino-5-methylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)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
 0JT  0JT  '(4R)-4-amino-5-methylhexanoic acid'  peptide  24  10  .  2022-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_0JT
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
 0JT  N22  N  NH2    0  -0.792  -1.2986   1.8031  -0.3725
 0JT  C18  C  CH1    0  -0.062  -1.2035   0.4650   0.2071
 0JT  C19  C  CH1    0  -0.210  -2.4224  -0.3536  -0.2517
 0JT  C21  C  CH3    0  -0.668  -2.3509  -1.8193   0.1690
 0JT  C20  C  CH3    0  -0.650  -3.7225   0.2625   0.2572
 0JT  C17  C  CH2    0  -0.415   0.1259  -0.2455  -0.0809
 0JT  C16  C  CH2    0  -0.596   1.3529   0.5859   0.2604
 0JT  C14  C  C      0   0.415   2.7082  -0.1367   0.1412
 0JT  O15  O  O      0  -0.609   2.7047  -1.3522  -0.1358
 0JT  H29  H  HNH2   0   0.345  -0.5960   2.4041   0.0395
 0JT  H30  H  HCH1   0   0.197  -1.2832   0.5881   1.2964
 0JT  H31  H  HCH1   0   0.201  -2.4365  -0.3205  -1.3500
 0JT  H32  H  HCH3   0   0.225  -3.2738  -2.3383  -0.0971
 0JT  H33  H  HCH3   0   0.229  -1.5296  -2.3524  -0.3095
 0JT  H34  H  HCH3   0   0.211  -2.2229  -1.9128   1.2508
 0JT  H35  H  HCH3   0   0.227  -3.7962   1.3169  -0.0033
 0JT  H36  H  HCH3   0   0.216  -4.5896  -0.2529  -0.1604
 0JT  H37  H  HCH3   0   0.205  -3.7874   0.1810   1.3458
 0JT  H38  H  HCH2   0   0.212   0.1644  -1.1756   0.4886
 0JT  H39  H  HCH2   0   0.195   0.1572  -0.5347  -1.1385
 0JT  H40  H  HCH2   0   0.212   1.3985   1.4780  -0.3721
 0JT  H41  H  HCH2   0   0.217   1.2662   0.9696   1.2855
 0JT  H2   H  HNH2   0   0.329  -1.0642   1.7520  -1.3586
 0JT  OXT  O  OC    -1  -0.635   3.7198   0.5696   0.3415

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
 0JT  N22  C18  single  1.461  0.020  1.461
 0JT  C20  C19  single  1.526  0.020  1.526
 0JT  C18  C19  single  1.538  0.020  1.538
 0JT  C18  C17  single  1.535  0.020  1.535
 0JT  C16  C14  single  1.541  0.020  1.541
 0JT  C16  C17  single  1.521  0.020  1.521
 0JT  C19  C21  single  1.527  0.020  1.527
 0JT  C14  O15  deloc   1.247  0.020  1.247
 0JT  N22  H29  single  0.890  0.020  1.040
 0JT  C18  H30  single  0.970  0.020  1.090
 0JT  C19  H31  single  0.970  0.020  1.090
 0JT  C21  H32  single  0.970  0.020  1.090
 0JT  C21  H33  single  0.970  0.020  1.090
 0JT  C21  H34  single  0.970  0.020  1.090
 0JT  C20  H35  single  0.970  0.020  1.090
 0JT  C20  H36  single  0.970  0.020  1.090
 0JT  C20  H37  single  0.970  0.020  1.090
 0JT  C17  H38  single  0.970  0.020  1.090
 0JT  C17  H39  single  0.970  0.020  1.090
 0JT  C16  H40  single  0.970  0.020  1.090
 0JT  C16  H41  single  0.970  0.020  1.090
 0JT  N22  H2   single  0.890  0.020  1.040
 0JT  C14  OXT  deloc   1.250  0.020  1.250

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
 0JT  H2   N22  H29  105.37  3.000
 0JT  H2   N22  C18  108.92  3.000
 0JT  H29  N22  C18  109.70  3.000
 0JT  H30  C18  C17  107.50  3.000
 0JT  H30  C18  C19  107.32  3.000
 0JT  C17  C18  C19  112.59  3.000
 0JT  H30  C18  N22  106.61  3.000
 0JT  C17  C18  N22  113.94  3.000
 0JT  C19  C18  N22  108.51  3.000
 0JT  H31  C19  C20  108.07  3.000
 0JT  H31  C19  C21  107.75  3.000
 0JT  C20  C19  C21  109.61  3.000
 0JT  H31  C19  C18  106.99  3.000
 0JT  C21  C19  C18  113.06  3.000
 0JT  C20  C19  C18  111.15  3.000
 0JT  H34  C21  H33  107.71  3.000
 0JT  H34  C21  H32  107.43  3.000
 0JT  H33  C21  H32  107.31  3.000
 0JT  H34  C21  C19  111.12  3.000
 0JT  H33  C21  C19  112.58  3.000
 0JT  H32  C21  C19  110.47  3.000
 0JT  H37  C20  H36  107.37  3.000
 0JT  H37  C20  H35  107.84  3.000
 0JT  H36  C20  H35  108.18  3.000
 0JT  H37  C20  C19  110.64  3.000
 0JT  H36  C20  C19  111.01  3.000
 0JT  H35  C20  C19  111.65  3.000
 0JT  H39  C17  H38  106.11  3.000
 0JT  H39  C17  C16  109.73  3.000
 0JT  H38  C17  C16  108.68  3.000
 0JT  H39  C17  C18  109.13  3.000
 0JT  H38  C17  C18  109.10  3.000
 0JT  C16  C17  C18  113.81  3.000
 0JT  H41  C16  H40  104.95  3.000
 0JT  H41  C16  C14  107.80  3.000
 0JT  H40  C16  C14  107.51  3.000
 0JT  H41  C16  C17  109.69  3.000
 0JT  H40  C16  C17  110.45  3.000
 0JT  C14  C16  C17  115.84  3.000
 0JT  OXT  C14  O15  126.07  3.000
 0JT  OXT  C14  C16  115.76  3.000
 0JT  O15  C14  C16  118.17  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
 0JT  Var_01  C14  C16  C17  C18  173.34  30.0  1
 0JT  Var_02  O15  C14  C16  C17   -4.53  30.0  3
 0JT  Var_03  H35  C20  C19  C18   52.85  30.0  3
 0JT  Var_04  H32  C21  C19  C18  174.85  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
 0JT  chir_01  C18  N22  C19  C17  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
 0JT  plan-1  C16  0.020
 0JT  plan-1  C14  0.020
 0JT  plan-1  O15  0.020
 0JT  plan-1  OXT  0.020

