# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:04:20 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3R,5R)-5-amino-3-methyl-D-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](N)N[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
 X7O  X7O  (3R,5R)-5-amino-3-methyl-D-proline  ligand  21  10  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_X7O
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
 X7O  C1    C  C      0   0.397  -0.2772   0.7450   0.7622
 X7O  C2    C  CH1    0  -0.216  -1.6061   0.5061   1.5188
 X7O  C3    C  CH1    0  -0.240  -1.5193   0.9418   2.9855
 X7O  C4    C  CH2    0  -0.483  -1.7928   2.4445   2.8691
 X7O  C5    C  CH1    0   0.070  -2.7103   2.6028   1.6390
 X7O  C6    C  CH3    0  -0.657  -2.5403   0.2291   3.8657
 X7O  O1    O  O      0  -0.605  -0.3085   1.4875  -0.2396
 X7O  N1    N  NH1    0  -0.616  -2.7382   1.2712   1.0278
 X7O  N2    N  NH2    0  -0.798  -4.0179   3.1204   1.9996
 X7O  O2    O  OC    -1  -0.620   0.7222   0.1478   1.2135
 X7O  HC2   H  HCH1   0   0.217  -1.8223  -0.5697   1.4555
 X7O  HC3   H  HCH1   0   0.227  -0.5217   0.7445   3.3803
 X7O  HC41  H  HCH2   0   0.230  -2.2513   2.8641   3.7670
 X7O  HC42  H  HCH2   0   0.237  -0.8597   2.9882   2.7093
 X7O  HC5   H  HCH1   0   0.209  -2.2748   3.3338   0.9499
 X7O  HC61  H  HCH3   0   0.220  -2.4877   0.5864   4.8959
 X7O  HC62  H  HCH3   0   0.216  -3.5608   0.3875   3.5116
 X7O  HC63  H  HCH3   0   0.220  -2.3622  -0.8481   3.8813
 X7O  HN1   H  HNH1   0   0.330  -2.6851   1.3508   0.0208
 X7O  HN21  H  HNH2   0   0.335  -4.5883   3.1953   1.1650
 X7O  HN22  H  HNH2   0   0.327  -4.4886   2.4409   2.5877

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
 X7O  C1  C2    single  1.548  0.020  1.548
 X7O  C1  O1    deloc   1.247  0.020  1.247
 X7O  C1  O2    deloc   1.249  0.020  1.249
 X7O  C2  C3    single  1.533  0.020  1.533
 X7O  C2  N1    single  1.452  0.020  1.452
 X7O  C2  HC2   single  0.970  0.020  1.090
 X7O  C3  C4    single  1.532  0.020  1.532
 X7O  C3  C6    single  1.525  0.020  1.525
 X7O  C3  HC3   single  0.970  0.020  1.090
 X7O  C4  C5    single  1.543  0.020  1.543
 X7O  C4  HC41  single  0.970  0.020  1.090
 X7O  C4  HC42  single  0.970  0.020  1.090
 X7O  C5  N1    single  1.465  0.020  1.465
 X7O  C5  N2    single  1.452  0.020  1.452
 X7O  C5  HC5   single  0.970  0.020  1.090
 X7O  C6  HC61  single  0.970  0.020  1.090
 X7O  C6  HC62  single  0.970  0.020  1.090
 X7O  C6  HC63  single  0.970  0.020  1.090
 X7O  N1  HN1   single  0.890  0.020  1.040
 X7O  N2  HN21  single  0.890  0.020  1.040
 X7O  N2  HN22  single  0.890  0.020  1.040

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
 X7O  O2    C1  O1    126.52  3.000
 X7O  O2    C1  C2    115.90  3.000
 X7O  O1    C1  C2    117.58  3.000
 X7O  HC2   C2  N1    110.06  3.000
 X7O  HC2   C2  C3    110.15  3.000
 X7O  N1    C2  C3    102.59  3.000
 X7O  HC2   C2  C1    106.96  3.000
 X7O  N1    C2  C1    115.02  3.000
 X7O  C3    C2  C1    112.04  3.000
 X7O  HC3   C3  C6    108.60  3.000
 X7O  HC3   C3  C4    111.61  3.000
 X7O  C6    C3  C4    112.51  3.000
 X7O  HC3   C3  C2    110.29  3.000
 X7O  C6    C3  C2    112.43  3.000
 X7O  C4    C3  C2    101.30  3.000
 X7O  HC42  C4  HC41  106.72  3.000
 X7O  HC42  C4  C5    109.91  3.000
 X7O  HC41  C4  C5    111.50  3.000
 X7O  HC42  C4  C3    110.31  3.000
 X7O  HC41  C4  C3    112.92  3.000
 X7O  C5    C4  C3    105.52  3.000
 X7O  HC5   C5  N2    106.05  3.000
 X7O  HC5   C5  N1    110.60  3.000
 X7O  N2    C5  N1    114.23  3.000
 X7O  HC5   C5  C4    109.50  3.000
 X7O  N2    C5  C4    111.97  3.000
 X7O  N1    C5  C4    104.51  3.000
 X7O  HC63  C6  HC62  107.47  3.000
 X7O  HC63  C6  HC61  107.55  3.000
 X7O  HC62  C6  HC61  107.68  3.000
 X7O  HC63  C6  C3    111.11  3.000
 X7O  HC62  C6  C3    111.77  3.000
 X7O  HC61  C6  C3    111.07  3.000
 X7O  HN1   N1  C5    110.04  3.000
 X7O  HN1   N1  C2    109.70  3.000
 X7O  C5    N1  C2    108.84  3.000
 X7O  HN22  N2  HN21  105.40  3.000
 X7O  HN22  N2  C5    108.85  3.000
 X7O  HN21  N2  C5    109.18  3.000

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
 X7O  chir_01  C2  C1  C3  N1  negativ
 X7O  chir_02  C3  C2  C4  C6  negativ
 X7O  chir_03  C5  N2  N1  C4  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
 X7O  plan-1  C1  0.020
 X7O  plan-1  C2  0.020
 X7O  plan-1  O1  0.020
 X7O  plan-1  O2  0.020

