# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 22:40:36 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (1R,2S,5S)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)[C@H]2CN[C@@H]([C@@H]12)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
 12L  12L  '(1R,2S,5S)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylic acid'  L-peptide  23  11  .  2022-03-10  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_12L
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
 12L  N19  N  NH1    0  -0.626   0.2811  -1.3167  -0.8922
 12L  C20  C  CH2    0  -0.260  -0.6928  -1.8648   0.0534
 12L  C21  C  CH1    0  -0.182   0.7237  -0.0099  -0.4135
 12L  C22  C  CH1    0  -0.271  -0.4018   0.4987   0.4624
 12L  C23  C  CH1    0  -0.279  -1.2940  -0.6735   0.7597
 12L  C24  C  CT     0   0.008  -1.8193   0.4845  -0.0440
 12L  C25  C  CH3    0  -0.657  -2.7648   1.4004   0.7030
 12L  C26  C  CH3    0  -0.681  -2.1597   0.3663  -1.5104
 12L  C27  C  C      0   0.399   2.0574  -0.0353   0.3738
 12L  O28  O  O      0  -0.605   2.6667  -1.1225   0.4323
 12L  H26  H  HCH2   0   0.203  -1.4422  -2.4661  -0.4735
 12L  H27  H  HCH2   0   0.206  -0.2329  -2.5173   0.8073
 12L  H28  H  HCH1   0   0.214   0.8780   0.6603  -1.2724
 12L  H29  H  HCH1   0   0.236  -0.1481   1.2265   1.2240
 12L  H30  H  HCH1   0   0.237  -1.7026  -0.8377   1.7513
 12L  H31  H  HCH3   0   0.221  -2.7443   2.4101   0.2861
 12L  H32  H  HCH3   0   0.220  -3.7944   1.0397   0.6406
 12L  H33  H  HCH3   0   0.222  -2.5061   1.4765   1.7607
 12L  H34  H  HCH3   0   0.242  -1.4966  -0.3140  -2.0400
 12L  H35  H  HCH3   0   0.215  -3.1843   0.0077  -1.6366
 12L  H36  H  HCH3   0   0.215  -2.1000   1.3434  -1.9966
 12L  H2   H  HNH1   0   0.338   1.0925  -1.9209  -0.9366
 12L  OXT  O  OC    -1  -0.616   2.4236   1.0516   0.8620

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
 12L  N19  C20  single  1.464  0.020  1.464
 12L  N19  C21  single  1.460  0.020  1.460
 12L  C20  C23  single  1.510  0.020  1.510
 12L  O28  C27  deloc   1.248  0.020  1.248
 12L  C27  C21  single  1.549  0.020  1.549
 12L  C21  C22  single  1.514  0.020  1.514
 12L  C23  C22  single  1.503  0.020  1.503
 12L  C23  C24  single  1.504  0.020  1.504
 12L  C22  C24  single  1.505  0.020  1.505
 12L  C26  C24  single  1.510  0.020  1.510
 12L  C24  C25  single  1.514  0.020  1.514
 12L  C20  H26  single  0.970  0.020  1.090
 12L  C20  H27  single  0.970  0.020  1.090
 12L  C21  H28  single  0.970  0.020  1.090
 12L  C22  H29  single  0.970  0.020  1.090
 12L  C23  H30  single  0.970  0.020  1.090
 12L  C25  H31  single  0.970  0.020  1.090
 12L  C25  H32  single  0.970  0.020  1.090
 12L  C25  H33  single  0.970  0.020  1.090
 12L  C26  H34  single  0.970  0.020  1.090
 12L  C26  H35  single  0.970  0.020  1.090
 12L  C26  H36  single  0.970  0.020  1.090
 12L  N19  H2   single  0.890  0.020  1.040
 12L  C27  OXT  deloc   1.246  0.020  1.246

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
 12L  H2   N19  C21  107.78  3.000
 12L  H2   N19  C20  109.76  3.000
 12L  C21  N19  C20  108.96  3.000
 12L  H27  C20  H26  106.89  3.000
 12L  H27  C20  C23  108.33  3.000
 12L  H26  C20  C23  112.68  3.000
 12L  H27  C20  N19  112.79  3.000
 12L  H26  C20  N19  110.48  3.000
 12L  C23  C20  N19  105.76  3.000
 12L  H28  C21  C27  106.62  3.000
 12L  H28  C21  C22  110.56  3.000
 12L  C27  C21  C22  110.58  3.000
 12L  H28  C21  N19  109.37  3.000
 12L  C22  C21  N19  105.36  3.000
 12L  C27  C21  N19  114.39  3.000
 12L  H29  C22  C24  117.60  3.000
 12L  H29  C22  C23  121.59  3.000
 12L  C24  C22  C23   60.01  3.000
 12L  H29  C22  C21  117.26  3.000
 12L  C24  C22  C21  120.14  3.000
 12L  C23  C22  C21  107.08  3.000
 12L  H30  C23  C24  118.25  3.000
 12L  H30  C23  C22  121.50  3.000
 12L  C24  C23  C22   60.08  3.000
 12L  H30  C23  C20  117.26  3.000
 12L  C24  C23  C20  119.77  3.000
 12L  C22  C23  C20  106.65  3.000
 12L  C26  C24  C25  112.69  3.000
 12L  C25  C24  C23  114.85  3.000
 12L  C26  C24  C23  122.51  3.000
 12L  C25  C24  C22  114.61  3.000
 12L  C26  C24  C22  122.66  3.000
 12L  C23  C24  C22   59.92  3.000
 12L  H33  C25  H32  107.56  3.000
 12L  H33  C25  H31  107.51  3.000
 12L  H32  C25  H31  107.51  3.000
 12L  H33  C25  C24  111.86  3.000
 12L  H32  C25  C24  111.14  3.000
 12L  H31  C25  C24  111.05  3.000
 12L  H36  C26  H35  107.05  3.000
 12L  H36  C26  H34  108.02  3.000
 12L  H35  C26  H34  108.07  3.000
 12L  H36  C26  C24  110.47  3.000
 12L  H35  C26  C24  110.43  3.000
 12L  H34  C26  C24  112.60  3.000
 12L  OXT  C27  O28  126.73  3.000
 12L  OXT  C27  C21  115.96  3.000
 12L  O28  C27  C21  117.29  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
 12L  Var_01  C22  C23  C20  N19  -14.51  30.0  1
 12L  Var_02  C21  C22  C23  C20   -0.22  30.0  1
 12L  Var_03  C23  C20  N19  C21   24.69  30.0  1
 12L  Var_04  H34  C26  C24  C22   38.08  30.0  3
 12L  Var_05  H31  C25  C24  C22   86.78  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
 12L  chir_01  C21  N19  C27  C22  positiv
 12L  chir_02  C22  C21  C23  C24  both
 12L  chir_03  C23  C24  C22  C20  both

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
 12L  plan-1  C21  0.020
 12L  plan-1  C27  0.020
 12L  plan-1  O28  0.020
 12L  plan-1  OXT  0.020

