# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 08:36:16 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (1S,2R)-2-[(S)-amino(carboxy)methyl]cyclobutanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H]1CC[C@@H]1C(O)=O)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
 G8M  G8M  '(1S,2R)-2-[(S)-amino(carboxy)methyl]cyclobutanecarboxylic acid'  L-peptide  21  12  .  2016-04-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G8M
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
 G8M  CD   C  C      0   0.405   5.6748  25.8346  20.8588
 G8M  OE1  O  O      0  -0.615   4.6340  25.3809  20.3384
 G8M  OE2  O  OC    -1  -0.612   6.2845  25.3322  21.8299
 G8M  CG   C  CH1    0  -0.356   6.2476  27.1261  20.2545
 G8M  C    C  C      0   0.411   7.6682  25.3358  17.6627
 G8M  OXT  O  OC    -1  -0.595   6.5590  25.7980  17.3340
 G8M  O    O  O      0  -0.615   8.3779  24.5636  16.9814
 G8M  CA   C  CH1    0  -0.240   8.2178  25.7089  19.0617
 G8M  N    N  NH2    0  -0.812   9.6761  25.8159  18.9963
 G8M  CB   C  CH1    0  -0.149   7.6655  27.0093  19.6182
 G8M  C6   C  CH2    0  -0.433   8.2644  27.5512  20.9324
 G8M  C7   C  CH2    0  -0.435   6.8694  28.0828  21.2967
 G8M  HG2  H  HCH1   0   0.186   5.5039  27.5751  19.5937
 G8M  HA   H  HCH1   0   0.188   7.9094  24.8928  19.7371
 G8M  H2   H  HNH2   0   0.328  10.0634  25.7045  19.9249
 G8M  H1   H  HNH2   0   0.327  10.0169  25.0361  18.4491
 G8M  HB2  H  HCH1   0   0.195   7.7601  27.7842  18.8499
 G8M  H9   H  HCH2   0   0.206   8.5718  26.7476  21.6024
 G8M  H10  H  HCH2   0   0.202   9.0814  28.2708  20.8543
 G8M  H11  H  HCH2   0   0.207   6.7480  29.1282  21.0049
 G8M  H12  H  HCH2   0   0.207   6.5440  27.9768  22.3322

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
 G8M  O    C    deloc   1.231  0.020  1.231
 G8M  OXT  C    deloc   1.246  0.020  1.246
 G8M  C    CA   single  1.525  0.021  1.525
 G8M  CA   N    single  1.458  0.019  1.458
 G8M  CA   CB   single  1.530  0.020  1.530
 G8M  CB   CG   single  1.558  0.020  1.558
 G8M  CB   C6   single  1.543  0.020  1.543
 G8M  CG   CD   single  1.537  0.020  1.537
 G8M  CG   C7   single  1.545  0.020  1.545
 G8M  OE1  CD   deloc   1.249  0.020  1.249
 G8M  C6   C7   single  1.537  0.020  1.537
 G8M  CD   OE2  deloc   1.252  0.020  1.252
 G8M  CG   HG2  single  0.970  0.020  1.090
 G8M  CA   HA   single  0.970  0.020  0.970
 G8M  N    H2   single  0.890  0.020  1.040
 G8M  N    H1   single  0.890  0.020  1.040
 G8M  CB   HB2  single  0.970  0.020  1.090
 G8M  C6   H9   single  0.970  0.020  1.090
 G8M  C6   H10  single  0.970  0.020  1.090
 G8M  C7   H11  single  0.970  0.020  1.090
 G8M  C7   H12  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
 G8M  CG   CD  OE2  117.44  3.000
 G8M  OE2  CD  OE1  125.68  3.000
 G8M  CG   CD  OE1  116.87  3.000
 G8M  HG2  CG  C7   115.32  3.000
 G8M  HG2  CG  CB   113.80  3.000
 G8M  C7   CG  CB    87.46  3.000
 G8M  HG2  CG  CD   109.26  3.000
 G8M  C7   CG  CD   113.90  3.000
 G8M  CB   CG  CD   115.89  3.000
 G8M  CA   C   O    120.80  1.700
 G8M  CA   C   OXT  117.71  3.000
 G8M  O    C   OXT  126.20  3.000
 G8M  HA   CA  CB   109.00  3.000
 G8M  HA   CA  N    110.00  3.000
 G8M  CB   CA  N    110.50  1.700
 G8M  HA   CA  C    109.00  3.000
 G8M  CB   CA  C    110.10  1.900
 G8M  N    CA  C    111.00  2.800
 G8M  H1   N   H2   106.41  3.000
 G8M  H1   N   CA   107.66  3.000
 G8M  H2   N   CA   109.40  3.000
 G8M  HB2  CB  C6   108.39  3.000
 G8M  HB2  CB  CA   108.50  3.000
 G8M  C6   CB  CA   118.16  3.000
 G8M  HB2  CB  CG   108.18  3.000
 G8M  C6   CB  CG    88.80  3.000
 G8M  CA   CB  CG   123.01  3.000
 G8M  H10  C6  H9   108.59  3.000
 G8M  H10  C6  C7   117.93  3.000
 G8M  H9   C6  C7   111.42  3.000
 G8M  H10  C6  CB   117.47  3.000
 G8M  H9   C6  CB   111.96  3.000
 G8M  C7   C6  CB    88.34  3.000
 G8M  H12  C7  H11  108.28  3.000
 G8M  H12  C7  C6   117.53  3.000
 G8M  H11  C7  C6   111.64  3.000
 G8M  H12  C7  CG   117.39  3.000
 G8M  H11  C7  CG   111.58  3.000
 G8M  C6   C7  CG    89.49  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
 G8M  Var_01  CB  C6  C7  CG  18.38  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
 G8M  chir_01  CG  CB  CD  C7  negativ
 G8M  chir_02  CA  N   CB  C   negativ
 G8M  chir_03  CB  CA  CG  C6  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
 G8M  plan-1  CD   0.020
 G8M  plan-1  OE1  0.020
 G8M  plan-1  OE2  0.020
 G8M  plan-1  CG   0.020
 G8M  plan-2  C    0.020
 G8M  plan-2  OXT  0.020
 G8M  plan-2  O    0.020
 G8M  plan-2  CA   0.020

