# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 10:20:15 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (3R,4R)-4-hydroxy-3-methyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@@H](O)CN[C@@H]1C(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
 05N  05N  (3R,4R)-4-hydroxy-3-methyl-L-proline  L-peptide  20  10  .  2022-09-22  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_05N
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
 05N  N3   N  NH1    0  -0.613   0.0638   1.5578  -0.1844
 05N  C19  C  CH1    0  -0.169  -0.4473   0.2085  -0.3571
 05N  C20  C  CH1    0  -0.273   0.5652  -0.6592   0.4230
 05N  C21  C  CH1    0   0.068   1.8200   0.2479   0.5338
 05N  C22  C  C      0   0.391  -1.9153   0.0416   0.0573
 05N  O9   O  OH1    0  -0.670   3.0005  -0.4380   0.1890
 05N  C52  C  CH2    0  -0.319   1.4907   1.4318  -0.3778
 05N  C53  C  CH3    0  -0.660   0.8090  -2.0057  -0.2381
 05N  H15  H  HCH1   0   0.195  -0.3837  -0.1041  -1.4183
 05N  H16  H  HCH1   0   0.227   0.1794  -0.8439   1.4294
 05N  H17  H  HCH1   0   0.202   1.8905   0.6211   1.5635
 05N  H40  H  HOH1   0   0.448   3.7415   0.1529   0.3527
 05N  H41  H  HCH2   0   0.183   1.7782   1.1784  -1.4124
 05N  H42  H  HCH2   0   0.221   2.0215   2.3458  -0.0977
 05N  H43  H  HCH3   0   0.209   1.2075  -1.8976  -1.2486
 05N  H44  H  HCH3   0   0.216   1.5031  -2.6241   0.3317
 05N  H45  H  HCH3   0   0.227  -0.1360  -2.5421  -0.3108
 05N  H2   H  HNH1   0   0.338  -0.3640   2.2101  -0.8262
 05N  O2   O  OC    -1  -0.612  -2.3254  -1.1333   0.1665
 05N  O3   O  O      0  -0.609  -2.5877   1.0782   0.2158

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
 05N  N3   C19  single  1.453  0.020  1.453
 05N  N3   H2   single  0.890  0.020  1.040
 05N  C19  C20  single  1.545  0.020  1.545
 05N  C19  C22  single  1.534  0.020  1.534
 05N  C19  H15  single  0.970  0.020  1.090
 05N  C20  C53  single  1.520  0.020  1.520
 05N  C20  H16  single  0.970  0.020  1.090
 05N  C21  C20  single  1.552  0.020  1.552
 05N  C21  H17  single  0.970  0.020  1.090
 05N  C22  O2   deloc   1.249  0.020  1.249
 05N  C22  O3   deloc   1.246  0.020  1.246
 05N  O9   C21  single  1.408  0.020  1.408
 05N  O9   H40  single  0.850  0.020  0.980
 05N  C52  N3   single  1.445  0.020  1.445
 05N  C52  C21  single  1.530  0.020  1.530
 05N  C52  H41  single  0.970  0.020  1.090
 05N  C52  H42  single  0.970  0.020  1.090
 05N  C53  H43  single  0.970  0.020  1.090
 05N  C53  H44  single  0.970  0.020  1.090
 05N  C53  H45  single  0.970  0.020  1.090

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
 05N  H2   N3   C52  112.91  3.000
 05N  C52  N3   C19  104.50  3.000
 05N  H2   N3   C19  112.03  3.000
 05N  H15  C19  C22  106.43  3.000
 05N  H15  C19  C20  106.71  3.000
 05N  C22  C19  C20  115.44  3.000
 05N  H15  C19  N3   110.83  3.000
 05N  C22  C19  N3   113.91  3.000
 05N  C20  C19  N3   103.35  3.000
 05N  H16  C20  C53  107.90  3.000
 05N  H16  C20  C21  108.56  3.000
 05N  C53  C20  C21  114.78  3.000
 05N  C21  C20  C19  103.75  3.000
 05N  H16  C20  C19  109.16  3.000
 05N  C53  C20  C19  112.53  3.000
 05N  H17  C21  C52  108.04  3.000
 05N  C52  C21  O9   114.29  3.000
 05N  H17  C21  O9   109.97  3.000
 05N  C52  C21  C20  103.63  3.000
 05N  O9   C21  C20  112.06  3.000
 05N  H17  C21  C20  108.52  3.000
 05N  O3   C22  O2   126.46  3.000
 05N  O3   C22  C19  117.41  3.000
 05N  O2   C22  C19  116.10  3.000
 05N  H40  O9   C21  107.76  3.000
 05N  H42  C52  H41  107.80  3.000
 05N  H42  C52  C21  112.94  3.000
 05N  H41  C52  C21  108.96  3.000
 05N  H42  C52  N3   111.84  3.000
 05N  H41  C52  N3   113.75  3.000
 05N  C21  C52  N3   101.55  3.000
 05N  H45  C53  H44  107.93  3.000
 05N  H45  C53  H43  107.68  3.000
 05N  H44  C53  H43  107.91  3.000
 05N  H45  C53  C20  109.04  3.000
 05N  H44  C53  C20  112.17  3.000
 05N  H43  C53  C20  111.93  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
 05N  Var_01  C21  C52  N3  C19  -49.02  30.0  1

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
 05N  chir_01  C19  N3   C20  C22  negativ
 05N  chir_02  C20  C19  C53  C21  negativ
 05N  chir_03  C21  O9   C20  C52  positiv

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
 05N  plan-1  C19  0.020
 05N  plan-1  C22  0.020
 05N  plan-1  O2   0.020
 05N  plan-1  O3   0.020

