# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:19:51 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S)-2-[(1S,2S)-2-aminocyclohexyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H]([C@@H]1CCCC[C@@H]1N)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
 GM8  GM8  '(2S)-2-[(1S,2S)-2-aminocyclohexyl]butanoic acid'  ligand  32  13  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GM8
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
 GM8  O     O  O     0  -0.446  -2.0676  -1.0806   1.3316
 GM8  C     C  C     0   0.539  -1.7689  -0.8906   0.1772
 GM8  CA    C  CH1   0  -0.346  -1.0094   0.3215  -0.3129
 GM8  CZ    C  CH2   0  -0.425  -1.8085   1.5805   0.0502
 GM8  CQ    C  CH3   0  -0.674  -3.2324   1.5839  -0.4924
 GM8  CB    C  CH1   0  -0.200   0.4104   0.3146   0.2953
 GM8  CG    C  CH1   0  -0.102   1.1572  -1.0071   0.0325
 GM8  N     N  NH2   0  -0.801   1.3085  -1.2379  -1.3994
 GM8  CD1   C  CH2   0  -0.442   2.5360  -0.9700   0.6904
 GM8  CE1   C  CH2   0  -0.419   3.3764   0.2087   0.2164
 GM8  CE2   C  CH2   0  -0.431   2.6324   1.5171   0.4462
 GM8  CD2   C  CH2   0  -0.419   1.2432   1.5043  -0.1866
 GM8  OXT   O  OH1   0  -0.590  -2.0858  -1.7392  -0.7960
 GM8  HG    H  HCH1  0   0.250  -0.9299   0.2758  -1.4036
 GM8  HZ1   H  HCH2  0   0.225  -1.8209   1.7016   1.1368
 GM8  HZ2   H  HCH2  0   0.243  -1.2841   2.4474  -0.3517
 GM8  HQ3   H  HCH3  0   0.224  -3.2465   1.4325  -1.5732
 GM8  HQ2   H  HCH3  0   0.224  -3.8538   0.8091  -0.0401
 GM8  HQ1   H  HCH3  0   0.238  -3.7150   2.5398  -0.2875
 GM8  HB    H  HCH1  0   0.220   0.2938   0.4010   1.3836
 GM8  HA    H  HCH1  0   0.214   0.5993  -1.8206   0.5228
 GM8  H2    H  HNH2  0   0.343   1.9162  -2.0351  -1.5444
 GM8  H3    H  HNH2  0   0.343   0.4217  -1.4996  -1.8107
 GM8  HD12  H  HCH2  0   0.219   2.3982  -0.9090   1.7746
 GM8  HD11  H  HCH2  0   0.228   3.0518  -1.9163   0.4998
 GM8  HE12  H  HCH2  0   0.222   4.3336   0.2197   0.7436
 GM8  HE11  H  HCH2  0   0.212   3.6054   0.0963  -0.8464
 GM8  HE22  H  HCH2  0   0.207   2.5315   1.6896   1.5236
 GM8  HE21  H  HCH2  0   0.225   3.2078   2.3589   0.0527
 GM8  HD21  H  HCH2  0   0.213   1.3327   1.4644  -1.2760
 GM8  HD22  H  HCH2  0   0.230   0.7429   2.4432   0.0559
 GM8  HXT   H  HOH1  0   0.477  -2.5596  -2.5022  -0.4299

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
 GM8  C    O     double  1.208  0.020  1.208
 GM8  C    CA    single  1.512  0.020  1.512
 GM8  CQ   CZ    single  1.524  0.020  1.524
 GM8  N    CG    single  1.458  0.020  1.458
 GM8  CA   CZ    single  1.535  0.020  1.535
 GM8  CA   CB    single  1.545  0.020  1.545
 GM8  CG   CB    single  1.541  0.020  1.541
 GM8  CG   CD1   single  1.528  0.020  1.528
 GM8  CB   CD2   single  1.530  0.020  1.530
 GM8  CD1  CE1   single  1.523  0.020  1.523
 GM8  CD2  CE2   single  1.527  0.020  1.527
 GM8  CE1  CE2   single  1.523  0.020  1.523
 GM8  C    OXT   single  1.330  0.020  1.330
 GM8  CA   HG    single  0.970  0.020  1.090
 GM8  CZ   HZ1   single  0.970  0.020  1.090
 GM8  CZ   HZ2   single  0.970  0.020  1.090
 GM8  CQ   HQ3   single  0.970  0.020  1.090
 GM8  CQ   HQ2   single  0.970  0.020  1.090
 GM8  CQ   HQ1   single  0.970  0.020  1.090
 GM8  CB   HB    single  0.970  0.020  1.090
 GM8  CG   HA    single  0.970  0.020  1.090
 GM8  N    H2    single  0.890  0.020  1.040
 GM8  N    H3    single  0.890  0.020  1.040
 GM8  CD1  HD12  single  0.970  0.020  1.090
 GM8  CD1  HD11  single  0.970  0.020  1.090
 GM8  CE1  HE12  single  0.970  0.020  1.090
 GM8  CE1  HE11  single  0.970  0.020  1.090
 GM8  CE2  HE22  single  0.970  0.020  1.090
 GM8  CE2  HE21  single  0.970  0.020  1.090
 GM8  CD2  HD21  single  0.970  0.020  1.090
 GM8  CD2  HD22  single  0.970  0.020  1.090
 GM8  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
 GM8  OXT   C    CA    113.21  3.000
 GM8  OXT   C    O     122.71  3.000
 GM8  CA    C    O     124.08  3.000
 GM8  HG    CA   CB    108.99  3.000
 GM8  HG    CA   CZ    107.93  3.000
 GM8  CB    CA   CZ    112.90  3.000
 GM8  HG    CA   C     109.03  3.000
 GM8  CB    CA   C     109.30  3.000
 GM8  CZ    CA   C     108.62  3.000
 GM8  HZ2   CZ   HZ1   106.49  3.000
 GM8  HZ2   CZ   CQ    108.45  3.000
 GM8  HZ1   CZ   CQ    110.06  3.000
 GM8  HZ2   CZ   CA    108.34  3.000
 GM8  HZ1   CZ   CA    109.39  3.000
 GM8  CQ    CZ   CA    113.84  3.000
 GM8  HQ1   CQ   HQ2   107.01  3.000
 GM8  HQ1   CQ   HQ3   107.58  3.000
 GM8  HQ2   CQ   HQ3   107.74  3.000
 GM8  HQ1   CQ   CZ    110.41  3.000
 GM8  HQ2   CQ   CZ    112.51  3.000
 GM8  HQ3   CQ   CZ    111.37  3.000
 GM8  HB    CB   CD2   107.99  3.000
 GM8  HB    CB   CG    106.74  3.000
 GM8  CD2   CB   CG    110.45  3.000
 GM8  HB    CB   CA    107.00  3.000
 GM8  CD2   CB   CA    111.89  3.000
 GM8  CG    CB   CA    112.47  3.000
 GM8  HA    CG   CD1   106.45  3.000
 GM8  HA    CG   N     111.88  3.000
 GM8  CD1   CG   N     109.45  3.000
 GM8  HA    CG   CB    108.19  3.000
 GM8  CD1   CG   CB    110.06  3.000
 GM8  N     CG   CB    110.71  3.000
 GM8  H3    N    H2    105.31  3.000
 GM8  H3    N    CG    110.43  3.000
 GM8  H2    N    CG    109.11  3.000
 GM8  HD11  CD1  HD12  106.26  3.000
 GM8  HD11  CD1  CE1   110.79  3.000
 GM8  HD12  CD1  CE1   109.55  3.000
 GM8  HD11  CD1  CG    109.22  3.000
 GM8  HD12  CD1  CG    108.31  3.000
 GM8  CE1   CD1  CG    112.49  3.000
 GM8  HE11  CE1  HE12  106.65  3.000
 GM8  HE11  CE1  CE2   109.73  3.000
 GM8  HE12  CE1  CE2   110.27  3.000
 GM8  HE11  CE1  CD1   109.79  3.000
 GM8  HE12  CE1  CD1   109.93  3.000
 GM8  CE2   CE1  CD1   110.39  3.000
 GM8  HE21  CE2  HE22  106.34  3.000
 GM8  HE21  CE2  CD2   109.65  3.000
 GM8  HE22  CE2  CD2   108.97  3.000
 GM8  HE21  CE2  CE1   110.51  3.000
 GM8  HE22  CE2  CE1   109.19  3.000
 GM8  CD2   CE2  CE1   112.01  3.000
 GM8  HD22  CD2  HD21  106.87  3.000
 GM8  HD22  CD2  CE2   108.53  3.000
 GM8  HD21  CD2  CE2   109.80  3.000
 GM8  HD22  CD2  CB    110.45  3.000
 GM8  HD21  CD2  CB    109.27  3.000
 GM8  CE2   CD2  CB    111.79  3.000
 GM8  HXT   OXT  C     110.02  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
 GM8  CONST_01  HXT  OXT  C    O      0.00   0.0  0
 GM8  Var_01    CE1  CE2  CD2  CB    55.00  30.0  1
 GM8  Var_02    CD2  CE2  CE1  CD1  -54.05  30.0  1
 GM8  Var_03    HQ3  CQ   CZ   CA   -55.00  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
 GM8  chir_01  CA  C    CZ   CB  negativ
 GM8  chir_02  CB  CD2  CG   CA  positiv
 GM8  chir_03  CG  N    CD1  CB  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
 GM8  plan-1  O    0.020
 GM8  plan-1  C    0.020
 GM8  plan-1  CA   0.020
 GM8  plan-1  OXT  0.020
 GM8  plan-1  HXT  0.020

