# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:50:38 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  25  10  .  2022-08-09  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (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  -1.2711   1.7950  -0.3989
 0JT  C18  C  CH1   0  -0.063  -1.1980   0.4651   0.1955
 0JT  C19  C  CH1   0  -0.213  -2.4200  -0.3482  -0.2645
 0JT  C21  C  CH3   0  -0.671  -2.3631  -1.8115   0.1668
 0JT  C20  C  CH3   0  -0.651  -3.7160   0.2835   0.2351
 0JT  C17  C  CH2   0  -0.435   0.1215  -0.2709  -0.0795
 0JT  C16  C  CH2   0  -0.592   1.3437   0.5680   0.2575
 0JT  C14  C  C     0   0.554   2.6425  -0.1745   0.1095
 0JT  O15  O  O     0  -0.446   2.7592  -1.3142  -0.2671
 0JT  H29  H  HNH2  0   0.349  -0.5955   2.4144   0.0295
 0JT  H30  H  HCH1  0   0.210  -1.2808   0.5985   1.2824
 0JT  H31  H  HCH1  0   0.206  -2.4278  -0.3215  -1.3627
 0JT  H32  H  HCH3  0   0.228  -3.2897  -2.3227  -0.1003
 0JT  H33  H  HCH3  0   0.230  -1.5461  -2.3573  -0.3051
 0JT  H34  H  HCH3  0   0.214  -2.2412  -1.8993   1.2497
 0JT  H35  H  HCH3  0   0.228  -3.7805   1.3363  -0.0339
 0JT  H36  H  HCH3  0   0.219  -4.5848  -0.2283  -0.1825
 0JT  H37  H  HCH3  0   0.207  -3.7856   0.2104   1.3239
 0JT  H38  H  HCH2  0   0.236   0.1484  -1.1886   0.5103
 0JT  H39  H  HCH2  0   0.222   0.1587  -0.5725  -1.1318
 0JT  H40  H  HCH2  0   0.271   1.4016   1.4552  -0.3798
 0JT  H41  H  HCH2  0   0.276   1.2833   0.9483   1.2830
 0JT  H2   H  HNH2  0   0.334  -1.0224   1.7429  -1.3807
 0JT  OXT  O  OH1   0  -0.599   3.6842   0.5843   0.4423
 0JT  HXT  H  HOH1  0   0.478   4.5052   0.0816   0.3348

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  1.458  0.020  1.458
 0JT  C20  C19  single  1.526  0.020  1.526
 0JT  C18  C19  single  1.538  0.020  1.538
 0JT  C18  C17  single  1.536  0.020  1.536
 0JT  C16  C14  single  1.503  0.020  1.503
 0JT  C16  C17  single  1.520  0.020  1.520
 0JT  C19  C21  single  1.527  0.020  1.527
 0JT  C14  O15  double  1.206  0.020  1.206
 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  single  1.331  0.020  1.331
 0JT  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
 0JT  H2   N22  H29  106.12  3.000
 0JT  H2   N22  C18  109.60  3.000
 0JT  H29  N22  C18  110.62  3.000
 0JT  H30  C18  C17  107.47  3.000
 0JT  H30  C18  C19  107.48  3.000
 0JT  C17  C18  C19  112.06  3.000
 0JT  H30  C18  N22  106.79  3.000
 0JT  C17  C18  N22  114.02  3.000
 0JT  C19  C18  N22  108.68  3.000
 0JT  H31  C19  C20  108.14  3.000
 0JT  H31  C19  C21  107.82  3.000
 0JT  C20  C19  C21  109.63  3.000
 0JT  H31  C19  C18  106.96  3.000
 0JT  C21  C19  C18  113.12  3.000
 0JT  C20  C19  C18  110.97  3.000
 0JT  H34  C21  H33  107.76  3.000
 0JT  H34  C21  H32  107.42  3.000
 0JT  H33  C21  H32  107.21  3.000
 0JT  H34  C21  C19  111.16  3.000
 0JT  H33  C21  C19  112.68  3.000
 0JT  H32  C21  C19  110.37  3.000
 0JT  H37  C20  H36  107.40  3.000
 0JT  H37  C20  H35  107.88  3.000
 0JT  H36  C20  H35  108.16  3.000
 0JT  H37  C20  C19  110.64  3.000
 0JT  H36  C20  C19  110.90  3.000
 0JT  H35  C20  C19  111.70  3.000
 0JT  H39  C17  H38  106.67  3.000
 0JT  H39  C17  C16  109.73  3.000
 0JT  H38  C17  C16  108.93  3.000
 0JT  H39  C17  C18  109.46  3.000
 0JT  H38  C17  C18  109.11  3.000
 0JT  C16  C17  C18  112.74  3.000
 0JT  H41  C16  H40  105.47  3.000
 0JT  H41  C16  C14  108.14  3.000
 0JT  H40  C16  C14  107.31  3.000
 0JT  H41  C16  C17  110.78  3.000
 0JT  H40  C16  C17  111.15  3.000
 0JT  C14  C16  C17  113.59  3.000
 0JT  OXT  C14  O15  122.76  3.000
 0JT  OXT  C14  C16  111.71  3.000
 0JT  O15  C14  C16  125.52  3.000
 0JT  HXT  OXT  C14  109.86  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  CONST_01  HXT  OXT  C14  C16  180.00   0.0  0
 0JT  Var_01    C14  C16  C17  C18  174.97  30.0  1
 0JT  Var_02    O15  C14  C16  C17    1.72  30.0  3
 0JT  Var_03    H35  C20  C19  C18   52.95  30.0  3
 0JT  Var_04    H32  C21  C19  C18  174.74  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
 0JT  plan-1  HXT  0.020

